Recent advances in rapid antimicrobial susceptibility testing systems

References

• Van Belkum A, Burnham CD, Rossen JWA, et al. Innovative and rapid antimicrobial susceptibility testing systems. Nat Rev Microbiol. 2020;18(5):299–311.
   PubMed Web of Science ®Google Scholar
• Vasala A, Hytonen VP, Laitinen OH. Modern tools for rapid diagnostics of antimicrobial resistance Front Cell Infect Microbiol. 2020;10(308). DOI:10.3389/fcimb.2020.00308
   PubMedGoogle Scholar
• World Health Organization. Landscape of diagnostics against antibacterial resistance, gaps and priorities. Geneva. 2019.
   Google Scholar
• Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing 30th informational supplement. CLSI document M100-S30. Wayne, PA.: Clinical and Laboratory Standards Institute; 2020.
   Google Scholar
• European committee on antimicrobial susceptibility testing. breakpoint tables for interpretations of MICs and zone diameters; v11.0 [cited 2021 Apr 24]. Available from: https://www.eucast.org/clinical_breakpoints/.
   Google Scholar
• Opota O, Croxatto A, Prod’hom G, et al. Blood culture-based diagnosis of bacteraemia: state of the art Clin Microbiol Infect. 2015;21(4):313–322.
   PubMed Web of Science ®Google Scholar
• Anton-Vazquez V, Hine P, Krishna S, et al. Rapid versus standard antibiotic susceptibility testing for treating bloodstream infections Cochrane Database Syst Rev. 2018;12:1–45.
   Google Scholar
• Bookstaver PB, Nimmich EB, Smith TJ, 3rd, et al. Cumulative effect of an antimicrobial stewardship and rapid diagnostic testing bundle on early streamlining of antimicrobial therapy in Gram-negative bloodstream infections Antimicrob Agents Chemother. 2017;61(9). doi: 10.1128/AAC.00189-17
   Web of Science ®Google Scholar
• Perez KK, Olsen RJ, Musick WL, et al. Integrating rapid pathogen identification and antimicrobial stewardship significantly decreases hospital costs Arch Pathol Lab Med. 2013;137(9):1247–1254.
   PubMed Web of Science ®Google Scholar
• Kahlmeter G, Giske CG, Kirn TJ, et al. Point-counterpoint: differences between the European committee on antimicrobial susceptibility testing and clinical and laboratory standards institute recommendations for reporting antimicrobial susceptibility results J Clin Microbiol. 2019;57(9). DOI:10.1128/JCM.01129-19
   PubMed Web of Science ®Google Scholar
• Akerlund A, Jonasson E, Matuschek E, et al. EUCAST rapid antimicrobial susceptibility testing (RAST) in blood cultures: validation in 55 European laboratories.J Antimicrob Chemother. 2020;75(11):3230–3238.
   PubMed Web of Science ®Google Scholar
• Endimiani A, Jacobs MR. The changing role of the clinical microbiology laboratory in defining resistance in Gram-negatives Infect Dis Clin North Am. 2016;30(2):323–345.
   PubMed Web of Science ®Google Scholar
• Behera B, Anil Vishnu GK, Chatterjee S, et al. Emerging technologies for antibiotic susceptibility testing Biosens Bioelectron. 2019;142(111552):111552.
   PubMedGoogle Scholar
• Van Den Poel B, Meersseman P, Debaveye Y, et al. Performance and potential clinical impact of Alfred60(AST) (Alifax(R)) for direct antimicrobial susceptibility testing on positive blood culture bottles Eur J Clin Microbiol Infect Dis. 2020;39(1):53–63.
   PubMed Web of Science ®Google Scholar
• Barnini S, Brucculeri V, Morici P, et al. A new rapid method for direct antimicrobial susceptibility testing of bacteria from positive blood cultures BMC Microbiol. 2016;16(1):185.
   PubMedGoogle Scholar
• Giordano C, Piccoli E, Brucculeri V, et al. Evaluation of two rapid phenotypical antimicrobial susceptibility technologies for the diagnostic Stewardship of Sepsis Biomed Res Int. 2018;6976923:2018.
   Google Scholar
• Sanchez-Carrillo C, Pescador P, Ricote R, et al. Evaluation of the Alfred AST(R) system for rapid antimicrobial susceptibility testing directly from positive blood cultures Eur J Clin Microbiol Infect Dis. 2019;38(9):1665–1670.
   PubMed Web of Science ®Google Scholar
• Charnot-Katsikas A, Tesic V, Love N, et al. Use of the accelerate pheno system for identification and antimicrobial susceptibility testing of pathogens in positive blood cultures and impact on time to results and workflow J Clin Microbiol. 2018;56(1).
   Web of Science ®Google Scholar
• Lutgring JD, Bittencourt C, McElvania TeKippe E, et al. Evaluation of the accelerate pheno system: results from two academic medical centers J Clin Microbiol. 2018;56(4). DOI:10.1128/JCM.01672-17
   Web of Science ®Google Scholar
• Pancholi P, Carroll KC, Buchan BW, et al. Multicenter evaluation of the accelerate PhenoTest BC kit for rapid identification and phenotypic antimicrobial susceptibility testing using morphokinetic cellular analysis. J Clin Microbiol. 2018;56(4). DOI:10.1128/JCM.01329-17.
   PubMed Web of Science ®Google Scholar
• Choi J, Yoo J, Lee M, et al. A rapid antimicrobial susceptibility test based on single-cell morphological analysis Sci Transl Med. 2014;6(267):267ra174.
