title: Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae.
abstract: Molecular typing has become indispensable in the detection of nosocomial transmission of bacterial pathogens and the identification of sources and routes of transmission in outbreak settings, but current methods are labor-intensive, are difficult to standardize, or have limited resolution. Whole-genome multilocus sequence typing (wgMLST) has emerged as a whole-genome sequencing (WGS)-based gene-by-gene typing method that may overcome these limitations and has been applied successfully for several species in outbreak settings. In this study, genus-, genetic-complex-, and species-specific wgMLST schemes were developed for Citrobacter spp., the Enterobacter cloacae complex, Escherichia coli, Klebsiella oxytoca, and Klebsiella pneumoniae and used to type a national collection of 1,798 extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E) isolates obtained from patients in Dutch hospitals. Genus-, genetic-complex-, and species-specific thresholds for genetic distance that accurately distinguish between epidemiologically related and unrelated isolates were defined for Citrobacter spp., the E. cloacae complex, E. coli, and K. pneumoniae wgMLST was shown to have higher discriminatory power and typeability than in silico MLST. In conclusion, the wgMLST schemes developed in this study facilitate high-resolution WGS-based typing of the most prevalent ESBL-producing species in clinical practice and may contribute to further elucidation of the complex epidemiology of antimicrobial-resistant Enterobacteriaceae wgMLST opens up possibilities for the creation of a Web-accessible database for the global surveillance of ESBL-producing bacterial clones.
authors.affiliation: Amphia Academy Infectious Disease Foundation, Amphia Hospital, Breda, the Netherlands marjoleinkluytmans@gmail.com.|Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands.
authors.forename: Marjolein F Q
authors.initials: MF
authors.lastname: Kluytmans-van den Bergh
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
authors.forename: John W A
authors.initials: JW
authors.lastname: Rossen
authors.affiliation: Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands.
authors.forename: Patricia C J
authors.initials: PC
authors.lastname: Bruijning-Verhagen
authors.affiliation: Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands.|Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands.
authors.forename: Marc J M
authors.initials: MJ
authors.lastname: Bonten
authors.affiliation: Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
authors.forename: Alexander W
authors.initials: AW
authors.lastname: Friedrich
authors.affiliation: Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands.
authors.forename: Christina M J E
authors.initials: CM
authors.lastname: Vandenbroucke-Grauls
authors.affiliation: Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands.
authors.forename: Rob J L
authors.initials: RJ
authors.lastname: Willems
authors.affiliation: Amphia Academy Infectious Disease Foundation, Amphia Hospital, Breda, the Netherlands.|Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands.
authors.forename: Jan A J W
authors.initials: JA
authors.lastname: Kluytmans
mesh_terms: D002954:Citrobacter / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics*; D016972:Enterobacter cloacae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D004755:Enterobacteriaceae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D004756:Enterobacteriaceae Infections / Q000382:microbiology*; D004926:Escherichia coli / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D041121:Klebsiella oxytoca / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D007711:Klebsiella pneumoniae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D058885:Multilocus Sequence Typing / Q000379:methods*; D001618:beta-Lactamases / Q000235:genetics* / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D001618:beta-Lactamases