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Background: Using genomic data, we determined the origin of MRSA ST398 isolates responsible for invasive infection in patients with no known livestock contact. Methods: We sequenced the genome of seven MSSA and four MRSA ST398 isolates from patients with invasive infections between 2013 and 2017, using the Illumina technique. Prophage-associated virulence genes and resistance genes were identified. To determine the origin of the isolates, their genome sequences were included in phylogenetic analysis also encompassing the ST398 genomes available on NCBI. Results: All isolates carried the φSa3 prophage, but with variations in the immune evasion cluster: type C in MRSA isolates, and type B in MSSA isolates. All MSSA belonged to the spa type t1451. MRSA strains had the same SCCmec type IVa (2B) cassette and belonged to spa types t899, t4132, t1939 and t2922. All MRSA harbored the tetracycline resistance gene, tet(M). Phylogenetic analysis revealed that MSSA isolates belonged to a cluster of human-associated isolates, while MRSA isolates belonged to a cluster containing livestock-associated MRSA. Conclusion: We showed that the clinical isolates MRSA and MSSA ST398 have different origins. An acquisition of virulence genes by livestock-associated MRSA isolates allows them to induce an invasive infection in human. [ABSTRACT FROM AUTHOR]

Background: Using genomic data, we determined the origin of MRSA ST398 isolates responsible for invasive infection in patients with no known livestock contact. Methods: We sequenced the genome of seven MSSA and four MRSA ST398 isolates from patients with invasive infections between 2013 and 2017, using the Illumina technique. Prophage-associated virulence genes and resistance genes were identified. To determine the origin of the isolates, their genome sequences were included in phylogenetic analysis also encompassing the ST398 genomes available on NCBI. Results: All isolates carried the φSa3 prophage, but with variations in the immune evasion cluster: type C in MRSA isolates, and type B in MSSA isolates. All MSSA belonged to the spa type t1451. MRSA strains had the same SCCmec type IVa (2B) cassette and belonged to spa types t899, t4132, t1939 and t2922. All MRSA harbored the tetracycline resistance gene, tet(M). Phylogenetic analysis revealed that MSSA isolates belonged to a cluster of human-associated isolates, while MRSA isolates belonged to a cluster containing livestock-associated MRSA. Conclusion: We showed that the clinical isolates MRSA and MSSA ST398 have different origins. An acquisition of virulence genes by livestock-associated MRSA isolates allows them to induce an invasive infection in human.

Summary: This study investigated the prevalence of MRSA in samples taken in households, with and without backyard pigs in villages in a rural area of Shandong Province, China. Community‐associated MRSA and livestock‐associated MRSA, belonging to ST59 and ST9, respectively, were identified in both humans and pigs. The genotypic and phenotypic comparison of isolates indicates that bidirectional transmission of MRSA has occurred between humans and pigs in the villages. [ABSTRACT FROM AUTHOR]

This study aimed to explore the association between occupational pig contact and human methicillin-resistant coagulase-negative staphylococci (MRCoNS) carriage. We conducted a cross-sectional study of pig exposed participants and controls in Guangdong, China, using a multi-stage sampling design. Participants provided a nasal swab for MRCoNS analysis and resulting isolates were tested for antibiotic susceptibility. The dose-response relation was examined using log binomial regression or Poisson regression models. The adjusted prevalence of MRCoNS carriage in pig exposed participants was 1.67 times (95% CI: 1.32–2.11) higher than in controls. The adjusted average number of resistance to different antibiotic classes of MRCoNS isolates from pig exposed participants was 1.67 times (95% CI: 1.46–1.91) higher than those from controls. Notably, we found the frequency and duration of occupational pig contact was associated with increased prevalence and increased number of resistance to different antibiotic classes of MRCoNS in a dose-response manner. When examining these relations by MRCoNS species, there was still evidence of similar exposure-response relations. Additionally, the proportion of tetracycline-resistant and tet (M) - containing MRCoNS isolates was significantly higher in pig exposed participants than in controls. These findings suggested a potential transmission of MRCoNS from livestock to humans by occupational livestock contact, and the presence of phenotypic and genotypic tetracycline resistance may aid in the differentiation of animal origins of MRCoNS isolates. [ABSTRACT FROM AUTHOR]