   PubMed Web of Science ®Google Scholar
• Kim JH, Kim TS, Song SH, et al. Direct rapid antibiotic susceptibility test (dRAST) for blood culture and its potential usefulness in clinical practice J Med Microbiol. 2018;67(3):325–331.
   PubMed Web of Science ®Google Scholar
• Bush K, Bush K. New beta-lactamases in gram-negative bacteria: diversity and impact on the selection of antimicrobial therapy Clin Infect Dis. 2001;32(7):1085–1089.
   PubMed Web of Science ®Google Scholar
• Paterson DL, Bonomo RA. Extended-spectrum beta-lactamases: a clinical update Clin Microbiol Rev. 2005;18(4):657–686.
   PubMed Web of Science ®Google Scholar
• Jacoby GA, Han P. Detection of extended-spectrum beta-lactamases in clinical isolates of Klebsiella pneumoniae and Escherichia coli J Clin Microbiol. 1996;34(4):908–911.
   PubMed Web of Science ®Google Scholar
• Jarlier V, Nicolas MH, Fournier G, et al. Extended broad-spectrum beta-lactamases conferring transferable resistance to newer beta-lactam agents in Enterobacteriaceae: hospital prevalence and susceptibility patterns Rev Infect Dis. 1988;10(4):867–878.
   PubMedGoogle Scholar
• Katsanis GP, Spargo J, Ferraro MJ, et al. Detection of Klebsiella pneumoniae and Escherichia coli strains producing extended-spectrum beta-lactamases J Clin Microbiol. 1994;32(3):691–696.
   PubMed Web of Science ®Google Scholar
• Moland ES, Sanders CC, Thomson KS. Can results obtained with commercially available MicroScan microdilution panels serve as an indicator of beta-lactamase production among escherichia coli and Klebsiella isolates with hidden resistance to expanded-spectrum cephalosporins and aztreonam? J Clin Microbiol. 1998;36(9):2575–2579.
   PubMed Web of Science ®Google Scholar
• Robberts FJ, Kohner PC, Patel R. Unreliable extended-spectrum beta-lactamase detection in the presence of plasmid-mediated AmpC in Escherichia coli clinical isolates J Clin Microbiol. 2009;47(2):358–361.
   PubMed Web of Science ®Google Scholar
• Patterson JE. Extended-spectrum beta-lactamases Semin Respir Infect. 2000;15(4):299–307.
   PubMedGoogle Scholar
• Bush K, Jacoby GA. Updated functional classification of beta-lactamases Antimicrob Agents Chemother. 2010;54(3):969–976.
   PubMed Web of Science ®Google Scholar
• Lee K, Chong Y, Shin HB, et al. Modified Hodge and EDTA-disk synergy tests to screen metallo-beta-lactamase-producing strains of Pseudomonas and Acinetobacter species Clin Microbiol Infect. 2001;7(2):88–91.
   PubMed Web of Science ®Google Scholar
• Hodge W, Ciak J, Tramont EC. Simple method for detection of penicillinase-producing Neisseria gonorrhoeae J Clin Microbiol. 1978;7(1):102–103.
   PubMed Web of Science ®Google Scholar
• Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing 19th informational supplement. CLSI document M100-S19. Wayne, PA.: Clinical and Laboratory Standards Institute; 2009.
   Google Scholar
• Nordmann P, Poirel L. Strategies for identification of carbapenemase-producing Enterobacteriaceae J Antimicrob Chemother. 2013;68(3):487–489.
   PubMed Web of Science ®Google Scholar
• Van Der Zwaluw K, De Haan A, Pluister GN, et al. The carbapenem inactivation method (CIM), a simple and low-cost alternative for the Carba NP test to assess phenotypic carbapenemase activity in gram-negative rods PLoS One. 2015;10(3):e0123690.
   PubMed Web of Science ®Google Scholar
• Laolerd W, Akeda Y, Preeyanon L, et al. Carbapenemase-producing carbapenem-resistant Enterobacteriaceae from Bangkok, Thailand, and their detection by the Carba NP and modified Carbapenem inactivation method tests Microb Drug Resist. 2018;24(7):1006–1011.
   PubMed Web of Science ®Google Scholar
• O’Callaghan CH, Morris A, Kirby SM, et al. Novel method for detection of beta-lactamases by using a chromogenic cephalosporin substrate Antimicrob Agents Chemother. 1972;1(4):283–288.
   PubMed Web of Science ®Google Scholar
• Papanicolas LE, Bell JM, Bastian I. Performance of phenotypic tests for detection of penicillinase in Staphylococcus aureus isolates from Australia J Clin Microbiol. 2014;52(4):1136–1138.
   PubMed Web of Science ®Google Scholar
• Nordmann P, Dortet L, Poirel L. Rapid detection of extended-spectrum-beta-lactamase-producing Enterobacteriaceae J Clin Microbiol. 2012;50(9):3016–3022.
   PubMed Web of Science ®Google Scholar
• Poirel L, Fernandez J, Nordmann P. Comparison of three biochemical tests for rapid detection of extended-spectrum-beta-lactamase-producing Enterobacteriaceae J Clin Microbiol. 2016;54(2):423–427.
   PubMed Web of Science ®Google Scholar
• Deepa R, Ravichandran M, Banu ST, et al. Evaluation of Nordmann, Dortet, and Poirel test for the identification of extended spectrum betalactamase production among urinary isolates of Escherichia coli J Lab Physicians. 2017;9(4):269–272.
