Recent updates in the development of molecular assays for the rapid identification and susceptibility testing of MRSA

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management.

AREAS COVERED

A literature search was conducted in PubMed and supplemented by citation searching. In this article, we provide a comprehensive review of molecular-based methods for MRSA screening and diagnostic tests including individual nucleic acid detection assays, syndromic panels, and sequencing technologies with a focus on their analytical performance.

EXPERT OPINION

Molecular based-assays for the detection of MRSA have improved in terms of accuracy and availability. Rapid turnaround enables earlier contact isolation and decolonization for MRSA. The availability of syndromic panel tests that include MRSA as a target has expanded from positive blood cultures to pneumonia and osteoarticular infections. Sequencing technologies allow detailed characterizations of novel methicillin-resistance mechanisms that can be incorporated into future assays. Next generation sequencing is capable of diagnosing MRSA infections that cannot be identified by conventional methods and metagenomic next-generation sequencing (mNGS) assays will likely move closer to implementation as front-line diagnostics in the near future.

Antimicrobial resistome of coagulase-negative staphylococci from nasotracheal cavities of nestlings of Ciconia ciconia in Southern Spain: Detection of mecC-SCCmec type-XI-carrying S. lentus

The antimicrobial resistance (AMR) genes of 268 non-duplicated coagulase-negative staphylococci (CoNS) previously obtained from nasotracheal cavities of nestling storks were characterized. They included S. sciuri isolates (n = 191), and non-sciuri-CoNS isolates (NSc-CoNS, n = 77). All S. sciuri carried the intrinsic salA gene (for clindamycin-resistance) and so, clindamycin was not considered for general analysis in this species. About 71.7%/41.6% of the S. sciuri/NSc-CoNS isolates were susceptible to all antibiotics tested; moreover, 14.1%/16.9% and 3.1%/20.8% of S. sciuri/NSc-CoNS showed single antibiotic resistance and multidrug resistance (MDR) phenotype, respectively. Of the ten mecA-positive CoNS isolates, six were associated with SCCmec types-III, -IV or -V elements. Remarkably was the detection of one MDR-S. lentus isolate carrying both mecA and mecC genes, as well as the SCCmec type-XI element. MDR-CoNS was relatively higher in nestlings of parent storks foraging in landfills (21.3%) than those in natural areas (9.7%) (χ² = 3.421, df=1, p = 0.064). AMR phenotypes (and genes detected) include penicillin (blaZ, bla_ARL), erythromycin-clindamycin-constitutive (ermA, ermC, ermT), clindamycin (lnuA, salA, vgaA), erythromycin (msrA, mphC), tetracycline (tetK, tetL, tetM), tobramycin (ant4'), tobramycin-gentamicin (aac6'-aph2″), sulfamethoxazole-trimethoprim (dfrA, dfrG, dfrK), chloramphenicol (fexA, fexB, catPC221), and mupirocin (mupA). Interestingly, one S. epidermidis isolate carried the ermT gene. About 29.9% of nestlings harboured more than one non-duplicated CoNS (with varied 2-5 AMR profiles). This study demonstrated that most of the CoNS isolates were susceptible to all the antibiotics tested (63.1%). However, AMR genes of public health importance were found, including the mecC-mediated methicillin resistance trait.

Genomic Evidence for Direct Transmission of mecC-MRSA between a Horse and Its Veterinarian

Methicillin-resistant Staphylococcus aureus bearing the mecC gene (mecC-MRSA) has been reported from animals and humans in recent years. This study describes the first mecC-MRSA isolates of human and equine origin in Hungary (two isolates from horses and one from a veterinarian, who treated one of the infected horses, but was asymptomatic). MRSA isolates were identified by cultivation and PCR detection of the species-specific spa gene and mecA/mecC methicillin resistance genes. The isolates were characterized by antibiotic susceptibility testing, MLST, spa, SCCmec typing, PFGE and whole genome sequencing (WGS). All three isolates belonged to the ST130-t843-SCCmec XI genotype, and carried the mecC and blaZ genes. Apart from beta-lactam drugs, they were sensitive to all tested antibiotics. The isolates of the infected horse and its veterinarian had the same PFGE pulsotype and showed only slight differences with WGS. Hence, this is the first description of direct transmission of a mecC-carrying MRSA between a horse and its veterinarian. The emergence of mecC in the country highlights the importance of the appropriate diagnostics in MRSA identification.

Frequent dissemination and carriage of an SCCmec-mecC hybrid in methicillin-resistant Mammaliicoccus sciuri in farm animals from Tunisia

OBJECTIVES

In this study, we aimed to assess the extent of dissemination of methicillin-resistant Mammaliicoccus sciuri in animal farms in Tunisia and evaluate the distribution of virulence and methicillin resistance genes in the M. sciuri population.

METHODS

Staphylococci and mammaliicocci isolated from unhealthy animals and healthy humans from adjacent farms in Tunisia were characterized for antimicrobial susceptibility, biofilm formation, agglutination, and hemolysis abilities. Mammaliicoccus sciuri relatedness and content in antibiotic resistance and virulence genes were analyzed by whole-genome sequencing (WGS).

RESULTS

Mammaliicoccus sciuri was the most prevalent species (46.2%), showing the highest resistance rates to fusidic acid (94.6%), oxacillin (73%), penicillin (40.5%), clindamycin (37%), ciprofloxacin (27%), and cefoxitin (24.3%). Some isolates carried genes encoding resistance to nine different antibiotic classes. mecA was found in 35% of M. sciuri and mecC in 16.2%. All isolates carrying mecC were of S. sciuri subspecies carnaticus and carried the hybrid element SCCmec-mecC. Mammaliicoccus sciuri were able to produce strong biofilm (27%) and have clumping ability (16%). Additionally, they carried genes for capsule production (cap8, 100%), iron-regulated surface determinants (isdE, 24%; isdG, 3%), and virulence regulation (clpC and clpP, 100%). Single nucleotide polymorphisms (SNPs) analysis showed that 17 M. sciuri cross-transmission events probably occurred between different animal species and farms. Moreover, SCCmec was estimated to have been acquired five times by S. sciuri subsp. carnaticus.

CONCLUSION

Multidrug resistant and pathogenic M. sciuri were frequently disseminated between different animal species within the farm environment. mecA and mecC can be disseminated by both frequent acquisition of the SCCmec element and clonal dissemination.

Distribution and Clonal Diversity of Staphylococcus aureus and Other Staphylococci in Surface Waters: Detection of ST425-t742 and ST130-t843 mecC-Positive MRSA Strains

Natural aquatic environments represent one of the most important vehicles of bacterial dissemination. Therefore, we aimed to isolate staphylococci from surface waters and to investigate the presence of antimicrobial resistance genes and virulence factors as well as the genetic lineages of all Staphylococcus aureus isolates. Staphylococci were recovered from water samples collected from 78 surface waters, including rivers, streams, irrigation ditches, dams, lakes, and fountains. The presence of antimicrobial resistance genes and virulence factors was investigated by PCR. Multilocus sequence typing and spa-typing were performed in all S. aureus isolates. From the 78 water samples, 33 S. aureus, one S. pseudintermedius, and 51 coagulase-negative staphylococci (CoNS) were identified. Among the S. aureus isolates, four MRSA were identified, and all harbored the mecC gene. Fourteen S. aureus were susceptible to all antimicrobials tested and the remaining showed resistance to penicillin, erythromycin and/or tetracycline encoded by the blaZ, ermT, msr(A/B), tetL, and vgaA genes. Regarding the clonal lineages, one mecC-MRSA isolate belonged to spa-type t843 and sequence type (ST) 130 and the other three to t742 and ST425. The remaining S. aureus were ascribed 14 spa-types and 17 sequence types. Eleven species of CoNS were isolated: S. sciuri, S. lentus, S. xylosus, S. epidermidis, S. cohnii spp. urealyticus, S. vitulinus, S. caprae, S. carnosus spp. Carnosus, S. equorum, S. simulans, and S. succinus. Thirteen CoNS isolates had a multidrug resistance profile and carried the following genes: mecA, msr(A/B), mph(C), aph(3′)-IIIa, aac(6′)-Ie–aph(2′’)-Ia, dfrA, fusB, cat_pC221, and tetK. A high diversity of staphylococci was isolated from surface waters including mecCMRSA strains and isolates presenting multidrug-resistance profiles. Studies on the prevalence of antibiotic-resistant staphylococci in surface waters are still very scarce but extremely important to estimate the contribution of the aquatic environment in the spread of these bacteria.