Background: It has been suggested that prophages in the ST398 S. aureus clone are responsible for expanding ST398's spectrum of action and increasing its ability to cause human infections. We carried out the first characterization of the various prophages carried by 76 ST398 bloodstream infection (BSI) isolates obtained over 9 years of observation. Results: Whole-genome sequencing of 22 representative isolates showed (1) the presence of the φ3-prophage and diverse genetic features typical of animal-associated isolates (i.e., SCCmec XI element, Tn916 transposon and non φ3-prophages) in a majority of BSI isolates, (2) one BSI isolate devoid of the φ3-prophage but otherwise similar to an animal-infecting isolate, (3) 35 prophages carrying numerous genes previously associated with virulence or immune evasion in animal models of staphylococcal infections. The analysis of prophage content in all 76 BSI isolates showed an increasing prevalence of polylysogeny over time. Overall, over the course of the last 10 years, the BSI isolates appear to have acquired increasing numbers of genetic features previously shown to contribute to bacterial adaptation and virulence in animal models of staphylococcal infections. Conclusions: We hypothesize that lysogeny has played a significant role in increasing the ability of the ST398 clone to cause infections in humans. Our findings highlight the risk that the ST398 lineage will increase its threat to public health by continuing to acquire virulence and/or multiple antibiotic-resistance genes from hospitalassociated clones of Staphylococcus aureus. [ABSTRACT FROM AUTHOR]

Whole-genome sequencing (WGS) was used to investigate the genetic features of the recently identified lsa (E) gene in porcine S. aureus ST9 isolates. Three quinupristin/dalfopristin-resistant isolates harboring the lsa (E) gene (two MRSA and one MSSA) were sequenced. Phylogenetic analysis of 184 S. aureus genomes showed that ST9 porcine isolates belong to a distinct sequence cluster. Further analysis showed that all isolates were deficient in the recently described type IV restriction-modification system and SCC mec type XII was identified in the two MRSA isolates, which included a rare class C2 mec gene complex. A 24 kb ΨSCC fragment was found in the MRSA and MSSA isolates sharing 99% nucleotide sequence homology with the ΨSCCJCSC6690 (O-2) element of a ST9 MRSA isolate from Thailand (accession number AB705453 ). Comparison of these ST9 isolates with 181 publically available S. aureus genomes identified 24 genes present in all (100%) ST9 isolates, that were absent from the most closely related human isolate. Our analysis suggests that the sequenced quinupristin/dalfopristin-resistant ST9 lineage represent a reservoir of mobile genetic elements associated with resistance and virulence features. [ABSTRACT FROM AUTHOR]

While some studies have defined Staphylococcus aureus based on its clonal complex and resistance pattern, few have explored the relations between the genetic lineages and antibiotic resistance patterns and immune evasion cluster (IEC) genes. Our aim was to investigate the potential relationship between phenotypic and molecular characteristics so as to reveal livestock-associated S. aureus in humans. The study participants were interviewed, and they provided two nasal swabs for S. aureus analysis. All S. aureus and methicillin-resistant S. aureus (MRSA) were tested for antibiotic susceptibility, multilocus sequence type and IEC genes. Of the 1162 participants, 9.3% carried S. aureus, including MRSA (1.4%) and multidrug-resistant S. aureus (MDRSA, 2.8%). The predominant multidrug-resistant pattern among MDRSA isolates was nonsusceptibility to erythromycin, clindamycin and tetracycline. The most common S. aureus genotypes were ST7, ST6, ST188 and ST59, and the predominant MRSA genotype was ST7. Notably, the livestock-associated S. aureus isolates (IEC-negative CC9, IEC-negative tetracycline-resistant CC398, and IEC-negative tetracycline-resistant CC5) were found in people with no occupational livestock contact. These findings reveal a potential relationship between S. aureus CCs and IEC genes and antibiotic resistance patterns in defining livestock-associated S. aureus in humans and support growing concern about the potential livestock-to-human transmission of livestock-associated S. aureus by non-occupational livestock contact.

