Performance of the Accelerate Pheno™ system for identification and antimicrobial susceptibility testing of a panel of multidrug-resistant Gram-negative bacilli directly from positive blood cultures

Performance of the Accelerate Pheno™ system for identification and antimicrobial susceptibility... Abstract Objectives To evaluate the performance of the Accelerate Pheno™ system for the identification and antimicrobial susceptibility testing (AST) of a panel of Gram-negative bacilli (GNB) with different resistance profiles (e.g. penicillinases, ESBLs, cephalosporinase overproduction, carbapenemases, impermeability) directly from positive blood cultures in <7 h. Methods A panel of 105 clinical strains previously characterized for the presence of β-lactamase-encoding genes was tested. Approximately 100 cfu of each isolate was inoculated into sterile blood culture bottles and incubated in a BD BACTEC™ FX automated system (Becton Dickinson, USA). Positive blood cultures were subjected to parallel testing using the Accelerate Pheno™ system and conventional culture methods [identification of isolated colonies by MALDI-TOF and VITEK® 2 system (bioMérieux, France), and AST by disc diffusion and Etest following EUCAST recommendations]. Results The overall identification agreement between the Accelerate Pheno™ system and conventional culture methods was 100% (105/105). The overall categorical agreement between the system and culture-based AST was 94.9% (1169/1232), with rates for minor errors of 4.1% (51/1232), major errors 0.3% (4/1232) and very major errors 0.7% (8/1232). The Accelerate Pheno™ system produced AST results indicative of third-generation cephalosporinases (26/26) and carbapenem-resistant strains (52/55). Conclusions The Accelerate Pheno™ system is an accurate, sensitive and easy-to-use test for the rapid identification and AST of MDR GNB in bloodstream infections. Given the burden of multidrug resistance, its implementation in the microbiology laboratory could be a useful tool for prompt management of sepsis. Introduction The incidence of bloodstream infections (BSIs) is reported to be ∼150 per 100 000 population.1 In ICUs, the incidence is ∼30% of admissions, a level that has remained stable over the last decade.1,2 Septic shock, the most severe form of sepsis, occurs in 10%–20% of ICU-admitted patients.1,3 It is responsible for increases in both length of stay and healthcare-related costs.4,5 Moreover, BSIs are a leading cause of death in critically ill patients worldwide, with an overall mortality rate of close to 40%.6,7 The spread of MDR Gram-negative bacilli (GNB) has become a major public health challenge directly related to the misuse and overuse of antibiotics.8 The rapid optimization of antibiotic therapy, according to the organism and its resistance profile, is a major goal both for individual patients and for public health.9 In severe sepsis and septic shock, the importance of early appropriate treatment is crucial, given the linear increase in the risk of mortality with each hour for which antibiotic administration is delayed.10 Current clinical microbiology methods are time consuming and are not validated for direct use on positive blood cultures. These methods require an overnight pure subculture on agar for subsequent identification of causative organisms and preparation of a standard inoculum for antimicrobial susceptibility testing (AST) according to the manufacturer’s guidelines. Faster identification and AST directly from positive blood cultures would have the potential to significantly improve time to diagnosis and initiation of appropriate antibiotic and patient management in ICUs. However, to our knowledge, none of the current technologies provide prompt AST with MICs that truly reflect the resistance profile of the bacteria involved in the BSI. In this study, we evaluated the performance of the Accelerate Pheno™ system (Accelerate Diagnostics Inc.) compared with routine laboratory analysis in order: (i) to provide a correct identification in 1.5 h; and (ii) to detect resistance in a panel of GNB, representative of the ecology of our region, within 7 h.11,12 Methods Bacterial panel A panel of 105 clinical GNB isolates belonging to a collection from our Regional MDR GNB Reference Lab (the CARB-LR group)13,14 in the Occitanie Region was tested (Table 1). Ninety-nine Enterobacteriaceae isolates were included with the following distribution: Escherichia coli (n = 36), Klebsiella pneumoniae (n = 34), Enterobacter cloacae (n = 14), Enterobacter aerogenes (n = 5), Klebsiella oxytoca (n = 5), Citrobacter freundii (n = 2), Citrobacter koseri (n = 2) and Proteus mirabilis (n = 1). Different β-lactam resistance profiles were selected with the following properties: (i) susceptibility to third-generation cephalosporins (3GC-S, n = 23); (ii) resistance to 3GCs (3GC-R, n = 26) mediated by ESBL (n = 17) or overexpressed/plasmid-mediated cephalosporinases (AmpC, n = 9); and (iii) resistance to carbapenems (n = 50) involving carbapenemase production (n = 33) or membrane permeability alterations (n = 17). Six Acinetobacter baumannii strains were also included: a wild-type phenotype (n = 1), and different carbapenemase-producing isolates [OXA-23, -24 or -58-type producers (n = 5)]. Table 1. Characteristics of the studied Gram-negative bacilli panel Group Resistance profile (no. of strains) Species (no. of strains) β-Lactamase content (no. of strains) Enterobacteriaceae 3GCa susceptible (23) no resistance to β-lactams (8) E. coli (8) none penicillinase (12) E. coli (6) TEM-1 (3) TEM-1 hyperproduction (2) inhibitor-resistant TEM (1) K. pneumoniae (4) SHV-1 (1) SHV-1 hyperproduction (2) inhibitor-resistant TEM (1) C. koseri (2) CKO (2) chromosomal cephalosporinase (3) E. aerogenes (2) AmpC (2) E. cloacae (1) AmpC (1) 3GC resistant (26) ESBL (17) E. coli (14) CTX-M-group 1 (7)b CTX-M-group 9 (5) CTX-M-group 8 (2) K. pneumoniae (2) SHV-5 (1) CTX-M-group 1 (1) P. mirabilis (1) CTX-M-group 1 (1) cephalosporinase overproduction (8) E. coli (2) AmpC hyperproduction (2) K. pneumoniae (2) DHA-1, SHV-1, TEM-1 (1) DHA-1, SHV-1 (1) E. cloacae (2) AmpC hyperproduction (2) C. freundii (2) AmpC hyperproduction (2) penicillinase overproduction (1) K. oxytoca (1) OXY hyperproduction (1) Carbapenem resistant (50) Class A carbapenemase (6) K. pneumoniae (5) KPC-2, CTX-M-group 1, SHV-1 (1) KPC-2 (4)c E. cloacae (1) IMI-1, AmpC (1) Class B carbapenemase (12) K. pneumoniae (6) NDM-1, SHV-1 (1) NDM-1, CTX-M-group 1, SHV-1 (3) VIM-1, SHV-1 (2) E. coli (4) NDM-1, CTX-M-group 1 (1) NDM-1, CTX-M-group 9 (1) NDM-1, DHA-1 (1) VIM-1 (1) E. cloacae (1) VIM-1, AmpC hyperproduced (1) E. aerogenes (1) NDM-1, CTX-M-group 1, AmpC (1) Class D carbapenemase (13) K. pneumoniae (6) OXA-48, SHV-1 (2) OXA-48, CTX-M-group 1, SHV-1 (4) E. coli (2) OXA-48 (1) OXA-181, CTX-M-group 1 (1) E. cloacae (2) OXA-48, CTX-M-group 1, AmpC (2) E. aerogenes (2) OXA-48, AmpC (2) K. oxytoca (1) OXA-48, OXY-1 (1) Class B + D carbapenemases (2) K. pneumoniae (2) OXA-48, NDM-1, CTX-M-group 1, SHV-1 (2) impermeability (17) K. pneumoniae (7) CTX-M-group 1, SHV-1 (1) DHA-1, SHV-1 (6) E. cloacae (7) AmpC hyperproduction (5) AmpC hyperproduction, CTX-M-group 9 (1) AmpC hyperproduction, SHV-5 (1) K. oxytoca (3) OXY hyperproduction (3) Non-fermenting Gram-negative bacilli wild-type (1) A. baumannii (1) AmpC (1) Class D carbapenemase (5) A. baumannii (5) OXA-23-type (3) OXA-24-type (1) OXA-23-type, OXA-58-type (1) Group Resistance profile (no. of strains) Species (no. of strains) β-Lactamase content (no. of strains) Enterobacteriaceae 3GCa susceptible (23) no resistance to β-lactams (8) E. coli (8) none penicillinase (12) E. coli (6) TEM-1 (3) TEM-1 hyperproduction (2) inhibitor-resistant TEM (1) K. pneumoniae (4) SHV-1 (1) SHV-1 hyperproduction (2) inhibitor-resistant TEM (1) C. koseri (2) CKO (2) chromosomal cephalosporinase (3) E. aerogenes (2) AmpC (2) E. cloacae (1) AmpC (1) 3GC resistant (26) ESBL (17) E. coli (14) CTX-M-group 1 (7)b CTX-M-group 9 (5) CTX-M-group 8 (2) K. pneumoniae (2) SHV-5 (1) CTX-M-group 1 (1) P. mirabilis (1) CTX-M-group 1 (1) cephalosporinase overproduction (8) E. coli (2) AmpC hyperproduction (2) K. pneumoniae (2) DHA-1, SHV-1, TEM-1 (1) DHA-1, SHV-1 (1) E. cloacae (2) AmpC hyperproduction (2) C. freundii (2) AmpC hyperproduction (2) penicillinase overproduction (1) K. oxytoca (1) OXY hyperproduction (1) Carbapenem resistant (50) Class A carbapenemase (6) K. pneumoniae (5) KPC-2, CTX-M-group 1, SHV-1 (1) KPC-2 (4)c E. cloacae (1) IMI-1, AmpC (1) Class B carbapenemase (12) K. pneumoniae (6) NDM-1, SHV-1 (1) NDM-1, CTX-M-group 1, SHV-1 (3) VIM-1, SHV-1 (2) E. coli (4) NDM-1, CTX-M-group 1 (1) NDM-1, CTX-M-group 9 (1) NDM-1, DHA-1 (1) VIM-1 (1) E. cloacae (1) VIM-1, AmpC hyperproduced (1) E. aerogenes (1) NDM-1, CTX-M-group 1, AmpC (1) Class D carbapenemase (13) K. pneumoniae (6) OXA-48, SHV-1 (2) OXA-48, CTX-M-group 1, SHV-1 (4) E. coli (2) OXA-48 (1) OXA-181, CTX-M-group 1 (1) E. cloacae (2) OXA-48, CTX-M-group 1, AmpC (2) E. aerogenes (2) OXA-48, AmpC (2) K. oxytoca (1) OXA-48, OXY-1 (1) Class B + D carbapenemases (2) K. pneumoniae (2) OXA-48, NDM-1, CTX-M-group 1, SHV-1 (2) impermeability (17) K. pneumoniae (7) CTX-M-group 1, SHV-1 (1) DHA-1, SHV-1 (6) E. cloacae (7) AmpC hyperproduction (5) AmpC hyperproduction, CTX-M-group 9 (1) AmpC hyperproduction, SHV-5 (1) K. oxytoca (3) OXY hyperproduction (3) Non-fermenting Gram-negative bacilli wild-type (1) A. baumannii (1) AmpC (1) Class D carbapenemase (5) A. baumannii (5) OXA-23-type (3) OXA-24-type (1) OXA-23-type, OXA-58-type (1) a 3GC, third-generation cephalosporins. b One CTX-M-producing E. coli harboured the plasmid-mediated colistin resistance gene mcr-1 (colistin MIC 4 mg/L). c Two KPC-producing K. pneumoniae harboured the aminoglycoside resistance methyltransferase gene armA. Table 1. Characteristics of the studied Gram-negative bacilli panel Group Resistance profile (no. of strains) Species (no. of strains) β-Lactamase content (no. of strains) Enterobacteriaceae 3GCa susceptible (23) no resistance to β-lactams (8) E. coli (8) none penicillinase (12) E. coli (6) TEM-1 (3) TEM-1 hyperproduction (2) inhibitor-resistant TEM (1) K. pneumoniae (4) SHV-1 (1) SHV-1 hyperproduction (2) inhibitor-resistant TEM (1) C. koseri (2) CKO (2) chromosomal cephalosporinase (3) E. aerogenes (2) AmpC (2) E. cloacae (1) AmpC (1) 3GC resistant (26) ESBL (17) E. coli (14) CTX-M-group 1 (7)b CTX-M-group 9 (5) CTX-M-group 8 (2) K. pneumoniae (2) SHV-5 (1) CTX-M-group 1 (1) P. mirabilis (1) CTX-M-group 1 (1) cephalosporinase overproduction (8) E. coli (2) AmpC hyperproduction (2) K. pneumoniae (2) DHA-1, SHV-1, TEM-1 (1) DHA-1, SHV-1 (1) E. cloacae (2) AmpC hyperproduction (2) C. freundii (2) AmpC hyperproduction (2) penicillinase overproduction (1) K. oxytoca (1) OXY hyperproduction (1) Carbapenem resistant (50) Class A carbapenemase (6) K. pneumoniae (5) KPC-2, CTX-M-group 1, SHV-1 (1) KPC-2 (4)c E. cloacae (1) IMI-1, AmpC (1) Class B carbapenemase (12) K. pneumoniae (6) NDM-1, SHV-1 (1) NDM-1, CTX-M-group 1, SHV-1 (3) VIM-1, SHV-1 (2) E. coli (4) NDM-1, CTX-M-group 1 (1) NDM-1, CTX-M-group 9 (1) NDM-1, DHA-1 (1) VIM-1 (1) E. cloacae (1) VIM-1, AmpC hyperproduced (1) E. aerogenes (1) NDM-1, CTX-M-group 1, AmpC (1) Class D carbapenemase (13) K. pneumoniae (6) OXA-48, SHV-1 (2) OXA-48, CTX-M-group 1, SHV-1 (4) E. coli (2) OXA-48 (1) OXA-181, CTX-M-group 1 (1) E. cloacae (2) OXA-48, CTX-M-group 1, AmpC (2) E. aerogenes (2) OXA-48, AmpC (2) K. oxytoca (1) OXA-48, OXY-1 (1) Class B + D carbapenemases (2) K. pneumoniae (2) OXA-48, NDM-1, CTX-M-group 1, SHV-1 (2) impermeability (17) K. pneumoniae (7) CTX-M-group 1, SHV-1 (1) DHA-1, SHV-1 (6) E. cloacae (7) AmpC hyperproduction (5) AmpC hyperproduction, CTX-M-group 9 (1) AmpC hyperproduction, SHV-5 (1) K. oxytoca (3) OXY hyperproduction (3) Non-fermenting Gram-negative bacilli wild-type (1) A. baumannii (1) AmpC (1) Class D carbapenemase (5) A. baumannii (5) OXA-23-type (3) OXA-24-type (1) OXA-23-type, OXA-58-type (1) Group Resistance profile (no. of strains) Species (no. of strains) β-Lactamase content (no. of strains) Enterobacteriaceae 3GCa susceptible (23) no resistance to β-lactams (8) E. coli (8) none penicillinase (12) E. coli (6) TEM-1 (3) TEM-1 hyperproduction (2) inhibitor-resistant TEM (1) K. pneumoniae (4) SHV-1 (1) SHV-1 hyperproduction (2) inhibitor-resistant TEM (1) C. koseri (2) CKO (2) chromosomal cephalosporinase (3) E. aerogenes (2) AmpC (2) E. cloacae (1) AmpC (1) 3GC resistant (26) ESBL (17) E. coli (14) CTX-M-group 1 (7)b CTX-M-group 9 (5) CTX-M-group 8 (2) K. pneumoniae (2) SHV-5 (1) CTX-M-group 1 (1) P. mirabilis (1) CTX-M-group 1 (1) cephalosporinase overproduction (8) E. coli (2) AmpC hyperproduction (2) K. pneumoniae (2) DHA-1, SHV-1, TEM-1 (1) DHA-1, SHV-1 (1) E. cloacae (2) AmpC hyperproduction (2) C. freundii (2) AmpC hyperproduction (2) penicillinase overproduction (1) K. oxytoca (1) OXY hyperproduction (1) Carbapenem