In the centre of an epidemic: Fifteen years of LA-MRSA CC398 at the University Hospital Münster

Whole-Genome Investigation of Zoonotic Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complex 398 Isolated from Pigs and Humans in Thailand

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has been widespread globally in pigs and humans for decades. Nasal colonization of LA-MRSA is regarded as an occupational hazard to people who are regularly involved in livestock production. Our previous study suggested pig-to-human transmission caused by LA-MRSA clonal complex (CC) 398, using traditional molecular typing methods. Instead, this study aimed to investigate the zoonotic transmission of LA-MRSA CC398 using whole genome sequencing (WGS) technologies. A total of 63 LA-MRSA isolates were identified and characterized in Thailand. Further, the 16 representatives of LA-MRSA CC9 and CC398, including porcine and worker isolates, were subjected to WGS on the Illumina Miseq platform. Core-genome single nucleotide polymorphism (SNP)-based analyses verify the zoonotic transmission caused by LA-MRSA CC398 in two farms. WGS-based characterization suggests the emergence of a novel staphylococcal cassette chromosome (SCC) mec type, consisting of multiple cassette chromosome recombinase (ccr) gene complexes via genetic recombination. Additionally, the WGS analyses revealed putative multi-resistant plasmids and several cross-resistance genes, conferring resistance against drugs of last resort used in humans such as quinupristin/dalfopristin and linezolid. Significantly, LA-MRSA isolates, in this study, harbored multiple virulence genes that may become a serious threat to an immunosuppressive population, particularly for persons who are in close contact with LA-MRSA carriers.

Genomic Diversity of Methicillin-Resistant Staphylococcus aureus CC398 Isolates Collected from Diseased Swine in the German National Resistance Monitoring Program GERM-Vet from 2007 to 2019

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex 398 (CC398) isolates (n = 178) collected in the national resistance monitoring program GERM-Vet from diseased swine in Germany from 2007 to 2019 were investigated for their genomic diversity with a focus on virulence and antimicrobial resistance (AMR) traits. Whole-genome sequencing was followed by molecular typing and sequence analysis. A minimum spanning tree based on core-genome multilocus sequence typing was constructed, and antimicrobial susceptibility testing was performed. Most isolates were assigned to nine clusters. They displayed close phylogenetic relationships but a wide molecular variety, including 13 spa types and 19 known and four novel dru types. Several toxin-encoding genes, including eta, seb, sek, sep, and seq, were detected. The isolates harbored a wide range of AMR properties mirroring the proportions of the classes of antimicrobial agents applied in veterinary medicine in Germany. Multiple novel or rare AMR genes were identified, including the phenicol-lincosamide-oxazolidinone-pleuromutilin-streptogramin A resistance gene cfr, the lincosamide-pleuromutilin-streptogramin A resistance gene vga(C), and the novel macrolide-lincosamide-streptogramin B resistance gene erm(54). Many AMR genes were part of small transposons or plasmids. Clonal and geographical correlations of molecular characteristics and resistance and virulence genes were more frequently observed than temporal relations. In conclusion, this study provides insight into population dynamics of the main epidemic porcine LA-MRSA lineage in Germany over a 13-year-period. The observed comprehensive AMR and virulence properties, most likely resulting from the exchange of genetic material between bacteria, highlighted the importance of LA-MRSA surveillance to prevent further dissemination among swine husbandry facilities and entry into the human community. IMPORTANCE The LA-MRSA-CC398 lineage is known for its low host specificity and frequent multiresistance to antimicrobial agents. Colonized swine and their related surroundings represent a considerable risk of LA-MRSA-CC398 colonization or infection for occupationally exposed people through which such isolates might be further disseminated within the human community. This study provides insight into the diversity of the porcine LA-MRSA-CC398 lineage in Germany. Clonal and geographical correlations of molecular characteristics and resistance and virulence traits were detected and may be associated with the spread of specific isolates through livestock trade, human occupational exposure, or dust emission. The demonstrated genetic variability underlines the lineage's ability to horizontally acquire foreign genetic material. Thus, LA-MRSA-CC398 isolates have the potential to become even more dangerous for various host species, including humans, due to increased virulence and/or limited therapeutic options for infection control. Full-scale LA-MRSA monitoring at the farm, community, and hospital level is therefore essential.

High-Throughput Mutagenesis Reveals a Role for Antimicrobial Resistance- and Virulence-Associated Mobile Genetic Elements in Staphylococcus aureus Host Adaptation

Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex 398 (CC398) is the dominant livestock-associated (LA) MRSA lineage in European livestock and an increasing cause of difficult-to-treat human disease. LA-CC398 MRSA evolved from a diverse human-associated methicillin-sensitive population, and this transition from humans to livestock was associated with three mobile genetic elements (MGEs). In this study, we apply transposon-directed insertion site sequencing (TraDIS), a high-throughput transposon mutagenesis approach, to investigate genetic signatures that contribute to LA-CC398 causing disease in humans. We identified 26 genes associated with LA-CC398 survival in human blood and 47 genes in porcine blood. We carried out phylogenetic reconstruction on 1,180 CC398 isolates to investigate the genetic context of all identified genes. We found that all genes associated with survival in human blood were part of the CC398 core genome, while 2/47 genes essential for survival in porcine blood were located on MGEs. Gene SAPIG0966 was located on the previously identified Tn916 transposon carrying a tetracycline resistance gene, which has been shown to be stably inherited within LA-CC398. Gene SAPIG1525 was carried on a phage element, which in part, matched phiSa2wa_st1, a previously identified bacteriophage carrying the Panton-Valentine leucocidin (PVL) virulence factor. Gene deletion mutants constructed in two LA-CC398 strains confirmed that the SAPIG0966 carrying Tn916 and SAPIG1525 were important for CC398 survival in porcine blood. Our study shows that MGEs that carry antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for host adaptation. IMPORTANCE CC398 is the dominant type of methicillin-resistant Staphylococcus aureus (MRSA) in European livestock and a growing cause of human infections. Previous studies have suggested MRSA CC398 evolved from human-associated methicillin-sensitive Staphylococcus aureus and is capable of rapidly readapting to human hosts while maintaining antibiotic resistance. Using high-throughput transposon mutagenesis, our study identified 26 and 47 genes important for MRSA CC398 survival in human and porcine blood, respectively. Two of the genes important for MRSA CC398 survival in porcine blood were located on mobile genetic elements (MGEs) carrying resistance or virulence genes. Our study shows that these MGEs carrying antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for blood infection and host adaptation.

Cyanidin chloride protects mice from methicillin-resistant Staphylococcus aureus-induced pneumonia by targeting Sortase A

Methicillin-resistant Staphylococcus aureus (MRSA) has been developing rapidly in recent years. It poses a severe peril to global health care, and the new strategies to against the MRSA is urgently needed. Sortase A (SrtA) regulates the anchoring of many surface proteins. Compounds repress Staphylococcus aureus (S. aureus) cysteine transpeptidase SrtA are considered adequate potent virulence inhibitors. Then, we describe the identification of an effective SrtA inhibitor, cyanidin chloride, a bioflavonoid compound isolated from various plants. It has a reversible inhibitory effect on SrtA activity at an IC₅₀ of 21.91 μg/mL. As a SrtA inhibitor, cyanidin chloride antagonizes SrtA-related virulence phenotypes due to its breadth and specificity, including fibrinogen adhesion, A549 cell invasion, biofilm formation, and surface protein (SpA) anchoring. Subsequently, molecular docking and fluorescence quenching revealed that SrtA and cyanidin chloride had robust mutual affinity. Further mechanistic studies revealed that Arg-197, Gly-167, and Sep-116 were the key-binding sites mediating the interaction between SrtA and cyanidin chloride. Notably, a significant therapeutic effect of cyanidin chloride in vivo was also observed on the mouse pneumonia model induced by MRSA. In conclusion, our study indicates that cyanidin chloride potentially represents a new candidate SrtA inhibitor for S. aureus and potentially be developed as a new antivirulence agent.

Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA

Mobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here, we fully characterise the evolutionary dynamics of these MGEs using a collection of 1180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline, and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398 have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised.

Antibiotic-resistant infections are a growing threat to human health. In 2019, these hard-to-treat infections resulted in 4.95 million deaths making them the third leading cause of death that year. Excessive use of antibiotics in humans is likely driving the emergence of drug-resistant bacteria. But there is a concern that use of antibiotics on livestock farms is also contributing. A type of bacteria traced back to livestock is a growing cause of human infections that do not respond to treatment with the antibiotic methicillin in Europe. It is called livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA).

Bacteria can share genes that make them drug resistant or more deadly. These genes are often carried on mobile genetic elements that promote their movement from one bacterial cell to another. The most common type of LA-MRSA in Europe is clonal-complex 398 (CC398). It has two mobile genetic elements carrying antibiotic-resistance genes, but generally lacks a mobile genetic element that helps the bacterium escape the human immune system. Learning more about how LA-MRSA acquired these genetic changes may help scientists develop better strategies to protect the public.

Matuszewska, Murray et al. analyzed the genomes of more than 1,000 samples of CC398 collected from humans, pigs and 13 other animal species in 28 countries over 27 years. They used this data to reconstruct the bacteria’s evolutionary history. Matuszewska, Murray et al. show that two mobile elements containing antibiotic resistance genes in CC398 were gained decades ago. One is more than 50 years old and was likely acquired around the time antibiotic use in livestock became common. While most CC398 in livestock do not have a mobile element that helps LA-MRSA evade the human immune system, they often gain it when they infect humans. This leads to highly drug-resistant human MRSA infections.

The results of this study suggest that LA-MRSA is a serious threat to human health. The resistance of this bacterium has persisted for decades, spreading across different livestock species and different countries. These drug-resistant bacteria in livestock readily infect humans. Current efforts to reduce antibiotic use in farms may take decades to mitigate these risks. Additionally, the ban on zinc-oxide use on livestock in the European Union (coming into force June 2022) may not help reduce LA-MRSA, because the genes conferring resistance to bacteria and zinc treatment are not always linked.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Staphylococcus aureus in cattle and horses

Staphylococcus aureus (S. aureus) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for cattle and horses in previous scientific opinions. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9, and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR S. aureus can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (60-90% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 4 (Categories A, B and D; 1-5%, 5-10% and 10-33% probability of meeting the criteria, respectively) and the AHAW Panel was uncertain whether it meets the criteria in Sections 3 and 5 (Categories C and E, 33-90% and 60-90% probability of meeting the criteria, respectively). The animal species to be listed for AMR S. aureus according to Article 8 criteria include mainly mammals, birds, reptiles and fish.

