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APMIS. 2017 Dec;125(12):1117-1124. doi: 10.1111/apm.12753. Epub 2017 Sep 28.

Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing.

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Department of Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden.
Department of Medicine and Optometry, Linnaeus University, Kalmar, Sweden.
Department of Clinical Microbiology, Växjö Central Hospital, Växjö, Sweden.
Division of Medical Diagnostics, Region Jönköping County, Jönköping, Sweden.
Department Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden.
Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden.


Enhanced precision of epidemiological typing in clinically suspected nosocomial outbreaks is crucial. Our aim was to investigate whether single nucleotide polymorphism (SNP) analysis and core genome (cg) multilocus sequence typing (MLST) of whole genome sequencing (WGS) data would more reliably identify a nosocomial outbreak, compared to earlier molecular typing methods. Sixteen isolates from a nosocomial outbreak of ESBL E. coli ST-131 in southeastern Sweden and three control strains were subjected to WGS. Sequences were explored by SNP analysis and cgMLST. cgMLST clearly differentiated between the outbreak isolates and the control isolates (>1400 differences). All clinically identified outbreak isolates showed close clustering (≥2 allele differences), except for two isolates (>50 allele differences). These data confirmed that the isolates with >50 differing genes did not belong to the nosocomial outbreak. The number of SNPs within the outbreak was ≤7, whereas the two discrepant isolates had >700 SNPs. Two of the ESBL E. coli ST-131 isolates did not belong to the clinically identified outbreak. Our results illustrate the power of WGS in terms of resolution, which may avoid overestimation of patients belonging to outbreaks as judged from epidemiological data and previously employed molecular methods with lower discriminatory ability.


Epidemiological typing; Escherichia coli ST-131; cgMLST; single nucleotide polymorphism; whole genome sequencing

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