resistant (50) Class A carbapenemase (6) K. pneumoniae (5) KPC-2, CTX-M-group 1, SHV-1 (1) KPC-2 (4)c E. cloacae (1) IMI-1, AmpC (1) Class B carbapenemase (12) K. pneumoniae (6) NDM-1, SHV-1 (1) NDM-1, CTX-M-group 1, SHV-1 (3) VIM-1, SHV-1 (2) E. coli (4) NDM-1, CTX-M-group 1 (1) NDM-1, CTX-M-group 9 (1) NDM-1, DHA-1 (1) VIM-1 (1) E. cloacae (1) VIM-1, AmpC hyperproduced (1) E. aerogenes (1) NDM-1, CTX-M-group 1, AmpC (1) Class D carbapenemase (13) K. pneumoniae (6) OXA-48, SHV-1 (2) OXA-48, CTX-M-group 1, SHV-1 (4) E. coli (2) OXA-48 (1) OXA-181, CTX-M-group 1 (1) E. cloacae (2) OXA-48, CTX-M-group 1, AmpC (2) E. aerogenes (2) OXA-48, AmpC (2) K. oxytoca (1) OXA-48, OXY-1 (1) Class B + D carbapenemases (2) K. pneumoniae (2) OXA-48, NDM-1, CTX-M-group 1, SHV-1 (2) impermeability (17) K. pneumoniae (7) CTX-M-group 1, SHV-1 (1) DHA-1, SHV-1 (6) E. cloacae (7) AmpC hyperproduction (5) AmpC hyperproduction, CTX-M-group 9 (1) AmpC hyperproduction, SHV-5 (1) K. oxytoca (3) OXY hyperproduction (3) Non-fermenting Gram-negative bacilli wild-type (1) A. baumannii (1) AmpC (1) Class D carbapenemase (5) A. baumannii (5) OXA-23-type (3) OXA-24-type (1) OXA-23-type, OXA-58-type (1) a 3GC, third-generation cephalosporins. b One CTX-M-producing E. coli harboured the plasmid-mediated colistin resistance gene mcr-1 (colistin MIC 4 mg/L). c Two KPC-producing K. pneumoniae harboured the aminoglycoside resistance methyltransferase gene armA. Isolates had been previously identified using the VITEK® MS and VITEK® 2 systems (bioMérieux, France). Susceptibility to antimicrobial agents was tested by the disc-diffusion method (BioRad, Marnes La Coquette, France) on Mueller–Hinton agar according to EUCAST-SFM 2016 recommendations (http://www.sfm-microbiologie.org). In addition, the MICs of carbapenems (ertapenem and meropenem) were determined by the Etest® method (bioMérieux). The MIC of colistin was determined using microbroth dilution (Umic®, Biocentric, France). The MICs were interpreted as specified by the EUCAST-SFM criteria. All isolates were typed by Check-MDR CT102/103® microarrays (Check-point, the Netherlands). Confirmation of the presence of β-lactamase-encoding genes was done by PCRs using specific primers and confirmed by sequencing the PCR products as previously described.15–19 Emerging resistance mechanisms (colistin resistance mcr-1 determinant and 16S rRNA methylase) were also characterized by PCR as previously described.20,21 The AST results of the studied strains are presented in Table S1 (available as Supplementary data at JAC Online). Sample preparation For each isolate, ∼100 cfu was spiked into sterile blood culture bottles [BD BACTEC™ Plus Aerobic/F and BD BACTEC™ Lytic/10 Anaerobic/F (BD Diagnostics)] containing 10 mL of fresh blood. Blood cultures were incubated in a BACTEC™ FX automated blood culture device until they flagged positive for microbial growth. All positive blood cultures were divided into two samples: (i) 1 mL for conventional comparator methods; and (ii) 0.5 mL for the Accelerate Pheno™ system. Conventional comparator methods All positive blood cultures were subcultured on blood agar plates (bioMérieux) for 18–24 h at 37 ± 2°C. Species-level identification was performed on isolated colonies by the VITEK® MS and VITEK® 2 systems. These methods were used as the comparators for bacterial identification. AST was determined by the agar disc-diffusion method according to EUCAST-SFM recommendations. Etest® (bioMérieux) was used to obtain MIC values for antibiotics included on the Accelerate Pheno™ system panel. The results of disc diffusion (and Etest® for carbapenems, colistin and all discrepant results) were used as the comparator for AST. Accelerate PhenoTest™ BC kit testing Accelerate PhenoTest™ BC kits were run on a two-module Accelerate Pheno™ system using software version 1.2.0.87. As recommended by the manufacturer, all positive blood cultures were tested within 8 h after the blood culture bottle flagged positive. A 500 μL sample of blood was introduced into the sample vial and loaded into the Accelerate Pheno™ system according to the manufacturer’s instructions. This system uses cocktails of fluorescently labelled oligonucleotide probes and in situ hybridization to identify bacterial species, and morphokinetic cellular analysis to measure distinct morphokinetic features (cell morphology, mass, division rate) of live microbial cells responding to antimicrobials to generate susceptibility results. An algorithm converts bacterial growth or inhibition in the presence of an antibiotic into an MIC value. Statistical analysis For identification, the Accelerate Pheno™ system results were compared with results from the VITEK® MS and VITEK® 2 systems. For AST, the Accelerate Pheno™ system results were compared with results from disc-diffusion and Etest® methods. Ampicillin/sulbactam was not evaluated in this study because this antibiotic is not used in France. The percentage of errors between comparator methods and the Accelerate Pheno™ system was evaluated. If a discrepant result was observed between the Accelerate Pheno™ system and Etest®, the two tests were repeated twice to rule out experimental error. If a concordant result [susceptible (S), intermediate (I) or resistant (R)] was obtained in two of the three test results, this result was considered correct. The total category agreement was determined and the discrepancies were categorized as follows: very major error (VME; false susceptibility by the Accelerate Pheno™ system), major error (ME; false resistance by the Accelerate Pheno™ system) and minor error (mE; I result reported by one method and S or R reported by the other method). The VME rate was expressed: (i) as the number of all VMEs detected between the system and culture-based AST out of the total number of MICs determined; (ii) as all the discrepant results detected between the system (reported S) and culture-based AST (reported I or R) out of the number of resistant strains for the tested antibiotics. The ME rate was expressed: (i) as the number of all MEs detected between the system and culture-based AST out of the total number of MICs determined; (ii) as all the discrepant results detected between the system (reported I or R) and culture-based AST (reported S) out of the number of susceptible strains for the tested antibiotics. Results and discussion Our evaluation of the Accelerate Pheno™ system assessed the potential for correct identification of bacterial genus. In the panel we studied, the Accelerate Pheno™ system exhibited 100% identification agreement with the VITEK® MS and VITEK® 2 systems. An analysis of the bacterial ecology of our university hospital in 2016 showed that the panel of aerobic GNB detected by this instrument (E. coli, Klebsiella spp., Enterobacter spp., Proteus spp., Citrobacter spp., Serratia marcescens, Pseudomonas aeruginosa and A. baumannii) represented 87.1% (590/677) and 93.6% (573/612) of aerobic GNB isolated in aerobic and anaerobic bottles, respectively (personal data). The Accelerate Pheno™ system accurately identified the main pathogens involved in BSIs. Moreover, as the result is reported in <1.5 h, it shows a clear advantage compared with routine laboratory procedures and is similar in speed to other solutions (e.g. Biofire® Film Array, Verigene® Nanosphere). Regarding the AST results from the panel studied here, the Accelerate Pheno™ system generated AST data for all of the tested samples. A total of 1232 AST results were produced and compared with disc-diffusion (S, I, R) and Etest® results. The overall category agreement between the Accelerate Pheno™ system and culture-based AST was 94.9% (1169/1232). Error rates were as follows: mE, 4.1% (51/1232); ME, 0.3% (4/1232); and VME, 0.7% (8/1232). After removing the bias of the prevalence of R and S strains in our panel, these error rates were: ME, 3.9% (26/668) and VME, 3.9% (22/564). The results are shown in Tables 2–4. Table 2. AST results for the Accelerate Pheno™ system compared with disc diffusion and Etest listed by resistance profile All strains Enterobacteriaceae A. baumannii Antibioticsa category agreements, n (%) discrepanciesc β-lactam resistance (n = 8) 3GCb susceptible (n = 15) ESBL-type (n = 17) high AmpCb and OXY-type (n = 9) carbapenemases (n = 33) carbapenem impermeability (n = 17) WTb (n = 1) OXA-type (n = 5) TZP 100 (95.2%) 4 mEs, 1 VME 100% 93.3% (1 VME) 88.2% (2 mEs) 88.9% (1 mE) 100% 94.1% (1 mE) 100% 100% CRO 98 (99.0%) 1 mE 100% 100% 100% 100% 97.0% (1 mE) 100% NAd NA CAZ 95 (96.0%) 2 mEs, 1 ME, 1 VME 100% 100% 88.2% (1 VME, 1 ME) 77.8% (2 mEs) 100% 100% NA NA FEP 89 (84.8%) 14 mEs, 2 VMEs 62.5% (3 mEs) 86.7% (2 mEs) 76.5% (3 mEs, 1 VME) 88.9% (1 mE) 84.8% (4 mEs, 1 VME) 94.1% (1 mE) 100% 100% ATM 88 (88.9%) 11 mEs 87.5% (1 mEs) 86.7% (2 mEs) 76.5% (4 mEs) 88.9% (1 mE) 93.9% (2 mEs) 94.1% (1 mE) NA NA ETP 91 (91.9%) 5 mEs, 3 VMEs 100% 100% 100% 100% 81.8% (3 mEs, 3 VMEs) 88.2% (2 mEs) NA NA MEM 98 (93.3%) 5 mEs, 1 ME, 1 VME 100% 100% 100% 100% 84.8% (4 mEs, 1 VME) 88.2% (1 mE, 1 ME) 100% 100% AMK 102 (97.1%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% 100% 100% TOB 96 (97.0%) 1 mE, 2 MEs 87.5% (1 ME) 100% 94.1% (1 ME) 88.9% (1 mE) 100% 100% NA NA GEN 96 (97.0%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% NA NA CIP 104 (99.1%) 1 mE 100% 100% 100% 88.9% (1 mE) 100% 100% 100% 100% CST 99 (100%) — 100% 100% 100% 100% 100% 100% NA NA MIN 13 (92.9%) 1 mEe 100% NA NA NA NA NA 100% 80% (1 mE) All strains Enterobacteriaceae A. baumannii Antibioticsa category agreements, n (%) discrepanciesc β-lactam resistance (n = 8) 3GCb susceptible (n = 15) ESBL-type (n = 17) high AmpCb and OXY-type (n = 9) carbapenemases (n = 33) carbapenem impermeability (n = 17) WTb (n = 1) OXA-type (n = 5) TZP 100 (95.2%) 4 mEs, 1 VME 100% 93.3% (1 VME) 88.2% (2 mEs) 88.9% (1 mE) 100% 94.1% (1 mE) 100% 100% CRO 98 (99.0%) 1 mE 100% 100% 100% 100% 97.0% (1 mE) 100% NAd NA CAZ 95 (96.0%) 2 mEs, 1 ME, 1 VME 100% 100% 88.2% (1 VME, 1 ME) 77.8% (2 mEs) 100% 100% NA NA FEP 89 (84.8%) 14 mEs, 2 VMEs 62.5% (3 mEs) 86.7% (2 mEs) 76.5% (3 mEs, 1 VME) 88.9% (1 mE) 84.8% (4 mEs, 1 VME) 94.1% (1 mE) 100% 100% ATM 88 (88.9%) 11 mEs 87.5% (1 mEs) 86.7% (2 mEs) 76.5% (4 mEs) 88.9% (1 mE) 93.9% (2 mEs) 94.1% (1 mE) NA NA ETP 91 (91.9%) 5 mEs, 3 VMEs 100% 100% 100% 100% 81.8% (3 mEs, 3 VMEs) 88.2% (2 mEs) NA NA MEM 98 (93.3%) 5 mEs, 1 ME, 1 VME 100% 100% 100% 100% 84.8% (4 mEs, 1 VME) 88.2% (1 mE, 1 ME) 100% 100% AMK 102 (97.1%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% 100% 100% TOB 96 (97.0%) 1 mE, 2 MEs 87.5% (1 ME) 100% 94.1% (1 ME) 88.9% (1 mE) 100% 100% NA NA GEN 96 (97.0%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% NA NA CIP 104 (99.1%) 1 mE 100% 100% 100% 88.9% (1 mE) 100% 100% 100% 100% CST 99 (100%) — 100% 100% 100% 100% 100% 100% NA NA MIN 13 (92.9%) 1 mEe 100% NA NA NA NA NA 100% 80% (1 mE) a TZP, piperacillin/tazobactam; CRO, ceftriaxone; CAZ, ceftazidime; FEP, cefepime; ATM, aztreonam; ETP, ertapenem; MEM, meropenem; AMK, amikacin; TOB, tobramycin; GEN, gentamicin; CIP, ciprofloxacin; CST, colistin; MIN, minocycline. b 3GC, third-generation cephalosporin; AmpC, cephalosporinase; WT, wild type. c VME, very major error (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). d NA, not applicable because not tested by Accelerate Pheno™ system. e Analysis restricted to some species. Table 2. AST results for the Accelerate Pheno™ system compared with disc diffusion and Etest listed by resistance profile All strains Enterobacteriaceae A. baumannii Antibioticsa category agreements, n (%) discrepanciesc β-lactam resistance (n = 8) 3GCb susceptible (n = 15) ESBL-type (n = 17) high AmpCb and OXY-type (n = 9) carbapenemases (n = 33) carbapenem impermeability (n = 17) WTb (n = 1) OXA-type (n = 5) TZP 100 (95.2%) 4 mEs, 1 VME 100% 93.3% (1 VME) 88.2% (2 mEs) 88.9% (1 mE) 100% 94.1% (1 mE) 100% 100% CRO 98 (99.0%) 1 mE 100% 100% 100% 100% 97.0% (1 mE) 100% NAd NA CAZ 95 (96.0%) 2 mEs, 1 ME, 1 VME 100% 100% 88.2% (1 VME, 1 ME) 77.8% (2 mEs) 100% 100% NA NA FEP 89 (84.8%) 14 mEs, 2 VMEs 62.5% (3 mEs) 86.7% (2 mEs) 76.5% (3 mEs, 1 VME) 88.9% (1 mE) 84.8% (4 mEs, 1 VME) 94.1% (1 mE) 100% 100% ATM 88 (88.9%) 11 mEs 87.5% (1 mEs) 86.7% (2 mEs) 76.5% (4 mEs) 88.9% (1 mE) 93.9% (2 mEs) 94.1% (1 mE) NA NA ETP 91 (91.9%) 5 mEs, 3 VMEs 100% 100% 100% 100% 81.8% (3 mEs, 3 VMEs) 88.2% (2 mEs) NA NA MEM 98 (93.3%) 5 mEs, 1 ME, 1 VME 100% 100% 100% 100% 84.8% (4 mEs, 1 VME) 88.2% (1 mE, 1 ME) 100% 100% AMK 102 (97.1%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% 100% 100% TOB 96 (97.0%) 1 mE, 2 MEs 87.5% (1 ME) 100% 94.1% (1 ME) 88.9% (1 mE) 100% 100% NA NA GEN 96 (97.0%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% NA NA CIP 104 (99.1%) 1 mE 100% 100% 100% 88.9% (1 mE) 100% 100% 100% 100% CST 99 (100%) — 100% 100% 100% 100% 100% 100% NA NA MIN 13 (92.9%) 1 mEe 100% NA NA NA NA NA 100% 80% (1 mE) All strains Enterobacteriaceae A. baumannii Antibioticsa category