Abstract
Community-associated spa type t127/t922 methicillin-resistant Staphylococcus aureus (MRSA) prevalence increased from 1%-7% in Ireland between 2010–2015. This study tracked the spread of 89 such isolates from June 2013-June 2016. These included 78 healthcare-associated and 11 community associated-MRSA isolates from a prolonged hospital outbreak (H1) (n = 46), 16 other hospitals (n = 28), four other healthcare facilities (n = 4) and community-associated sources (n = 11). Isolates underwent antimicrobial susceptibility testing, DNA microarray profiling and whole-genome sequencing. Minimum spanning trees were generated following core-genome multilocus sequence typing and pairwise single nucleotide variation (SNV) analysis was performed. All isolates were sequence type 1 MRSA staphylococcal cassette chromosome mec type IV (ST1-MRSA-IV) and 76/89 were multidrug-resistant. Fifty isolates, including 40/46 from H1, were high-level mupirocin-resistant, carrying a conjugative 39 kb iles2-encoding plasmid. Two closely related ST1-MRSA-IV strains (I and II) and multiple sporadic strains were identified. Strain I isolates (57/89), including 43/46 H1 and all high-level mupirocin-resistant isolates, exhibited ≤80 SNVs. Two strain I isolates from separate H1 healthcare workers differed from other H1/strain I isolates by 7–47 and 12–53 SNVs, respectively, indicating healthcare worker involvement in this outbreak. Strain II isolates (19/89), including the remaining H1 isolates, exhibited ≤127 SNVs. For each strain, the pairwise SNVs exhibited by healthcare-associated and community-associated isolates indicated recent transmission of ST1-MRSA-IV within and between multiple hospitals, healthcare facilities and communities in Ireland. Given the interchange between healthcare-associated and community-associated isolates in hospitals, the risk factors that inform screening for MRSA require revision.
Highlights
Staphylococcus aureus can cause a wide variety of diseases ranging in severity from superficial skin infections to life-threatening invasive infections such as necrotizing pneumonia, endocarditis and sepsis [1, 2]
This study revealed the recent emergence and extensive spread of several strains of a predominantly MDR CA-methicillin-resistant S. aureus (MRSA) clone, CC1-ST1-MRSA-IV, within and between hospitals/healthcare facilities (HCFs) and communities throughout Ireland
Increased prevalence of a MDR CA-MRSA clone, pvl-positive CC1-ST772-MRSA-V, was previously reported in Ireland [22]. This clone did not spread as extensively as the CC1-ST1-MRSA-IV clone investigated here, this pattern reflects the relatively recent worldwide trend of CA-MRSA spreading into hospitals
Summary
Staphylococcus aureus can cause a wide variety of diseases ranging in severity from superficial skin infections to life-threatening invasive infections such as necrotizing pneumonia, endocarditis and sepsis [1, 2]. Data from S. aureus sequence types (STs) ST22, ST2257, ST30 and ST36 showed that multiple colonies recovered from a single patient swab can vary by up 40 SNVs [15] This 40 SNV intra-host strain variation threshold has since been used to infer relatedness between isolates and to identify transmission events [10, 16]. In addition to SNV analysis, whole-genome MLST (wgMLST), involving >1,800 genome-wide loci, has been applied to investigate relationships between MRSA isolates [17]. This approach currently provides the optimal resolution to infer phylogenetic relatedness among isolates, permitting the identification of possible, probable, or unlikely cases of epidemiological linkage. Core-genome MLST (cgMLST), which excludes accessory genome loci, is a refinement of wgMLST based on genes present in each isolate genome [18]
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