The UK Antimicrobial Resistance Strategy 2013–18: A Qualitative Study of International and Domestic Policy and Action Related to Livestock and the Food Chain

Antimicrobial resistance (AMR) is an increasingly important challenge within global health, and growing action is being taken by countries across the world. The UK Government established a national AMR Strategy in 2013, encompassing human and animal health. An evaluation of the implementation of the Strategy was commissioned, to feed into a refresh of the Strategy in 2018. This article addresses the implementation of the parts of the Strategy related to food sourced from animals. It is based on 15 semi-structured interviews with policy officials and professionals from UK and international agencies. Four themes comprise the findings from thematic analysis. (1) The UK's advocacy and leadership at the global level to encourage international action, which was praised. However, the UK's actions were limited in permeating complex international food supply chains. (2) Integrating a One Health approach, adopted in the Strategy, which had successfully facilitated bringing together human and animal health sectors, but still lacked input from environmental agencies and integration of the role of environmental factors in understanding and tackling AMR. (3) Changes in antimicrobial use and attempts to reduce AMR brought about by the Strategy, including the disparity in variations of actions and progress between livestock sectors, the pros and cons of antimicrobial usage reduction targets—felt to be best when adapted for each livestock species sector, the preference for voluntary sector-led approaches to reduction in antimicrobial use, and the need for changes in production systems and animal husbandry. (4) The challenges relating to costs, drivers and incentives identified to reduce antimicrobial use, and how research, data and surveillance systems support continued action. In particular, the need for adequate investment and financial incentives to enable changes in production and husbandry to take a more preventative approach, the importance of working with different actors throughout the food chain in each livestock sector, and the need for adequate and consistent surveillance data to measure antimicrobial use and continued research to understand AMR. The findings have implications for how to implement further changes at both farm and policy level, how to implement harmonized surveillance whilst maintaining sectoral autonomy, the need for a whole food chain approach, and greater integration of research, actions and actors working on environmental factors of AMR.

Knowledge about Hand Hygiene and Related Infectious Disease Awareness among Primary School Children in Germany

Hand hygiene is a cornerstone of infection prevention. However, few data are available for school children on their knowledge of infectious diseases and their prevention. The aim of the study was to develop and apply a standardized questionnaire for children when visiting primary schools to survey their knowledge about infectious diseases, pathogen transmission and prevention measures. Enrolling thirteen German primary schools, 493 questionnaires for grade three primary school children were included for further analyses, comprising 257 (52.1%) girls and 236 (47.9%) boys with an age range of 8–11 years. Out of 489 children, 91.2% participants indicated that they knew about human-to-human transmissible diseases. Of these, 445 children responded in detail, most frequently mentioning respiratory and gastrointestinal diseases, followed by childhood diseases. Addressing putative hygiene awareness-influencing factors, it was worrisome that more than 40.0% of the children avoided visiting the sanitary facilities at school. Most of the children (82.9%) noted that they did not like to use the sanitary facilities at school because of their uncleanliness and the poor hygienic behavior of their classmates. In conclusion, basic infection awareness exists already in primary school age children. Ideas about the origin and prevention of infections are retrievable, however, this knowledge is not always accurate and adequately contextualized. Since the condition of sanitary facilities has a strong influence on usage behavior, the child’s perspective should be given more consideration in the design and maintenance of sanitary facilities.

An outbreak of livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex 398 in a Regional Burns Centre

BACKGROUND

MRSA outbreaks have previously been reported in burns centres with resulting mortality and morbidity. We describe the first human associated outbreak in the UK caused by a strain of mupirocin-resistant (MuR) livestock-associated meticillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398) in an Adult Burns Centre. The centre historically had a very low prevalence of MRSA infections.

AIM

This report describes the clinical and epidemiological context of how the outbreak was identified and contained using a range of infection prevention and control (IPC) measures guided by both traditional and genetic methods.

METHODS

A cluster of MuR-MRSA led to an outbreak investigation. Cases were detected via retrospective search and real-time laboratory surveillance. Isolates were sent continuously for whole genome sequencing (WGS). A live timeline of cases and interventions was produced throughout the period.

FINDINGS

The outbreak consisted of twelve cases, seven males and five females, aged between 22 to 70 years. Patients were identified between May and October 2020. All patients were colonized rather than infected. The strain acquired the plasmid bearing MupA while colonizing the index case before dissemination. The index case was found to be a chicken farmer. This outbreak was eventually controlled using IPC measures, audits and blind staff decolonization guided by the insight from WGS.

CONCLUSION

We could not determine how the strain entered the centre or if a staff carrier was involved. The outbreak demonstrated the potential for continued transmissions for months despite active surveillance and stringent control measures.