agreements, n (%) discrepanciesc β-lactam resistance (n = 8) 3GCb susceptible (n = 15) ESBL-type (n = 17) high AmpCb and OXY-type (n = 9) carbapenemases (n = 33) carbapenem impermeability (n = 17) WTb (n = 1) OXA-type (n = 5) TZP 100 (95.2%) 4 mEs, 1 VME 100% 93.3% (1 VME) 88.2% (2 mEs) 88.9% (1 mE) 100% 94.1% (1 mE) 100% 100% CRO 98 (99.0%) 1 mE 100% 100% 100% 100% 97.0% (1 mE) 100% NAd NA CAZ 95 (96.0%) 2 mEs, 1 ME, 1 VME 100% 100% 88.2% (1 VME, 1 ME) 77.8% (2 mEs) 100% 100% NA NA FEP 89 (84.8%) 14 mEs, 2 VMEs 62.5% (3 mEs) 86.7% (2 mEs) 76.5% (3 mEs, 1 VME) 88.9% (1 mE) 84.8% (4 mEs, 1 VME) 94.1% (1 mE) 100% 100% ATM 88 (88.9%) 11 mEs 87.5% (1 mEs) 86.7% (2 mEs) 76.5% (4 mEs) 88.9% (1 mE) 93.9% (2 mEs) 94.1% (1 mE) NA NA ETP 91 (91.9%) 5 mEs, 3 VMEs 100% 100% 100% 100% 81.8% (3 mEs, 3 VMEs) 88.2% (2 mEs) NA NA MEM 98 (93.3%) 5 mEs, 1 ME, 1 VME 100% 100% 100% 100% 84.8% (4 mEs, 1 VME) 88.2% (1 mE, 1 ME) 100% 100% AMK 102 (97.1%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% 100% 100% TOB 96 (97.0%) 1 mE, 2 MEs 87.5% (1 ME) 100% 94.1% (1 ME) 88.9% (1 mE) 100% 100% NA NA GEN 96 (97.0%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% NA NA CIP 104 (99.1%) 1 mE 100% 100% 100% 88.9% (1 mE) 100% 100% 100% 100% CST 99 (100%) — 100% 100% 100% 100% 100% 100% NA NA MIN 13 (92.9%) 1 mEe 100% NA NA NA NA NA 100% 80% (1 mE) a TZP, piperacillin/tazobactam; CRO, ceftriaxone; CAZ, ceftazidime; FEP, cefepime; ATM, aztreonam; ETP, ertapenem; MEM, meropenem; AMK, amikacin; TOB, tobramycin; GEN, gentamicin; CIP, ciprofloxacin; CST, colistin; MIN, minocycline. b 3GC, third-generation cephalosporin; AmpC, cephalosporinase; WT, wild type. c VME, very major error (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). d NA, not applicable because not tested by Accelerate Pheno™ system. e Analysis restricted to some species. Table 3. AST results of the Accelerate Pheno™ system compared with disc diffusion and Etest listed by species Klebsiella spp. (n = 39) E. coli (n = 36) Enterobacter spp. (n = 19) Citrobacter spp. (n = 4) Proteus spp. (n = 1) A. baumannii (n = 6) Antibiotic category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa TZP 36 (92.3) 1 VME, 2 mEs 34 (94.4) 2 mEs 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 CRO 38 (97.4) 1 mE 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NAb NA CAZ 38 (97.4) 1 mE 32 (88.9) 1 VME, 1 ME, 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 NA NA FEP 35 (89.7) 1 VME, 3 mEs 28 (77.8) 8 mEs 15 (79.0) 1 VME, 3 mEs 4 (100) 0 1 (100) 0 6 (100) 0 ATM 37 (94.9) 2 mEs 30 (83.3) 6 mEs 16 (84.2) 3 mEs 4 (100) 0 1 (100) 0 NA NA ETP 37 (94.9) 2 mEs 33 (91.7) 2 VMEs, 1 mE 17 (89.5) 1 VME, 1 mE 4 (100) 0 1 (100) 0 NA NA MEM 35 (89.7) 1 ME, 3 mEs 34 (94.4) 2 mEs 18 (94.7) 1 VME 4 (100) 0 1 (100) 0 6 (100) 0 AMK 37 (94.9) 2 mEs 35 (97.2) 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 TOB 38 (97.4) 1 mE 34 (94.4) 2 MEs 19 (100) 0 4 (100) 0 1 (100) 0 NA NA GEN 36 (92.3) 3 mEs 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA CIP 39 (100) 0 36 (100) 0 18 (94.7) 1 mE 4 (100) 0 1 (100) 0 6 (100) 0 CST 39 (100) 0 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA MIN NA NA NA NA NA NA NA NA NA NA 5 (83.3) 1 mE Klebsiella spp. (n = 39) E. coli (n = 36) Enterobacter spp. (n = 19) Citrobacter spp. (n = 4) Proteus spp. (n = 1) A. baumannii (n = 6) Antibiotic category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa TZP 36 (92.3) 1 VME, 2 mEs 34 (94.4) 2 mEs 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 CRO 38 (97.4) 1 mE 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NAb NA CAZ 38 (97.4) 1 mE 32 (88.9) 1 VME, 1 ME, 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 NA NA FEP 35 (89.7) 1 VME, 3 mEs 28 (77.8) 8 mEs 15 (79.0) 1 VME, 3 mEs 4 (100) 0 1 (100) 0 6 (100) 0 ATM 37 (94.9) 2 mEs 30 (83.3) 6 mEs 16 (84.2) 3 mEs 4 (100) 0 1 (100) 0 NA NA ETP 37 (94.9) 2 mEs 33 (91.7) 2 VMEs, 1 mE 17 (89.5) 1 VME, 1 mE 4 (100) 0 1 (100) 0 NA NA MEM 35 (89.7) 1 ME, 3 mEs 34 (94.4) 2 mEs 18 (94.7) 1 VME 4 (100) 0 1 (100) 0 6 (100) 0 AMK 37 (94.9) 2 mEs 35 (97.2) 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 TOB 38 (97.4) 1 mE 34 (94.4) 2 MEs 19 (100) 0 4 (100) 0 1 (100) 0 NA NA GEN 36 (92.3) 3 mEs 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA CIP 39 (100) 0 36 (100) 0 18 (94.7) 1 mE 4 (100) 0 1 (100) 0 6 (100) 0 CST 39 (100) 0 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA MIN NA NA NA NA NA NA NA NA NA NA 5 (83.3) 1 mE a VME, very major errors (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). b NA, not applicable because not tested by Accelerate Pheno™ system. Table 3. AST results of the Accelerate Pheno™ system compared with disc diffusion and Etest listed by species Klebsiella spp. (n = 39) E. coli (n = 36) Enterobacter spp. (n = 19) Citrobacter spp. (n = 4) Proteus spp. (n = 1) A. baumannii (n = 6) Antibiotic category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa TZP 36 (92.3) 1 VME, 2 mEs 34 (94.4) 2 mEs 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 CRO 38 (97.4) 1 mE 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NAb NA CAZ 38 (97.4) 1 mE 32 (88.9) 1 VME, 1 ME, 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 NA NA FEP 35 (89.7) 1 VME, 3 mEs 28 (77.8) 8 mEs 15 (79.0) 1 VME, 3 mEs 4 (100) 0 1 (100) 0 6 (100) 0 ATM 37 (94.9) 2 mEs 30 (83.3) 6 mEs 16 (84.2) 3 mEs 4 (100) 0 1 (100) 0 NA NA ETP 37 (94.9) 2 mEs 33 (91.7) 2 VMEs, 1 mE 17 (89.5) 1 VME, 1 mE 4 (100) 0 1 (100) 0 NA NA MEM 35 (89.7) 1 ME, 3 mEs 34 (94.4) 2 mEs 18 (94.7) 1 VME 4 (100) 0 1 (100) 0 6 (100) 0 AMK 37 (94.9) 2 mEs 35 (97.2) 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 TOB 38 (97.4) 1 mE 34 (94.4) 2 MEs 19 (100) 0 4 (100) 0 1 (100) 0 NA NA GEN 36 (92.3) 3 mEs 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA CIP 39 (100) 0 36 (100) 0 18 (94.7) 1 mE 4 (100) 0 1 (100) 0 6 (100) 0 CST 39 (100) 0 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA MIN NA NA NA NA NA NA NA NA NA NA 5 (83.3) 1 mE Klebsiella spp. (n = 39) E. coli (n = 36) Enterobacter spp. (n = 19) Citrobacter spp. (n = 4) Proteus spp. (n = 1) A. baumannii (n = 6) Antibiotic category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa TZP 36 (92.3) 1 VME, 2 mEs 34 (94.4) 2 mEs 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 CRO 38 (97.4) 1 mE 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NAb NA CAZ 38 (97.4) 1 mE 32 (88.9) 1 VME, 1 ME, 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 NA NA FEP 35 (89.7) 1 VME, 3 mEs 28 (77.8) 8 mEs 15 (79.0) 1 VME, 3 mEs 4 (100) 0 1 (100) 0 6 (100) 0 ATM 37 (94.9) 2 mEs 30 (83.3) 6 mEs 16 (84.2) 3 mEs 4 (100) 0 1 (100) 0 NA NA ETP 37 (94.9) 2 mEs 33 (91.7) 2 VMEs, 1 mE 17 (89.5) 1 VME, 1 mE 4 (100) 0 1 (100) 0 NA NA MEM 35 (89.7) 1 ME, 3 mEs 34 (94.4) 2 mEs 18 (94.7) 1 VME 4 (100) 0 1 (100) 0 6 (100) 0 AMK 37 (94.9) 2 mEs 35 (97.2) 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 TOB 38 (97.4) 1 mE 34 (94.4) 2 MEs 19 (100) 0 4 (100) 0 1 (100) 0 NA NA GEN 36 (92.3) 3 mEs 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA CIP 39 (100) 0 36 (100) 0 18 (94.7) 1 mE 4 (100) 0 1 (100) 0 6 (100) 0 CST 39 (100) 0 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA MIN NA NA NA NA NA NA NA NA NA NA 5 (83.3) 1 mE a VME, very major errors (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). b NA, not applicable because not tested by Accelerate Pheno™ system. Table 4. Major and very major errors of AST results produced by the Accelerate Pheno™ system compared with Etests MIC, mg/L (interpretation)a Strain Testb TZP CAZ CRO FEP ETP MEM TOB Errorc β-Lactam resistance mechanismsd K. pneumoniae N1008720875 AXDX <4 (S) – – – – – – VME IRT Etest 32 (R) – – – – – – E. coli MECB5 AXDX – 1 (S) 4 (R) – – – – VME CTX-M-15 Etest – 8 (R) 16 (R) – – – – E. coli N1008665740 AXDX – >8 (R) >8 (R) – – – – ME CTX-M-15 Etest – 0.5 (S) >32 (R) – – – – K. pneumoniae NKP124 AXDX – – – ≤1 (S) – – – VME SHV-5 Etest – – – 8 (R) – – – E. aerogenes ARS662 AXDX – – – ≤1 (S) 0.25 (S) ≤0.25 (S) – VME (2) NDM-1 Etest – – – 8 (R) >32 (R) 1.5 (S) – E. coli ARS603 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME NDM-1, CTX-M-15 Etest – – – – >32 (R) 4 (I) – E. coli OHY12035985 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME VIM-1, CMY-2 Etest – – – – 1.5 (R) 0.75 (S) – K. pneumoniae O1122816060 AXDX – – – – 1 (I) >8 (R) – ME impermeability Etest – – – – 0.75 (I) 0.094 (S) – E. cloacae ARS769 AXDX – – – – 2 (R) 0.5 (S) – VME IMI Etest – – – – >32 (R) >32 (R) – E. coli N1008560953 AXDX – – – – – – 8 (R) ME none Etest – – – – – – 0.25 (S) E. coli NECM9 AXDX – – – – – – 8 (R) ME CTX-M-9 Etest – – – – – – 0.5 (S) MIC, mg/L (interpretation)a Strain Testb TZP CAZ CRO FEP ETP MEM TOB Errorc β-Lactam resistance mechanismsd K. pneumoniae N1008720875 AXDX <4 (S) – – – – – – VME IRT Etest 32 (R) – – – – – – E. coli MECB5 AXDX – 1 (S) 4 (R) – – – – VME CTX-M-15 Etest – 8 (R) 16 (R) – – – – E. coli N1008665740 AXDX – >8 (R) >8 (R) – – – – ME CTX-M-15 Etest – 0.5 (S) >32 (R) – – – – K. pneumoniae NKP124 AXDX – – – ≤1 (S) – – – VME SHV-5 Etest – – – 8 (R) – – – E. aerogenes ARS662 AXDX – – – ≤1 (S) 0.25 (S) ≤0.25 (S) – VME (2) NDM-1 Etest – – – 8 (R) >32 (R) 1.5 (S) – E. coli ARS603 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME NDM-1, CTX-M-15 Etest – – – – >32 (R) 4 (I) – E. coli OHY12035985 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME VIM-1, CMY-2 Etest – – – – 1.5 (R) 0.75 (S) – K. pneumoniae O1122816060 AXDX – – – – 1 (I) >8 (R) – ME impermeability Etest – – – – 0.75 (I) 0.094 (S) – E. cloacae ARS769 AXDX – – – – 2 (R) 0.5 (S) – VME IMI Etest – – – – >32 (R) >32 (R) – E. coli N1008560953 AXDX – – – – – – 8 (R) ME none Etest – – – – – – 0.25 (S) E. coli NECM9 AXDX – – – – – – 8 (R) ME CTX-M-9 Etest – – – – – – 0.5 (S) S, susceptible; I, intermediate; R, resistant. The total numbers of VMEs and MEs respectively were: 7.6% and 0% for TZP, 0% and 3% for CRO, 4.4% and 3.2% for CAZ, 3.5% and 11.9% for ATM, 3.7 and 23.5% for FEP, 7.3% and 0% for ETP, 24% and 1.3% for MEM, 0% and 3.1% for AMK, 0% and 4.2% for TOB, 0% and 0% for GEN, 0% and 2.3% for CIP, and 0% and 0% for MIN. a Dark grey shading indicates discrepant results; light grey shading indicates AST results, which allow for the deduction of the mechanism of resistance expressed by the bacteria. b AXDX, Accelerate Pheno™ system. c VME, very major error (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). d IRT, inhibitor-resistant TEM. Table 4. Major and very major errors of AST results produced by the Accelerate Pheno™ system compared with Etests MIC, mg/L (interpretation)a Strain Testb TZP CAZ CRO FEP ETP MEM TOB Errorc β-Lactam resistance mechanismsd K. pneumoniae N1008720875 AXDX <4 (S) – – – – – – VME IRT Etest 32 (R) – – – – – – E. coli MECB5 AXDX – 1 (S) 4 (R) – – – – VME CTX-M-15 Etest – 8 (R) 16 (R) – – – – E. coli N1008665740 AXDX – >8 (R) >8 (R) – – – – ME CTX-M-15 Etest – 0.5 (S) >32 (R) – – – – K. pneumoniae NKP124 AXDX – – – ≤1 (S) – – – VME SHV-5 Etest – – – 8 (R) – – – E. aerogenes ARS662 AXDX – – – ≤1 (S) 0.25 (S) ≤0.25 (S) – VME (2) NDM-1 Etest – – – 8 (R) >32 (R) 1.5 (S) – E. coli ARS603 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME NDM-1, CTX-M-15 Etest – – – – >32 (R) 4 (I) – E. coli OHY12035985 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME VIM-1, CMY-2 Etest – – – – 1.5 (R) 0.75 (S) – K. pneumoniae O1122816060 AXDX – – – – 1 (I) >8 (R) – ME impermeability Etest – – – – 0.75 (I) 0.094 (S) – E. cloacae ARS769 AXDX – – – – 2 (R) 0.5 (S) – VME IMI Etest – – – – >32 (R) >32 (R) – E. coli N1008560953 AXDX – – – – – – 8 (R) ME none Etest – – – – – – 0.25 (S) E. coli NECM9 AXDX – – – – – – 8 (R) ME CTX-M-9 Etest – – – – – – 0.5 (S) MIC, mg/L (interpretation)a Strain Testb TZP CAZ CRO FEP ETP MEM TOB Errorc β-Lactam resistance mechanismsd K. pneumoniae N1008720875 AXDX <4 (S) – – – – – – VME IRT Etest 32 (R) – – – – – – E. coli MECB5 AXDX – 1 (S) 4 (R) – – – – VME CTX-M-15 Etest – 8 (R) 16 (R) – – – – E. coli N1008665740 AXDX – >8 (R) >8 (R) – – – – ME CTX-M-15 Etest – 0.5 (S) >32 (R) – – – – K. pneumoniae NKP124 AXDX – – – ≤1 (S) – – – VME SHV-5 Etest – – – 8 (R) – – – E. aerogenes ARS662 AXDX – – – ≤1 (S) 0.25 (S) ≤0.25 (S) – VME (2) NDM-1 Etest – – – 8 (R) >32 (R) 1.5 (S) – E. coli ARS603 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME NDM-1, CTX-M-15 Etest – – – – >32 (R) 4 (I) – E. coli OHY12035985 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME VIM-1, CMY-2 Etest – – – – 1.5 (R) 0.75 (S) – K. pneumoniae O1122816060 AXDX – – – – 1 (I) >8 (R) – ME impermeability Etest – – – – 0.75 (I) 0.094 (S) – E. cloacae ARS769 AXDX – – – – 2 (R) 0.5 (S) – VME IMI Etest – – – – >32 (R) >32 (R) – E. coli N1008560953 AXDX – – – – – – 8 (R) ME none Etest – – – – – – 0.25 (S) E. coli NECM9 AXDX – – – – – – 8 (R) ME CTX-M-9 Etest – – – – – – 0.5 (S) S, susceptible; I, intermediate; R, resistant. The total numbers of VMEs and MEs respectively were: 7.6% and 0% for TZP, 0% and 3% for CRO, 