Unknown

Dataset Information

0

Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.


ABSTRACT: Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n=19), methicillin-resistant Staphylococcus aureus (n=17), and Acinetobacter baumannii (n=15). WGS was highly reproducible (average?0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P=5.6×10(-8) to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. For A. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing.

SUBMITTER: Salipante SJ 

PROVIDER: S-EPMC4365209 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

altmetric image

Publications

Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.

Salipante Stephen J SJ   SenGupta Dhruba J DJ   Cummings Lisa A LA   Land Tyler A TA   Hoogestraat Daniel R DR   Cookson Brad T BT  

Journal of clinical microbiology 20150128 4


Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococ  ...[more]

Similar Datasets

| S-EPMC6997133 | biostudies-literature
| S-EPMC6873635 | biostudies-literature
| S-EPMC8875922 | biostudies-literature
| S-EPMC7660531 | biostudies-literature
| S-EPMC6398925 | biostudies-literature
| S-EPMC6107157 | biostudies-literature
| S-EPMC7666501 | biostudies-literature
| S-EPMC5741664 | biostudies-literature
| S-EPMC4447836 | biostudies-literature
| S-EPMC5328449 | biostudies-literature