In addition to being a human pathogen, Staphylococcus aureus causes an array of infections in economically important livestock animals, particularly pigs. In Asia, there have been few reports on livestock-associated meticillin-resistant S. aureus (LA-MRSA), mostly from developed countries, with very few data available from resource-limited countries, not because of low prevalence but probably due to a shortage of diagnostic facilities. Unlike the wide spread of sequence type 398 (ST398) LA-MRSA in European countries and North America, ST9 predominates in most Asian countries. The prevalence of LA-MRSA among pigs in Asian countries varied widely (0.9–42.5%). The prevalence may vary by geographic location, age of pigs and sampling methodologies. Among pig farmers, the prevalence of nasal MRSA colonisation varied from 5.5% in Malaysia to 15% in China and 19.2% in Taiwan. Although most LA-MRSA isolates in Asia are of the same ST, molecular characteristics are not all the same. Dominant isolates in China were characterised as spa type t899-SCC mec III and t899-SCC mec IVb or V for isolates in Hong Kong, and t899-untypeable SCC mec for Taiwan. Dominant isolates in Malaysia were spa type t4358-SCC mec V and t337-SCC mec IX for isolates in Thailand. In addition, MRSA ST221 was reported in Japan and MRSA ST398 was isolated from commercial pigs in South Korea. Attention should be paid because pigs could become an important reservoir for MRSA and spread them to humans, as observed in many countries. There is a potential risk from the livestock reservoir to community and hospitals. [ABSTRACT FROM AUTHOR]

Quinupristin/dalfopristin (Q/D) is a valuable alternative to vancomycin for the treatment of meticillin-resistant Staphylococcus aureus (MRSA) infections. However, not long after Q/D was approved, bacteria with resistance to this newer antimicrobial agent were reported. To investigate the prevalence of Q/D resistance, a total of 1476 non-duplicate S. aureus isolates, including 775 MRSA, from a Chinese tertiary hospital were selected randomly from 2003 to 2013. Of the 775 MRSA, 3 (0.4%) were resistant to Q/D. All meticillin-susceptible S. aureus were susceptible to Q/D. The prevalence of Q/D resistance among S. aureus was 0.2% (3/1476). The three isolates with Q/D resistance had the same antimicrobial resistance profile, except for cefaclor and chloramphenicol. All three Q/D-resistant MRSA were positive for five streptogramin B resistance genes ( ermA , ermB , ermC , msrA and msrB ) and two streptogramin A resistance genes ( vatC and vgaA ) as determined by PCR and DNA sequencing. MRSA WZ1031 belonged to ST9-MRSA-SCC mec V-t899, whilst MRSA WZ414 and WZ480 belonged to ST9-MRSA-SCC mec NT(non-typeable)-t899. ST9 has been reported predominantly in livestock-associated (LA) MRSA in some Asian countries. The three patients with these MRSA isolates were not livestock handlers and did not keep close contact with livestock. The origin of these important LA-MRSA isolates causing human infections is not known. Taken together, Q/D resistance, which was caused by a combination of ermA–ermB – ermC – msrA – msrB – vatC – vgaA , was first found among S. aureus clinical isolates in China. The present study is the first report of the emergence of human infections caused by ST9 LA-MRSA isolates with Q/D resistance. [ABSTRACT FROM AUTHOR]