4.4% and 3.2% for CAZ, 3.5% and 11.9% for ATM, 3.7 and 23.5% for FEP, 7.3% and 0% for ETP, 24% and 1.3% for MEM, 0% and 3.1% for AMK, 0% and 4.2% for TOB, 0% and 0% for GEN, 0% and 2.3% for CIP, and 0% and 0% for MIN. a Dark grey shading indicates discrepant results; light grey shading indicates AST results, which allow for the deduction of the mechanism of resistance expressed by the bacteria. b AXDX, Accelerate Pheno™ system. c VME, very major error (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). d IRT, inhibitor-resistant TEM. The highest number of discrepancies occurred for aztreonam (11.1%) and cefepime (15.2%) (Table 2). For aztreonam, all the discrepant results corresponded to mEs in Enterobacteriaceae irrespective of the β-lactamase resistance profile. For cefepime, 14 mEs were observed, equally distributed among the resistance profiles, and two VMEs were detected in one ESBL-producing K. pneumoniae and one NDM-producing E. aerogenes (Table 4). However, aztreonam and cefepime are not used for first-line management of either sepsis or septic shock.22 The other minor errors were equally distributed among the different isolates of our panel irrespective of resistance profile (Table 2). Interestingly, some discrepant results were observed for cephalosporinase-overproducing isolates, with two isolates considered S instead of I for ceftazidime. However, in these two isolates, the ceftriaxone MICs were categorized as R by the Accelerate Pheno™ system, which allowed the isolates to be considered R to 3GC. In the same way, we observed two errors among ESBL-producers, with a VME and an ME in the ceftazidime results from two CTX-M-producing E. coli isolates (Table 4). In these two cases, however, if we use an interpretative reading of the AST results (which enables the possible mechanism of resistance expressed by the bacteria to be deduced),23 the ceftriaxone MIC results indicate the possibility of an ESBL with a clear resistance profile consistent with cefotaximase producers. More importantly, we observed VMEs [0.5% (3/564) and 0.2% (1/564) for ertapenem and meropenem, respectively] or MEs [0.2% (1/668) for meropenem] in the carbapenem results of five carbapenem-resistant Enterobacteriaceae. Three of the five discrepancies were noted for class B metallo-β-lactamases (two NDM- and one VIM-type producer) (Table 4). In these three cases, the susceptible meropenem result did not allow for correction of the false-susceptible ertapenem result. This could result in inappropriate therapeutic management of patients. In contrast, the results of two other cases of an ME and a VME with meropenem (due to impermeability and IMI production, respectively) could be called into question based on ertapenem MIC results which could have guided antibiotic treatment. Overall, 3/14 class B carbapenemase-producing Enterobacteriaceae showed discrepant results for ertapenem, with two VMEs out of ten NDM-producers and one VME out of four VIM-producers. One hypothesis to explain these results is that the discrepancies could be related to the zinc concentration of the medium used for bacterial growth. Zinc enables complete expression of the metallo-β-lactamases, which are known to use zinc ions in their catalytic sites.24,25 In 3GC-S strains, only one VME was observed for piperacillin/tazobactam with K. pneumoniae. By species, the major discrepant results (VMEs and MEs) were observed with E. coli (n = 6), Klebsiella spp. (n = 3) and Enterobacter spp. (n = 2) (Table 4). Only one isolate (NDM-producing E. aerogenes) produced two VMEs (0.9% of the studied panel). On the other hand, no MEs or VMEs for Citrobacter spp., Proteus spp. or A. baumannii were observed, irrespective of the resistance profile, though only small numbers of strains were tested in these species. Furthermore, isolates harbouring emerging co-resistant determinants (one MCR-1-producing E. coli and two armA-producing K. pneumoniae) produced correct AST results. Some limitations of this study should be noted. The number of susceptible strains was limited for some antibiotics. Moreover, the panel of studied strains was representative of the MDR organisms actually observed in France and was not exhaustive. However, the aim of our study was to focus on the potential of the Accelerate Pheno™ system to detect these local MDR bacteria. Early susceptibility results are crucial for the initiation of appropriate antimicrobial therapy for critically ill patients, including those in settings challenged by MDR bacteria, such as ICUs. Failure to initiate appropriate empirical therapy in patients with sepsis and septic shock is associated with a substantial increase in morbidity and mortality.22 To date, no tool gives a phenotypic AST result in <7 h directly from specimens such as positive blood cultures. Three recent studies by Marschal et al.,12 Brazelton de Cárdenas et al.26 and Charnot-Katsikas et al.27 have demonstrated the performance of the Accelerate Pheno™ system in a routine diagnostic setting. However, owing to the scarcity of MDR bacteria, these studies have not challenged the instrument on a large characterized panel of MDR GNB. In this study, we demonstrated the high performance of a new technology to obtain fast identification and AST results directly from positive blood cultures. This system may enable clinicians to adjust antimicrobial treatment earlier to facilitate patient management and outcomes as well as antimicrobial stewardship. Acknowledgements We thank Accelerate Diagnostics, Inc., Tucson, AZ, USA, for providing two Accelerate Pheno™ system modules and the test reagents. This company had no role in the study design, data collection or interpretation of the results.  We thank R. Bonnet and F. Robin for providing the mcr-1-positive control strain. Funding This work was supported by Institut National de la Sante et de la Recherche Medicale and University Hospital of Nîmes. Transparency declarations None to declare. Supplementary data Table S1 is available as Supplementary data at JAC Online. References 1 Laupland KB. Incidence of bloodstream infection: a review of population-based studies . Clin Microbiol Infect 2013 ; 19 : 492 – 500 . Google Scholar CrossRef Search ADS PubMed 2 Vincent JL , Marshall JC , Namendys-Silva SA et al. Assessment of the worldwide burden of critical illness: the intensive care over nations (ICON) audit . Lancet Respir Med 2014 ; 2 : 380 – 6 . Google Scholar CrossRef Search ADS PubMed 3 Constantin JM , Leone M , Jaber S et al. [Activity and the available human resources working in 66 French southern intensive care units] . Ann Fr Anesth Reanim 2010 ; 29 : 512 – 7 . Google Scholar CrossRef Search ADS PubMed 4 Barnett AG , Page K , Campbell M et al. The increased risks of death and extra lengths of hospital and ICU stay from hospital-acquired bloodstream infections: a case-control study . BMJ Open 2013 ; 3 : e003587. Google Scholar CrossRef Search ADS PubMed 5 Laupland KB , Lee H , Gregson DB et al. Cost of intensive care unit-acquired bloodstream infections . J Hosp Infect 2006 ; 63 : 124 – 32 . Google Scholar CrossRef Search ADS PubMed 6 Angus DC , van der Poll T. Severe sepsis and septic shock . N Engl J Med 2013 ; 369 : 840 – 51 . Google Scholar CrossRef Search ADS PubMed 7 Singer M , Deutschman CS , Seymour CW et al. The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) . JAMA 2016 ; 315 : 801 – 10 . Google Scholar CrossRef Search ADS PubMed 8 Laxminarayan R , Duse A , Wattal C et al. Antibiotic resistance—the need for global solutions . Lancet Infect Dis 2013 ; 13 : 1057 – 98 . Google Scholar CrossRef Search ADS PubMed 9 Roca I , Akova M , Baquero F et al. The global threat of antimicrobial resistance: science for intervention . New Microbes New Infect 2015 ; 6 : 22 – 9 . Google Scholar CrossRef Search ADS PubMed 10 Ferrer R , Martin-Loeches I , Phillips G et al. Empiric antibiotic treatment reduces mortality in severe sepsis and septic shock from the first hour: results from a guideline-based performance improvement program . Crit Care Med 2014 ; 42 : 1749 – 55 . Google Scholar CrossRef Search ADS PubMed 11 Chantell C. Multiplexed automated digital microscopy for rapid identification and antimicrobial susceptibility testing of bacteria and yeast directly from clinical samples . Clin Microbiol Newsl 2015 ; 37 : 161 – 7 . Google Scholar CrossRef Search ADS 12 Marschal M , Bachmaier J , Autenrieth I et al. Evaluation of the Accelerate Pheno system for fast identification and antimicrobial susceptibility testing from positive blood cultures in bloodstream infections caused by Gram-negative pathogens . J Clin Microbiol 2017 ; 55 : 2116 – 26 . Google Scholar CrossRef Search ADS PubMed 13 Pantel A , Boutet-Dubois A , Jean-Pierre H et al. French regional surveillance program of carbapenemase-producing Gram-negative bacilli: results from a 2-year period . Eur J Clin Microbiol Infect Dis 2014 ; 33 : 2285 – 92 . Google Scholar CrossRef Search ADS PubMed 14 Robert J , Pantel A , Mérens A et al. Incidence rates of carbapenemase-producing Enterobacteriaceae clinical isolates in France: a prospective nationwide study in 2011-12 . J Antimicrob Chemother 2014 ; 69 : 2706 – 12 . Google Scholar CrossRef Search ADS PubMed 15 Pitout JD , Hossain A , Hanson ND. Phenotypic and molecular detection of CTX-M-beta-lactamases produced by Escherichia coli and Klebsiella spp . J Clin Microbiol 2004 ; 42 : 5715 – 21 . Google Scholar CrossRef Search ADS PubMed 16 Aubron C , Poirel L , Ash RJ et al. Carbapenemase-producing Enterobacteriaceae, U.S. rivers . Emerg Infect Dis 2005 ; 11 : 260 – 4 . Google Scholar CrossRef Search ADS PubMed 17 Poirel L , Walsh TR , Cuvillier V et al. Multiplex PCR for detection of acquired carbapenemase genes . Diagn Microbiol Infect Dis 2011 ; 70 : 119 – 23 . Google Scholar CrossRef Search ADS PubMed 18 Perez-Perez FJ , Hanson ND. Detection of plasmid-mediated AmpC β-lactamase genes in clinical isolates by using multiplex PCR . J Clin Microbiol 2002 ; 40 : 2153 – 62 . Google Scholar CrossRef Search ADS PubMed 19 Woodford N , Ellington MJ , Coelho JM et al. Multiplex PCR for genes encoding prevalent OXA carbapenemases in Acinetobacter spp . Int J Antimicrob Agents 2006 ; 27 : 351 – 3 . Google Scholar CrossRef Search ADS PubMed 20 Liu YY , Wang Y , Walsh TR et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study . Lancet Infect Dis 2016 ; 16 : 161 – 8 . Google Scholar CrossRef Search ADS PubMed 21 Hidalgo L , Hopkins KL , Gutierrez B et al. Association of the novel aminoglycoside resistance determinant RmtF with NDM carbapenemase in Enterobacteriaceae isolated in India and the UK . J Antimicrob Chemother 2013 ; 68 : 1543 – 50 . Google Scholar CrossRef Search ADS PubMed 22 Rhodes A , Evans LE , Alhazzani W et al. Surviving Sepsis Campaign: international guidelines for management of sepsis and septic shock: 2016 . Intensive Care Med 2017 ; 43 : 304 – 77 . Google Scholar CrossRef Search ADS PubMed 23 Livermore DM , Winstanley TG , Shannon KP. Interpretative reading: recognizing the unusual and inferring resistance mechanisms from resistance phenotypes . J Antimicrob Chemother 2001 ; 48 : 87 – 102 . Google Scholar CrossRef Search ADS PubMed 24 Lee K , Lim YS , Yong D et al. Evaluation of the Hodge test and the imipenem-EDTA double-disk synergy test for differentiating metallo-β-lactamase-producing isolates of Pseudomonas spp. and Acinetobacter spp . J Clin Microbiol 2003 ; 41 : 4623 – 9 . Google Scholar CrossRef Search ADS PubMed 25 Dortet L , Bréchard L , Poirel L et al. Impact of the isolation medium for detection of carbapenemase-producing Enterobacteriaceae using an updated version of the Carba NP test . J Med Microbiol 2014 ; 63 : 772 – 6 . Google Scholar CrossRef Search ADS PubMed 26 Brazelton de Cárdenas JN , Su Y , Rodriguez A et al. Evaluation of rapid phenotypic identification and antimicrobial susceptibility testing in a pediatric oncology center . Diagn Microbiol Infect Dis 2017 ; 89 : 52 – 7 . Google Scholar CrossRef Search ADS PubMed 27 Charnot-Katsikas A , Tesic V , Love N et al. Use of Accelerate Pheno™ system for identification and antimicrobial susceptibility testing (ID/AST) of pathogens in positive blood cultures and impact on time to results and workflow . J Clin Microbiol 2017 ; 56 : pii=e01166-17. © The Author(s) 2018. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/about_us/legal/notices) http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Antimicrobial Chemotherapy Oxford University Press

Performance of the Accelerate Pheno™ system for identification and antimicrobial susceptibility testing of a panel of multidrug-resistant Gram-negative bacilli directly from positive blood cultures

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Oxford University Press
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© The Author(s) 2018. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
ISSN
0305-7453
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1460-2091
D.O.I.