Antimicrobial Resistance and Genetic Lineages of Staphylococcus aureus from Wild Rodents: First Report of mecC-Positive Methicillin-Resistant S. aureus (MRSA) in Portugal

The frequent carriage of Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), by wild animals along with its zoonotic potential poses a public health problem. Furthermore, the repeated detection of the mecA gene homologue, mecC, in wildlife raises the question whether these animals may be a reservoir for mecC-MRSA. Thus, we aimed to isolate S. aureus and MRSA from wild rodents living in port areas and to characterize their antimicrobial resistance and genetic lineages. Mouth and rectal swab samples were recovered from 204 wild rodents. The samples were incubated in BHI broth with 6.5% of NaCl and after 24 h at 37 °C the inoculum was seeded onto Baird-Parker agar, Mannitol Salt agar and ORSAB (supplemented with 2 mg/L of oxacillin) plates. Species identification was confirmed by MALDI-TOF MS. The antimicrobial susceptibility testing was performed by the Kirby-Bauer disc diffusion method against 14 antibiotics. The presence of virulence and resistance genes was performed by PCR. The immune evasion cluster (IEC) system was investigated in all S. aureus. All isolates were characterized by MLST, spa- and agr typing. From 204 samples, 38 S. aureus were isolated of which six MRSA were detected. Among the six MRSA isolates, three harbored the mecC gene and the other three, the mecA gene. All mecC-MRSA isolates were ascribed to sequence type (ST) 1945 (which belongs to CC130) and spa-type t1535 whereas the mecA isolates belonged to ST22 and ST36 and spa-types t747 and t018. Twenty-five S. aureus were susceptible to all antibiotics tested. S. aureus isolates were ascribed to 11 MLST and 12 spa-types. S. aureus presents a great diversity of genetic lineages in wild rodents. This is the first report of mecC-MRSA in Portugal.

First report of methicillin-resistant Staphylococcus aureus carrying the mecC gene in human samples from Iran: prevalence and molecular characteristics

There is a lack of information concerning mecC clinical methicillin-resistant Staphylococcus aureus (MRSA) strains throughout the world. In the present survey, 345 MRSA strains were characterized by antimicrobial susceptibility testing and staphylococcal cassette chromosome mec element (SCCmec) typing. mecC-positive MRSA isolates were characterized by study of biofilm formability, adhesion and virulence analysis, multilocus sequence typing, accessory gene regulator (agr) typing, S. aureus protein A locus (spa) typing and staphylocoagulase typing. The present study found ten SCCmec types, with the majority being SCCmec type III (38.3%). The presence of mecC was confirmed in three isolates from skin wounds (two isolates) and burn wounds (one isolate). All the mecC-positive isolates carried SCCmec XI and belonged to coa type III. Molecular typing showed that these isolates belonged to clonal complex/ST130-spa type t843-agr type III (two isolates) and clonal complex/ST599-spa type 5930-agr type I. The presence of SCCmec type IV confirms the hypothesis of extensive infiltration from the community to the hospital. Detection of MRSA isolates harbouring the mecC gene highlights the need to perform routine detection methods and molecular investigations in order to identify these emerging strains and limit their transfer in hospitals and communities.

Changing Epidemiology of Presumptive Community-associated-methicillin-resistant Staphylococcus Aureus in Slovenia in 2014-2015 Compared To 2010

Introduction

Although the distinction between the Community-Associated-Methicillin-Resistant Staphylococcus aureus (CA-MRSA) and Hospital-Associated-Methicillin-Resistant S. aureus (HA-MRSA) has blurred in recent years, the CA-MRSA is an important group because of its potential to cause fulminant and severe infections. Its importance has further increased with the emergence of Livestock-Associated-Methicillin-Resistant S. aureus (LA-MRSA).

Methods

In the present study we analysed clonal distributions and virulence factors in presumptive CA-MRSA isolated from January 2014 to December 2015 and compared the results with our previous study from 2010. Phenotypic definition for presumptive CA-MRSA was based on resistance to cefoxitin and oxacillin and susceptibility to at least two of the following four antibiotics: ciprofloxacin, erythromycin, clindamycin and gentamicin.

Results

In 2014 and 2015 altogether 304 MRSA isolates fulfilled our screening phenotypic definition, 45 isolates were cultivated from clinical specimens and 259 from screening specimens. Sequence types ST398, LA-MRSA and mecC MRSA increased significantly in 2015 compared to 2010 (p-value <0.05) and were spread over Slovenia.

Conclusion

The clonal distribution of presumptive CA-MRSA has changed within the study period in Slovenia. In 2015 the most frequent clone among clinical and screening specimens was a pig-associated clone, ST398, but the number of confirmed ST398 infections remains low. While previously ST398 and mecC positive MRSA strains were geographically limited, they have spread throughout the country since 2010.

First report of meticillin-resistant Staphylococcus aureus harboring mecC gene in milk samples from cows with mastitis in southeastern Brazil

MRSA infection and colonization have been reported in both companion and food-chain animals, highlighting MRSA as an important veterinary and zoonotic pathogen. Another mec allele, the mecC gene, also confers beta-lactam resistance in Staphylococcus aureus and shows 69% nucleotide identity to mecA. The main aim of this study was to investigate the genotypic and clonal profile of methicillin-resistant S. aureus (MRSA) from cows with mastitis in dairy herds. Thirty-five samples suggestive of bovine subclinical mastitis were evaluated, and S. aureus were detected in all of them using both phenotypic and molecular approaches. According to the multilocus sequence typing (MLST), the S. aureus isolates were assigned in five different STs, 21 (60%) showed ST 742, 6 (17%) ST97, 4 (11%) ST1, 2 (6%) ST30, and 2 (6%) ST126. The presence of mecA was not observed in any of these isolates whereas mecC was detected in nine of them (9/35; 26%). The Panton-Valentine leukocidin (PVL) genes were detected in a total of 4 isolates. Among the 35 isolates analyzed, 26 showed resistance to penicillin. Changes in the S. aureus epidemiology due to the detection of MRSA in milk samples from cows presenting with bovine subclinical mastitis may have consequences for public health in Brazil, challenging the empirical therapy and animal management, with potential medical and social outcomes. To the best of our knowledge, this is the first report describing mecC MRSA in Southeastern Brazil.

First report of mecC gene in clinical methicillin resistant S. aureus (MRSA) from tertiary care hospital Islamabad, Pakistan

BACKGROUND

Staphylococcus aureus (S. aureus) is one of the leading causes of community and hospital acquired infections globally. The objective of the study was to assess the prevalence, study the carriage of antibiotic resistance genes and evaluate the molecular typing of S. aureus isolates from a tertiary care hospital in Islamabad.

METHODS

A total of 1528 staphylococci isolates were included in this study. Standard microbiological procedures were applied to identify S. aureus. Antimicrobial susceptability was evaluated using the disk diffusion method and Minimum Inhibitory Concentrations (MICs) were determined using microbroth dilution method following Clinical and Laboratory Standards Institute (CLSI) guidelines. Multiplex PCR was used to detect antibiotic resistance genes, and molecular typing was performed using agr, SCCmec, spa, and Multi-Locus Sequence Typing (MLST) and clonal relatedness by Pulse Field Gel Electrophoresis (PFGE) methods.

RESULTS

Overall 65% were MRSA and 35% were methicillin sensitive Staphylococcus aureus (MSSA). Among MRSA isolates, 83% were multi-drug resistant and mecA was found in 54% isolates, mecC was in 3% while 1 MRSA carried both mecA and mecC genes. agrI (22%) was most prevalent group in MRSA, while agrIII (16%) was observed in MSSA. SCCmec types I, II, III, IV, and VI were detected, with high prevalence of type III while type V was absent. The prevelant spa type in MRSA was t657 with SCCmecIII elelments while in MSSA it was t021. One NEW spa type identified in MSSA isolates. In a subset of isolates, ST772 with SCCmecIV, ST1 carrying PVL marker, and ST1535 was reported first time from Pakistan.

CONCLUSIONS

The study presents a comprehensive analysis of prevalent S. aureus types and their antibiotic resistance profiles. It also reports for the first time SCCmec type VI and clinical MRSA isolates with mecC alone and in combination with mecA from Islamabad, Pakistan. This calls for further detailed investigations in other hospital settings in the region.

Novel strategies for rapid identification and susceptibility testing of MRSA

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs. Rapid diagnosis of MRSA infections has been associated with positive impact on clinical outcomes.

AREAS COVERED

We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review describes screening and diagnostic test methods for MRSA and their analytical performances with a focus on rapid molecular-based assays including those that are on the horizon. Future novel technologies will allow more rapid detection of phenotypic resistance. In the case of whole-genome sequencing, detection of mutations may predict resistance, transmission, and virulence.