   PubMedGoogle Scholar
• Demord A, Poirel L, D’Emidio F, et al. Rapid ESBL NP test for rapid detection of expanded-spectrum beta-lactamase producers in Enterobacterales Microb Drug Resist. 2020, doi:10.1089/mdr.2020.0391.
   PubMed Web of Science ®Google Scholar
• Saeed A, Tabl H, Mogahed M. Evaluation of the NDP test, a novel chromogenic test for rapid detection of extended spectrum beta-lactamase producing Enterobacteriaciae Microbiol Res J Int. 2017;18(6):1–8.
   Google Scholar
• Dortet L, Poirel L, Nordmann P. Rapid detection of extended-spectrum-beta-lactamase-producing enterobacteriaceae from urine samples by use of the ESBL NDP test. J Clin Microbiol. 2014;52(10):3701–3706.
   PubMed Web of Science ®Google Scholar
• Nordmann P, Poirel L, Dortet L. Rapid detection of carbapenemase-producing Enterobacteriaceae. Emerg Infect Dis. 2012;18(9):1503–1507.
   PubMed Web of Science ®Google Scholar
• Tijet N, Boyd D, Patel SN, et al. Evaluation of the Carba NP test for rapid detection of carbapenemase-producing Enterobacteriaceae and Pseudomonas aeruginosa. Antimicrob Agents Chemother. 2013;57(9):4578–4580.
   PubMedGoogle Scholar
• Simner PJ, Johnson JK, Brasso WB, et al. Multicenter evaluation of the modified Carbapenem inactivation method and the Carba NP for detection of Carbapenemase-producing Pseudomonas aeruginosa and Acinetobacter baumannii. J Clin Microbiol. 2018;;56(1):e01369-17.
   Web of Science ®Google Scholar
• Pires J, Novais A, Peixe L. Blue-carba, an easy biochemical test for detection of diverse carbapenemase producers directly from bacterial cultures. J Clin Microbiol. 2013;51(12):4281–4283.
   PubMed Web of Science ®Google Scholar
• Pasteran F, Veliz O, Ceriana P, et al. Evaluation of the Blue-Carba test for rapid detection of carbapenemases in gram-negative bacilli. J Clin Microbiol. 2015;53(6):1996–1998.
   PubMed Web of Science ®Google Scholar
• Jia L, Han L, Cai HX, et al. AI-Blue-Carba: a rapid and Improved Carbapenemase producer detection assay using Blue-Carba with deep learning. Front Microbiol. 2020;11(585417). DOI:10.3389/fmicb.2020.585417.
   Google Scholar
• Nordmann P, Sadek M, Demord A, et al. NitroSpeed-Carba NP test for rapid detection and differentiation between different classes of Carbapenemases in Enterobacterales. J Clin Microbiol. 2020;58(9):e00932-20.
   Web of Science ®Google Scholar
• Sadek M, Poirel L, Nordmann P. Rapid detection of carbapenemase-producing Pseudomonas spp. using the NitroSpeed-Carba NP test. Diagn Microbiol Infect Dis. 2021;99(3):115280.
   PubMed Web of Science ®Google Scholar
• Bishop JD, Hsieh HV, Gasperino DJ, et al. Sensitivity enhancement in lateral flow assays: a systems perspective. Lab Chip. 2019;19(15):2486–2499.
   PubMed Web of Science ®Google Scholar
• Cointe A, Bonacorsi S, Truong J, et al. Detection of Carbapenemase-producing Enterobacteriaceae in positive blood culture using an immunochromatographic RESIST-4 O.K.N.V. assay. Antimicrob Agents Chemother. 2018;62(12). DOI:10.1128/AAC.01828-18.
   PubMed Web of Science ®Google Scholar
• Greissl C, Saleh A, Hamprecht A. Rapid detection of OXA-48-like, KPC, NDM, and VIM carbapenemases in Enterobacterales by a new multiplex immunochromatographic test. Eur J Clin Microbiol Infect Dis. 2019;38(2):331–335.
   PubMed Web of Science ®Google Scholar
• Saleh A, Gottig S, Hamprecht AG. Multiplex immunochromatographic detection of OXA-48, KPC, and NDM Carbapenemases: impact of inoculum, antibiotics, and agar. J Clin Microbiol. 2018;56(5):5.
   Web of Science ®Google Scholar
• Jenkins S, Ledeboer NA, Westblade LF, et al. Evaluation of NG-test Carba 5 for rapid phenotypic detection and differentiation of five common Carbapenemase families: results of a multicenter clinical evaluation. J Clin Microbiol. 2020;58(7). DOI:10.1128/JCM.00344-20.
   Web of Science ®Google Scholar
• Potron A, Fournier D, Emeraud C, et al. Evaluation of the immunochromatographic NG-test Carba 5 for rapid identification of Carbapenemase in nonfermenters. Antimicrob Agents Chemother. 2019;63(9). DOI:10.1128/AAC.00968-19.
   Web of Science ®Google Scholar
• Takissian J, Bonnin RA, Naas T, et al. NG-test Carba 5 for rapid detection of Carbapenemase-producing Enterobacterales from positive blood cultures. Antimicrob Agents Chemother. 2019;63(5). DOI:10.1128/AAC.00011-19
   Web of Science ®Google Scholar
• Volland H, Girlich D, Laguide M, et al. Improvement of the Immunochromatographic NG-test Carba 5 assay for the detection of IMP variants previously undetected. Antimicrob Agents Chemother. 2019;64(1). DOI:10.1128/AAC.01940-19.
