Next-Generation Sequencing Confirms Presumed Nosocomial Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in the Netherlands

Abstract

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) was detected in 2003 and rapidly became the predominant MRSA clade in the Netherlands. Studies have shown that transmissions are difficult to identify, since this MRSA variant represents a genetically homogenous clade when current typing techniques are used. Here, next-generation sequencing was performed on 206 LA-MRSA isolates to assess the capability of LA-MRSA to be transmitted between humans. The usefulness of single nucleotide variants (SNVs), the composition of the SCCmec region, and the presence of plasmids to identify transmission of LA-MRSA were assessed. In total, 30 presumed putative nosocomial transmission events and 2 LA-MRSA outbreaks were studied; in most cases, SNV analysis revealed that the isolates of the index patient and the contact(s) clustered closely together. In three presumed events, the isolates did not cluster together, indicating that transmission was unlikely. The composition of the SCCmec region corroborated these findings. However, plasmid identification did not support our SNV analysis, since different plasmids were present in several cases where SNV and SCCmec analysis suggested that transmission was likely. Next-generation sequencing shows that transmission of LA-MRSA does occur in Dutch health care settings. Transmission was identified based on SNV analysis combined with epidemiological data and in the context of epidemiologically related and unrelated isolates. Analysis of the SCCmec region provided limited, albeit useful, information to corroborate conclusions on transmissions, but plasmid identification did not. IMPORTANCE In 2003, a variant of methicillin-resistant Staphylococcus aureus (MRSA) isolated from pigs was also found in pig farmers inFrance and the Netherlands. Soon thereafter, this livestock-associated MRSA (LA-MRSA) was identified in many other countries. Transmission of LA-MRSA between humans, particularly in the health care setting, is regarded to occur sporadically. Moreover, studies that describe LA-MRSA transmission used molecular characterization of isolates with limited discriminatory power, making the validity of the conclusion that transmission occurred questionable. In our study, we sequenced the complete genomes of 206 LA-MRSA isolates, obtained from more than 30 presumed LA-MRSA transmission events. Analysis of the data showed that transmission of LA-MRSA between humans had indeed occurred in more than 90% of these events. We conclude that transmission of LA-MRSA between humans does occur in Dutch health care settings; therefore, a decision to discontinue the search and destroy policy for LA-MRSA should be taken with caution. M ethicillin-resistant Staphylococcus aureus (MRSA) is an important cause of hospital-acquired and community-acquired infections (1). In 2003, an MRSA variant cultured from pigs and pig farmers emerged in the Netherlands and France (2, 3). This clonal lineage was designated MLST clonal complex 398 (CC398), and a large number of countries reported ...

Prevalence of Antibiotic and Heavy Metal Resistance Determinants and Virulence-Related Genetic Elements in Plasmids of Staphylococcus aureus

“…The presence of TA system pemIK-Sa1 likely stabilizes its maintenance as the system has been demonstrated to display required properties (Bukowski et al, 2013). Conversely, homologs of group II plasmids, pRIVM4390 (pMCCL5) and pRIVM1295-2 (GenBank accessions CP013623 and CP013618), were reported recently in an opposite context, namely in livestock-associated MRSA (LA-MRSA) strains transmitted from farmed animals to humans in Netherlands, which dated back to 2003 (Bosch et al, 2016). It is noteworthy that pRIVM1295-2 found here in ph1 strain, which belongs to sequence type 1347 (ST1347) according to multilocus sequence typing (MLST, Maiden et al, 1998), was reported before by Lowder et al (2009) regarding a single human-to-poultry host jump and radiation among broiler chicken of unique to Poland, human ST5 clonal lineage that was roughly estimated to have occurred around 1970s.…”

“…Mass scale use of antibacterial drugs, especially in farming, increases the pressure for resistance determinants spread in natural environment and their exchange among free-living bacteria as well as animal commensals (Martinez, 2009; Fluit, 2012; He et al, 2014; Cuny et al, 2017; Kumar et al, 2017; Lau et al, 2017). Temporary colonization of humans by animal strains leading to the interaction with human microbiota or stable colonization (host jump) are not a rare phenomenon and the last part of the route (Armand-Lefevre et al, 2005; Voss et al, 2005; Bosch et al, 2016). Indeed, commensal strains of the same species or genus constitute a vast reservoir for antibiotic resistance determinants for those displaying pathogenic potential as it is observed for staphylococci (Tulinski et al, 2012; Hung et al, 2015; Morgenstern et al, 2016; Savini et al, 2016).…”

Methicillin-resistant Staphylococcus aureus among animals: current overview

“…Small hospital outbreaks of MRSA ST398 have occurred, the first in a Dutch hospital in 2007, but this phenomenon is still infrequent. Nevertheless, a recent study in which the genomes of 206 LA-MRSA isolates were fully sequenced showed that transmission of LA-MRSA between humans occurs in Dutch healthcare settings [53].…”

Characterization of Staphylococcal Cassette Chromosome mec Elements from Methicillin-Resistant Staphylococcus pseudintermedius Infections in Australian Animals

“…Instead, the isolates harbored a recombinase gene with 99% homology to ccrC6 , recently identified in a 43,922-bp SCC mec element in ST84 MRSP ( 15 ) and methicillin-resistant S. schleiferi (MRSS) ( 25 ). This element is also present in ST398 MRSA RIVM3897 ( 26 ), but the RIVM3987 element lacks the final 8,164 bp at the 3′ end of the SCC mec cassette in ST84 MRSP and MRSS. The nine isolates in this study showed 99% homology to the entire SCC mec cassette from MRSP NA45, which contained heavy metal resistance genes arsB, arsC , arsR (arsenic resistance) and copA (copper resistance) but no antimicrobial resistance genes.…”