10.1093/jac/dky032
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Abstract

Abstract Objectives To evaluate the performance of the Accelerate Pheno™ system for the identification and antimicrobial susceptibility testing (AST) of a panel of Gram-negative bacilli (GNB) with different resistance profiles (e.g. penicillinases, ESBLs, cephalosporinase overproduction, carbapenemases, impermeability) directly from positive blood cultures in <7 h. Methods A panel of 105 clinical strains previously characterized for the presence of β-lactamase-encoding genes was tested. Approximately 100 cfu of each isolate was inoculated into sterile blood culture bottles and incubated in a BD BACTEC™ FX automated system (Becton Dickinson, USA). Positive blood cultures were subjected to parallel testing using the Accelerate Pheno™ system and conventional culture methods [identification of isolated colonies by MALDI-TOF and VITEK® 2 system (bioMérieux, France), and AST by disc diffusion and Etest following EUCAST recommendations]. Results The overall identification agreement between the Accelerate Pheno™ system and conventional culture methods was 100% (105/105). The overall categorical agreement between the system and culture-based AST was 94.9% (1169/1232), with rates for minor errors of 4.1% (51/1232), major errors 0.3% (4/1232) and very major errors 0.7% (8/1232). The Accelerate Pheno™ system produced AST results indicative of third-generation cephalosporinases (26/26) and carbapenem-resistant strains (52/55). Conclusions The Accelerate Pheno™ system is an accurate, sensitive and easy-to-use test for the rapid identification and AST of MDR GNB in bloodstream infections. Given the burden of multidrug resistance, its implementation in the microbiology laboratory could be a useful tool for prompt management of sepsis. Introduction The incidence of bloodstream infections (BSIs) is reported to be ∼150 per 100 000 population.1 In ICUs, the incidence is ∼30% of admissions, a level that has remained stable over the last decade.1,2 Septic shock, the most severe form of sepsis, occurs in 10%–20% of ICU-admitted patients.1,3 It is responsible for increases in both length of stay and healthcare-related costs.4,5 Moreover, BSIs are a leading cause of death in critically ill patients worldwide, with an overall mortality rate of close to 40%.6,7 The spread of MDR Gram-negative bacilli (GNB) has become a major public health challenge directly related to the misuse and overuse of antibiotics.8 The rapid optimization of antibiotic therapy, according to the organism and its resistance profile, is a major goal both for individual patients and for public health.9 In severe sepsis and septic shock, the importance of early appropriate treatment is crucial, given the linear increase in the risk of mortality with each hour for which antibiotic administration is delayed.10 Current clinical microbiology methods are time consuming and are not validated for direct use on positive blood cultures. These methods require an overnight pure subculture on agar for subsequent identification of causative organisms and preparation of a standard inoculum for antimicrobial susceptibility testing (AST) according to the manufacturer’s guidelines. Faster identification and AST directly from positive blood cultures would have the potential to significantly improve time to diagnosis and initiation of appropriate antibiotic and patient management in ICUs. However, to our knowledge, none of the current technologies provide prompt AST with MICs that truly reflect the resistance profile of the bacteria involved in the BSI. In this study, we evaluated the performance of the Accelerate Pheno™ system (Accelerate Diagnostics Inc.) compared with routine laboratory analysis in order: (i) to provide a correct identification in 1.5 h; and (ii) to detect resistance in a panel of GNB, representative of the ecology of our region, within 7 h.11,12 Methods Bacterial panel A panel of 105 clinical GNB isolates belonging to a collection from our Regional MDR GNB Reference Lab (the CARB-LR group)13,14 in the Occitanie Region was tested (Table 1). Ninety-nine Enterobacteriaceae isolates were included with the following distribution: Escherichia coli (n = 36), Klebsiella pneumoniae (n = 34), Enterobacter cloacae (n = 14), Enterobacter aerogenes (n = 5), Klebsiella oxytoca (n = 5), Citrobacter freundii (n = 2), Citrobacter koseri (n = 2) and Proteus mirabilis (n = 1). Different β-lactam resistance profiles were selected with the following properties: (i) susceptibility to third-generation cephalosporins (3GC-S, n = 23); (ii) resistance to 3GCs (3GC-R, n = 26) mediated by ESBL (n = 17) or overexpressed/plasmid-mediated cephalosporinases (AmpC, n = 9); and (iii) resistance to carbapenems (n = 50) involving carbapenemase production (n = 33) or membrane permeability alterations (n = 17). Six Acinetobacter baumannii strains were also included: a wild-type phenotype (n = 1), and different carbapenemase-producing isolates [OXA-23, -24 or -58-type producers (n = 5)]. Table 1. Characteristics of the studied Gram-negative bacilli panel Group Resistance profile (no. of strains) Species (no. of strains) β-Lactamase content (no. of strains) Enterobacteriaceae 3GCa susceptible (23) no resistance to β-lactams (8) E. coli (8) none penicillinase (12) E. coli (6) TEM-1 (3) TEM-1 hyperproduction (2) inhibitor-resistant TEM (1) K. pneumoniae (4) SHV-1 (1) SHV-1 hyperproduction (2) inhibitor-resistant TEM (1) C. koseri (2) CKO (2) chromosomal cephalosporinase (3) E. aerogenes (2) AmpC (2) E. cloacae (1) AmpC (1) 3GC resistant (26) ESBL (17) E. coli (14) CTX-M-group 1 (7)b CTX-M-group 9 (5) CTX-M-group 8 (2) K. pneumoniae (2) SHV-5 (1) CTX-M-group 1 (1) P. mirabilis (1) CTX-M-group 1 (1) cephalosporinase overproduction (8) E. coli (2) AmpC hyperproduction (2) K. pneumoniae (2) DHA-1, SHV-1, TEM-1 (1) DHA-1, SHV-1 (1) E. cloacae (2) AmpC hyperproduction (2) C. freundii (2) AmpC hyperproduction (2) penicillinase overproduction (1) K. oxytoca (1) OXY hyperproduction (1) Carbapenem resistant (50) Class A carbapenemase (6) K. pneumoniae (5) KPC-2, CTX-M-group 1, SHV-1 (1) KPC-2 (4)c E. cloacae (1) IMI-1, AmpC (1) Class B carbapenemase (12) K. pneumoniae (6) NDM-1, SHV-1 (1) NDM-1, CTX-M-group 1, SHV-1 (3) VIM-1, SHV-1 (2) E. coli (4) NDM-1, CTX-M-group 1 (1) NDM-1, CTX-M-group 9 (1) NDM-1, DHA-1 (1) VIM-1 (1) E. cloacae (1) VIM-1, AmpC hyperproduced (1) E. aerogenes (1) NDM-1, CTX-M-group 1, AmpC (1) Class D carbapenemase (13) K. pneumoniae (6) OXA-48, SHV-1 (2) OXA-48, CTX-M-group 1, SHV-1 (4) E. coli (2) OXA-48 (1) OXA-181, CTX-M-group 1 (1) E. cloacae (2) OXA-48, CTX-M-group 1, AmpC (2) E. aerogenes (2) OXA-48, AmpC (2) K. oxytoca (1) OXA-48, OXY-1 (1) Class B + D carbapenemases (2) K. pneumoniae (2) OXA-48, NDM-1, CTX-M-group 1, SHV-1 (2) impermeability (17) K. pneumoniae (7) CTX-M-group 1, SHV-1 (1) DHA-1, SHV-1 (6) E. cloacae (7) AmpC hyperproduction (5) AmpC hyperproduction, CTX-M-group 9 (1) AmpC hyperproduction, SHV-5 (1) K. oxytoca (3) OXY hyperproduction (3) Non-fermenting Gram-negative bacilli wild-type (1) A. baumannii (1) AmpC (1) Class D carbapenemase (5) A. baumannii (5) OXA-23-type (3) OXA-24-type (1) OXA-23-type, OXA-58-type (1) Group Resistance profile (no. of strains) Species (no. of strains) β-Lactamase content (no. of strains) Enterobacteriaceae 3GCa susceptible (23) no resistance to β-lactams (8) E. coli (8) none penicillinase (12) E. coli (6) TEM-1 (3) TEM-1 hyperproduction (2) inhibitor-resistant TEM (1) K. pneumoniae (4) SHV-1 (1) SHV-1 hyperproduction (2) inhibitor-resistant TEM (1) C. koseri (2) CKO (2) chromosomal cephalosporinase (3) E. aerogenes (2) AmpC (2) E. cloacae (1) AmpC (1) 3GC resistant (26) ESBL (17) E. coli (14) CTX-M-group 1 (7)b CTX-M-group 9 (5) CTX-M-group 8 (2) K. pneumoniae (2) SHV-5 (1) CTX-M-group 1 (1) P. mirabilis (1) CTX-M-group 1 (1) cephalosporinase overproduction (8) E. coli (2) AmpC hyperproduction (2) K. pneumoniae (2) DHA-1, SHV-1, TEM-1 (1) DHA-1, SHV-1 (1) E. cloacae (2) AmpC hyperproduction (2) C. freundii (2) AmpC hyperproduction (2) penicillinase overproduction (1) K. oxytoca (1) OXY hyperproduction (1) Carbapenem resistant (50) Class A carbapenemase (6) K. pneumoniae (5) KPC-2, CTX-M-group 1, SHV-1 (1) KPC-2 (4)c E. cloacae (1) IMI-1, AmpC (1) Class B carbapenemase (12) K. pneumoniae (6) NDM-1, SHV-1 (1) NDM-1, CTX-M-group 1, SHV-1 (3) VIM-1, SHV-1 (2) E. coli (4) NDM-1, CTX-M-group 1 (1) NDM-1, CTX-M-group 9 (1) NDM-1, DHA-1 (1) VIM-1 (1) E. cloacae (1) VIM-1, AmpC hyperproduced (1) E. aerogenes (1) NDM-1, CTX-M-group 1, AmpC (1) Class D carbapenemase (13) K. pneumoniae (6) OXA-48, SHV-1 (2) OXA-48, CTX-M-group 1, SHV-1 (4) E. coli (2) OXA-48 (1) OXA-181, CTX-M-group 1 (1) E. cloacae (2) OXA-48, CTX-M-group 1, AmpC (2) E. aerogenes (2) OXA-48, AmpC (2) K. oxytoca (1) OXA-48, OXY-1 (1) Class B + D carbapenemases (2) K. pneumoniae (2) OXA-48, NDM-1, CTX-M-group 1, SHV-1 (2) impermeability (17) K. pneumoniae (7) CTX-M-group 1, SHV-1 (1) DHA-1, SHV-1 (6) E. cloacae (7) AmpC hyperproduction (5) AmpC hyperproduction, CTX-M-group 9 (1) AmpC hyperproduction, SHV-5 (1) K. oxytoca (3) OXY hyperproduction (3) Non-fermenting Gram-negative bacilli wild-type (1) A. baumannii (1) AmpC (1) Class D carbapenemase (5) A. baumannii (5) OXA-23-type (3) OXA-24-type (1) OXA-23-type, OXA-58-type (1) a 3GC, third-generation cephalosporins. b One CTX-M-producing E. coli harboured the plasmid-mediated colistin resistance gene mcr-1 (colistin MIC 4 mg/L). c Two KPC-producing K. pneumoniae harboured the aminoglycoside resistance methyltransferase gene armA. Table 1. Characteristics of the studied Gram-negative bacilli panel Group Resistance profile (no. of strains) Species (no. of strains) β-Lactamase content (no. of strains) Enterobacteriaceae 3GCa susceptible (23) no resistance to β-lactams (8) E. coli (8) none penicillinase (12) E. coli (6) TEM-1 (3) TEM-1 hyperproduction (2) inhibitor-resistant TEM (1) K. pneumoniae (4) SHV-1 (1) SHV-1 hyperproduction (2) inhibitor-resistant TEM (1) C. koseri (2) CKO (2) chromosomal cephalosporinase (3) E. aerogenes (2) AmpC (2) E. cloacae (1) AmpC (1) 3GC resistant (26) ESBL (17) E. coli (14) CTX-M-group 1 (7)b CTX-M-group 9 (5) CTX-M-group 8 (2) K. pneumoniae (2) SHV-5 (1) CTX-M-group 1 (1) P. mirabilis (1) CTX-M-group 1 (1) cephalosporinase overproduction (8) E. coli (2) AmpC hyperproduction (2) K. pneumoniae (2) DHA-1, SHV-1, TEM-1 (1) DHA-1, SHV-1 (1) E. cloacae (2) AmpC hyperproduction (2) C. freundii (2) AmpC hyperproduction (2) penicillinase overproduction (1) K. oxytoca (1) OXY hyperproduction (1) Carbapenem resistant (50) Class A carbapenemase (6) K. pneumoniae (5) KPC-2, CTX-M-group 1, SHV-1 (1) KPC-2 (4)c E. cloacae (1) IMI-1, AmpC (1) Class B carbapenemase (12) K. pneumoniae (6) NDM-1, SHV-1 (1) NDM-1, CTX-M-group 1, SHV-1 (3) VIM-1, SHV-1 (2) E. coli (4) NDM-1, CTX-M-group 1 (1) NDM-1, CTX-M-group 9 (1) NDM-1, DHA-1 (1) VIM-1 (1) E. cloacae (1) VIM-1, AmpC hyperproduced (1) E. aerogenes (1) NDM-1, CTX-M-group 1, AmpC (1) Class D carbapenemase (13) K. pneumoniae (6) OXA-48, SHV-1 (2) OXA-48, CTX-M-group 1, SHV-1 (4) E. coli (2) OXA-48 (1) OXA-181, CTX-M-group 1 (1) E. cloacae (2) OXA-48, CTX-M-group 1, AmpC (2) E. aerogenes (2) OXA-48, AmpC (2) K. oxytoca (1) OXA-48, OXY-1 (1) Class B + D carbapenemases (2) K. pneumoniae (2) OXA-48, NDM-1, CTX-M-group 1, SHV-1 (2) impermeability (17) K. pneumoniae (7) CTX-M-group 1, SHV-1 (1) DHA-1, SHV-1 (6) E. cloacae (7) AmpC hyperproduction (5) AmpC hyperproduction, CTX-M-group 9 (1) AmpC hyperproduction, SHV-5 (1) K. oxytoca (3) OXY hyperproduction (3) Non-fermenting Gram-negative bacilli wild-type (1) A. baumannii (1) AmpC (1) Class D carbapenemase (5) A. baumannii (5) OXA-23-type (3) OXA-24-type (1) OXA-23-type, OXA-58-type (1) Group Resistance profile (no. of strains) Species (no. of strains) β-Lactamase content (no. of strains) Enterobacteriaceae 3GCa susceptible (23) no resistance to β-lactams (8) E. coli (8) none penicillinase (12) E. coli (6) TEM-1 (3) TEM-1 hyperproduction (2) inhibitor-resistant TEM (1) K. pneumoniae (4) SHV-1 (1) SHV-1 hyperproduction (2) inhibitor-resistant TEM (1) C. koseri (2) CKO (2) chromosomal