Correlations of Host and Bacterial Characteristics with Clinical Parameters and Survival in Staphylococcus aureus Bacteremia

Staphylococcus aureus bacteremia (SAB) is a frequent, severe condition that occurs in patients of all age groups and affects clinical departments of all medical fields. It is associated with a high mortality rate of 20-30%. In this study, we analyzed patient mortality associated with SAB at our tertiary care university hospital, assessed the clinical management in terms of administered antimicrobial therapy, and determined which factors have an impact on the clinical course and outcome of patients with this disease. We collected clinical data and blood culture isolates of 178 patients diagnosed with SAB between May 2013 and July 2015. For this study, bacteria were cultured and analyzed concerning their phenotype, hemolysis activity, biofilm formation, nuclease activity, prevalence of toxin genes, spa and agr type. Overall mortality was 24.2% and 30-day mortality was 14.6%. Inadequate initial therapy was administered to 26.2% of patients and was associated with decreased survival (p = 0.041). Other factors associated with poor survival were patient age (p = 0.003), agr type 4 (p ≤ 0.001) and pathological leukocyte counts (p = 0.029 if elevated and p = 0.003 if lowered). The type of infection focus, spa clonal complex and enterotoxin genes seg and sei had an impact on severity of inflammation. Our results indicate that mortality and burden of disease posed by SAB are high at our university hospital.

Livestock-Associated and Non-Livestock-Associated Staphylococcus aureus Carriage in Humans is Associated with Pig Exposure in a Dose-Response Manner

Background

The distinction between livestock-associated and human-associated methicillin-resistant Staphylococcus aureus (MRSA) has become more and more blurred. This study aimed to reveal the transmission risk of livestock-associated and non-livestock-associated S. aureus (including MRSA and multidrug-resistant S. aureus [MDRSA]) by occupational pig exposure.

Methods

A total of 591 pig-exposed workers and 1178 non-exposed workers were enrolled in this study. All nasal S. aureus isolates were tested for antibiotic susceptibility and molecular characteristics. Logistic regression models were used to examine the dose–response relationships between occupational pig exposure and S. aureus carriage.

Results

Pig-exposed workers had significantly higher carriage rates of MRSA (OR=6.29, 95% CI: 3.38~11.68) and MDRSA (OR=3.17, 95% CI: 2.03~4.96) than non-exposed workers. Notably, we found dose–response relationships between occupational pig exposure and MRSA or MDRSA carriage. Using genotypic and phenotypic markers for differentiating livestock-associated and non-livestock-associated S. aureus, we also revealed dose–response relationships occupational pig exposure and livestock-associated or non-livestock-associated S. aureus carriage.

Conclusion

Our findings provide sufficient epidemiological evidence for revealing the high transmission risk of livestock-associated S. aureus and the low transmission risk of non-livestock-associated S. aureus by occupational pig exposure.

Methicillin-Resistant Staphylococci and Macrococci at the Interface of Human and Animal Health

The global impact of methicillin-resistant Staphylococcus aureus (MRSA) clonal lineages on human and animal health continues, even considering the decreasing MRSA rates in some parts of the world [...].

Animal petting zoos as sources of Shiga toxin-producing Escherichia coli, Salmonella and extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae

Animal petting zoos and farm fairs provide the opportunity for children and adults to interact with animals, but contact with animals carries a risk of exposure to zoonotic pathogens and antimicrobial-resistant bacteria. The aim of this study was to assess the occurrence of Shiga toxin-producing Escherichia coli (STEC), Salmonella, extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA) in animal faeces from six animal petting zoos and one farm fair in Switzerland. Furthermore, hygiene facilities on the venues were evaluated. Of 163 faecal samples, 75 contained stx1, stx2 or stx1/stx2 genes, indicating the presence of STEC. Samples included faeces from sika deer (100%), sheep (92%), goats (88%), mouflons (80%), camels (62%), llamas (50%), yaks (50%), pigs (29%) and donkeys (6%), whereas no stx genes were isolated from faeces of calves, guinea pigs, hens, ostriches, ponies, zebras or zebus. Salmonella enterica subsp. enterica serovar Stourbridge (S. Stourbridge) was detected in faecal samples from camels. A total of four ESBL-producing E. coli strains were isolated from faeces of goats, camels and pigs. PCR and sequencing identified the presence of bla_CTX-M-15 in three and bla_CTX-M-65 in one E. coli. Antimicrobial resistance profiling using the disk diffusion method revealed two multidrug-resistant (MDR) E. coli with resistance to ciprofloxacin, gentamicin and azithromycin, all of which are critically important drugs for human medicine. Multilocus sequence typing identified E. coli ST162, E. coli ST2179, extraintestinal high-risk E. coli ST410 and E. coli ST4553, which belongs to the emerging extraintestinal clonal complex (CC) 648. No MRSA was detected. On all animal petting venues, there were inadequacies with regard to access to hygiene information and handwashing hygiene facilities. This study provides data that underscore the importance of hygiene measures to minimize the risk of transmission of zoonotic pathogens and MDR, ESBL-producing E. coli to visitors of animal petting venues.

