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We report the utility of whole-genome sequencing (WGS) conducted in a clinically relevant time frame (ie, sufficient for guiding management decision), in managing a Streptococcus pyogenes outbreak, and present a comparison of its performance with emm typing.
A 2,000-bed tertiary-care psychiatric hospital.
Active surveillance was conducted to identify new cases of S. pyogenes. WGS guided targeted epidemiological investigations, and infection control measures were implemented. Single-nucleotide polymorphism (SNP)–based genome phylogeny, emm typing, and multilocus sequence typing (MLST) were performed. We compared the ability of WGS and emm typing to correctly identify person-to-person transmission and to guide the management of the outbreak.
The study included 204 patients and 152 staff. We identified 35 patients and 2 staff members with S. pyogenes. WGS revealed polyclonal S. pyogenes infections with 3 genetically distinct phylogenetic clusters (C1–C3). Cluster C1 isolates were all emm type 4, sequence type 915 and had pairwise SNP differences of 0–5, which suggested recent person-to-person transmissions. Epidemiological investigation revealed that cluster C1 was mediated by dermal colonization and transmission of S. pyogenes in a male residential ward. Clusters C2 and C3 were genomically diverse, with pairwise SNP differences of 21–45 and 26–58, and emm 11 and mostly emm120, respectively. Clusters C2 and C3, which may have been considered person-to-person transmissions by emm typing, were shown by WGS to be unlikely by integrating pairwise SNP differences with epidemiology.
WGS had higher resolution than emm typing in identifying clusters with recent and ongoing person-to-person transmissions, which allowed implementation of targeted intervention to control the outbreak.
To investigate the molecular epidemiology of carbapenem-resistant Acinetobacter baumannii-calcoaceticus complex isolates in a tertiary care hospital where the prevalence of carbapenem resistance among these organisms is high.
The study was a prospective, observational study performed during an 8-month period (May 1 through December 31, 2004). A. baumannii isolates recovered from all clinical samples during the study period were included in the study. Antibiotic susceptibility testing was performed using the disk diffusion method, and all carbapenem-resistant strains were typed by a polymerase chain reaction-based typing method.
An 800-bed hospital in Singapore.
More than half of recovered isolates were clonally unrelated, with the remaining isolates grouped into 4 genotypes.
The results of the study suggest that the high prevalence of carbapenem resistance among Acinetobacter organisms in this institution is not caused by the spread of a predominant clone and that other factors may need to be investigated.
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