EXPERT OPINION

Currently there are many diagnostic options for the detection of MRSA in surveillance and clinical samples. In general, these are highly accurate and have resulted in improvements in targeted management and reduction in hospital or intensive care unit length of stay for both MSSA and MRSA. Impact on mortality has been variable. Promising novel technologies will not only accurately identify pathogens and detect their resistance markers but will allow discovery of virulence determinants that might further affect patient management.

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.

Phenotype and Genotype Characteristics of Staphylococcus aureus Resistant to Methicillin/Oxacillin Carrying Gene mecC in the Czech Republic from 2002 to 2017

The aim of this study was to detect and characterize isolates of methicillin-/oxacillin-resistant Staphylococcus aureus (MRSA) carrying gene mecC (MRSA/mecC) and occurring in the Czech Republic within the period from 2002 to 2017. Altogether, 18 from 3,472 isolates of MRSA were mecC positive (0.52%). The first detection of MRSA/mecC in the Czech Republic is dated to 2004. MRSA/mecC isolates were susceptible to almost all tested antibiotics with few exceptions. Resistances to erythromycin (n = 2), clindamycin (n = 1), trimethoprim-sulfamethoxazole (n = 1), and rifampicin (n = 1) were found in the collection. Multilocus sequence typing and spa typing revealed a genetic heterogeneity of MRSA/mecC strains: three CCs (130, 425, and 2361), five STs (1245, 130, 2361, 425, and a new ST5480), and eight spa types (t843, t978, t1048, t1535, t1736, t6104, t8842, and t17153), which were detected in the study, with the highest prevalence of CC130/t843 lineage (n = 8, 44%). Except for two strains, none from 18 examined isolates harbored genes encoding any of S. aureus toxins: enterotoxins a-u, exfoliative toxins A, B, and D, toxic shock syndrome toxin-1, and the Panton-Valentine leukocidin.

Low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 and mecC MRSA among human isolates in North-West England

AIMS

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an important public health problem in many countries. Despite reports of such isolates being found in both animals and humans in the United Kingdom few data are available on the prevalence in humans of such isolates. A prevalence study was therefore undertaken in the north-west of England.

METHODS AND RESULTS

One thousand two hundred and forty-two human MRSA isolates collected during 2015 were screened by PCR to detect two of the major forms of LA-MRSA: clonal complex (CC)398 and mecC MRSA. Isolates identified were further characterized by antimicrobial susceptibility testing and whole-genome sequencing using HiSeq technology. A single mecC MRSA isolate and three CC398 LA-MRSA were identified among the isolates screened. All four isolates were from MRSA screening. A phylogenetic analysis, including previously sequenced isolates from the United Kingdom, provided strong evidence for the genomic and epidemiological linkage between a pair of animal and human isolates of CC398 LA-MRSA in England. These data are indicative of animal and humans isolates of CC398 LA-MRSA being involved in the same transmission network and is the first demonstration of such closely linked animal and human isolates of this lineage in the UK.

CONCLUSIONS

The study indicates there is a low prevalence of CC398 LA-MRSA and mecC MRSA among MRSA isolates in the sampled population.

SIGNIFICANCE AND IMPACT OF THE STUDY

While the study demonstrates that LA-MRSA were rare among human MRSA isolates in the sampled population, the data provide a baseline for the future surveillance of what is a significant public health challenge in some regions. The demonstration of linked human and animal isolates of CC398 LA-MRSA, supported by genomic and epidemiological data, reinforces the need for such surveillance and for continued awareness of the risks that LA-MRSA may pose in the UK.

First mecC and mecA Positive Livestock-Associated Methicillin Resistant Staphylococcus aureus (mecC MRSA/LA-MRSA) from Dairy Cattle in Malaysia

Livestock associated Methicillin resistant Staphylococcus aureus (S. aureus) (LA-MRSA) was reported to be zoonotic and may transmit to farmers and veterinarians. The objectives of this study were to investigate the occurrence of LA-MRSA from dairy cattle and to evaluate the antimicrobial resistance profiles of the isolates. A total of 63 milk and 32 nasal swab samples were randomly collected from dairy cattle. The samples were processed to isolate S. aureus, MRSA and LA-MRSA using both phenotypic and molecular methods using PCR. The confirmed S. aureus isolates were cultured on oxacillin resistant screening agar base (ORSAB) to detect MRSA and the isolates were further confirmed by PCR targeting the mecA gene. Detection of the novel mecA gene, mecC gene was conducted by PCR amplification. The antimicrobial susceptibility tests were conducted using disc diffusion method. Results revealed 17/95 (17.89%) and 15/95 (15.79%) were positive for mecA and mecC genes respectively. Out of the 15 mecC positive isolates, 12 were positive for both mecA and mecC. The MRSA isolates showed multidrug resistance. The findings showed high prevalence of mecC-positive LA-MRSA in Malaysia and highlight the public health risks to people that may come in contact with the carrier animals or those who may consume unpasteurized milk products from these animals.

Genomic epidemiology of methicillin-resistant Staphylococcus sciuri carrying a SCCmec-mecC hybrid element

The recognition in 2011 of the methicillin resistance determinate mecC among staphylococci has raised many questions over its evolution and epidemiology. While mecC has been best studied in Staphylococcus aureus it has also been described in at least nine other species of staphylococci. In most cases these studies are limited to single isolates. In the widespread animal commensal Staphylococcus sciuri mecC has been described in two isolates and is located within a distinct SCCmec-mecC composite element. In this study, a further 11 mecA/mecC S. sciuri isolated from dairy farms in England and Wales in 2015 and 2016 were genome sequenced and characterised. The results show that two variants of the SCCmec-mecC element are present in S. sciuri, differentiated by different ccr alleles and likely to have arisen by homologous recombination. A phylogeny of sixty genome-sequenced S. sciuri isolates was made using core genome multi-locus sequence typing and reveals a diverse population with the SCCmec-mecC element present in four distinct branches, indicative of four independent acquisitions by S. sciuri. Finally, the study identified the rapid clonal expansion of a mecA/mecC lineage of S. sciuri among dairy farms across a wide geographical area which may contribute to the future dissemination of this methicillin resistance cassette.

LA-MRSA CC398 in Dairy Cattle and Veal Calf Farms Indicates Spillover From Pig Production

The possible spillover from pigs into other production animals incites concern for unresolved reservoirs of human exposure. The present investigation was therefore initiated, to elucidate if Danish veal and dairy farms constitute a reservoir of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) CC398 and to potentially identify the source of introduction. We collected nasal swab samples from 17 Danish veal farms, 2 slaughterhouses, and received bulk tank milk samples from 286 dairy farms. All samples were analyzed by culturing and screening on MRSA selective plates and presumed MRSA was verified by MALDI-TOF and PCR. MRSA isolates were subjected to spa typing and whole-genome sequencing. LA-MRSA was found on two veal farms in one and three calves, respectively, with subsequent follow-up samples found negative. Eight of 286 dairy farms (2.8%) were found LA-MRSA positive and follow-up samples, from five farms showed intermittent detection of LA-MRSA. The spa types, t034 and t011, were the most common while a single isolate from a dairy farm belonged to spa type t843 associated to mecC-MRSA CC130 and is the first report of mecC-MRSA in the Danish dairy production. A phylogenetic analysis showed that some of the isolates grouped within or close to the dominant Danish pig clusters, suggesting spillover into cattle farms. Other isolates clustered outside the dominant pig clusters suggesting that other routes of introduction cannot be excluded. Results of the investigation indicated a contamination of veal farms while some dairy farms seemed to be a permanent reservoir. Thus, Danish cattle represent a low prevalence reservoir of LA-MRSA CC398, which at present, is not of major human health concern.