   PubMed Web of Science ®Google Scholar
• Bianco G, Boattini M, Van Asten SAV, et al. RESIST-5 O.O.K.N.V. and NG-test Carba 5 assays for the rapid detection of carbapenemase-producing Enterobacterales from positive blood cultures: a comparative study. J Hosp Infect. 2020;105(2):162–166.
   PubMed Web of Science ®Google Scholar
• Hu Y, Huang Y, Lizou Y, et al. Evaluation of Staphylococcus aureus subtyping module for methicillin-resistant Staphylococcus aureus detection based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Front Microbiol. 2019;10(2504). DOI:10.3389/fmicb.2019.02504
   Google Scholar
• Rhoads DD, Wang H, Karichu J, et al. The presence of a single MALDI-TOF mass spectral peak predicts methicillin resistance in staphylococci. Diagn Microbiol Infect Dis. 2016;86(3):257–261.
   PubMed Web of Science ®Google Scholar
• Lau AF, Wang H, Weingarten RA, et al. A rapid matrix-assisted laser desorption ionization-time of flight mass spectrometry-based method for single-plasmid tracking in an outbreak of carbapenem-resistant Enterobacteriaceae. J Clin Microbiol. 2014;52(8):2804–2812.
   PubMed Web of Science ®Google Scholar
• Nagy E, Becker S, Soki J, et al. Differentiation of division I (cfiA-negative) and division II (cfiA-positive) Bacteroides fragilis strains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Med Microbiol. 2011;60(11):1584–1590.
   PubMed Web of Science ®Google Scholar
• Wybo I, De Bel A, Soetens O, et al. Differentiation of cfiA-negative and cfiA-positive Bacteroides fragilis isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol. 2011;49(5):1961–1964.
   PubMed Web of Science ®Google Scholar
• Oviano M, Bou G. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the rapid detection of antimicrobial resistance mechanisms and beyond. Clin Microbiol Rev. 2019;32(1). DOI:10.1128/CMR.00037-18
   PubMed Web of Science ®Google Scholar
• Dortet L, Tande D, De Briel D, et al. MALDI-TOF for the rapid detection of carbapenemase-producing Enterobacteriaceae: comparison of the commercialized MBT STAR(R)-Carba IVD Kit with two in-house MALDI-TOF techniques and the RAPIDEC(R) CARBA NP. J Antimicrob Chemother. 2018;73(9):2352–2359.
   PubMed Web of Science ®Google Scholar
• Rapp E, Samuelsen O, Sundqvist M. Detection of carbapenemases with a newly developed commercial assay using matrix assisted laser desorption ionization-time of flight. J Microbiol Methods. 2018;146(37):37–39.
   PubMedGoogle Scholar
• Idelevich EA, Storck LM, Sparbier K, et al. Rapid direct susceptibility testing from positive blood cultures by the matrix-assisted laser desorption ionization-time of flight mass spectrometry-based direct-on-target microdroplet growth assay. J Clin Microbiol. 2018;56(10). DOI:10.1128/JCM.00913-18
   Web of Science ®Google Scholar
• Lee GH, Pang S, Coombs GW. Misidentification of Staphylococcus aureus by the Cepheid Xpert MRSA/SA BC Assay due to deletions in the spa gene. J Clin Microbiol. 2018;56(7). DOI:10.1128/JCM.00530-18
   Web of Science ®Google Scholar
• Wolk DM, Struelens MJ, Pancholi P, et al. Rapid detection of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in wound specimens and blood cultures: multicenter preclinical evaluation of the Cepheid Xpert MRSA/SA skin and soft tissue and blood culture assays. J Clin Microbiol. 2009;47(3):823–826.
   PubMed Web of Science ®Google Scholar
• Dubouix-Bourandy A, De Ladoucette A, Pietri V, et al. Direct detection of Staphylococcus osteoarticular infections by use of Xpert MRSA/SA SSTI real-time PCR. J Clin Microbiol. 2011;49(12):4225–4230.
   PubMed Web of Science ®Google Scholar
• Sambri A, Pignatti G, Romagnoli M, et al. Intraoperative diagnosis of Staphylococcus aureus and coagulase-negative Staphylococcus using Xpert MRSA/SA SSTI assay in prosthetic joint infection. New Microbiol. 2017;40(2):130–134.
   PubMed Web of Science ®Google Scholar
• Yarbrough ML, Warren DK, Allen K, et al. Multicenter evaluation of the Xpert MRSA NxG Assay for detection of methicillin-resistant Staphylococcus aureus in nasal swabs. J Clin Microbiol. 2018;56(1).
   Web of Science ®Google Scholar
• Buchan BW, Allen S, Burnham CA, et al. Comparison of the next-generation Xpert MRSA/SA BC assay and the GeneOhm StaphSR assay to routine culture for identification of Staphylococcus aureus and methicillin-resistant S. aureus in positive-blood-culture broths. J Clin Microbiol. 2015;53(3):804–809.
   PubMed Web of Science ®Google Scholar
• Hombach M, Pfyffer GE, Roos M, et al. Detection of methicillin-resistant Staphylococcus aureus (MRSA) in specimens from various body sites: performance characteristics of the BD GeneOhm MRSA assay, the Xpert MRSA assay, and broth-enriched culture in an area with a low prevalence of MRSA infections. J Clin Microbiol. 2010;48(11):3882–3887.