Not only is Asia the most populous region in the world, but inappropriate therapy, including self-medication with over-the-counter antimicrobial agents, is a common response to infectious diseases. The high antibiotic selective pressure among the overcrowded inhabitants creates an environment that is suitable for the rapid development and efficient spread of numerous multidrug-resistant pathogens. Indeed, Asia is among the regions with the highest prevalence rates of healthcare-associated methicillin-resistant Staphylococcus aureus ( HA- MRSA) and community-associated methicillin-resistant S. aureus ( CA- MRSA) in the world. Most hospitals in Asia are endemic for multidrug-resistant methicillin-resistant S. aureus ( MRSA), with an estimated proportion from 28% (in Hong Kong and Indonesia) to >70% (in Korea) among all clinical S. aureus isolates in the early 2010s. Isolates with reduced susceptibility or a high level of resistance to glycopeptides have also been increasingly identified in the past few years. In contrast, the proportion of MRSA among community-associated S. aureus infections in Asian countries varies markedly, from <5% to >35%. Two pandemic HA- MRSA clones, namely multilocus sequence type ( ST) 239 and ST5, are disseminated internationally in Asia, whereas the molecular epidemiology of CA- MRSA in Asia is characterized by clonal heterogeneity, similar to that in Europe. In this review, the epidemiology of S. aureus in both healthcare facilities and communities in Asia is addressed, with an emphasis on the prevalence, clonal structure and antibiotic resistant profiles of the MRSA strains. The novel MRSA strains from livestock animals have been considered to constitute a public health threat in western countries. The emerging livestock-associated MRSA strains in Asia are also included in this review. [ABSTRACT FROM AUTHOR]

Abstract: Equine methicillin-resistant Staphylococcus aureus (MRSA) carriage entails a risk of both equine and zoonotic transmission and infection. In Europe, CC398, the livestock-associated (LA-)MRSA is highly prevalent in horses and veterinary personnel at equine clinics. The extent of the MRSA reservoir created by healthy horses from the general population and associated health hazard for their daily caretakers is, however, unknown. This study aimed at screening healthy horse-caretaker couples from a broad range of home farms. At five equine gatherings, 166 couples were selected for MRSA screening in the anterior nares and participation in an epidemiologic survey. All MRSA isolates were subjected to genotyping and antimicrobial susceptibility testing. Only 4 humans (2.4%) and 2 of their horses (1.2%) tested MRSA positive. Within the 2 couples where both partners were positive, man and horse carried isolates belonging to identical, livestock-associated spa types (t011 and t2330) and demonstrating equal antimicrobial susceptibility patterns. For all LA-MRSA positive humans (n =3) and animals (n =2) regular (in)direct contact with the veterinary sector was reported. A significant association between the horses’ carriage status and transportation to an event could not be demonstrated (P =1.00). In conclusion, outside equine clinics, the extent of the MRSA reservoir in horses and their caretakers was low. Travel to an equine gathering could not be withheld as a risk factor for equine MRSA carriage, whereas indications were found that contact with veterinary care may predispose both healthy horses and their handlers to carriage. [Copyright &y& Elsevier]