cephalosporinase (3) E. aerogenes (2) AmpC (2) E. cloacae (1) AmpC (1) 3GC resistant (26) ESBL (17) E. coli (14) CTX-M-group 1 (7)b CTX-M-group 9 (5) CTX-M-group 8 (2) K. pneumoniae (2) SHV-5 (1) CTX-M-group 1 (1) P. mirabilis (1) CTX-M-group 1 (1) cephalosporinase overproduction (8) E. coli (2) AmpC hyperproduction (2) K. pneumoniae (2) DHA-1, SHV-1, TEM-1 (1) DHA-1, SHV-1 (1) E. cloacae (2) AmpC hyperproduction (2) C. freundii (2) AmpC hyperproduction (2) penicillinase overproduction (1) K. oxytoca (1) OXY hyperproduction (1) Carbapenem resistant (50) Class A carbapenemase (6) K. pneumoniae (5) KPC-2, CTX-M-group 1, SHV-1 (1) KPC-2 (4)c E. cloacae (1) IMI-1, AmpC (1) Class B carbapenemase (12) K. pneumoniae (6) NDM-1, SHV-1 (1) NDM-1, CTX-M-group 1, SHV-1 (3) VIM-1, SHV-1 (2) E. coli (4) NDM-1, CTX-M-group 1 (1) NDM-1, CTX-M-group 9 (1) NDM-1, DHA-1 (1) VIM-1 (1) E. cloacae (1) VIM-1, AmpC hyperproduced (1) E. aerogenes (1) NDM-1, CTX-M-group 1, AmpC (1) Class D carbapenemase (13) K. pneumoniae (6) OXA-48, SHV-1 (2) OXA-48, CTX-M-group 1, SHV-1 (4) E. coli (2) OXA-48 (1) OXA-181, CTX-M-group 1 (1) E. cloacae (2) OXA-48, CTX-M-group 1, AmpC (2) E. aerogenes (2) OXA-48, AmpC (2) K. oxytoca (1) OXA-48, OXY-1 (1) Class B + D carbapenemases (2) K. pneumoniae (2) OXA-48, NDM-1, CTX-M-group 1, SHV-1 (2) impermeability (17) K. pneumoniae (7) CTX-M-group 1, SHV-1 (1) DHA-1, SHV-1 (6) E. cloacae (7) AmpC hyperproduction (5) AmpC hyperproduction, CTX-M-group 9 (1) AmpC hyperproduction, SHV-5 (1) K. oxytoca (3) OXY hyperproduction (3) Non-fermenting Gram-negative bacilli wild-type (1) A. baumannii (1) AmpC (1) Class D carbapenemase (5) A. baumannii (5) OXA-23-type (3) OXA-24-type (1) OXA-23-type, OXA-58-type (1) a 3GC, third-generation cephalosporins. b One CTX-M-producing E. coli harboured the plasmid-mediated colistin resistance gene mcr-1 (colistin MIC 4 mg/L). c Two KPC-producing K. pneumoniae harboured the aminoglycoside resistance methyltransferase gene armA. Isolates had been previously identified using the VITEK® MS and VITEK® 2 systems (bioMérieux, France). Susceptibility to antimicrobial agents was tested by the disc-diffusion method (BioRad, Marnes La Coquette, France) on Mueller–Hinton agar according to EUCAST-SFM 2016 recommendations (http://www.sfm-microbiologie.org). In addition, the MICs of carbapenems (ertapenem and meropenem) were determined by the Etest® method (bioMérieux). The MIC of colistin was determined using microbroth dilution (Umic®, Biocentric, France). The MICs were interpreted as specified by the EUCAST-SFM criteria. All isolates were typed by Check-MDR CT102/103® microarrays (Check-point, the Netherlands). Confirmation of the presence of β-lactamase-encoding genes was done by PCRs using specific primers and confirmed by sequencing the PCR products as previously described.15–19 Emerging resistance mechanisms (colistin resistance mcr-1 determinant and 16S rRNA methylase) were also characterized by PCR as previously described.20,21 The AST results of the studied strains are presented in Table S1 (available as Supplementary data at JAC Online). Sample preparation For each isolate, ∼100 cfu was spiked into sterile blood culture bottles [BD BACTEC™ Plus Aerobic/F and BD BACTEC™ Lytic/10 Anaerobic/F (BD Diagnostics)] containing 10 mL of fresh blood. Blood cultures were incubated in a BACTEC™ FX automated blood culture device until they flagged positive for microbial growth. All positive blood cultures were divided into two samples: (i) 1 mL for conventional comparator methods; and (ii) 0.5 mL for the Accelerate Pheno™ system. Conventional comparator methods All positive blood cultures were subcultured on blood agar plates (bioMérieux) for 18–24 h at 37 ± 2°C. Species-level identification was performed on isolated colonies by the VITEK® MS and VITEK® 2 systems. These methods were used as the comparators for bacterial identification. AST was determined by the agar disc-diffusion method according to EUCAST-SFM recommendations. Etest® (bioMérieux) was used to obtain MIC values for antibiotics included on the Accelerate Pheno™ system panel. The results of disc diffusion (and Etest® for carbapenems, colistin and all discrepant results) were used as the comparator for AST. Accelerate PhenoTest™ BC kit testing Accelerate PhenoTest™ BC kits were run on a two-module Accelerate Pheno™ system using software version 1.2.0.87. As recommended by the manufacturer, all positive blood cultures were tested within 8 h after the blood culture bottle flagged positive. A 500 μL sample of blood was introduced into the sample vial and loaded into the Accelerate Pheno™ system according to the manufacturer’s instructions. This system uses cocktails of fluorescently labelled oligonucleotide probes and in situ hybridization to identify bacterial species, and morphokinetic cellular analysis to measure distinct morphokinetic features (cell morphology, mass, division rate) of live microbial cells responding to antimicrobials to generate susceptibility results. An algorithm converts bacterial growth or inhibition in the presence of an antibiotic into an MIC value. Statistical analysis For identification, the Accelerate Pheno™ system results were compared with results from the VITEK® MS and VITEK® 2 systems. For AST, the Accelerate Pheno™ system results were compared with results from disc-diffusion and Etest® methods. Ampicillin/sulbactam was not evaluated in this study because this antibiotic is not used in France. The percentage of errors between comparator methods and the Accelerate Pheno™ system was evaluated. If a discrepant result was observed between the Accelerate Pheno™ system and Etest®, the two tests were repeated twice to rule out experimental error. If a concordant result [susceptible (S), intermediate (I) or resistant (R)] was obtained in two of the three test results, this result was considered correct. The total category agreement was determined and the discrepancies were categorized as follows: very major error (VME; false susceptibility by the Accelerate Pheno™ system), major error (ME; false resistance by the Accelerate Pheno™ system) and minor error (mE; I result reported by one method and S or R reported by the other method). The VME rate was expressed: (i) as the number of all VMEs detected between the system and culture-based AST out of the total number of MICs determined; (ii) as all the discrepant results detected between the system (reported S) and culture-based AST (reported I or R) out of the number of resistant strains for the tested antibiotics. The ME rate was expressed: (i) as the number of all MEs detected between the system and culture-based AST out of the total number of MICs determined; (ii) as all the discrepant results detected between the system (reported I or R) and culture-based AST (reported S) out of the number of susceptible strains for the tested antibiotics. Results and discussion Our evaluation of the Accelerate Pheno™ system assessed the potential for correct identification of bacterial genus. In the panel we studied, the Accelerate Pheno™ system exhibited 100% identification agreement with the VITEK® MS and VITEK® 2 systems. An analysis of the bacterial ecology of our university hospital in 2016 showed that the panel of aerobic GNB detected by this instrument (E. coli, Klebsiella spp., Enterobacter spp., Proteus spp., Citrobacter spp., Serratia marcescens, Pseudomonas aeruginosa and A. baumannii) represented 87.1% (590/677) and 93.6% (573/612) of aerobic GNB isolated in aerobic and anaerobic bottles, respectively (personal data). The Accelerate Pheno™ system accurately identified the main pathogens involved in BSIs. Moreover, as the result is reported in <1.5 h, it shows a clear advantage compared with routine laboratory procedures and is similar in speed to other solutions (e.g. Biofire® Film Array, Verigene® Nanosphere). Regarding the AST results from the panel studied here, the Accelerate Pheno™ system generated AST data for all of the tested samples. A total of 1232 AST results were produced and compared with disc-diffusion (S, I, R) and Etest® results. The overall category agreement between the Accelerate Pheno™ system and culture-based AST was 94.9% (1169/1232). Error rates were as follows: mE, 4.1% (51/1232); ME, 0.3% (4/1232); and VME, 0.7% (8/1232). After removing the bias of the prevalence of R and S strains in our panel, these error rates were: ME, 3.9% (26/668) and VME, 3.9% (22/564). The results are shown in Tables 2–4. Table 2. AST results for the Accelerate Pheno™ system compared with disc diffusion and Etest listed by resistance profile All strains Enterobacteriaceae A. baumannii Antibioticsa category agreements, n (%) discrepanciesc β-lactam resistance (n = 8) 3GCb susceptible (n = 15) ESBL-type (n = 17) high AmpCb and OXY-type (n = 9) carbapenemases (n = 33) carbapenem impermeability (n = 17) WTb (n = 1) OXA-type (n = 5) TZP 100 (95.2%) 4 mEs, 1 VME 100% 93.3% (1 VME) 88.2% (2 mEs) 88.9% (1 mE) 100% 94.1% (1 mE) 100% 100% CRO 98 (99.0%) 1 mE 100% 100% 100% 100% 97.0% (1 mE) 100% NAd NA CAZ 95 (96.0%) 2 mEs, 1 ME, 1 VME 100% 100% 88.2% (1 VME, 1 ME) 77.8% (2 mEs) 100% 100% NA NA FEP 89 (84.8%) 14 mEs, 2 VMEs 62.5% (3 mEs) 86.7% (2 mEs) 76.5% (3 mEs, 1 VME) 88.9% (1 mE) 84.8% (4 mEs, 1 VME) 94.1% (1 mE) 100% 100% ATM 88 (88.9%) 11 mEs 87.5% (1 mEs) 86.7% (2 mEs) 76.5% (4 mEs) 88.9% (1 mE) 93.9% (2 mEs) 94.1% (1 mE) NA NA ETP 91 (91.9%) 5 mEs, 3 VMEs 100% 100% 100% 100% 81.8% (3 mEs, 3 VMEs) 88.2% (2 mEs) NA NA MEM 98 (93.3%) 5 mEs, 1 ME, 1 VME 100% 100% 100% 100% 84.8% (4 mEs, 1 VME) 88.2% (1 mE, 1 ME) 100% 100% AMK 102 (97.1%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% 100% 100% TOB 96 (97.0%) 1 mE, 2 MEs 87.5% (1 ME) 100% 94.1% (1 ME) 88.9% (1 mE) 100% 100% NA NA GEN 96 (97.0%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% NA NA CIP 104 (99.1%) 1 mE 100% 100% 100% 88.9% (1 mE) 100% 100% 100% 100% CST 99 (100%) — 100% 100% 100% 100% 100% 100% NA NA MIN 13 (92.9%) 1 mEe 100% NA NA NA NA NA 100% 80% (1 mE) All strains Enterobacteriaceae A. baumannii Antibioticsa category agreements, n (%) discrepanciesc β-lactam resistance (n = 8) 3GCb susceptible (n = 15) ESBL-type (n = 17) high AmpCb and OXY-type (n = 9) carbapenemases (n = 33) carbapenem impermeability (n = 17) WTb (n = 1) OXA-type (n = 5) TZP 100 (95.2%) 4 mEs, 1 VME 100% 93.3% (1 VME) 88.2% (2 mEs) 88.9% (1 mE) 100% 94.1% (1 mE) 100% 100% CRO 98 (99.0%) 1 mE 100% 100% 100% 100% 97.0% (1 mE) 100% NAd NA CAZ 95 (96.0%) 2 mEs, 1 ME, 1 VME 100% 100% 88.2% (1 VME, 1 ME) 77.8% (2 mEs) 100% 100% NA NA FEP 89 (84.8%) 14 mEs, 2 VMEs 62.5% (3 mEs) 86.7% (2 mEs) 76.5% (3 mEs, 1 VME) 88.9% (1 mE) 84.8% (4 mEs, 1 VME) 94.1% (1 mE) 100% 100% ATM 88 (88.9%) 11 mEs 87.5% (1 mEs) 86.7% (2 mEs) 76.5% (4 mEs) 88.9% (1 mE) 93.9% (2 mEs) 94.1% (1 mE) NA NA ETP 91 (91.9%) 5 mEs, 3 VMEs 100% 100% 100% 100% 81.8% (3 mEs, 3 VMEs) 88.2% (2 mEs) NA NA MEM 98 (93.3%) 5 mEs, 1 ME, 1 VME 100% 100% 100% 100% 84.8% (4 mEs, 1 VME) 88.2% (1 mE, 1 ME) 100% 100% AMK 102 (97.1%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% 100% 100% TOB 96 (97.0%) 1 mE, 2 MEs 87.5% (1 ME) 100% 94.1% (1 ME) 88.9% (1 mE) 100% 100% NA NA GEN 96 (97.0%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% NA NA CIP 104 (99.1%) 1 mE 100% 100% 100% 88.9% (1 mE) 100% 100% 100% 100% CST 99 (100%) — 100% 100% 100% 100% 100% 100% NA NA MIN 13 (92.9%) 1 mEe 100% NA NA NA NA NA 100% 80% (1 mE) a TZP, piperacillin/tazobactam; CRO, ceftriaxone; CAZ, ceftazidime; FEP, cefepime; ATM, aztreonam; ETP, ertapenem; MEM, meropenem; AMK, amikacin; TOB, tobramycin; GEN, gentamicin; CIP, ciprofloxacin; CST, colistin; MIN, minocycline. b 3GC, third-generation cephalosporin; AmpC, cephalosporinase; WT, wild type. c VME, very major error (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). d NA, not applicable because not tested by Accelerate Pheno™ system. e Analysis restricted to some species. Table 2. AST results for the Accelerate Pheno™ system compared with disc diffusion and Etest listed by resistance profile All strains Enterobacteriaceae A. baumannii Antibioticsa category agreements, n (%) discrepanciesc β-lactam resistance (n = 8) 3GCb susceptible (n = 15) ESBL-type (n = 17) high