   PubMed Web of Science ®Google Scholar
• Rabaan AA, Bazzi AM. Variation in MRSA identification results from different generations of Xpert MRSA real-time PCR testing kits from nasal swabs. J Infect Public Health. 2017;10(6):799–802.
   PubMed Web of Science ®Google Scholar
• Gazin M, Lammens C, Goossens H, Gazin M, Lammens C, Goossens H, Malhotra-Kumar S, Team MWS. Evaluation of GeneOhm VanR and Xpert vanA/vanB molecular assays for the rapid detection of vancomycin-resistant enterococci. Eur J Clin Microbiol Infect Dis. 2012;31(3):273–276.
   PubMed Web of Science ®Google Scholar
• Both A, Berneking L, Berinson B, et al. Rapid identification of the vanA/vanB resistance determinant in Enterococcus sp. from blood cultures using the Cepheid Xpert vanA/vanB cartridge system. Diagn Microbiol Infect Dis. 2020;96(4):114977.
   PubMed Web of Science ®Google Scholar
• Holzknecht BJ, Hansen DS, Nielsen L, et al. Screening for vancomycin-resistant enterococci with Xpert® vanA/vanB: diagnostic accuracy and impact on infection control decision making. New Microbes New Infect. 2017;16(54):54–59.
   PubMedGoogle Scholar
• Rasoanandrasana S, Decousser JW, Cattoir V, et al. Use of ESwab in the Xpert(R) vanA/vanB PCR assay. Eur J Clin Microbiol Infect Dis. 2017;36(4):755–756.
   PubMed Web of Science ®Google Scholar
• Steingart KR, Sohn H, Schiller I, et al. Xpert(R) MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev. 2013;(1):CD009593. DOI:10.1002/14651858.CD009593.pub2.
   PubMed Web of Science ®Google Scholar
• Horne DJ, Kohli M, Zifodya JS, et al. Xpert MTB/RIF and Xpert MTB/RIF Ultra for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev. 2019;6(CD009593). DOI:10.1002/14651858.CD009593.pub4.
   PubMedGoogle Scholar
• Donovan J, Thu DDA, Phu NH, et al. Xpert MTB/RIF Ultra versus Xpert MTB/RIF for the diagnosis of tuberculous meningitis: a prospective, randomised, diagnostic accuracy study. Lancet Infect Dis. 2020;20(3):299–307.
   PubMed Web of Science ®Google Scholar
• Traczewski MM, Carretto E, Canton R, et al. Multicenter evaluation of the Xpert Carba-R Assay for detection of Carbapenemase genes in Gram-negative isolates. J Clin Microbiol. 2018;56(8). DOI:10.1128/JCM.00272-18
   Web of Science ®Google Scholar
• Tato M, Ruiz-Garbajosa P, Traczewski M, et al. Multisite evaluation of Cepheid Xpert Carba-R Assay for detection of carbapenemase-producing organisms in rectal Swabs. J Clin Microbiol. 2016;54(7):1814–1819.
   PubMed Web of Science ®Google Scholar
• Moore NM, Canton R, Carretto E, et al. Rapid identification of five classes of Carbapenem resistance genes directly from rectal swabs by use of the Xpert Carba-R Assay. J Clin Microbiol. 2017;55(7):2268–2275.
   PubMed Web of Science ®Google Scholar
• Cointe A, Walewski V, Hobson CA, et al. Rapid Carbapenemase detection with Xpert Carba-R V2 directly on positive blood vials. Infect Drug Resist. 2019;12(12):3311–3316.
   PubMedGoogle Scholar
• Salimnia H, Fairfax MR, Lephart PR, et al. Evaluation of the filmarray blood culture identification panel: results of a multicenter controlled trial. J Clin Microbiol. 2016;54(3):687–698.
   PubMed Web of Science ®Google Scholar
• Kang CM, Chen XJ, Chih CC, et al. Rapid identification of bloodstream bacterial and fungal pathogens and their antibiotic resistance determinants from positively flagged blood cultures using the BioFire filmarray blood culture identification panel. J Microbiol Immunol Infect. 2020;53(6):882–891.
   PubMedGoogle Scholar
• Payne M, Champagne S, Lowe C, et al. Evaluation of the filmarray blood culture identification panel compared to direct MALDI-TOF MS identification for rapid identification of pathogens. J Med Microbiol. 2018;67(9):1253–1256.
   PubMed Web of Science ®Google Scholar
• Pulido MR, Moreno-Martinez P, Gonzalez-Galan V, et al. Application of BioFire filmarray blood culture identification panel for rapid identification of the causative agents of ventilator-associated pneumonia. Clin Microbiol Infect. 2018;24(11):1213 e1211–1213 e1214.
   Web of Science ®Google Scholar
• Southern TR, VanSchooneveld TC, Bannister DL, et al. Implementation and performance of the BioFire filmArray(R) blood culture Identification panel with antimicrobial treatment recommendations for bloodstream infections at a midwestern academic tertiary hospital. Diagn Microbiol Infect Dis. 2015;81(2):96–101.
   PubMed Web of Science ®Google Scholar
• Cortazzo V, D’Inzeo T, Giordano L, et al. Comparing BioFire filmArray BCID2 and BCID panels for direct detection of bacterial pathogens and antimicrobial resistance genes from positive blood cultures. J Clin Microbiol. 2021;59(4). DOI:10.1128/JCM.03163-20.