Investigation of In-Vitro Adaptation toward Sodium Bituminosulfonate in Staphylococcus aureus

The global increase in antimicrobial resistance has revived the interest in “old” substances with antimicrobial activity such as sodium bituminosulfonate. However, for those “old” compounds, scientific studies are still sparse and the ones available do not mostly meet the current standards. Since this compound is used for topical applications, investigation of a potential increase in minimal inhibitory concentrations (MICs) is of particular importance. For selection of phenotypes with decreased susceptibility, a collection of 30 genetically diverse methicillin-susceptible (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) strains were cultured on bi-layered linear gradient agar plates containing sub-inhibitory concentrations of the active agents. The stability of phenotypes with increased MICs was determined by serial passage on agent-free medium. Within 10 passages, only slight and, in most cases, reversible increases in MSSA and MRSA MIC levels toward sodium bituminosulfonate were obtained. Fusidic acid, used as a control, showed exponential expansions in MIC based on mutations in the fusA gene (elongation factor G or EF-G) with no reduction during the recovery phase. The only marginal and largely reversible changes of S. aureus MICs after exposition to sodium bituminosulfonate indicate a low potential for resistance development.

The occurrence and distribution of livestock-associated methicillin-resistant Staphylococcus aureus ST398 on German dairy farms

The objective of this study was to investigate the occurrence and distribution of methicillin-resistant Staphylococcus aureus (MRSA) on 20 German dairy farms. Farms were selected based on previous MRSA reports from phenotypic susceptibility testing of mastitis pathogens. Samples were collected from predefined groups of cows, young stock, farm personnel, and the environment. A high MRSA-positive test rate was detected in swab samples from milk-fed calves (22.7%; 46/203). In postweaning calves, the MRSA-positive test rate was 9.1% (17/187). From prefresh heifers, both nasal swabs and udder cleft swabs were collected if possible. Including both sample types, the MRSA-positive test rate in prefresh heifers was 13.0% (26/200). The positive test rate was 8.9% (17/191) in nasal swabs and 6.5% (11/170) in udder cleft swabs. In quarter milk samples (QMS), the MRSA-positive test rate was 2.9% (67/2347), and on cow level, 7.9% (47/597) of the dairy cows were affected. Among all cows included in this study, the geometric mean of somatic cell counts was higher in QMS that carried MRSA (345,000 cells/mL) in comparison to all QMS (114,000 cells/mL). No differences in parity or the affected mammary quarter position on the udder were observed among the 47 infected cows. Methicillin-resistant S. aureus was also detected in boot swab samples (dust), teat liners, and in suckers from automatic calf feeders. All isolates belonged to livestock-associated sequence type 398 and most common staphylococcal protein A (spa)-types were t011 and t034. Most isolates harbored the staphylococcal cassette chromosome mec (SCCmec)-type V, with the exception of some isolates with SCCmec-type IVa on 1 farm. Similar MRSA genotypes in samples from humans and dairy cows underline the possible zoonotic and reverse-zoonotic transmission of livestock-associated MRSA strains from dairy farms. Similar MRSA genotypes in pig and cattle barns were detected on only 1 of 5 farms that kept both cattle and pigs. Similar MRSA spa-types were detected in samples from different sources (dairy cows, young stock, environment, and humans), suggesting a possible contagious transmission on some of the farms. Sporadically, up to 3 different MRSA spa-types were detected in QMS from the respective farms. On MRSA-affected farms, improper milking hygiene procedures and elevated bulk-tank milk somatic cell counts (>250,000 cells/mL) were observed. The occurrence of livestock-associated MRSA ST398 in different samples from dairy farms, and especially in young calves, should be considered for future MRSA-monitoring programs and biosecurity guidelines.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

The Virulence Potential of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Cultured from the Airways of Cystic Fibrosis Patients

Staphylococcus aureus is one of the most common pathogens that infects the airways of patients with cystic fibrosis (CF) and contributes to respiratory failure. Recently, livestock-associated methicillin-resistant S. aureus (LA-MRSA), usually cultured in farm animals, were detected in CF airways. Although some of these strains are able to establish severe infections in humans, there is limited knowledge about the role of LA-MRSA virulence in CF lung disease. To address this issue, we analyzed LA-MRSA, hospital-associated (HA-) MRSA and methicillin-susceptible S.aureus (MSSA) clinical isolates recovered early in the course of airway infection and several years after persistence in this hostile environment from pulmonary specimens of nine CF patients regarding important virulence traits such as their hemolytic activity, biofilm formation, invasion in airway epithelial cells, cytotoxicity, and antibiotic susceptibility. We detected that CF LA-MRSA isolates were resistant to tetracycline, more hemolytic and cytotoxic than HA-MRSA, and more invasive than MSSA. Despite the residence in the animal host, LA-MRSA still represent a serious threat to humans, as such clones possess a virulence potential similar or even higher than that of HA-MRSA. Furthermore, we confirmed that S. aureus individually adapts to the airways of CF patients, which eventually impedes the success of antistaphylococcal therapy of airway infections in CF.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

The Porcine Nasal Microbiota with Particular Attention to Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Germany-A Culturomic Approach

