Detection of three distinct genetic lineages in methicillin-resistant Staphylococcus aureus (MRSA) isolates from animals and veterinary personnel

Comparative genomics of MRSA strains from human and canine origins reveals similar virulence gene repertoire

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen associated with a wide variety of infections in humans. The ability of MRSA to infect companion animals has gained increasing attention in the scientific literature. In this study, 334 dogs were screened for MRSA in two cities located in Rio de Janeiro State. The prevalence of MRSA in dogs was 2.7%. Genotyping revealed isolates from sequence types (ST) 1, 5, 30, and 239 either colonizing or infecting dogs. The genome of the canine ST5 MRSA (strain SA112) was compared with ST5 MRSA from humans-the main lineage found in Rio de Janeiro hospitals-to gain insights in the origin of this dog isolate. Phylogenetic analysis situated the canine genome and human strain CR14-035 in the same clade. Comparative genomics revealed similar virulence profiles for SA112 and CR14-035. Both genomes carry S. aureus genomic islands νSAα, νSAβ, and νSAγ. The virulence potential of the canine and human strains was similar in a Caenorhabditis elegans model. Together, these results suggest a potential of canine MRSA to infect humans and vice versa. The circulation in community settings of a MRSA lineage commonly found in hospitals is an additional challenge for public health surveillance authorities.

Molecular Epidemiology of Staphylococcus aureus Lineages in Wild Animals in Europe: A Review

Staphylococcus aureus is an opportunist pathogen that is responsible for numerous types of infections. S. aureus is known for its ability to easily acquire antibiotic resistance determinants. Methicillin-resistant S. aureus (MRSA) is a leading cause of infections both in humans and animals and is usually associated with a multidrug-resistant profile. MRSA dissemination is increasing due to its capability of establishing new reservoirs and has been found in humans, animals and the environment. Despite the fact that the information on the incidence of MRSA in the environment and, in particular, in wild animals, is scarce, some studies have reported the presence of these strains among wildlife with no direct contact with antibiotics. This shows a possible transmission between species and, consequently, a public health concern. The aim of this review is to better understand the distribution, prevalence and molecular lineages of MRSA in European free-living animals.

Burden and antimicrobial resistance of S. aureus in dairy farms in Mekelle, Northern Ethiopia

Background

Staphylococcus aureus is a frequent colonizer of human and several animal species, including dairy cows. It is the most common cause of intramammary infections in dairy cows. Its public health importance increases inline to the continuous emergence of drug-resistant strains; such as Methicillin-resistant S. aureus (MRSA). Indeed, the recent emergence of human and veterinary adapted MRSA demands serious attention. The aim of this study was to determine the burden and drug resistance pattern of S. aureus in dairy farms in Mekelle and determine the molecular characteristics of MRSA.

Results

This study was done on 385 lactating dairy cows and 71 dairy farmers. The ages of the cows and farmworkers were between 3 and 14 and 17–63 years respectively. S. aureus was isolated from 12.5% of cows and 31% of farmworkers. Highest resistance was observed for penicillin (> 90%) followed by tetracycline (32–35%) and trimethoprim-sulphamethoxazole (10–27%). But no resistance was observed for vancomycin, daptomycin, and rifampin. Only one isolate was MRSA both phenotypically and harboring mecA. This isolate was from nasal of a farmworker and was MRSA SCCmec Iva, spa type t064 of CC8. Multi-drug resistance was observed in 6.2% of cow isolates and 13.6% of nasal isolates.

Conclusions

In this study, S. aureus infected 12.5% of dairy cows and colonized 31% of farmworkers. Except for penicillin, resistance to other drugs was rare. Although no MRSA was found from dairy cows the existence of the human and animal adapted and globally spread strain, MRSA SCCmec IVa spa t064, warrants for a coordinated action to tackle AMR in both human and veterinary in the country.

Methicillin-resistant Staphylococcus aureus from infections in horses in Germany are frequent colonizers of veterinarians but rare among MRSA from infections in humans

A total of 272 methicillin-resistant Staphylococcus aureus (MRSA) from equine infections originating from 17 equine hospitals and 39 veterinary practices in Germany as well as 67 isolates from personnel working at equine clinics were subjected to molecular typing. The majority of isolates from horses was attributed to clonal complex (CC) 398 (82.7%). Within CC398, 66% of isolates belonged to a subpopulation (clade) of CC398, which is associated with equine clinics.