   PubMed Web of Science ®Google Scholar
• Murphy CN, Fowler R, Balada-Llasat JM, et al. Multicenter evaluation of the Biofire filmarray Pneumonia/Pneumonia plus panel for detection and quantification of agents of lower respiratory tract infection. J Clin Microbiol. 2020;58(7). DOI:10.1128/JCM.00128-20.
   Web of Science ®Google Scholar
• Edin A, Eilers H, Allard A. Evaluation of the Biofire filmarray Pneumonia panel plus for lower respiratory tract infections. Infect Dis (Lond). 2020;52(7):479–488.
   PubMed Web of Science ®Google Scholar
• Webber DM, Wallace MA, Burnham CA, et al. Evaluation of the BioFire filmarray Pneumonia panel for detection of viral and bacterial pathogens in lower respiratory tract specimens in the setting of a tertiary care academic medical center. J Clin Microbiol. 2020;58(7). DOI:10.1128/JCM.00343-20
   Web of Science ®Google Scholar
• Gastli N, Loubinoux J, Daragon M, et al. Multicentric evaluation of BioFire filmarray Pneumonia panel for rapid bacteriological documentation of pneumonia. Clin Microbiol Infect. 2020. DOI:10.1016/j.cmi.2020.11.014.
   PubMedGoogle Scholar
• Buchan BW, Windham S, Balada-Llasat JM, et al. Practical comparison of the BioFire filmArray Pneumonia panel to routine diagnostic methods and potential impact on antimicrobial stewardship in adult hospitalized patients with lower respiratory tract infections. J Clin Microbiol. 2020;58(7). DOI:10.1128/JCM.00135-20.
   Web of Science ®Google Scholar
• Gilbert DN, Leggett JE, Wang L, et al. Enhanced detection of community-acquired Pneumonia pathogens with the BioFire(R) Pneumonia filmArray(R) panel. Diagn Microbiol Infect Dis. 2021;99(3):115246.
   PubMed Web of Science ®Google Scholar
• Bryant S, Almahmoud I, Pierre I, et al. Evaluation of microbiological performance and the potential clinical impact of the ePlex((R)) blood culture identification panels for the rapid diagnosis of bacteremia and fungemia. Front Cell Infect Microbiol. 2020;10(594951). DOI:10.3389/fcimb.2020.594951.
   PubMedGoogle Scholar
• Carroll KC, Reid JL, Thornberg A, et al. Clinical performance of the novel GenMark Dx ePlex blood culture ID Gram-positive panel. J Clin Microbiol. 2020;58(4). DOI:10.1128/JCM.01730-19.
   Web of Science ®Google Scholar
• Huang TD, Melnik E, Bogaerts P, et al. Evaluation of the ePlex blood culture identification panels for detection of pathogens in bloodstream infections. J Clin Microbiol. 2019;57(2). DOI:10.1128/JCM.01597-18
   Web of Science ®Google Scholar
• Krifors A, Radberg G, Golbob S, et al. The clinical impact of implementing GenMark ePlex blood culture panels for around-the-clock blood culture identification; a prospective observational study. Infect Dis (Lond). 2020;52(10):705–712.
   PubMed Web of Science ®Google Scholar
• Voulgari E, Miliotis G, Siatravani E, et al. Evaluation of the performance of Acuitas(R) resistome test and the Acuitas Lighthouse(R) software for the detection of beta-lactamase-producing microorganisms. J Glob Antimicrob Resist. 2020;22(184):184–189.
   PubMedGoogle Scholar
• Walker GT, Quan J, Higgins SG, et al. Predicting antibiotic resistance in Gram-negative Bacilli from resistance genes. Antimicrob Agents Chemother. 2019;63(4). DOI:10.1128/AAC.02462-18.
   Web of Science ®Google Scholar
• Vanstone GL, Woodhead S, Roulston K, et al. Improving the detection of carbapenemase-producing organisms (CPO) in a low-prevalence setting: evaluation of four commercial methods and implementation of an algorithm of testing. J Med Microbiol. 2018;67(2):208–214.
   PubMed Web of Science ®Google Scholar
• Evans SR, Tran TTT, Hujer AM, et al. Rapid molecular diagnostics to inform Empiric use of Ceftazidime/Avibactam and Ceftolozane/Tazobactam against Pseudomonas aeruginosa: PRIMERS IV. Clin Infect Dis. 2019;68(11):1823–1830.
   PubMed Web of Science ®Google Scholar
• Sadek M, Demord A, Poirel L, et al. Fast and reliable detection of carbapenemase genes in various Gram negatives using a new commercially available fluorescence-based real-time polymerase chain reaction platform. Diagn Microbiol Infect Dis. 2020;98(3):115127.
   PubMed Web of Science ®Google Scholar
• Bissonnette L, Bergeron MG. The GenePOC platform a rational solution for extreme point-of-care testing. Micromach (Basel). 2016;7:6.
   Web of Science ®Google Scholar
• Lucena Baeza L, Pfennigwerth N, Hamprecht A. Rapid and easy detection of carbapenemases in enterobacterales in the routine laboratory using the new GenePOC Carba/Revogene Carba C Assay. J Clin Microbiol. 2019;57(9). DOI:10.1128/JCM.00597-19
   PubMed Web of Science ®Google Scholar
• Lucena Baeza L, Hamprecht A. A profile of the GenePOC Carba C assay for the detection and differentiation of gene sequences associated with carbapenem-non-susceptibility. Expert Rev Mol Diagn. 2020;20(8):757–769.