Background: The Netherlands is one of the most densely populated countries in the world, with extensive livestock of pigs. In 2005, the emergence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) was a fact, with a relatively high MRSA colonisation among pig farmers. These MRSA isolates mostly belonged to sequence type 398 (ST398). Compared to hospital-associated MRSA (HA-MRSA), severe infections due to LA-MRSA and transmission between individuals are still relatively rare. Therefore, LA-MRSA may warrant less stringent containment measures than HA-MRSA in hospital settings. Results: The aim of this study was to develop a rapid diagnostic tool to distinguish LA-MRSA from non-LA-MRSA in aid of infection control. Here, we show that ST398 strains can be readily detected with real-time polymerase chain reaction (PCR). Analysis of a large panel of related and unrelated microorganisms confirmed that the real-time ST398 PCR (ST398-qPCR) assay does not cross-react with other microorganisms or with non-LA- S. aureus strains. ST398-qPCR analysis of MRSA isolates collected in 2010, 2011 and 2012 at the Jeroen Bosch Hospital ( n = 275) showed that an average of 78 % of MRSA belonged to sequence type ST398. Conclusion: We conclude that the ST398 real-time PCR is a reliable assay to detect LA- S. aureus and anticipate that the use of this assay can prevent the unnecessary closing of hospital wards, which may lead to substantial savings for the health care system. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus is not only part of normal flora but also an opportunistic pathogen relevant to microbial genomics, public health, and veterinary medicine. In addition to being a well-known human pathogen, S. aureus causes various infections in economically important livestock animals such as cows, sheep, goats, and pigs. There are very few studies that have examined the pan-genome of S. aureus or the host-specific strains' pan-genomes. We report on livestock-associated S. aureus' (LA- SA ) pan-genome and suggest that virulence is not the primary interest in evolution of its genome. LA- SA ' complete genomes were retrieved from the NCBI and pan-genome was constructed by high-speed Roary pipeline. The pan-genome size was 4637 clusters, whereas 42.46% of the pan-genome was associated with the core genome. We found 1268 genes were associated with the strain-unique genome, and the remaining 1432 cluster with the accessory genome. COG (clusters of orthologous group of proteins) analysis of the core genes revealed 34% of clusters related to metabolism responsible for amino acid and inorganic ion transport (COG categories E and P), followed by carbohydrate metabolism (category G). Virulent gene analysis revealed the core genes responsible for antiphagocytosis and iron uptake. The fluidity of pan-genome was calculated as 0.082 ± 0.025. Importantly, the positive selection analysis suggested a slower rate of evolution among the LA- SA genomes. We call for comparative microbial and pan-genome research between human and LA -SA that can help further understand the evolution of virulence and thus inform future microbial diagnostics and drug discovery.

Currently, surveillance of livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) in humans in Europe is not systematic but mainly event-based. In September 2014, the European Centre for Disease Prevention and Control (ECDC) initiated a questionnaire to collect data on the number of LA-MRSA from human samples (one isolate per patient) from national/regional reference laboratories in European Union/European Economic Area (EU/EEA) countries in 2013. Identification of LA-MRSA as clonal complex (CC) 398 by multilocus sequence typing (MLST) was preferred, although surrogate methods such as spa -typing were also accepted. The questionnaire was returned by 28 laboratories in 27 EU/EEA countries. Overall, LA-MRSA represented 3.9% of 13,756 typed MRSA human isolates, but it represented ≥ 10% in five countries (Belgium, Denmark, Spain, the Netherlands and Slovenia). Seven of the reference laboratories did not type MRSA isolates in 2013. To monitor the dispersion of LA-MRSA and facilitate targeted control measures, we advocate periodic systematic surveys or integrated multi-sectorial surveillance.

While some studies have defined Staphylococcus aureus based on its clonal complex and resistance pattern, few have explored the relations between the genetic lineages and antibiotic resistance patterns and immune evasion cluster (IEC) genes. Our aim was to investigate the potential relationship between phenotypic and molecular characteristics so as to reveal livestock-associated S. aureus in humans. The study participants were interviewed, and they provided two nasal swabs for S. aureus analysis. All S. aureus and methicillin-resistant S. aureus (MRSA) were tested for antibiotic susceptibility, multilocus sequence type and IEC genes. Of the 1162 participants, 9.3% carried S. aureus , including MRSA (1.4%) and multidrug-resistant S. aureus (MDRSA, 2.8%). The predominant multidrug-resistant pattern among MDRSA isolates was non-susceptibility to erythromycin, clindamycin and tetracycline. The most common S. aureus genotypes were ST7, ST6, ST188, and ST59, and the predominant MRSA genotype was ST7. Notably, the livestock-associated S. aureus isolates (IEC-negative CC9, IEC-negative tetracycline-resistant CC398, and IEC-negative tetracycline-resistant CC5) were found in people with no occupational livestock contact. These findings reveal a potential relationship between S. aureus CCs and IEC genes and antibiotic resistance patterns in defining livestock-associated S. aureus in humans and support growing concern about the potential livestock-to-human transmission of livestock-associated S. aureus by non-occupational livestock contact.