OBJECTIVES: Phenotypic and genotypic methods for the detection of antimicrobial resistance (AMR) in enteroaggregative Escherichia coli (EAEC) were compared and evaluated. METHODS: WGS data from 155 isolates of EAEC isolated between June 2015 and December 2016 were mapped to genes known to be associated with phenotypic AMR. RESULTS: Phenotypic and genotypic testing of 155 isolates against 10 antimicrobial classes resulted in a total of 25 (1.6%) discordant results of a possible 1550 isolate/antimicrobial combinations. Twenty-three of the mismatches were observed in streptomycin or sulphonamide resistance profiles. These discrepancies were associated with either insertions or truncations in the genes predicted to confer resistance, or in their promotors, rendering them non-functional, or with the presence of aadA variants associated with reduced expression. The most common resistances detected were to ampicillin (56.1%), the sulphonamides (49.7%) and trimethoprim (48.4%). The presence of CTX-M ESBL variants and/or acquired AmpC was detected in 87 of 155 (56.1%) isolates and 18 of 155 (11.6%) isolates were resistant to ciprofloxacin. Eighty-eight (56.8%) isolates were MDR. CONCLUSIONS: Phenotypic and genome-derived AMR comparisons showed good correlation for EAEC. A better understanding of the role of allelic variants, specific gene combinations and promoter/attenuator mechanisms in the phenotypic manifestation will improve our ability to provide a robust interpretation of the data for surveillance purposes and, ultimately, in the clinical setting.
OBJECTIVES: Phenotypic and genotypic methods for the detection of antimicrobial resistance (AMR) in enteroaggregative Escherichia coli (EAEC) were compared and evaluated. METHODS: WGS data from 155 isolates of EAEC isolated between June 2015 and December 2016 were mapped to genes known to be associated with phenotypic AMR. RESULTS: Phenotypic and genotypic testing of 155 isolates against 10 antimicrobial classes resulted in a total of 25 (1.6%) discordant results of a possible 1550 isolate/antimicrobial combinations. Twenty-three of the mismatches were observed in streptomycin or sulphonamide resistance profiles. These discrepancies were associated with either insertions or truncations in the genes predicted to confer resistance, or in their promotors, rendering them non-functional, or with the presence of aadA variants associated with reduced expression. The most common resistances detected were to ampicillin (56.1%), the sulphonamides (49.7%) and trimethoprim (48.4%). The presence of CTX-M ESBL variants and/or acquired AmpC was detected in 87 of 155 (56.1%) isolates and 18 of 155 (11.6%) isolates were resistant to ciprofloxacin. Eighty-eight (56.8%) isolates were MDR. CONCLUSIONS: Phenotypic and genome-derived AMR comparisons showed good correlation for EAEC. A better understanding of the role of allelic variants, specific gene combinations and promoter/attenuator mechanisms in the phenotypic manifestation will improve our ability to provide a robust interpretation of the data for surveillance purposes and, ultimately, in the clinical setting.
Authors: Michael Feldgarden; Vyacheslav Brover; Daniel H Haft; Arjun B Prasad; Douglas J Slotta; Igor Tolstoy; Gregory H Tyson; Shaohua Zhao; Chih-Hao Hsu; Patrick F McDermott; Daniel A Tadesse; Cesar Morales; Mustafa Simmons; Glenn Tillman; Jamie Wasilenko; Jason P Folster; William Klimke Journal: Antimicrob Agents Chemother Date: 2019-10-22 Impact factor: 5.191
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Authors: Alex van Belkum; Carey-Ann D Burnham; John W A Rossen; Frederic Mallard; Olivier Rochas; William Michael Dunne Journal: Nat Rev Microbiol Date: 2020-02-13 Impact factor: 60.633
Authors: Nicole Jackson; Clarissa A Borges; Nicole J Tarlton; Angel Resendez; Aubrianne K Milton; Tara R de Boer; Cheyenne R Butcher; Niren Murthy; Lee W Riley Journal: J Microbiol Methods Date: 2021-02-04 Impact factor: 2.363
Authors: Ana Sofia Ribeiro Duarte; Katharina D C Stärk; Patrick Munk; Pimlapas Leekitcharoenphon; Alex Bossers; Roosmarijn Luiken; Steven Sarrazin; Oksana Lukjancenko; Sünje Johanna Pamp; Valeria Bortolaia; Jakob Nybo Nissen; Philipp Kirstahler; Liese Van Gompel; Casper Sahl Poulsen; Rolf Sommer Kaas; Maria Hellmér; Rasmus Borup Hansen; Violeta Munoz Gomez; Tine Hald Journal: Front Public Health Date: 2020-02-25