   PubMed Web of Science ®Google Scholar
• Powell EA, Haslam D, Mortensen JE. Performance of the check-points check-MDR CT103XL assay utilizing the CDC/FDA antimicrobial resistance isolate bank. Diagn Microbiol Infect Dis. 2017;88(3):219–221.
   PubMed Web of Science ®Google Scholar
• Powell EA, Khalil N, DeBurger B, et al. Combined molecular and Phenotypic Antimicrobial susceptibility testing is beneficial in detection of ESBL and AmpC Beta-Lactamase producing isolates of Enterobacteriaceae in pediatric patients with bloodstream infections. Microb Drug Resist. 2020;26(7):825–830.
   PubMed Web of Science ®Google Scholar
• Uddin F, McHugh TD, Roulston K, et al. Detection of carbapenemases AmpC and ESBL genes in Acinetobacter isolates from ICUs by DNA microarray. J Microbiol Methods. 2018;155:19–23.
   PubMed Web of Science ®Google Scholar
• Forster CS, Powell EA, DeBurger B, et al. Association of systemic antimicrobials with the expression of beta-lactamases in bacteria cultured from urological patients. Diagn Microbiol Infect Dis. 2019;94(4):391–394.
   PubMed Web of Science ®Google Scholar
• Wojewoda CM, Sercia L, Navas M, et al. Evaluation of the Verigene Gram-positive blood culture nucleic acid test for rapid detection of bacteria and resistance determinants. J Clin Microbiol. 2013;51(7):2072–2076.
   PubMed Web of Science ®Google Scholar
• Beal SG, Ciurca J, Smith G, et al. Evaluation of the nanosphere verigene gram-positive blood culture assay with the VersaTREK blood culture system and assessment of possible impact on selected patients. J Clin Microbiol. 2013;51(12):3988–3992.
   PubMed Web of Science ®Google Scholar
• Vareechon C, Mestas J, Polanco CM, et al. A 5-year study of the performance of the Verigene Gram-positive blood culture panel in a pediatric hospital. Eur J Clin Microbiol Infect Dis. 2018;37(11):2091–2096.
   PubMed Web of Science ®Google Scholar
• De Angelis G, Grossi A, Menchinelli G, et al. Rapid molecular tests for detection of antimicrobial resistance determinants in Gram-negative organisms from positive blood cultures: a systematic review and meta-analysis. Clin Microbiol Infect. 2020;26(3):271–280.
   PubMed Web of Science ®Google Scholar
• Ledeboer NA, Lopansri BK, Dhiman N, et al. Identification of Gram-negative bacteria and genetic resistance determinants from positive blood culture broths by use of the Verigene Gram-negative blood culture multiplex microarray-based molecular assay. J Clin Microbiol. 2015;53(8):2460–2472.
   PubMed Web of Science ®Google Scholar
• Hayakawa K, Mezaki K, Kobayakawa M, et al. Impact of rapid identification of positive blood cultures using the Verigene system on antibiotic prescriptions: a prospective study of community-onset bacteremia in a tertiary hospital in Japan. PLoS One. 2017;12(7):e0181548.
   PubMed Web of Science ®Google Scholar
• Belknap A, Grosser DS, Hale DA, et al. Clinical uptake of antimicrobial stewardship recommendations following Nanosphere Verigene blood culture Gram-negative reporting. Proc (Bayl Univ Med Cent). 2017;30(4):395–399.
   PubMedGoogle Scholar
• Hinic V, Ziegler J, Straub C, et al. Extended-spectrum beta-lactamase (ESBL) detection directly from urine samples with the rapid isothermal amplification-based eazyplex(R) SuperBug CRE assay: proof of concept. J Microbiol Methods. 2015;119(203):203–205.
   PubMedGoogle Scholar
• Garcia-Fernandez S, Morosini MI, Marco F, et al. Evaluation of the eazyplex(R) SuperBug CRE system for rapid detection of carbapenemases and ESBLs in clinical Enterobacteriaceae isolates recovered at two Spanish hospitals. J Antimicrob Chemother. 2015;70(4):1047–1050.
   PubMed Web of Science ®Google Scholar
• Land M, Hauser L, Jun SR, et al. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015;15(2):141–161.
   PubMed Web of Science ®Google Scholar
• Gautam SS, Kc R, Leong KW, et al. A step-by-step beginner’s protocol for whole genome sequencing of human bacterial pathogens. J Biol Methods. 2019;6(1):e110.
   PubMedGoogle Scholar
• Rossen JWA, Friedrich AW, Moran-Gilad J. ESCMID study group for genomic molecular diagnostics. practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology. Clin Microbiol Infect. 2018;24(4):355–360.
   PubMed Web of Science ®Google Scholar
• Rhoads DD, Ledeboer NA. Lowering the barriers to routine whole-genome sequencing of bacteria in the clinical microbiology laboratory. J Clin Microbiol. 2018;56(9). DOI:10.1128/JCM.00813-18
   PubMed Web of Science ®Google Scholar
• Didelot X, Bowden R, Wilson DJ, et al. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet. 2012;13(9):601–612.
   PubMed Web of Science ®Google Scholar
• Reuter S, Ellington MJ, Cartwright EJ, et al. Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Intern Med. 2013;173(15):1397–1404.