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) remains a serious public health threat. Porcine nasal cavities are predominant habitats of LA-MRSA. Hence, components of their microbiota might be of interest as putative antagonistically acting competitors. Here, an extensive culturomics approach has been applied including 27 healthy pigs from seven different farms; five were treated with antibiotics prior to sampling. Overall, 314 different species with standing in nomenclature and 51 isolates representing novel bacterial taxa were detected. Staphylococcus aureus was isolated from pigs on all seven farms sampled, comprising ten different spa types with t899 (n = 15, 29.4%) and t337 (n = 10, 19.6%) being most frequently isolated. Twenty-six MRSA (mostly t899) were detected on five out of the seven farms. Positive correlations between MRSA colonization and age and colonization with Streptococcus hyovaginalis, and a negative correlation between colonization with MRSA and Citrobacter spp. were found (p < 0.05). Of 209 non-S. aureus members of the Staphylococcaceae family, 25 isolates (12.0%) from three out of the seven farms exhibited methicillin resistance, including two Macrococcus goetzii isolates carrying the mecB gene. Among 125 Enterobacterales, none tested positive for extended-spectrum beta-lactamase (ESBL) and carbapenemase production. The high frequency of methicillin-resistant staphylococci supports the need for enhanced efforts within the “One Health” concept to manage the antibiotic resistance crisis in the human and veterinary medicine sector.

Prevention and Control of Multidrug-Resistant Bacteria in The Netherlands and Germany-The Impact of Healthcare Structures

The Netherlands and Germany are neighbouring countries within the European Union but are differently affected by multidrug-resistant microorganisms (MDRO). In this narrative review, we summarize data about antibiotic use, the occurrence of MDRO and healthcare-associated infections in these two countries, as well as data about organizational and structural differences between the Dutch and German healthcare systems. These results are discussed with a focus on whether or how the organization of healthcare influences MDRO prevention. We found that from the point of view of MDRO prevention, a higher density of inpatient care, a higher number of hospitals, a longer length of stay and lower staffing ratios might facilitate MDRO dissemination in German hospitals.

Prevalence and characterisation of methicillin-resistant staphylococci from bovine bulk tank milk in England and Wales

OBJECTIVES

To investigate the prevalence and characteristics of methicillin-resistant staphylococci on dairy farms in England and Wales including zoonotic MRSA.

METHODS

Bulk tank milk was sampled from 363 dairy farms in 2015-2016 and methicillin-resistant staphylococci were isolated by salt broth enrichment and plating on MRSA Brilliance selective agar. Isolates were characterised through antimicrobial susceptibility testing and whole-genome sequencing.

RESULTS

Methicillin-resistant staphylococci were isolated from ∼5% of dairy farms and belonged to six different species, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus lentus, Staphylococcus saprophyticus, Staphylococcus fleurettii and Staphylococcus sciuri. Whole-genome sequencing revealed a large variety of antimicrobial resistance genes and SCCmec elements were present, including mecA and mecC alleles. Potentially zoonotic methicillin-resistance S. aureus were found at a low prevalence (0.83% of sampled dairy farms). Whole-genome sequencing also provided evidence for the mobility of a primordial mec gene complex, independently of a SCCmec element, which appears to have been acquired by S. saprophyticus from S. fleurettii.

CONCLUSIONS

These data give new insight into the epidemiology of veterinary methicillin-resistant staphylococci to inform future surveillance and zoonotic risk evaluation. Our data indicate that MRSA has likely decreased in prevalence since earlier survey work in England and Wales during 2011-12 and highlights the diversity of methicillin resistance and other resistance determinants among bovine-associated staphylococci with implications for veterinary and human medicine.

Overview of Evidence of Antimicrobial Use and Antimicrobial Resistance in the Food Chain

Antimicrobial resistance (AMR) is a global health problem. Bacteria carrying resistance genes can be transmitted between humans, animals and the environment. There are concerns that the widespread use of antimicrobials in the food chain constitutes an important source of AMR in humans, but the extent of this transmission is not well understood. The aim of this review is to examine published evidence on the links between antimicrobial use (AMU) in the food chain and AMR in people and animals. The evidence showed a link between AMU in animals and the occurrence of resistance in these animals. However, evidence of the benefits of a reduction in AMU in animals on the prevalence of resistant bacteria in humans is scarce. The presence of resistant bacteria is documented in the human food supply chain, which presents a potential exposure route and risk to public health. Microbial genome sequencing has enabled the establishment of some links between the presence of resistant bacteria in humans and animals but, for some antimicrobials, no link could be established. Research and monitoring of AMU and AMR in an integrated manner is essential for a better understanding of the biology and the dynamics of antimicrobial resistance.

Molecular Epidemiology of Methicillin-Susceptible and Methicillin-Resistant Staphylococcus aureus in Wild, Captive and Laboratory Rats: Effect of Habitat on the Nasal S. aureus Population

Rats are a reservoir of human- and livestock-associated methicillin-resistant Staphylococcus aureus (MRSA). However, the composition of the natural S. aureus population in wild and laboratory rats is largely unknown. Here, 144 nasal S. aureus isolates from free-living wild rats, captive wild rats and laboratory rats were genotyped and profiled for antibiotic resistances and human-specific virulence genes. The nasal S. aureus carriage rate was higher among wild rats (23.4%) than laboratory rats (12.3%). Free-living wild rats were primarily colonized with isolates of clonal complex (CC) 49 and CC130 and maintained these strains even in husbandry. Moreover, upon livestock contact, CC398 isolates were acquired. In contrast, laboratory rats were colonized with many different S. aureus lineages—many of which are commonly found in humans. Five captive wild rats were colonized with CC398-MRSA. Moreover, a single CC30-MRSA and two CC130-MRSA were detected in free-living or captive wild rats. Rat-derived S. aureus isolates rarely harbored the phage-carried immune evasion gene cluster or superantigen genes, suggesting long-term adaptation to their host. Taken together, our study revealed a natural S. aureus population in wild rats, as well as a colonization pressure on wild and laboratory rats by exposure to livestock- and human-associated S. aureus, respectively.

