Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system

Abstract

BackgroundIn the past decade, several countries have seen gradual replacement of endemic multi-resistant healthcare-associated methicillin-resistant Staphylococcus aureus (MRSA) with clones that are more susceptible to antibiotic treatment. One example is Singapore, where MRSA ST239, the dominant clone since molecular profiling of MRSA began in the mid-1980s, has been replaced by ST22 isolates belonging to EMRSA-15, a recently emerged pandemic lineage originating from Europe.ResultsWe investigated the population structure of MRSA in Singaporean hospitals spanning three decades, using whole genome sequencing. Applying Bayesian phylogenetic methods we report that prior to the introduction of ST22, the ST239 MRSA population in Singapore originated from multiple introductions from the surrounding region; it was frequently transferred within the healthcare system resulting in a heterogeneous hospital population. Following the introduction of ST22 around the beginning of the millennium, this clone spread rapidly through Singaporean hospitals, supplanting the endemic ST239 population. Coalescent analysis revealed that although the genetic diversity of ST239 initially decreased as ST22 became more dominant, from 2007 onwards the genetic diversity of ST239 began to increase once more, which was not associated with the emergence of a sub-clone of ST239. Comparative genomic analysis of the accessory genome of the extant ST239 population identified that the Arginine Catabolic Mobile Element arose multiple times, thereby introducing genes associated with enhanced skin colonization into this population.ConclusionsOur results clearly demonstrate that, alongside clinical practice and antibiotic usage, competition between clones also has an important role in driving the evolution of nosocomial pathogen populations.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0643-z) contains supplementary material, which is available to authorized users.

Temporally Varying Relative Risks for Infectious Diseases

“…A parallel literature in molecular epidemiology of pathogens (e.g. [63]) documents the rise and fall of particular pathogen lineages over time, with less attention to which kinds of hosts tend to get infected with which genetic variants. Combining epidemiologic analysis of host risk factors (and their change over time) with molecular analysis of pathogen characteristics (and their change over time) may be a fertile route to understanding the relationship between who gets infected and which pathogen or strain infects them.…”

Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice

“…Tagged DNA libraries were created using a method adapted from a standard Illumina Indexing protocol, as described previously [31]. Whole genome sequencing was performed on the Illumina HiSeq 2000 platform with 100-bp paired-end reads.…”

Genomic insights into the emergence and spread of international clones of healthcare-, community- and livestock-associated meticillin-resistant Staphylococcus aureus : Blurring of the traditional definitions

“…The human EMRSA-15 epidemic has also spread into the companion animal population [22,23], with veterinary hospitals also being healthcare settings that may experience high levels of transmission [24]. A c c e p t e d M a n u s c r i p t 12 documented in Portugal, Singapore and Australia [25][26][27]. One feature that may contribute to its success is the SCCmec IV element that this clone carries, which has a lower fitness cost than the larger SCCmec elements such as SCCmec types II and III that were prevalent in earlier HA-MRSA clones [28].…”