AmpCb and OXY-type (n = 9) carbapenemases (n = 33) carbapenem impermeability (n = 17) WTb (n = 1) OXA-type (n = 5) TZP 100 (95.2%) 4 mEs, 1 VME 100% 93.3% (1 VME) 88.2% (2 mEs) 88.9% (1 mE) 100% 94.1% (1 mE) 100% 100% CRO 98 (99.0%) 1 mE 100% 100% 100% 100% 97.0% (1 mE) 100% NAd NA CAZ 95 (96.0%) 2 mEs, 1 ME, 1 VME 100% 100% 88.2% (1 VME, 1 ME) 77.8% (2 mEs) 100% 100% NA NA FEP 89 (84.8%) 14 mEs, 2 VMEs 62.5% (3 mEs) 86.7% (2 mEs) 76.5% (3 mEs, 1 VME) 88.9% (1 mE) 84.8% (4 mEs, 1 VME) 94.1% (1 mE) 100% 100% ATM 88 (88.9%) 11 mEs 87.5% (1 mEs) 86.7% (2 mEs) 76.5% (4 mEs) 88.9% (1 mE) 93.9% (2 mEs) 94.1% (1 mE) NA NA ETP 91 (91.9%) 5 mEs, 3 VMEs 100% 100% 100% 100% 81.8% (3 mEs, 3 VMEs) 88.2% (2 mEs) NA NA MEM 98 (93.3%) 5 mEs, 1 ME, 1 VME 100% 100% 100% 100% 84.8% (4 mEs, 1 VME) 88.2% (1 mE, 1 ME) 100% 100% AMK 102 (97.1%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% 100% 100% TOB 96 (97.0%) 1 mE, 2 MEs 87.5% (1 ME) 100% 94.1% (1 ME) 88.9% (1 mE) 100% 100% NA NA GEN 96 (97.0%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% NA NA CIP 104 (99.1%) 1 mE 100% 100% 100% 88.9% (1 mE) 100% 100% 100% 100% CST 99 (100%) — 100% 100% 100% 100% 100% 100% NA NA MIN 13 (92.9%) 1 mEe 100% NA NA NA NA NA 100% 80% (1 mE) All strains Enterobacteriaceae A. baumannii Antibioticsa category agreements, n (%) discrepanciesc β-lactam resistance (n = 8) 3GCb susceptible (n = 15) ESBL-type (n = 17) high AmpCb and OXY-type (n = 9) carbapenemases (n = 33) carbapenem impermeability (n = 17) WTb (n = 1) OXA-type (n = 5) TZP 100 (95.2%) 4 mEs, 1 VME 100% 93.3% (1 VME) 88.2% (2 mEs) 88.9% (1 mE) 100% 94.1% (1 mE) 100% 100% CRO 98 (99.0%) 1 mE 100% 100% 100% 100% 97.0% (1 mE) 100% NAd NA CAZ 95 (96.0%) 2 mEs, 1 ME, 1 VME 100% 100% 88.2% (1 VME, 1 ME) 77.8% (2 mEs) 100% 100% NA NA FEP 89 (84.8%) 14 mEs, 2 VMEs 62.5% (3 mEs) 86.7% (2 mEs) 76.5% (3 mEs, 1 VME) 88.9% (1 mE) 84.8% (4 mEs, 1 VME) 94.1% (1 mE) 100% 100% ATM 88 (88.9%) 11 mEs 87.5% (1 mEs) 86.7% (2 mEs) 76.5% (4 mEs) 88.9% (1 mE) 93.9% (2 mEs) 94.1% (1 mE) NA NA ETP 91 (91.9%) 5 mEs, 3 VMEs 100% 100% 100% 100% 81.8% (3 mEs, 3 VMEs) 88.2% (2 mEs) NA NA MEM 98 (93.3%) 5 mEs, 1 ME, 1 VME 100% 100% 100% 100% 84.8% (4 mEs, 1 VME) 88.2% (1 mE, 1 ME) 100% 100% AMK 102 (97.1%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% 100% 100% TOB 96 (97.0%) 1 mE, 2 MEs 87.5% (1 ME) 100% 94.1% (1 ME) 88.9% (1 mE) 100% 100% NA NA GEN 96 (97.0%) 3 mEs 100% 100% 100% 100% 90.9% (3 mEs) 100% NA NA CIP 104 (99.1%) 1 mE 100% 100% 100% 88.9% (1 mE) 100% 100% 100% 100% CST 99 (100%) — 100% 100% 100% 100% 100% 100% NA NA MIN 13 (92.9%) 1 mEe 100% NA NA NA NA NA 100% 80% (1 mE) a TZP, piperacillin/tazobactam; CRO, ceftriaxone; CAZ, ceftazidime; FEP, cefepime; ATM, aztreonam; ETP, ertapenem; MEM, meropenem; AMK, amikacin; TOB, tobramycin; GEN, gentamicin; CIP, ciprofloxacin; CST, colistin; MIN, minocycline. b 3GC, third-generation cephalosporin; AmpC, cephalosporinase; WT, wild type. c VME, very major error (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). d NA, not applicable because not tested by Accelerate Pheno™ system. e Analysis restricted to some species. Table 3. AST results of the Accelerate Pheno™ system compared with disc diffusion and Etest listed by species Klebsiella spp. (n = 39) E. coli (n = 36) Enterobacter spp. (n = 19) Citrobacter spp. (n = 4) Proteus spp. (n = 1) A. baumannii (n = 6) Antibiotic category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa TZP 36 (92.3) 1 VME, 2 mEs 34 (94.4) 2 mEs 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 CRO 38 (97.4) 1 mE 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NAb NA CAZ 38 (97.4) 1 mE 32 (88.9) 1 VME, 1 ME, 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 NA NA FEP 35 (89.7) 1 VME, 3 mEs 28 (77.8) 8 mEs 15 (79.0) 1 VME, 3 mEs 4 (100) 0 1 (100) 0 6 (100) 0 ATM 37 (94.9) 2 mEs 30 (83.3) 6 mEs 16 (84.2) 3 mEs 4 (100) 0 1 (100) 0 NA NA ETP 37 (94.9) 2 mEs 33 (91.7) 2 VMEs, 1 mE 17 (89.5) 1 VME, 1 mE 4 (100) 0 1 (100) 0 NA NA MEM 35 (89.7) 1 ME, 3 mEs 34 (94.4) 2 mEs 18 (94.7) 1 VME 4 (100) 0 1 (100) 0 6 (100) 0 AMK 37 (94.9) 2 mEs 35 (97.2) 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 TOB 38 (97.4) 1 mE 34 (94.4) 2 MEs 19 (100) 0 4 (100) 0 1 (100) 0 NA NA GEN 36 (92.3) 3 mEs 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA CIP 39 (100) 0 36 (100) 0 18 (94.7) 1 mE 4 (100) 0 1 (100) 0 6 (100) 0 CST 39 (100) 0 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA MIN NA NA NA NA NA NA NA NA NA NA 5 (83.3) 1 mE Klebsiella spp. (n = 39) E. coli (n = 36) Enterobacter spp. (n = 19) Citrobacter spp. (n = 4) Proteus spp. (n = 1) A. baumannii (n = 6) Antibiotic category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa TZP 36 (92.3) 1 VME, 2 mEs 34 (94.4) 2 mEs 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 CRO 38 (97.4) 1 mE 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NAb NA CAZ 38 (97.4) 1 mE 32 (88.9) 1 VME, 1 ME, 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 NA NA FEP 35 (89.7) 1 VME, 3 mEs 28 (77.8) 8 mEs 15 (79.0) 1 VME, 3 mEs 4 (100) 0 1 (100) 0 6 (100) 0 ATM 37 (94.9) 2 mEs 30 (83.3) 6 mEs 16 (84.2) 3 mEs 4 (100) 0 1 (100) 0 NA NA ETP 37 (94.9) 2 mEs 33 (91.7) 2 VMEs, 1 mE 17 (89.5) 1 VME, 1 mE 4 (100) 0 1 (100) 0 NA NA MEM 35 (89.7) 1 ME, 3 mEs 34 (94.4) 2 mEs 18 (94.7) 1 VME 4 (100) 0 1 (100) 0 6 (100) 0 AMK 37 (94.9) 2 mEs 35 (97.2) 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 TOB 38 (97.4) 1 mE 34 (94.4) 2 MEs 19 (100) 0 4 (100) 0 1 (100) 0 NA NA GEN 36 (92.3) 3 mEs 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA CIP 39 (100) 0 36 (100) 0 18 (94.7) 1 mE 4 (100) 0 1 (100) 0 6 (100) 0 CST 39 (100) 0 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA MIN NA NA NA NA NA NA NA NA NA NA 5 (83.3) 1 mE a VME, very major errors (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). b NA, not applicable because not tested by Accelerate Pheno™ system. Table 3. AST results of the Accelerate Pheno™ system compared with disc diffusion and Etest listed by species Klebsiella spp. (n = 39) E. coli (n = 36) Enterobacter spp. (n = 19) Citrobacter spp. (n = 4) Proteus spp. (n = 1) A. baumannii (n = 6) Antibiotic category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa TZP 36 (92.3) 1 VME, 2 mEs 34 (94.4) 2 mEs 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 CRO 38 (97.4) 1 mE 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NAb NA CAZ 38 (97.4) 1 mE 32 (88.9) 1 VME, 1 ME, 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 NA NA FEP 35 (89.7) 1 VME, 3 mEs 28 (77.8) 8 mEs 15 (79.0) 1 VME, 3 mEs 4 (100) 0 1 (100) 0 6 (100) 0 ATM 37 (94.9) 2 mEs 30 (83.3) 6 mEs 16 (84.2) 3 mEs 4 (100) 0 1 (100) 0 NA NA ETP 37 (94.9) 2 mEs 33 (91.7) 2 VMEs, 1 mE 17 (89.5) 1 VME, 1 mE 4 (100) 0 1 (100) 0 NA NA MEM 35 (89.7) 1 ME, 3 mEs 34 (94.4) 2 mEs 18 (94.7) 1 VME 4 (100) 0 1 (100) 0 6 (100) 0 AMK 37 (94.9) 2 mEs 35 (97.2) 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 TOB 38 (97.4) 1 mE 34 (94.4) 2 MEs 19 (100) 0 4 (100) 0 1 (100) 0 NA NA GEN 36 (92.3) 3 mEs 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA CIP 39 (100) 0 36 (100) 0 18 (94.7) 1 mE 4 (100) 0 1 (100) 0 6 (100) 0 CST 39 (100) 0 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA MIN NA NA NA NA NA NA NA NA NA NA 5 (83.3) 1 mE Klebsiella spp. (n = 39) E. coli (n = 36) Enterobacter spp. (n = 19) Citrobacter spp. (n = 4) Proteus spp. (n = 1) A. baumannii (n = 6) Antibiotic category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa category agreements, n (%) discrepanciesa TZP 36 (92.3) 1 VME, 2 mEs 34 (94.4) 2 mEs 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 CRO 38 (97.4) 1 mE 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NAb NA CAZ 38 (97.4) 1 mE 32 (88.9) 1 VME, 1 ME, 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 NA NA FEP 35 (89.7) 1 VME, 3 mEs 28 (77.8) 8 mEs 15 (79.0) 1 VME, 3 mEs 4 (100) 0 1 (100) 0 6 (100) 0 ATM 37 (94.9) 2 mEs 30 (83.3) 6 mEs 16 (84.2) 3 mEs 4 (100) 0 1 (100) 0 NA NA ETP 37 (94.9) 2 mEs 33 (91.7) 2 VMEs, 1 mE 17 (89.5) 1 VME, 1 mE 4 (100) 0 1 (100) 0 NA NA MEM 35 (89.7) 1 ME, 3 mEs 34 (94.4) 2 mEs 18 (94.7) 1 VME 4 (100) 0 1 (100) 0 6 (100) 0 AMK 37 (94.9) 2 mEs 35 (97.2) 1 mE 19 (100) 0 4 (100) 0 1 (100) 0 6 (100) 0 TOB 38 (97.4) 1 mE 34 (94.4) 2 MEs 19 (100) 0 4 (100) 0 1 (100) 0 NA NA GEN 36 (92.3) 3 mEs 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA CIP 39 (100) 0 36 (100) 0 18 (94.7) 1 mE 4 (100) 0 1 (100) 0 6 (100) 0 CST 39 (100) 0 36 (100) 0 19 (100) 0 4 (100) 0 1 (100) 0 NA NA MIN NA NA NA NA NA NA NA NA NA NA 5 (83.3) 1 mE a VME, very major errors (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). b NA, not applicable because not tested by Accelerate Pheno™ system. Table 4. Major and very major errors of AST results produced by the Accelerate Pheno™ system compared with Etests MIC, mg/L (interpretation)a Strain Testb TZP CAZ CRO FEP ETP MEM TOB Errorc β-Lactam resistance mechanismsd K. pneumoniae N1008720875 AXDX <4 (S) – – – – – – VME IRT Etest 32 (R) – – – – – – E. coli MECB5 AXDX – 1 (S) 4 (R) – – – – VME CTX-M-15 Etest – 8 (R) 16 (R) – – – – E. coli N1008665740 AXDX – >8 (R) >8 (R) – – – – ME CTX-M-15 Etest – 0.5 (S) >32 (R) – – – – K. pneumoniae NKP124 AXDX – – – ≤1 (S) – – – VME SHV-5 Etest – – – 8 (R) – – – E. aerogenes ARS662 AXDX – – – ≤1 (S) 0.25 (S) ≤0.25 (S) – VME (2) NDM-1 Etest – – – 8 (R) >32 (R) 1.5 (S) – E. coli ARS603 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME NDM-1, CTX-M-15 Etest – – – – >32 (R) 4 (I) – E. coli OHY12035985 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME VIM-1, CMY-2 Etest – – – – 1.5 (R) 0.75 (S) – K. pneumoniae O1122816060 AXDX – – – – 1 (I) >8 (R) – ME impermeability Etest – – – – 0.75 (I) 0.094 (S) – E. cloacae ARS769 AXDX – – – – 2 (R) 0.5 (S) – VME IMI Etest – – – – >32 (R) >32 (R) – E. coli N1008560953 AXDX – – – – – – 8 (R) ME none Etest – – – – – – 0.25 (S) E. coli NECM9 AXDX – – – – – – 8 (R) ME CTX-M-9 Etest – – – – – – 0.5 (S) MIC, mg/L (interpretation)a Strain Testb TZP CAZ CRO FEP ETP MEM TOB Errorc β-Lactam resistance mechanismsd K. pneumoniae N1008720875 AXDX <4 (S) – – – – – – VME IRT Etest 32 (R) – – – – – – E. coli MECB5 AXDX – 1 (S) 4 (R) – – – – VME CTX-M-15 Etest – 8 (R) 16 (R) – – – – E. coli N1008665740 AXDX – >8 (R) >8 (R) – – – – ME CTX-M-15 Etest – 0.5 (S) >32 (R) – – – – K. pneumoniae NKP124 AXDX – – – ≤1 (S) – – – VME SHV-5 Etest – – – 8 (R) – – – E. aerogenes ARS662 AXDX – – – ≤1 (S) 0.25 (S) ≤0.25 (S) – VME (2) NDM-1 Etest – – – 8 (R) >32 (R) 1.5 (S) – E. coli ARS603 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME NDM-1, CTX-M-15 Etest – – – – >32 (R) 4 (I) – E. coli OHY12035985 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME VIM-1, CMY-2 Etest – – – – 1.5 (R) 0.75 (S) – K. pneumoniae O1122816060 AXDX – – – – 1 (I) >8 (R) – ME impermeability Etest – – – – 0.75 (I) 0.094 (S) – E. cloacae ARS769 AXDX – – – – 2 (R) 0.5 (S) – VME IMI Etest – – – – >32 (R) >32 (R) – E. coli N1008560953 AXDX – – – – – – 8 (R) ME none Etest – – – – – – 0.25 (S) E. coli NECM9 AXDX – – – – – – 8 (R) ME CTX-M-9 Etest – – – – – – 0.5 (S) S, susceptible; I, intermediate; R, resistant. The total numbers of VMEs and MEs respectively were: 7.6% and 0% for TZP, 0% and 3% for CRO, 4.4% and 3.2% for CAZ, 3.5% and 11.9% for ATM, 3.7 and 23.5% for FEP, 7.3% and 0% for ETP, 24% and 1.3% for MEM, 0% and 3.1% for AMK, 0% and 4.2% for TOB, 0% and 0% for GEN, 0% and 2.3% for CIP, and 0% and 0% for MIN. a Dark grey shading indicates discrepant results; light grey shading indicates AST results, which allow for the deduction of the mechanism of resistance expressed by the bacteria. b AXDX, Accelerate Pheno™ system. c VME, very major error (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). d IRT, inhibitor-resistant TEM. Table 4. Major and very major errors of AST results produced by the Accelerate Pheno™ system compared with Etests MIC, mg/L (interpretation)a Strain Testb TZP CAZ CRO FEP ETP MEM TOB Errorc β-Lactam resistance mechanismsd K. pneumoniae N1008720875 AXDX <4 (S) – – – – – – VME IRT Etest 32 (R) – – – – – – E. coli MECB5 AXDX – 1 (S) 4 (R) – – – – VME CTX-M-15 Etest – 8 (R) 16 (R) – – – – E. coli N1008665740 AXDX – >8 (R) >8 (R) – – – – ME CTX-M-15 Etest – 