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.

The Evolutionary Genomics of Host Specificity in Staphylococcus aureus

Staphylococcus aureus is an important human bacterial pathogen that has a cosmopolitan host range, including livestock, companion and wild animal species. Genomic and epidemiological studies show that S. aureus has jumped between host species many times over its evolutionary history. These jumps have involved the dynamic gain and loss of host-specific adaptive genes, usually located on mobile genetic elements. The same functional elements are often consistently gained in jumps into a particular species. Further sampling of diverse animal species is likely to uncover an even broader host range and greater genetic diversity of S. aureus than is already known, and understanding S. aureus host specificity in these hosts will mitigate the risks of emergent human and livestock strains.

Epidemiology and antimicrobial resistance of methicillin-resistant Staphylococcus aureus isolates colonizing pigs with different exposure to antibiotics

Background

In 2016, very high rates of methicillin-resistant Staphylococcus aureus (MRSA)-ST398 (99%) were found in Portuguese pig farms that used colistin, amoxicillin, and zinc oxide as feed additives. Since then, farms A and B banned the use of colistin, and farm C banned the use of both antibiotics.

Objective

The aim of the present study was to evaluate the impact of the ban of colistin and amoxicillin on pig MRSA carriage rates, clonal types and antimicrobial resistance, compared to the results obtained in 2016.

Methods

In 2018, 103 pigs (52 from farm B using amoxicillin only as a feed additive and 51 from farm C where no antibiotics were included in the feed regimen) were nasally swabbed for MRSA colonization. Isolates were tested for antimicrobial susceptibility, and characterised by spa typing, SCCmec typing and MLST. Whole genome sequencing (WGS) was performed for representative isolates.

Results

Overall, 96% of the pigs swabbed in 2018 carried MRSA, mostly ST398-SCCmec V-spa types t011/t108. MRSA from pigs not receiving antibiotics in the feed regimen showed susceptibility to a higher number of antibiotics, namely erythromycin, ciprofloxacin, gentamicin, and chloramphenicol. Notably, most of these isolates (n = 52) presented an unusual erythromycin-susceptibility/clindamycin-resistance phenotype. WGS showed that these isolates lacked the erm and the lnu genes encoding resistance to macrolides and lincosamides, respectively, but carried the vgaA_LC gene encoding resistance to lincosamides, which is here firstly identified in S. aureus ST398.

Conclusion

After two years the ban of colistin and amoxicillin as feed additives had no significant impact on the MRSA nasal carriage rates. Nevertheless, the MRSA strains circulating in those farms showed resistance to a lower number of antibiotic classes.

Characterization of an Oxacillin-Susceptible mecA-Positive Staphylococcus aureus Isolate from an Imported Meat Product

Methicillin-resistant Staphylococcus aureus (MRSA) isolates that carry mecA but are oxacillin susceptible (OS-MRSA; oxacillin minimum inhibitory concentration [MIC] ≤2 μg/mL) are increasingly reported worldwide in the past decade. In this study, an OS-MRSA isolate FC1102921 from an imported meat sample was characterized and the oxacillin resistance mutation frequency and mutant prevention concentration (MPC) to oxacillin was determined. Isolate FC1102921 was pvl negative and contained SCCmec V (5C2&5), the sequence type and spa type were identified as ST398-t034. The MPCs of isolate FC1102921 to oxacillin was 16 μg/mL. The resistance mutation frequency of isolate FC1102921 to oxacillin was 0.036%. The expression of mecA in isolate FC1102921 was detectable, but the mecA expression in the mutant isolate FC1102921m increased 13.8-folds. Our data indicated that S. aureus FC1102921 was not a hypermutator, and the high-resistance mutation frequency of S. aureus FC1102921 was specific to oxacillin and penicillin. SCCmec V region of isolate FC1102921 and FC1102921m was identical, functional blaI and blaR1 were identified in SCCmec region of both isolates, and no plasmid loss was identified in mutant isolate FC1102921m. To the best of our knowledge, this is the first report of the resistance mutation frequency and MPC study of an OS-MRSA ST398-t034 isolate. The high oxacillin MPC value and high oxacillin resistance mutation frequency was not related to a curable plasmid as previously reported, which further highlighted that an in-depth study should be carried out to clarify the mechanism and role of the OS-MRSA isolates in the emergence and transmission of MRSA ST398-t034.

Susceptibility of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) to chlorhexidine digluconate, octenidine dihydrochloride, polyhexanide, PVP-iodine and triclosan in comparison to hospital-acquired MRSA (HA-MRSA) and community-aquired MRSA (CA-MRSA): a standardized comparison

Background

Recent publications have raised concerns of reduced susceptibilities of clinical bacterial isolates towards biocides. This study presents a comparative investigation of the susceptibility of livestock-associated Methicillin-resistant Staphylococcus aureus (LA-MRSA), hospital-acquired MRSA (HA-MRSA) and community-aquired MRSA (CA-MRSA) to the commonly used antiseptics chlorhexidine (CHX), octenidine (OCT), polyhexanide (PHMB), PVP-iodine (PVP-I) and triclosan (TCX) based on internationally accepted standards.