MRSA attributed to CC8 (ST254, t009, t036, SCCmecIV; ST8, t064, SCCmecIV) were less frequent (16.5%). Single isolates were attributed to ST1, CC22, ST130, and ST1660. The emergence of MRSA CC22 and ST130 in horses was not reported so far. Nasal MRSA colonization was found in 19.5% of veterinary personnel with occupational exposure to horses. The typing characteristics of these isolates corresponded to isolates from equine infections.

Comparing typing characteristics of equine isolates with those of a substantial number of isolates from human infections typed at the German Reference Center for Staphylococci and Enterococci (2006–2014; n = 10864) yielded that the proportion of isolates exhibiting characteristics of MRSA from equine medicine is very low (< 0.5%). As this low proportion was also found among MRSA originating from nasal screenings of human carriers not suffering from a staphylococcal infection (n = 5546) transmission of MRSA from equine clinics to the community seems to be rare so far.

Extensive genetic diversity identified among sporadic methicillin-resistant Staphylococcus aureus isolates recovered in Irish hospitals between 2000 and 2012

Clonal replacement of predominant nosocomial methicillin-resistant Staphylococcus aureus (MRSA) strains has occurred several times in Ireland during the last 4 decades. However, little is known about sporadically occurring MRSA in Irish hospitals or in other countries. Eighty-eight representative pvl-negative sporadic MRSA isolates recovered in Irish hospitals between 2000 and 2012 were investigated. These yielded unusual pulsed-field gel electrophoresis and antibiogram-resistogram typing patterns distinct from those of the predominant nosocomial MRSA clone, ST22-MRSA-IV, during the study period. Isolates were characterized by spa typing and DNA microarray profiling for multilocus sequence type (MLST) clonal complex (CC) and/or sequence type (ST) and SCCmec type assignment, as well as for detection of virulence and antimicrobial resistance genes. Conventional PCR-based SCCmec subtyping was undertaken when necessary. Extensive diversity was detected, including 38 spa types, 13 MLST-CCs (including 18 STs among 62 isolates assigned to STs), and 25 SCCmec types (including 2 possible novel SCCmec elements and 7 possible novel SCCmec subtypes). Fifty-four MLST-spa-SCCmec type combinations were identified. Overall, 68.5% of isolates were assigned to nosocomial lineages, with ST8-t190-MRSA-IID/IIE±SCCM1 predominating (17.4%), followed by CC779/ST779-t878-MRSA-ψSCCmec-SCC-SCCCRISPR (7.6%) and CC22/ST22-t032-MRSA-IVh (5.4%). Community-associated clones, including CC1-t127/t386/t2279-MRSA-IV, CC59-t216-MRSA-V, CC8-t008-MRSA-IVa, and CC5-t002/t242-MRSA-IV/V, and putative animal-associated clones, including CC130-t12399-MRSA-XI, ST8-t064-MRSA-IVa, ST398-t011-MRSA-IVa, and CC6-t701-MRSA-V, were also identified. In total, 53.3% and 47.8% of isolates harbored genes for resistance to two or more classes of antimicrobial agents and two or more mobile genetic element-encoded virulence-associated factors, respectively. Effective ongoing surveillance of sporadic nosocomial MRSA is warranted for early detection of emerging clones and reservoirs of virulence, resistance, and SCCmec genes.

Methicillin-resistant staphylococci: implications for our food supply?

Food-borne intoxication, caused by heat-stable enterotoxins produced by Staphylococcus aureus, causes over 240,000 cases of food-borne illness in the United States annually. Other staphylococci commonly associated with animals may also produce these enterotoxins. Foods may be contaminated by infected food handlers during slaughter and processing of livestock or by cross-contamination during food preparation. S. aureus also causes a variety of mild to severe skin and soft tissue infections in humans and other animals. Antibiotic resistance is common in staphylococci. Hospital-associated (HA) S. aureus are resistant to numerous antibiotics, with methicillin-resistant S. aureus (MRSA) presenting significant challenges in health care facilities for over 40 years. During the mid-1990s new human MRSA strains developed outside of hospitals and were termed community-associated (CA). A few years later, MRSA was isolated from horses and methicillin resistance was detected in Staphylococcus intermedius/pseudintermedius from dogs and cats. In 2003, a livestock-associated (LA) MRSA strain was first detected in swine. These methicillin-resistant staphylococci pose additional food safety and occupational health concerns. MRSA has been detected in a small percentage of retail meat and raw milk samples indicating a potential risk for food-borne transmission of MRSA. Persons working with animals or handling meat products may be at increased risk for antibiotic-resistant infections. This review discusses the scope of the problem of methicillin-resistant staphylococci and some strategies for control of these bacteria and prevention of illness.