Prevalence of meticillin-resistant and -susceptible coagulase-negative staphylococci with the first detection of the mecC gene among cows, humans and manure in Tunisia

In Europe, a novel mecA homologue - mecC (formerly mecA_LGA251) - has emerged recently in staphylococci from animals, humans and the environment. This paper reports the first occurrence of the mecC gene in Staphylococcus sciuri from cows and manure in Tunisia and Africa. Forty-nine coagulase-negative staphylococci (CNS) were isolated from the milk of cows with mastitis (n=20), manure (n=20) and human nares (n=9), including 16 Staphylococcus equoruim (32.6%), 12 S. xylosus (24.5%), 12 S. sciuri (24.5%), two S. saprophyticus (4.1%), two S. haemolyticus (4.1%), two S. lentus (4.1%), two S. vitulinus (4.1%) and one S. cohnii (2%). CNS from the three origins carried various resistance genes [mecA, blaZ, tet(K), erm(A), erm(B), msr(A)], suggesting an ongoing genetic exchange among CNS from the three niches. The mecA gene was detected in CNS (n=11) recovered from cows, manure and humans, whereas the mecC gene (n=3) was only detected in CNS from cows and manure. Various staphylococcal cassette chromosome mec (SCCmec) - SCCmec type I (n=1), II (n=3), IV (n=2), V/VII (n=2) and untypeable (n=3) - and diverse pulsed-field gel electrophoresis (PFGE) patterns were observed in mecA-positive CNS. Otherwise, similar SCCmec types and PFGE patterns were found in meticillin-resistant CNS within different farms and origins, showing the potential of SCCmec interspecies exchange and circulation of the same clones of meticillin-resistant CNS in the human-animal-environment interface. This study provides baseline data to support clonal dissemination of CNS between cows, humans and manure, and indicates the possible transmission of the mecC gene to humans in contact with cows and manure.

Staphylococcus pseudoxylosus sp. nov., isolated from bovine mastitis

Strain S04009T, a Gram-stain-positive, coagulase-negative staphylococcus, was isolated from bovine mastitis in France. 16S rRNA gene analysis revealed it to be closely related to the coagulase-negative species Staphylococcusxylosus, Staphylococcussaprophyticus, Staphylococcuscaeli and Staphylococcus edaphicus. At the whole-genome level, strain S04009T had an average nucleotide identity value <95 % and an inferred DNA-DNA hybridization value <70 % when compared to these species. Furthermore, phenotypic characteristics distinguished S04009T from those species. From these related species only strain S04009T and S. xylosus are able to ferment xylose and these two can be distinguished by the inability of strain S04009T to express urease activity. Based on the genotypic and phenotypic results, it is proposed that this isolate is a novel species, with the name Staphylococcus pseudoxylosus sp. nov. The type strain is S04009T (=DSM 107950T=CCUG 72763T=NCTC 14184T).

Increased genetic diversity of methicillin-resistant Staphylococcus aureus (MRSA) isolated from companion animals

The aim of the present study was to investigate the diversity of methicillin-resistant Staphylococcus aureus (MRSA) that originated from Austrian companion animals during the last five-year period. A total of 90 non-repetitive MRSA isolates were obtained during diagnostic activities from autumn 2013 to autumn 2018. They originated from horses (n = 62), cats (n = 13), dogs (n = 10), rabbits (n = 2), a domestic canary, a zoo-kept hammer-headed bat (Hypsignathus monstrosus) and a semi-captive northern bald ibis (Geronticus eremita). Antimicrobial susceptibility testing was performed. All isolates were mecA-positive and mecC-negative. The isolates were genotyped by SCCmec, spa and dru typing, Multiple-Locus Variable number of tandem repeat Analyses (MLVA), S. aureus DNA microarray, and whole-genome sequencing (WGS). Eight sequence types (STs - ST398, ST5275 (new ST), ST225, ST8, ST22, ST152, ST1, and ST45), three SCCmec types (II, IV, and V), sixteen spa types (t003, t008, t011, t015, t032, t034, t1381, t1928, t1985, t223, t334, t355, t430, t6447, t6867, and t7105), fourteen dru types (dt10a, dt10az, dt10q, dt10r, dt11a, dt5e, dt6j, dt9a, dt9ak, dt9g, and four new types dt8as, dt7ak, dt4j, dt14n), and thirty-five MLVA types were detected. WGS-based core genome MLST (cgMLST) displayed five main clusters. Compared to the time period 2004-2013, the results of the present study show not only a higher diversity among the MRSA isolates within the population of Austrian companion animals, but also the introduction of new clones. Although ST398 isolates remained predominant, mainly due to high presence of this lineage among horses, increasing isolation rates of human-associated MRSA clones were observed in cats and dogs.

Isolation and Molecular Identification of Virulence, Antimicrobial and Heavy Metal Resistance Genes in Livestock-Associated Methicillin-Resistant Staphylococcus aureus

Staphylococcus aureus is one of the most important pathogens of humans and animals. Livestock production contributes a significant proportion to the South African Gross Domestic Product. Consequently, the aim of this study was to determine for the first time the prevalence, virulence, antibiotic and heavy metal resistance in livestock-associated S. aureus isolated from South African livestock production systems. Microbial phenotypic methods were used to detect the presence of antibiotic and heavy metal resistance. Furthermore, molecular DNA based methods were used to genetically determine virulence as well as antibiotic and heavy metal resistance determinants. Polymerase chain reaction (PCR) confirmed 217 out of 403 (53.8%) isolates to be S. aureus. Kirby-Bauer disc diffusion method was conducted to evaluate antibiotic resistance and 90.8% of S. aureus isolates were found to be resistant to at least three antibiotics, and therefore, classified as multidrug resistant. Of the antibiotics tested, 98% of the isolates demonstrated resistance towards penicillin G. High resistance was shown against different heavy metals, with 90% (196/217), 88% (192/217), 86% (188/217) and 84% (183/217) of the isolates resistant to 1500 µg/mL concentration of Cadmium (Cd), Zinc (Zn), Lead (Pb) and Copper (Cu) respectively. A total of 10 antimicrobial resistance and virulence genetic determinants were screened for all livestock associated S. aureus isolates. Methicillin-resistant S. aureus (MRSA) isolates were identified, by the presence of mecC, in 27% of the isolates with a significant relationship (p < 0.001)) with the host animal. This is the first report of mecC positive LA-MRSA in South Africa and the African continent. The gene for tetracycline resistance (tetK) was the most frequently detected of the screened genes with an overall prevalence of 35% and the highest prevalence percentage was observed for goats (56.76%) followed by avian species (chicken, duck and wild birds) (42.5%). Virulence-associated genes were observed across all animal host species. The study reports the presence of luks/pv, a gene encoding the PVL toxin previously described to be a marker for community acquired-MRSA, suggesting the crossing of species between human and livestock. The high prevalence of S. aureus from the livestock indicates a major food security and healthcare threat. This threat is further compounded by the virulence of the pathogen, which causes numerous clinical manifestations. The phenomenon of co-selection is observed in this study as isolates exhibited resistance to both antibiotics and heavy metals. Further, all the screened antibiotic and heavy metal resistance genes did not correspond with the phenotypic resistance.

Methicillin-Resistant Staphylococcus aureus Harboring mecC Still Eludes Us in East London, United Kingdom

Reports of methicillin-resistant Staphylococcus aureus (MRSA) harboring the mecC gene have increased in the UK since first being described. To our diagnostic S. aureus multiplex PCR, a mecC primer set was designed and implemented, and then the prevalence in our patient population was investigated. Fewer than 1% of the clinical isolates possessed the mecC gene, confirming that mecA remains the dominant genetic determinant of MRSA in East London.

Characterization of mecC gene-carrying coagulase-negative Staphylococcus spp. isolated from various animals

The presence of the methicillin resistance gene mecC in coagulase-negative Staphylococcus spp. (CoNS) is scarce. The aim of this study was to characterize mecC-positive CoNS isolated from various wild and domestic animals. The presence of the mecC gene was screened in 4299 samples from wild animals and domestic animals. Fifteen coagulase-negative staphylococci, that displayed a cefoxitin-resistant phenotype, were tested mecC-positive by PCR. Antimicrobial susceptibility testing was performed for all isolates. The 15 isolates were genotyped by sequencing of the entire class E mec gene complex (blaZ-mecC-mecR1-mecI), the ccrA and ccrB recombinase genes and other determinants within the type XI SCCmec element. DNA microarray analysis was performed and five selected isolates were additionally whole genome sequenced and analyzed. S. stepanovicii (n = 3), S. caprae (n = 1), S. warneri (n = 1), S. xylosus (n = 1) and S. sciuri (n = 9) were detected. All but the S. sciuri isolates were found to be susceptible to all non-beta lactams. The entire class E mec gene complex was detected in all isolates but ccrA and ccrB genes were not identified in S. stepanovicii and S. xylosus. The genes erm(B) and fexA (n = 4, each) were the most predominant non-beta lactam resistance genes detected in the S. sciuri isolates. Even though the presence of the mecC gene among CoNS is a rare observation, this study further expands our knowledge by showing that the mecC gene, including its allotypes, are present in more staphylococcal species from different animal species than has been previously described.

Absence of the mecC gene in methicillin-resistant Staphylococcus aureus isolated from various clinical samples: The first multi-centered study in Turkey

BACKGROUND

mecA is a predefined gene causing methicillin resistance in Staphylococcus aureus (S. aureus) isolates; however, it has been shown that some methicillin-resistant S. aureus (MRSA) strains do not carry this gene. Recently, in isolates found to be MRSA-positive but mecA-negative, a new resistance gene called mecC, which is a homolog of mecA, has been reported. This study aimed to investigate the mecC and mecA genes in MRSA strains isolated from different geographic regions in Turkey.