0.5 (S) >32 (R) – – – – K. pneumoniae NKP124 AXDX – – – ≤1 (S) – – – VME SHV-5 Etest – – – 8 (R) – – – E. aerogenes ARS662 AXDX – – – ≤1 (S) 0.25 (S) ≤0.25 (S) – VME (2) NDM-1 Etest – – – 8 (R) >32 (R) 1.5 (S) – E. coli ARS603 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME NDM-1, CTX-M-15 Etest – – – – >32 (R) 4 (I) – E. coli OHY12035985 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME VIM-1, CMY-2 Etest – – – – 1.5 (R) 0.75 (S) – K. pneumoniae O1122816060 AXDX – – – – 1 (I) >8 (R) – ME impermeability Etest – – – – 0.75 (I) 0.094 (S) – E. cloacae ARS769 AXDX – – – – 2 (R) 0.5 (S) – VME IMI Etest – – – – >32 (R) >32 (R) – E. coli N1008560953 AXDX – – – – – – 8 (R) ME none Etest – – – – – – 0.25 (S) E. coli NECM9 AXDX – – – – – – 8 (R) ME CTX-M-9 Etest – – – – – – 0.5 (S) MIC, mg/L (interpretation)a Strain Testb TZP CAZ CRO FEP ETP MEM TOB Errorc β-Lactam resistance mechanismsd K. pneumoniae N1008720875 AXDX <4 (S) – – – – – – VME IRT Etest 32 (R) – – – – – – E. coli MECB5 AXDX – 1 (S) 4 (R) – – – – VME CTX-M-15 Etest – 8 (R) 16 (R) – – – – E. coli N1008665740 AXDX – >8 (R) >8 (R) – – – – ME CTX-M-15 Etest – 0.5 (S) >32 (R) – – – – K. pneumoniae NKP124 AXDX – – – ≤1 (S) – – – VME SHV-5 Etest – – – 8 (R) – – – E. aerogenes ARS662 AXDX – – – ≤1 (S) 0.25 (S) ≤0.25 (S) – VME (2) NDM-1 Etest – – – 8 (R) >32 (R) 1.5 (S) – E. coli ARS603 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME NDM-1, CTX-M-15 Etest – – – – >32 (R) 4 (I) – E. coli OHY12035985 AXDX – – – – 0.25 (S) ≤0.25 (S) – VME VIM-1, CMY-2 Etest – – – – 1.5 (R) 0.75 (S) – K. pneumoniae O1122816060 AXDX – – – – 1 (I) >8 (R) – ME impermeability Etest – – – – 0.75 (I) 0.094 (S) – E. cloacae ARS769 AXDX – – – – 2 (R) 0.5 (S) – VME IMI Etest – – – – >32 (R) >32 (R) – E. coli N1008560953 AXDX – – – – – – 8 (R) ME none Etest – – – – – – 0.25 (S) E. coli NECM9 AXDX – – – – – – 8 (R) ME CTX-M-9 Etest – – – – – – 0.5 (S) S, susceptible; I, intermediate; R, resistant. The total numbers of VMEs and MEs respectively were: 7.6% and 0% for TZP, 0% and 3% for CRO, 4.4% and 3.2% for CAZ, 3.5% and 11.9% for ATM, 3.7 and 23.5% for FEP, 7.3% and 0% for ETP, 24% and 1.3% for MEM, 0% and 3.1% for AMK, 0% and 4.2% for TOB, 0% and 0% for GEN, 0% and 2.3% for CIP, and 0% and 0% for MIN. a Dark grey shading indicates discrepant results; light grey shading indicates AST results, which allow for the deduction of the mechanism of resistance expressed by the bacteria. b AXDX, Accelerate Pheno™ system. c VME, very major error (false susceptibility); ME, major error (false resistance); mE, minor error (intermediate result instead of susceptible or resistant). d IRT, inhibitor-resistant TEM. The highest number of discrepancies occurred for aztreonam (11.1%) and cefepime (15.2%) (Table 2). For aztreonam, all the discrepant results corresponded to mEs in Enterobacteriaceae irrespective of the β-lactamase resistance profile. For cefepime, 14 mEs were observed, equally distributed among the resistance profiles, and two VMEs were detected in one ESBL-producing K. pneumoniae and one NDM-producing E. aerogenes (Table 4). However, aztreonam and cefepime are not used for first-line management of either sepsis or septic shock.22 The other minor errors were equally distributed among the different isolates of our panel irrespective of resistance profile (Table 2). Interestingly, some discrepant results were observed for cephalosporinase-overproducing isolates, with two isolates considered S instead of I for ceftazidime. However, in these two isolates, the ceftriaxone MICs were categorized as R by the Accelerate Pheno™ system, which allowed the isolates to be considered R to 3GC. In the same way, we observed two errors among ESBL-producers, with a VME and an ME in the ceftazidime results from two CTX-M-producing E. coli isolates (Table 4). In these two cases, however, if we use an interpretative reading of the AST results (which enables the possible mechanism of resistance expressed by the bacteria to be deduced),23 the ceftriaxone MIC results indicate the possibility of an ESBL with a clear resistance profile consistent with cefotaximase producers. More importantly, we observed VMEs [0.5% (3/564) and 0.2% (1/564) for ertapenem and meropenem, respectively] or MEs [0.2% (1/668) for meropenem] in the carbapenem results of five carbapenem-resistant Enterobacteriaceae. Three of the five discrepancies were noted for class B metallo-β-lactamases (two NDM- and one VIM-type producer) (Table 4). In these three cases, the susceptible meropenem result did not allow for correction of the false-susceptible ertapenem result. This could result in inappropriate therapeutic management of patients. In contrast, the results of two other cases of an ME and a VME with meropenem (due to impermeability and IMI production, respectively) could be called into question based on ertapenem MIC results which could have guided antibiotic treatment. Overall, 3/14 class B carbapenemase-producing Enterobacteriaceae showed discrepant results for ertapenem, with two VMEs out of ten NDM-producers and one VME out of four VIM-producers. One hypothesis to explain these results is that the discrepancies could be related to the zinc concentration of the medium used for bacterial growth. Zinc enables complete expression of the metallo-β-lactamases, which are known to use zinc ions in their catalytic sites.24,25 In 3GC-S strains, only one VME was observed for piperacillin/tazobactam with K. pneumoniae. By species, the major discrepant results (VMEs and MEs) were observed with E. coli (n = 6), Klebsiella spp. (n = 3) and Enterobacter spp. (n = 2) (Table 4). Only one isolate (NDM-producing E. aerogenes) produced two VMEs (0.9% of the studied panel). On the other hand, no MEs or VMEs for Citrobacter spp., Proteus spp. or A. baumannii were observed, irrespective of the resistance profile, though only small numbers of strains were tested in these species. Furthermore, isolates harbouring emerging co-resistant determinants (one MCR-1-producing E. coli and two armA-producing K. pneumoniae) produced correct AST results. Some limitations of this study should be noted. The number of susceptible strains was limited for some antibiotics. Moreover, the panel of studied strains was representative of the MDR organisms actually observed in France and was not exhaustive. However, the aim of our study was to focus on the potential of the Accelerate Pheno™ system to detect these local MDR bacteria. Early susceptibility results are crucial for the initiation of appropriate antimicrobial therapy for critically ill patients, including those in settings challenged by MDR bacteria, such as ICUs. Failure to initiate appropriate empirical therapy in patients with sepsis and septic shock is associated with a substantial increase in morbidity and mortality.22 To date, no tool gives a phenotypic AST result in <7 h directly from specimens such as positive blood cultures. Three recent studies by Marschal et al.,12 Brazelton de Cárdenas et al.26 and Charnot-Katsikas et al.27 have demonstrated the performance of the Accelerate Pheno™ system in a routine diagnostic setting. However, owing to the scarcity of MDR bacteria, these studies have not challenged the instrument on a large characterized panel of MDR GNB. In this study, we demonstrated the high performance of a new technology to obtain fast identification and AST results directly from positive blood cultures. This system may enable clinicians to adjust antimicrobial treatment earlier to facilitate patient management and outcomes as well as antimicrobial stewardship. Acknowledgements We thank Accelerate Diagnostics, Inc., Tucson, AZ, USA, for providing two Accelerate Pheno™ system modules and the test reagents. This company had no role in the study design, data collection or interpretation of the results.  We thank R. Bonnet and F. Robin for providing the mcr-1-positive control strain. Funding This work was supported by Institut National de la Sante et de la Recherche Medicale and University Hospital of Nîmes. Transparency declarations None to declare. Supplementary data Table S1 is available as Supplementary data at JAC Online. References 1 Laupland KB. Incidence of bloodstream infection: a review of population-based studies . Clin Microbiol Infect 2013 ; 19 : 492 – 500 . Google Scholar CrossRef Search ADS PubMed 2 Vincent JL , Marshall JC , Namendys-Silva SA et al. 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Multiplexed automated digital microscopy for rapid identification and antimicrobial susceptibility testing of bacteria and yeast directly from clinical samples . Clin Microbiol Newsl 2015 ; 37 : 161 – 7 . Google Scholar CrossRef Search ADS 12 Marschal M , Bachmaier J , Autenrieth I et al. Evaluation of the Accelerate Pheno system for fast identification and antimicrobial susceptibility testing from positive blood cultures in bloodstream infections caused by Gram-negative pathogens . J Clin Microbiol 2017 ; 55 : 2116 – 26 . Google Scholar CrossRef Search ADS PubMed 13 Pantel A , Boutet-Dubois A , Jean-Pierre H et al. French regional surveillance program of carbapenemase-producing Gram-negative bacilli: results from a 2-year period . Eur J Clin Microbiol Infect Dis 2014 ; 33 : 2285 – 92 . Google Scholar CrossRef Search ADS PubMed 14 Robert J , Pantel A , Mérens A et al. Incidence rates of carbapenemase-producing Enterobacteriaceae clinical isolates in France: a prospective nationwide study in 2011-12 . J Antimicrob Chemother 2014 ; 69 : 2706 – 12 . Google Scholar CrossRef Search ADS PubMed 15 Pitout JD , Hossain A , Hanson ND. Phenotypic and molecular detection of CTX-M-beta-lactamases produced by Escherichia coli and Klebsiella spp . J Clin Microbiol 2004 ; 42 : 5715 – 21 . Google Scholar CrossRef Search ADS PubMed 16 Aubron C , Poirel L , Ash RJ et al. Carbapenemase-producing Enterobacteriaceae, U.S. rivers . Emerg Infect Dis 2005 ; 11 : 260 – 4 . Google Scholar CrossRef Search ADS PubMed 17 Poirel L , Walsh TR , Cuvillier V et al. Multiplex PCR for detection of acquired carbapenemase genes . Diagn Microbiol Infect Dis 2011 ; 70 : 119 – 23 . Google Scholar CrossRef Search ADS PubMed 18 Perez-Perez FJ , Hanson ND. Detection of plasmid-mediated AmpC β-lactamase genes in clinical isolates by using multiplex PCR . 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Surviving Sepsis Campaign: international guidelines for management of sepsis and septic shock: 2016 . Intensive Care Med 2017 ; 43 : 304 – 77 . Google Scholar CrossRef Search ADS PubMed 23 Livermore DM , Winstanley TG , Shannon KP. Interpretative reading: recognizing the unusual and inferring resistance mechanisms from resistance phenotypes . J Antimicrob Chemother 2001 ; 48 : 87 – 102 . Google Scholar CrossRef Search ADS PubMed 24 Lee K , Lim YS , Yong D et al. Evaluation of the Hodge test and the imipenem-EDTA double-disk synergy test for differentiating metallo-β-lactamase-producing isolates of Pseudomonas spp. and Acinetobacter spp . J Clin Microbiol 2003 ; 41 : 4623 – 9 . Google Scholar CrossRef Search ADS PubMed 25 Dortet L , Bréchard L , Poirel L et al. Impact of the isolation medium for detection of carbapenemase-producing Enterobacteriaceae using an updated version of the Carba NP test . J Med Microbiol 2014 ; 63 : 772 – 6 . Google Scholar CrossRef Search ADS PubMed 26 Brazelton de Cárdenas JN , Su Y , Rodriguez A et al. Evaluation of rapid phenotypic identification and antimicrobial susceptibility testing in a pediatric oncology center . Diagn Microbiol Infect Dis 2017 ; 89 : 52 – 7 . Google Scholar CrossRef Search ADS PubMed 27 Charnot-Katsikas A , Tesic V , Love N et al. Use of Accelerate Pheno™ system for identification and antimicrobial susceptibility testing (ID/AST) of pathogens in positive blood cultures and impact on time to results and workflow . J Clin Microbiol 2017 ; 56 : pii=e01166-17. © The Author(s) 2018. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com. This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/about_us/legal/notices)

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Journal of Antimicrobial ChemotherapyOxford University Press

Published: Feb 20, 2018

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