MRSA carriage in the equine community: an investigation of horse-caretaker couples

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.

Environmental contamination by dog&#8217;s faeces: a public health problem?

The risk to public health from the large number of dog stools present on streets of urban areas is cause for concern. Dog faeces may be a serious hazard because they may contain microorganisms that are both pathogenic to humans and resistant to several classes of antibiotics. The aim of this study was to evaluate the potential for zoonotic infections and for the presence of antibiotic resistant bacteria in canine faeces which contaminates the urban environment. A total of 418 canine faecal samples were collected from streets in seven areas of Bari, Southern Italy. We have isolated multi-drug resistant Enterococci and meticillin-resistant Staphylococcus aureus from these dog faecal samples. The presence of the resistant bacteria in an urban environment may represent a public health hazard which requires control measures by competent authorities. No Salmonella, Yersinia or Campylobacter species were isolated. Giardia cysts were detected in 1.9% of the samples. The predominant Enterococcus species were E. faecium (61.6%), E. gallinarum (23.3%) and E. casseliflavus (5.5%). Other species, including E. faecalis were also isolated. These strains were resistant to clindamycin (86.3%), tetracycline (65.7%), erythromycin (60.27%) and ampicillin (47.9%). High-level aminoglycoside resistance (HLAR) was found in 65.7% of enterococci. Resistance to three or more antibiotics and six or more antibiotics were observed in 67.12% and 38.4% of Enterococcus spp., respectively. Resistance to vancomycin and teicoplanin was not detected in any of the Enterococcus spp. isolated. Methicillin-resistant Staphylococcus aureus was isolated in 0.7% of the faecal samples. Canine faeces left on the streets may represent a risk factor for transmission of microorganisms and a reservoir of multidrug- resistant bacteria thus contributing to the spread of resistance genes into an urban area.

Are all meticillin-resistant Staphylococcus aureus (MRSA) equal in all hosts? Epidemiological and genetic comparison between animal and human MRSA

Meticillin-resistant Staphylococcus aureus (MRSA) continues to pose a major threat to human health. In animals, MRSA has become established as a veterinary pathogen in pets and horses; in livestock, it presents a concern for public health as a reservoir that can infect humans and as a source of transferrable resistance genes. Genetic analyses have revealed that the epidemiology of MRSA is different in different animal hosts. While human hospital-associated MRSA lineages are most commonly involved in pet infection and carriage, horse-specific MRSA most often represent 'traditional' equine S. aureus lineages. A recent development in the epidemiology of animal MRSA is the emergence of pig-adapted strains, such as CC398 and CC9, which appear to have arisen independently in the pig population. Recent insight into the genome structure and the evolution of S. aureus has helped to explain key aspects of these three distinct epidemiological scenarios. This nonsystematic literature review summarizes the structure and variations of the S. aureus genome and gives an overview of the current distribution of MRSA lineages in various animal species. It also discusses present knowledge about the emergence and evolution of MRSA in animals, adaptation to different host species and response to selective pressure from animal-specific environments. An improved understanding of the genetics and selective pressure that underpin the adaptive behaviour of S. aureus may be used in the future to predict new developments in staphylococcal diseases and to investigate novel control strategies required at a time of increasing resistance to antimicrobial agents.

Investigation of the persistence and transmission of MRSA CC 5 in pigs following intra-nasal inoculation

MRSA CC5 spa type t002 appears to have a broad host range, has been isolated from animals and in-contact humans in Ireland and could potentially become established in pigs in Ireland. The aims of this study were to determine if MRSA CC5 spa type t002 could persist in the tissues of the porcine upper respiratory tract following intra-nasal inoculation; to determine the relative importance of environmental and animal sources of the bacterium in the transmission cycle and to determine the importance of the pharynx as a carriage site of Staphylococcus aureus and MRSA. Twelve pigs were inoculated intra-nasally with MRSA CC5 t002. After 1 or 6 days, the inoculated pigs were removed from the contaminated environment, were washed in an antiseptic solution and placed in a clean house with a group of naive pigs (in-contact group). Another group of naive pigs was placed in the contaminated environment to assess transmission from the environment (environmental group). Nasal swabs, environmental swabs and tissue samples from the upper respiratory tract were taken for MRSA culture. Infection rates were calculated for each group of exposed pigs. MRSA persisted in the pharyngeal tissues of 6 inoculated pigs for at least 30 days and higher counts of S. aureus were found in pharyngeal tissues than in other sites. In this study we were able to demonstrate the establishment of colonisation by MRSA CC5 spa type t002 in commercially sourced pigs already colonised by S. aureus; however, colonisation was sporadic despite the inoculation of large doses. Onward transmission via pig-to-pig contact or environmental contamination was possible and a significant difference was found between the proportion of pigs infected in the environmental group and the proportion infected in the in-contact group during the first 5 days. However, no significant difference was detected in overall infection rates between the 2 groups. The tissues of the pharynx were found to carry greater numbers of S. aureus than other tissues of the upper respiratory tract; therefore, pharyngeal carriage of MRSA and S. aureus in pigs may be more significant than previously thought.