METHODS

The sample of the study consisted of 494 MRSA strains isolated from seven geographical regions in Turkey between 2013 and 2016. The strains were obtained from 17 centers, comprising 13 university hospitals, three education and research hospitals, and one state hospital. Methicillin resistance in S. aureus strains was determined using the agar disk diffusion method with a cefoxitin disk and the agar dilution method with oxacillin. The mecC and mecA genes in MRSA strains was investigated by Polymerase Chain Reaction (PCR).

RESULTS

Of the MRSA strains investigated, 47.9% were isolated from intensive care units. Concerning sample type, 36.7% were detected in the respiratory tract (tracheal aspirate, sputum, etc.), 24.8% in blood, 18.7% in skin and soft tissues, 9.3% in nasal swabs, 5.4% in urine, 4.1% in ears, and 1% in sterile body fluid. Using PCR, mecC was not identified in any of the S. aureus strains isolated from different clinical microbiology laboratories. mecA gene positivity was found in 315 of the MRSA strains (63.8%). Staphylococcal Cassette Chromosome mec (SCCmec) type was identified in 232 strains (46.9%), of which 136 (58.7%) were type II, 75 (32.4%) were type IV, 12 (5.1%) were type IIIb, six (2.5%) were type I, and three (1.3%) were type III.

CONCLUSION

This is the first multi-centered study to investigate MRSA strains isolated from different regions in Turkey. The mecC gene was not detected in any of the MRSA strains. We believe that this study will constitute an important basis for monitoring possible future changes.

Persistence and Diffusion of mecC-Positive CC130 MRSA Isolates in Dairy Farms in Meurthe-et-Moselle County (France)

Background: Methicillin resistance in Staphylococcus aureus (MRSA) is classically conferred by the acquisition of the mecA gene encoding an additional penicillin binding protein with low affinity for beta-lactams. A mecA variant, named mecC, was described in 2011. MRSA isolates harboring mecC of both animal and human origin have since been collected in different European countries. In France, animal cases were reported in 4 dairy farms between 2008 and 2013 in the Meurthe-et-Moselle county, all located in a 30 km perimeter, suggesting a possible dissemination of mecC-positive MRSA strains. We performed a prospective study to evaluate the local epidemiology of such strains in terms of (i) dissemination among animals, humans and in the environment, and (ii) persistence in Meurthe-et-Moselle dairy cattle farms. Methods: The 4 French dairy farms with previous reports of mecC-positive MRSA strains and 14 farms in the same perimeter were included in this study. In each farm, nasal swabs, rectal swabs and milk samples were collected from 10 randomly selected cows, as well as nasal samples from family pets, volunteer farmers and veterinarians. One farm (E0), in which mecC-MRSA isolates were detected, was selected to study more deeply the dissemination of mecC-positive strains within the farm. After pre-enrichment of swabs and milk, they were subcultured on MSSA/MRSA chromogenic selective agar plates. S. aureus colonies were tested with a multiplex PCR to detect the mecA and mecC genes. The mecC-positive strains were characterized using DNA microarray. Results: mecC-positive strains were recovered in four farms, corresponding to the ones with previous reports of mecC-positive MRSA strains, and originated only from dairy cow samples. The screening in the E0 farm showed that 22% of the dairy cows carried mecC-positive MRSA. Three strains were also isolated from the environmental samples. All mecC-positive strains belonged to the clonal complex CC130 and harbored the same spa-type t1736. Conclusion: This study found that mecC-positive MRSA isolates are able to persist within the same farms for several years after being introduced in this setting and are able to widely disseminate but only among dairy cows suggesting that milking machines might be a key player.

SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data

Typing of methicillin-resistant Staphylococcus aureus (MRSA) is important in infection control and surveillance. The current nomenclature of MRSA includes the genetic background of the S. aureus strain determined by multilocus sequence typing (MLST) or equivalent methods like spa typing and typing of the mobile genetic element staphylococcal cassette chromosome mec (SCCmec), which carries the mecA or mecC gene. Whereas MLST and spa typing are relatively simple, typing of SCCmec is less trivial because of its heterogeneity. Whole-genome sequencing (WGS) provides the essential data for typing of the genetic background and SCCmec, but so far, no bioinformatic tools for SCCmec typing have been available. Here, we report the development and evaluation of SCCmecFinder for characterization of the SCCmec element from S. aureus WGS data. SCCmecFinder is able to identify all SCCmec element types, designated I to XIII, with subtyping of SCCmec types IV (2B) and V (5C2). SCCmec elements are characterized by two different gene prediction approaches to achieve correct annotation, a Basic Local Alignment Search Tool (BLAST)-based approach and a k-mer-based approach. Evaluation of SCCmecFinder by using a diverse collection of clinical isolates (n = 93) showed a high typeability level of 96.7%, which increased to 98.9% upon modification of the default settings. In conclusion, SCCmecFinder can be an alternative to more laborious SCCmec typing methods and is freely available at https://cge.cbs.dtu.dk/services/SCCmecFinder. IMPORTANCE SCCmec in MRSA is acknowledged to be of importance not only because it contains the mecA or mecC gene but also for staphylococcal adaptation to different environments, e.g., in hospitals, the community, and livestock. Typing of SCCmec by PCR techniques has, because of its heterogeneity, been challenging, and whole-genome sequencing has only partially solved this since no good bioinformatic tools have been available. In this article, we describe the development of a new bioinformatic tool, SCCmecFinder, that includes most of the needs for infection control professionals and researchers regarding the interpretation of SCCmec elements. The software detects all of the SCCmec elements accepted by the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements, and users will be prompted if diverging and potential new elements are uploaded. Furthermore, SCCmecFinder will be curated and updated as new elements are found and it is easy to use and freely accessible.

Comparison of Different Phenotypic Approaches To Screen and Detect mecC-Harboring Methicillin-Resistant Staphylococcus aureus

Similar to mecA, mecC confers resistance against beta-lactams, leading to the phenotype of methicillin-resistant Staphylococcus aureus (MRSA). However, mecC-harboring MRSA strains pose special difficulties in their detection. The aim of this study was to assess and compare different phenotypic systems for screening, identification, and susceptibility testing of mecC-positive MRSA isolates. A well-characterized collection of mecC-positive S. aureus isolates (n = 111) was used for evaluation. Routinely used approaches were studied to determine their suitability to correctly identify mecC-harboring MRSA, including three (semi)automated antimicrobial susceptibility testing (AST) systems and five selective chromogenic agar plates. Additionally, a cefoxitin disk diffusion test and an oxacillin broth microdilution assay were examined. All mecC-harboring MRSA isolates were able to grow on all chromogenic MRSA screening plates tested. Detection of these isolates in AST systems based on cefoxitin and/or oxacillin testing yielded overall positive agreements with the mecC genotype of 97.3% (MicroScan WalkAway; Siemens), 91.9% (Vitek 2; bioMérieux), and 64.9% (Phoenix, BD). The phenotypic resistance pattern most frequently observed by AST devices was "cefoxitin resistance/oxacillin susceptibility," ranging from 54.1% (Phoenix) and 83.8% (Vitek 2) to 92.8% (WalkAway). The cefoxitin disk diffusion and oxacillin broth microdilution assays categorized 100% and 61.3% of isolates to be MRSA, respectively. The chromogenic media tested confirmed their suitability to reliably screen for mecC-harboring MRSA. The AST systems showed false-negative results with varying numbers, misidentifying mecC-harboring MRSA as methicillin-susceptible S. aureus This study underlines cefoxitin's status as the superior surrogate mecC-positive MRSA marker.