   PubMed Web of Science ®Google Scholar
• Quainoo S, Coolen JPM, Van Hijum S, et al. Whole-genome sequencing of bacterial pathogens: the future of Nosocomial outbreak analysis. Clin Microbiol Rev. 2017;30(4):1015–1063.
   PubMed Web of Science ®Google Scholar
• Nezami BG, Jani M, Alouani D, et al. Helicobacter pylori mutations detected by next-generation sequencing in formalin-fixed paraffin-embedded gastric biopsy specimens are associated with treatment failure. J Clin Microbiol. 2019;57:7.
   Web of Science ®Google Scholar
• Tamma PD, Fan Y, Bergman Y, et al. Applying rapid whole-genome sequencing to predict phenotypic antimicrobial susceptibility testing results among Carbapenem-resistant Klebsiella pneumoniae clinical isolates. Antimicrob Agents Chemother. 2019;63(1).
   Web of Science ®Google Scholar
• Stoesser N, Batty EM, Eyre DW, et al. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother. 2013;68(10):2234–2244.
   PubMed Web of Science ®Google Scholar
• Davis JJ, Boisvert S, Brettin T, et al. Antimicrobial resistance prediction in PATRIC and RAST. Sci Rep. 2016;6(1). DOI:10.1038/srep27930.
   Google Scholar
• Pesesky MW, Hussain T, Wallace M, et al. Evaluation of machine learning and rules-based approaches for predicting antimicrobial resistance profiles in Gram-negative Bacilli from whole genome sequence data. Front Microbiol. 2016;7(1887). DOI:10.3389/fmicb.2016.01887.
   PubMedGoogle Scholar
• Nguyen M, Long SW, McDermott PF, et al. Using machine learning to predict antimicrobial MICs and associated genomic features for Nontyphoidal Salmonella. J Clin Microbiol. 2019;57(2). DOI:10.1128/JCM.01260-18.
   Web of Science ®Google Scholar
• Ferreira I, Beisken S, Lueftinger L, et al. Species identification and antibiotic resistance prediction by analysis of whole-genome sequence data by use of aresdb: an analysis of isolates from the Unyvero lower respiratory tract infection trial. J Clin Microbiol. 2020;58(7). DOI:10.1128/JCM.00273-20.
   PubMed Web of Science ®Google Scholar
• He G, Li Y, Chen X, et al. Prediction of treatment outcomes for multidrug-resistant tuberculosis by whole-genome sequencing. Int J Infect Dis. 2020;96(68):68–72.
   PubMedGoogle Scholar
• Kizny Gordon A, Marais B, Walker TM, et al. Clinical and public health utility of Mycobacterium tuberculosis whole genome sequencing. Int J Infect Dis. 2021. DOI:10.1016/j.ijid.2021.02.114
   PubMedGoogle Scholar
• Rhoads DD, Sintchenko V, Rauch CA, et al. Clinical microbiology informatics. Clin Microbiol Rev. 2014;27(4):1025–1047.
   PubMed Web of Science ®Google Scholar
• Grad YH, Harris SR, Kirkcaldy RD, et al. Genomic Epidemiology of Gonococcal resistance to extended-spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013. J Infect Dis. 2016;214(10):1579–1587.
   PubMed Web of Science ®Google Scholar
• Yee R, Breitwieser FP, Hao S, et al. Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms. Eur J Clin Microbiol Infect Dis. 2021;40(1):95–102.
   PubMed Web of Science ®Google Scholar
• Clancy CJ, Potoski BA, Buehrle D, et al. Estimating the treatment of Carbapenem-resistant Enterobacteriaceae infections in the United States using antibiotic prescription data. Open Forum Infect Dis. 2019;6(8):ofz344.
   PubMed Web of Science ®Google Scholar
• Vandenberg O, Durand G, Hallin M, et al. Consolidation of clinical microbiology laboratories and introduction of transformative technologies. Clin Microbiol Rev. 2020;33(2). DOI:10.1128/CMR.00057-19.
   PubMed Web of Science ®Google Scholar
• Vickers RJ, Bassetti M, Clancy CJ, et al. Combating resistance while maintaining innovation: the future of antimicrobial stewardship. Future Microbiol. 2019;14(15):1331–1341.
   PubMed Web of Science ®Google Scholar
• D’Onofrio V, Salimans L, Bedenic B, et al. The clinical impact of rapid molecular microbiological diagnostics for pathogen and resistance gene identification in patients with Sepsis: a systematic review. Open Forum Infect Dis. 2020;7(10):ofaa352.
   PubMed Web of Science ®Google Scholar
• Beal SG, Assarzadegan N, Rand KH. Sample-to-result molecular infectious disease assays: clinical implications, limitations and potential. Expert Rev Mol Diagn. 2016;16(3):323–341.
   PubMed Web of Science ®Google Scholar
• Doyle RM, O’Sullivan DM, Aller SD, et al. Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study. Microb Genom. 2020;6(2). DOI:10.1099/mgen.0.000335.
   PubMed Web of Science ®Google Scholar
• Ellington MJ, Ekelund O, Aarestrup FM, et al. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST subcommittee. Clin Microbiol Infect. 2017;23(1):2–22.
   PubMed Web of Science ®Google Scholar
• EUCAST. EUCAST guidelines for detection of resistance mechanisms and specific resistances of clinical and/or epidemiological importance. (2017).
   Google Scholar