Cross-sectional study of antimicrobial-resistant bacteria in horses. Part 1: Prevalence of antimicrobial-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus

REASONS FOR PERFORMING STUDY

The increasing prevalence of antimicrobial-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) and antimicrobial-resistant Escherichia coli represents a significant problem. However, the carriage of such bacteria by horses in the UK has not been well characterised.

OBJECTIVES

To estimate the prevalence of nasal carriage of MRSA and faecal carriage of antimicrobial-resistant E. coli amongst horses in the general equine community of the mainland UK.

METHODS

A cross-sectional study of horses recruited by 65 randomly selected equine veterinary practices was conducted, with nasal swabs and faecal samples collected. Faecal samples were cultured for antimicrobial-resistant E. coli. Nasal swabs were cultured for staphylococcal species; methicillin-resistant isolates identified as S. aureus were characterised by SCCmec and spa gene typing. Multilevel logistic regression models were used to calculate prevalence estimates with adjustment for clustering at practice and premises levels. Spatial variation in risk of antimicrobial resistance was also examined.

RESULTS

In total, 650 faecal samples and 678 nasal swabs were collected from 692 horses located on 525 premises. The prevalence of faecal carriage of E. coli with resistance to any antimicrobial was 69.5% (95% CI 65.9-73.1%) and the prevalence of extended-spectrum β-lactamase (ESBL)-producing E. coli was 6.3% (95% CI 4.1-9.6%). The prevalence of nasal carriage of MRSA was 0.6% (95% CI 0.2-1.5%). Spatial analysis indicated variation across the UK for risk of carriage of resistant and multidrug-resistant (resistant to more than 3 antimicrobial classes) E. coli.

CONCLUSIONS AND POTENTIAL RELEVANCE

Carriage of MRSA by horses in the community appears rare, but the prevalence of antimicrobial-resistant E. coli (including ESBL-producing E. coli) is higher. A high prevalence of antimicrobial-resistant bacteria could have significant health implications for the horse population of the UK.

Detection of staphylococcal cassette chromosome mec type XI carrying highly divergent mecA, mecI, mecR1, blaZ, and ccr genes in human clinical isolates of clonal complex 130 methicillin-resistant Staphylococcus aureus

Methicillin resistance in staphylococci is mediated by penicillin binding protein 2a (PBP 2a), encoded by mecA on mobile staphylococcal cassette chromosome mec (SCCmec) elements. In this study, two clonal complex 130 (CC130) methicillin-resistant Staphylococcus aureus (MRSA) isolates from patients in Irish hospitals were identified that were phenotypically PBP 2a positive but lacked mecA by conventional PCR and by DNA microarray screening. The isolates were identified as methicillin-susceptible S. aureus using the GeneXpert real-time PCR assay. Whole-genome sequencing of one isolate (M10/0061) revealed a 30-kb SCCmec element encoding a class E mec complex with highly divergent blaZ-mecA-mecR1-mecI, a type 8 cassette chromosome recombinase (ccr) complex consisting of ccrA1-ccrB3, an arsenic resistance operon, and flanking direct repeats (DRs). The SCCmec element was almost identical to that of SCCmec type XI (SCCmec XI) identified by the Sanger Institute in sequence type 425 bovine MRSA strain LGA251 listed on the website of the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements. The open reading frames (ORFs) identified within SCCmec XI of M10/0061 exhibited 21 to 93% amino acid identity to ORFs in GenBank. A third DR was identified ca. 3 kb downstream of SCCmec XI, indicating the presence of a possible SCC remnant. SCCmec XI was also identified in the second CC130 MRSA isolate by PCR and sequencing. The CC130 MRSA isolates may be of animal origin as previously reported CC130 S. aureus strains were predominantly from bovine sources. The highly divergent nature of SCCmec XI relative to other SCCmec elements indicates that it may have originated in another taxon.