Characterization of Livestock-Associated Methicillin-Resistant Staphylococcus aureus CC398 and mecC-positive CC130 from Zoo Animals in the United Kingdom

Little is known about the characteristics and diseases associated with methicillin-resistant Staphylococcus aureus (MRSA) in nondomestic animals. Four presumptive MRSA isolates, obtained from clinical (n = 3) and surveillance specimens (n = 1) from dwarf (Helogale parvula) and yellow mongooses (Cynictis penicillata) from a United Kingdom zoo, were analyzed by PCR for detection of mecA and mecC-mediated methicillin resistance, and virulence genes. Isolates were genotyped by multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) and spa sequence typing. Three isolates, obtained from the dwarf mongooses, carried mecA, tetK, and fexA resistance and virulence genes (icaA, icaD, and sec) and were typed to SCCmec IVa, spa type t899, and clonal complex (CC) 398. The fourth MRSA isolate, obtained from the femoral bone marrow of a yellow mongoose showing postmortem findings consistent with septicemia, carried mecC and was oxacillin/cefoxitin susceptible, when tested at 37°C but showed a characteristic MRSA susceptibility profile at 25°C ± 2°C. Furthermore, this isolate exhibited a different genetic background (SCCmecXI/t843/CC130) and had biofilm-associated genes (bap, icaA, and icaD) and tetK tetracycline resistance genes. This work describes the first isolation of livestock-associated MRSA CC398 from two zoo mongoose species where it was associated with both clinical disease and colonization, and the first isolation of mecC MRSA from a zoo species in the United Kingdom. Both reports highlight the potential for zoo species to act as reservoirs for these zoonotic agents.

Wild rodents and shrews are natural hosts of Staphylococcus aureus

Laboratory mice are the most commonly used animal model for Staphylococcus aureus infection studies. We have previously shown that laboratory mice from global vendors are frequently colonized with S. aureus. Laboratory mice originate from wild house mice. Hence, we investigated whether wild rodents, including house mice, as well as shrews are naturally colonized with S. aureus and whether S. aureus adapts to the wild animal host. 295 animals of ten different species were caught in different locations over four years (2012-2015) in Germany, France and the Czech Republic. 45 animals were positive for S. aureus (15.3%). Three animals were co-colonized with two different isolates, resulting in 48 S. aureus isolates in total. Positive animals were found in Germany and the Czech Republic in each studied year. The S. aureus isolates belonged to ten different spa types, which grouped into six lineages (clonal complex (CC) 49, CC88, CC130, CC1956, sequence type (ST) 890, ST3033). CC49 isolates were most abundant (17/48, 35.4%), followed by CC1956 (14/48, 29.2%) and ST890 (9/48, 18.8%). The wild animal isolates lacked certain properties that are common among human isolates, e.g., a phage-encoded immune evasion cluster, superantigen genes on mobile genetic elements and antibiotic resistance genes, which suggests long-term adaptation to the wild animal host. One CC130 isolate contained the mecC gene, implying wild rodents might be both reservoir and vector for methicillin-resistant . In conclusion, we demonstrated that wild rodents and shrews are naturally colonized with S. aureus, and that those S. aureus isolates show signs of host adaptation.

Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus

Denmark is a country with high prevalence of livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) clonal complex (CC) 398 in pigs. Even though pig farming is regarded as the main source of human infection or colonization with MRSA CC398, 10-15% of the human cases appear not to be linked to pigs. Following the recent reports of MRSA CC398 in horses in other European countries and the lack of knowledge on S. aureus carriage in this animal species, we carried out a study to investigate whether horses constitute a reservoir of MRSA CC398 in Denmark, and to gain knowledge on the frequency and genetic diversity of S. aureus in horses, including both methicillin-resistant and -susceptible S. aureus (MSSA). Nasal swabs were collected from 401 horses originating from 74 farms, either at their farms or prior to admission to veterinary clinics. Following culture on selective media, species identification by MALDI-TOF MS and MRSA confirmation by standard PCR-based methods, S. aureus and MRSA were detected in 54 (13%) and 17 (4%) horses originating from 30 (40%) and 7 (9%) farms, respectively. Based on spa typing, MSSA differed genetically from MRSA isolates. The spa type prevalent among MSSA isolates was t127 (CC1), which was detected in 12 horses from 11 farms and represents the most common S. aureus clone isolated from human bacteremia cases in Denmark. Among the 17 MRSA carriers, 10 horses from three farms carried CC398 t011 harboring the immune evasion cluster (IEC), four horses from two farms carried IEC-negative CC398 t034, and three horses from two farms carried a mecC-positive MRSA lineage previously associated with wildlife and domestic ruminants (CC130 t528). Based on whole-genome phylogenetic analysis of the 14 MRSA CC398, t011 isolates belonged to the recently identified horse-adapted clone in Europe and were closely related to human t011 isolates from three Danish equine veterinarians, whereas t034 isolates belonged to pig-adapted clones. Our study confirms that horses carry an equine-specific clone of MRSA CC398 that can be transmitted to veterinary personnel, and reveals that these animals are exposed to MRSA and MSSA clones that are likely to originate from livestock and humans, respectively.

Full-Genome Sequencing Identifies in the Genetic Background Several Determinants That Modulate the Resistance Phenotype in Methicillin-Resistant Staphylococcus aureus Strains Carrying the Novel mecC Gene

Most methicillin-resistant Staphylococcus aureus (MRSA) strains are resistant to beta-lactam antibiotics due to the presence of the mecA gene, encoding an extra penicillin-binding protein (PBP2A) that has low affinity for virtually all beta-lactam antibiotics. Recently, a new resistance determinant-the mecC gene-was identified in S. aureus isolates recovered from humans and dairy cattle. Although having typically low MICs to beta-lactam antibiotics, MRSA strains with the mecC determinant are also capable of expressing high levels of oxacillin resistance when in an optimal genetic background. In order to test the impact of extensive beta-lactam selection on the emergence of mecC-carrying strains with high levels of antibiotic resistance, we exposed the prototype mecC-carrying MRSA strain, LGA251, to increasing concentrations of oxacillin. LGA251 was able to rapidly adapt to high concentrations of oxacillin in growth medium. In such laboratory mutants with increased levels of oxacillin resistance, we identified mutations in genes with no relationship to the mecC regulatory system, indicating that the genetic background plays an important role in the establishment of the levels of oxacillin resistance. Our data also indicate that the stringent stress response plays a critical role in the beta-lactam antibiotic resistance phenotype of MRSA strains carrying the mecC determinant.

Comparison of the BD MAX MRSA XT to the Cepheid™ Xpert® MRSA assay for the molecular detection of methicillin-resistant Staphylococcus aureus from nasal swabs

INTRODUCTION

Variation in MRSA genotypes may affect the sensitivity of molecular assays to detect this organism.

METHODS

We compared 2 commonly used screening assays, the Cepheid™ Xpert® MRSA and the BD MAX™ MRSA XT on consecutively obtained nasal swabs from 479 subjects. Specimens giving discordant results were subjected to additional microbiologic and molecular testing.

RESULTS

Six hundred forty-two (97.6%) of the 658 test results were concordant. Of the 16 discordant results from 12 subjects, additional results suggested that 9 (60%) of the 15 MRSA XT assays were likely correct, and 6 (40%) of the 15 Xpert® assays were likely correct. One discordant result could not be resolved. A mecA dropout and novel mec right-extremity junction (MREJ) sites led to false-positive and negative results by Xpert®.

CONCLUSION

While both assays performed well, continued vigilance is needed to monitor for Staphylococcus aureus with novel MREJ sites, mecA dropouts, and mecC, leading to inaccurate results in screening assays.

Methicillin-resistant Staphylococcus aureus among animals: current overview

Currently, methicillin-resistant Staphylococcus aureus (MRSA) is a universal threat. After being well established in the healthcare setting, it has emerged in the community among people with no risk factors for MRSA acquisition, therefore imposing a new threat. The subsequent detection of MRSA colonizing or infecting animals as well as in food of animal origin was of major concern, revealing new reservoirs for MRSA. The major MRSA clonal lineages circulating in the different settings, i.e. in hospitals, in the community and among animals, are described here, differentiating between clones colonizing companion and food-chain animals. Particular attention is given to the widely spread livestock-associated MRSA clonal complex (CC) 398, which is mainly associated with professional exposure but may be of high pathogenicity. The recent detection of a mecA homologue, designated mecC, with a wide geographical distribution in Europe, and including a large diversity of hosts (food-chain, companion and wildlife animals and also detected in water samples) adds to the threat. Domestication as well as globalization of the livestock industry have intensified exchanges between human and animal bacteria. We report here several cases of transmission of MRSA between companion or food-chain animals and humans, as well as some MRSA clones of human origin that have adapted to new animal hosts eventually by losing useless virulence factors or acquiring new mobile genetic elements.

Methicillin-resistant Staphylococcus aureus isolates with SCCmec type V and spa types t437 or t1081 associated to discordant susceptibility results between oxacillin and cefoxitin, Central Taiwan

Staphylococcus aureus isolates with discordant susceptibility results between oxacillin and cefoxitin obtained using automated microbiology systems are infrequently observed. From April 2013 to December 2014, 1956 methicillin-resistant S. aureus (MRSA) and 1761 methicillin-susceptible S. aureus isolates were obtained from different patients. Forty isolates (1.1% and 2% in case of S. aureus and MRSA, respectively) with discordant susceptibility results (oxacillin susceptible and cefoxitin resistant) and carrying mecA gene were obtained. Except 2 SCCmec type IV isolates, 38 MRSA isolates were all SCCmec type V (V_T or non-V_T), which were further divided into V_T (n=22) and non-V_T (n=16). The most common spa type in V_T and non-V_T isolates were t437 (n=19) and t1081 (n=13), respectively. Only 55% of patients received effective antimicrobial agents; 2 mortalities were not attributable to MRSA infection. Using standard agar dilution, 17 MRSA isolates (0.46% and 0.87% in case of S. aureus and MRSA, respectively) had oxacillin MIC in the susceptible ranges (oxacillin-susceptible MRSA [OS-MRSA]); all carried SCCmec type V (V_T, n=8; non-V_T, n=9). The most common spa-MLST types of OS-MRSA in V_T and non-V_T were t437-ST59 (n=4) and t1081-ST45 (n=7), respectively. Concomitant testing by both cefoxitin- and oxacillin-based methods is a practical strategy for OS-MRSA detection in the clinical laboratories. Continuous monitoring of OS-MRSA isolates is necessary to elucidate their impact in clinical infectious diseases.

In vitro activity of ceftaroline against mecC-positive MRSA isolates

Ceftaroline is a new cephalosporin with activity against methicillin-resistant Staphylococcus aureus (MRSA). A collection of 17 clinical and veterinary mecC-positive MRSA isolates was tested to evaluate the in vitro efficacy of ceftaroline against recently emerged mecC-MRSA isolates. Minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) of ceftaroline for the 17 isolates were determined by broth microdilution using the methodology and interpretive criteria of the Clinical and Laboratory Standards Institute (CLSI). Additional susceptibility tests were performed using ceftaroline M.I.C.Evaluator (M.I.C.E.™) strips. All isolates showed susceptibility according to CLSI breakpoints, with MICs of ceftaroline ranging from 0.125mg/L to 0.25mg/L. MBCs were identical or up to a twofold dilution step higher. In conclusion, all tested isolates, from various sources and belonging to several clonal complexes (CCs), but predominantly to CC130, were found to be susceptible to ceftaroline. Ceftaroline could thus be an option for the treatment of mecC-MRSA infections.

Increase of genetic diversity and clonal replacement of epidemic methicillin-resistant Staphylococcus aureus strains in South-East Austria

Spa-typing and microarray techniques were used to study epidemiological changes in methicillin-resistant Staphylococcus aureus (MRSA) in South-East Austria. The population structure of 327 MRSA isolated between 2002 and 2012 was investigated. MRSA was assigned to 58 different spa types and 14 different MLST CC (multilocus sequence type clonal complexes); in particular, between 2007 and 2012, an increasing diversity in MRSA clones could be observed. The most abundant clonal complex was CC5. On the respective SCCmec cassettes, the CC5 isolates differed clearly within this decade and CC5/SCCmecI, the South German MRSA, predominant in 2002, was replaced by CC5/SCCmecII, the Rhine-Hesse MRSA in 2012. Whereas in many European countries MLST CC22-MRSA (EMRSA 15, the Barnim epidemic MRSA) is predominant, this clone occurred in Austria nearly 10 years later than in neighbouring countries. CC45, the Berlin EMRSA, epidemic in Germany, was only sporadically found in South-East Austria. The Irish ST8-MRSA-II represented by spa-type t190 was frequently found in 2002 and 2007, but disappeared in 2012. Our results demonstrate clonal replacement of MRSA clones within the last years in Austria. Ongoing surveillance is warranted for detection of changes within the MRSA population.

Changes in the epidemiology of MRSA clones in Austria.

Ability of the GENSPEED(®) MRSA test kit to detect the novel mecA homologue mecC in Staphylococcus aureus

The aim of this study was to evaluate the GENSPEED(®) MRSA Test Kit that in addition to the traditional MRSA gene mecA, also incorporates a probe for detection of the newly described mecA homologue mecC. So far only one commercial system is able to detect this new gene. The specific objective was to evaluate the ability of the kit to detect and separate Stapyhylococcus aureus containing either mecA, mecC or no methicillin-resistance determinant. Ninety-five MRSA isolates from humans were included in the test and additional mecC-positive isolates from animals and methicillin-sensitive S. aureus were tested. The kit demonstrated 100% sensitivity and 100% specificity compared to a standard PCR method. The kit provides the ability to perform rapid and reliable detection of both mecA-MRSA and mecC-MRSA.

High prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carrying the mecC gene in a semi-extensive red deer (Cervus elaphus hispanicus) farm in Southern Spain

The objective was to determine the prevalence of Staphylococcus aureus nasal carriage in red deer of a semi-extensive farm and in humans in contact with the estate animals, and to characterize obtained isolates. Nasal swabs of 65 deer and 15 humans were seeded on mannitol-salt-agar and oxacillin-resistance-screening-agar-base. Isolates were identified by microbiological and molecular methods. Antimicrobial susceptibility profile was determined for 16 antibiotics by disk-diffusion and the presence of eight antibiotic resistance genes, seven virulence genes and genes of immune-evasion-cluster (IEC) was analyzed by PCR. S. aureus was typed by PFGE-SmaI, spa, agr, SCCmec and MLST. Isolates were detected in 16 deer (24.6%). Eleven S. aureus isolates were methicillin-resistant (MRSA), and five were methicillin-susceptible (MSSA). All MRSA harbored mecC gene and were agr-III/SCCmecXI/ST1945 (four spa-t843 and seven spa-t1535). All mecC-MRSA carried blaZ-SCCmecXI and etd2, were IEC-type-E, and belonged to the same PFGE pattern. The five MSSA were typed as spa-t2420/agr-I/ST133. Regarding humans, S. aureus was recovered from six samples (40%). The isolates were MSSA and were typed as spa-t002/agr-II, spa-t012/agr-III or spa-t822/agr-III and showed different IEC types (A, B, D and F). blaZ and erm(A) genes were detected, as well as cna and tst genes. As conclusion, red deer analyzed in this study are frequent carriers of mecC-MRSA CC130 (16.9%), they are characterized by few resistance and virulence determinants, and by the presence of IEC type-E. Deer could be a source of mecC-MRSA which could potentially be transmitted to other animals, or even to humans.

First report of mecC MRSA in human samples from Austria: molecular characteristics and clinical data

Reports of mecC methicillin-resistant Staphylococcus aureus (MRSA) strains have been published from several European countries. We describe the first six mecC MRSA isolates of human origin from Austria and report the application of a rapid PCR test. Candidate isolates (n = 295) received between 2009 and 2013 were investigated phenotypically by cefoxitin screening and streaking on ChromID MRSA plates. The presence of mecC was confirmed in six isolates from blood cultures, wound swabs and screening samples of four female and two male patients (age range 7–89 years) by an in-house PCR method and the new Genspeed MRSA test (Greiner Bio-One, Kremsmünster, Austria). The mecC MRSA were further characterized by whole genome sequencing, multilocus sequence and spa typing. Antimicrobial susceptibility testing was performed by Eucast disk-diffusion method and Vitek 2. The six mecC MRSA isolates were from two clonal lineages (CC130, including a new single-locus variant, and CC599) and four different spa types (t843, t1535, t3256, t5930). Analysis for virulence factor genes yielded lukED, eta, etd2 and edin-B (CC130 isolates) and tst, lukED, eta and sel (ST599 isolates). The Genspeed MRSA test identified mecC in all isolates whereas Vitek 2 failed to detect methicillin resistance in one isolate. The strains were susceptible to a wide range of non-β-lactam antibiotics. All patients were successfully treated or decolonized. mecC MRSA are present in Austria as colonizers but may also cause infections. Thus, laboratories must choose appropriate test methods such as cefoxitin screening and confirmation using molecular assays specifically targeting mecC.

In vitro activities of oritavancin and comparators against meticillin-resistant Staphylococcus aureus (MRSA) isolates harbouring the novel mecC gene

Meticillin-resistant Staphylococcus aureus (MRSA) is routinely detected by amplification of the mecA gene. Recently, MRSA isolates harbouring a novel mec gene (mecC) that is not detected by mecA amplification have been reported. In this study, the activities of the lipoglycopeptide oritavancin as well as the comparators vancomycin, daptomycin and linezolid against 14 mecC MRSA isolates were studied by broth microdilution minimum inhibitory concentration (MIC) and time-kill assays at clinically relevant concentrations of each antibacterial agent. Oritavancin, vancomycin, daptomycin and linezolid MIC90 values (MIC required to inhibit 90% of the isolates) against the mecC isolates were 0.06, 1, 1 and 2mg/L, respectively. In time-kill assays, oritavancin at concentrations reflective of its free peak in plasma of patients receiving a single 1200 mg intravenous dose and the level 24h thereafter was bactericidal against all isolates tested, attaining 3 log kill relative to the starting inoculum between 5 min and 15 min. Vancomycin both at its free peak and free trough concentrations was also bactericidal against all isolates, attaining bactericidal activity between 6h and 24h. Daptomycin was bactericidal only at its free peak concentration, attaining bactericidal activity between 30 min and 4h against the tested isolates. Linezolid was bacteriostatic (<3 log kill relative to the starting inoculum) against the tested isolates. Oritavancin's in vitro activity against mecC MRSA isolates was indistinguishable from that against mecA MRSA isolates both in MIC and time-kill assays.

Multiple cases of methicillin-resistant CC130 Staphylococcus aureus harboring mecC in milk and swab samples from a Bavarian dairy herd

The discovery of a new mecA homolog, mecC, necessitates a modification of diagnostic procedures for the identification of methicillin-resistant Staphylococcus aureus (MRSA), as most assays used for the genotypic and phenotypic mecA detection cannot currently recognize mecC. Although the prevalence, distribution, and importance of mecC are not yet completely understood, an exchange of mecC-MRSA between humans and animals seems possible. All previously reported observations of mecC-positive strains have been sporadic. To the best of our knowledge, this is the first report about multiple cases of mecC-positive Staph. aureus in 1 dairy herd. Clonal complex 130 Staph. aureus harboring mecC were found in milk samples from 16 of 56 lactating cows kept in a herd in Bavaria, Germany. Almost all quarter milk samples positive for mecC-MRSA had the lowest possible California Mastitis Test score; composite somatic cell counts obtained from monthly milk recordings showed a mean of 51,600 cells/mL in mecC-MRSA affected cows. Additionally, mecC-positive clonal complex 130 Staph. aureus were detected in swab samples from the mammary skin and a teat lesion of 1 cow from this herd. This report suggests that mecC-carrying strains are able to spread among livestock, and that they have the ability to cause multiple cases in single herds. Therefore, future studies targeting MRSA in dairy cows need to consider mecC.

[Antimicrobial spectrum of ceftaroline. In vitro activity against methicillin-resistant staphylococci]

Because of the increase in bacterial resistance, there is a need for new antimicrobial agents. In particular, Staphylococcus aureus is a frequent cause of severe infections and has an extraordinary capacity to develop antibiotic multiresistance, including resistance to glycopeptides, linezolid, and daptomycin. Although the incidence of methicillin-resistant S. aureus (MRSA) seems to have stabilized in the last few years, its wide dissemination in healthcare settings and in the community is a cause of concern. Ceftaroline is a new broad-spectrum cephalosporin with bactericidal activity against Gram-positive bacteria, including MRSA and multidrug-resistant Streptococcus pneumoniae. In addition, this drug is active against staphylococci showing resistance to glycopeptides, linezolid, and daptomycin. The ceftaroline MIC90 against MRSA ranges from 0.5-2mg/L and that against methicillin-resistant coagulase-negative staphylococci is 0.5mg/L. Ceftaroline has also good activity against respiratory pathogens including Haemophilus influenzae and Moraxella catarrhalis. Although this drug is active against Enterobacteriaceae, it does not retain activity when these isolates produce extended-spectrum beta-lactamases, carbapenemases or hyperproduce AmpC. Ceftaroline is not active against nonfermentative Gram-negative bacilli. Ceftaroline is an interesting addition to the therapeutic armamentarium against MRSA and constitutes an important option for the treatment of polymicrobial infections caused by multidrug-resistant Gram-positive microorganisms.

Prevalence of methicillin-resistant Staphylococcus aureus carrying mecA or mecC in dairy cattle

In the Netherlands, livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has been found in pigs, veal calves, horses and poultry. However, little is known about its prevalence in healthy dairy cattle. Recently, a new mec gene, called mecC, has been found in methicillin-resistant S. aureus (MRSA) isolates from humans and animals in several countries. The objective of our pilot study was to investigate the prevalence of MRSA (mecA and mecC) in dairy cows at a large slaughterhouse. Samples from the skin between the udder and hind leg were taken from 411 cows. The samples were incubated in Mueller-Hinton enrichment broth with 6.5% NaCl, followed by selective enrichment and plated onto Columbia agar with 5% sheep blood, Brilliance MRSA 2 agar and Baird-Parker agar. Suspected colonies were tested by PCR for a S. aureus specific DNA fragment, the mecA and mecC genes and the Panton-Valentine leucotoxin (PVL) genes. All MRSA isolates and methicillin-susceptible S. aureus (MSSA) isolates were typed by spa typing and MLVA typing. Sixteen of 411 (3.9%) cows, all originating from different farms, were found to be MRSA positive and this prevalence is lower than in Dutch pigs, veal calves and broilers. All MRSA isolates belonging to livestock-associated MLVA complex 398, were PVL-negative and spa type t011 predominated. MSSA isolates (n=39) were of many different MLVA types and spa type t543 was found most often. Four MSSA isolates belonging to MLVA clonal complex 398 and spa types t011 (n=2), t108 and t034 were isolated from different MRSA-negative animals. In conclusion, the prevalence of MRSA in dairy cows was low and isolates carrying the mecC gene were not found, indicating that it is absent or has a low prevalence (<0.73%) in Dutch dairy cows.

The emergence of mecC methicillin-resistant Staphylococcus aureus

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A novel mecA homologue, mecC, confers methicillin resistance to methicillin-resistant Staphylococcus aureus (MRSA).

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mecC MRSA produce negative results with common diagnostic tools.

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Reported from throughout Western Europe. Recent increase in Denmark.

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Found in a range of host species and may pose a zoonotic risk to humans.

The report of methicillin-resistant Staphylococcus aureus (MRSA) encoding a divergent mecA gene in 2011 was highly significant. This homologue, designated mecC, poses diagnostic problems with the potential to be misdiagnosed as methicillin-sensitive S. aureus, with important potential consequences for individual patients and for the surveillance of MRSA. mecC MRSA have now been reported from 13 European countries and have been isolated from 14 different host species, with evidence of a recent increase in Denmark. The emergence of mecC MRSA is a topic of interest to human and veterinary microbiology, and we consider it timely to review here its discovery and subsequent investigation.

Novel mutations in penicillin-binding protein genes in clinical Staphylococcus aureus isolates that are methicillin resistant on susceptibility testing, but lack the mec gene

Objectives

Methicillin-resistant Staphylococcus aureus (MRSA) is an important global health problem. MRSA resistance to β-lactam antibiotics is mediated by the mecA or mecC genes, which encode an alternative penicillin-binding protein (PBP) 2a that has a low affinity to β-lactam antibiotics. Detection of mec genes or PBP2a is regarded as the gold standard for the diagnosis of MRSA. We identified four MRSA isolates that lacked mecA or mecC genes, but were still phenotypically resistant to pencillinase-resistant β-lactam antibiotics.

Methods

The four human S. aureus isolates were investigated by whole genome sequencing and a range of phenotypic assays.

Results

We identified a number of amino acid substitutions present in the endogenous PBPs 1, 2 and 3 that were found in the resistant isolates but were absent in closely related susceptible isolates and which may be the basis of resistance. Of particular interest are three identical amino acid substitutions in PBPs 1, 2 and 3, occurring independently in isolates from at least two separate multilocus sequence types. Two different non-conservative substitutions were also present in the same amino acid of PBP1 in two isolates from two different sequence types.

Conclusions

This work suggests that phenotypically resistant MRSA could be misdiagnosed using molecular methods alone and provides evidence of alternative mechanisms for β-lactam resistance in MRSA that may need to be considered by diagnostic laboratories.

Genomic Basis for Methicillin Resistance in Staphylococcus aureus

Since the discovery of the first strain in 1961 in England, MRSA, the most notorious multidrug-resistant hospital pathogen, has spread all over the world. MRSA repeatedly turned down the challenges by number of chemotherapeutics, the fruits of modern organic chemistry. Now, we are in short of effective therapeutic agents against MRSA prevailing among immuno-compromised patients in the hospital. On top of this, we recently became aware of the rise of diverse clones of MRSA, some of which have increased pathogenic potential compared to the classical hospital-associated MRSA, and the others from veterinary sources. They increased rapidly in the community, and started menacing otherwise healthy individuals by causing unexpected acute infection. This review is intended to provide a whole picture of MRSA based on its genetic makeup as a versatile pathogen and our tenacious colonizer.