Methods

In total, 28 (18 LA-, 5 HA- and 5 CA) genetically characterized MRSA strains representing a broad spectrum of hosts, clonal complexes and spa-types, as well as the reference methicillin-sensitive Staphylococcus aureus (MSSA) strain ATCC 6538, were selected. Minimal inhibitory concentration (MIC) and minimal microbicidal concentration (MBC) were determined in accordance with DIN 58940-7, 58940-8 and DIN EN ISO 20776-1. The microbicidal efficacy was determined in accordance with DIN EN 1040.

Results

Results from the MIC/MBC and quantitative suspension tests revealed differences between antiseptic substances but not between epidemiological groups of MRSA strains. OCT and PHMB were the most active substances with a minimal MIC of 1 mg/L, followed by CHX (2 mg/L), TCX (32 mg/L) and finally PVP-I (1024 mg/L). The MSSA reference strain showed a tendency to a higher susceptibility compared to the MRSA strains.

Conclusions

This investigation of the susceptibility of a range of LA-, HA- and CA-MRSA strains using standardized conditions gave no indication that LA-MRSA strains are less susceptible to commonly used antiseptics compared to HA- and CA-MRSA strains.

Zoonotic multidrug-resistant microorganisms among non-hospitalized horses from Germany

Colonization with multidrug-resistant organisms (MDROs) belonging to the genus Staphylococcus and the order Enterobacterales poses a particular threat to populations at risk. While previous studies focused on MDRO carriage among livestock or companion animals, respective epidemiological data on the general equine population are limited. Here, carriage of methicillin-resistant Staphylococcus aureus (MRSA) and extended spectrum beta-lactamase (ESBL) producing Enterobacteriaceae (ESBL-E) in non-hospitalized horses living on private farms in the rural area in Northwest Germany was assessed. Intranasal and perianal swab samples were cultured on solid chromogenic media directly and after enrichment in tryptic soy broth, respectively. S. aureus isolates were spa-typed, MRSA and ESBL-E were further classified by phenotypic and molecular methods. Additionally, a subgroup of the first 20 samples was used to isolate and characterize staphylococci other than S. aureus. Among 223 horses, fifteen (6.8%) carried S. aureus. Two isolates were identified as MRSA (0.9% of all horses, mecA-positive) and classified as spa types t011 and t6867, both known as members of the livestock-associated MRSA MLST clonal complex 398. Nine horses (4.0%) were colonized by ESBL-Escherichia coli positive for bla_CTX-M and/or bla_TEM. ESBL-E carriage was associated with prior antibiotic treatment (4/31 vs. 5/183; p = 0.0362) and veterinary examinations (4/31 vs. 5/183; p = 0.0362). In the subgroup, nine different staphylococcal species other than S. aureus were found. The high prevalence of ESBL-E. coli in non-hospitalized horses underlines the necessity to raise awareness for strain dissemination across different hosts in order to do justice to the “One Health” concept.

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The prevalence of equine ESBL-E carriage is 4.0%.

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0.9% of horses carry MRSA.

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Risk factors for ESBL-E carriage: antibiotic treatment and veterinary examinations.

Zoonotic multidrug-resistant microorganisms among small companion animals in Germany

Antimicrobial multidrug-resistant microorganisms (MDRO) can be transmitted between companion animals and their human owners. Aim of this study was to determine the prevalence of extended spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) and Staphylococcus aureus including methicillin-resistant S. aureus (MRSA) in different companion animal species. Dogs (n = 192), cats (n = 74), and rabbits (n = 17), treated in a veterinary practice and hospital or living in an animal shelter and private households, were sampled. All facilities were located in a region characterized by a high density of pig production. Nasal, buccal and perianal swabs were enriched and cultured on solid chromogenic selective media. A subgroup of 20 animals (13 dogs, 3 cats, 4 rabbits) was analyzed for the presence of staphylococci other than S. aureus. Amongst all animals (n = 283), twenty dogs (10.4%) and six cats (8.1%) carried S. aureus. MRSA was found in five dogs (2.6%) and two cats (2.7%). Isolates were of spa types t011, t034, t108 (all mecA-positive, ST398), and t843 (mecC-positive, ST130), typical for livestock-associated (LA)-MRSA. Except for one dog, MRSA-positive animals did not have direct contact to husbandry. ESBL-Escherichia coli (bla_CTX-M/bla_TEM/bla_SHV genes) were present in seven dogs (3.6%), one cat (1.4%) possessed a cefotaxime-resistant Citrobacter freundii isolate (bla_TEM/bla_CMY-2 genes). MDRO carriage was associated with animals from veterinary medical settings (p<0.05). One dog and one rabbit carried methicillin-resistant coagulase-negative staphylococci. The exclusive occurrence of MRSA lineages typically described for livestock stresses the impact of MDRO strain dissemination across species barriers in regional settings. Presence of ESBL-E and LA-MRSA among pets and probable dissemination in clinical settings support the necessity of a “One Health” approach to address the potential threats due to MDRO-carrying companion animals.

Equine Methicillin-Resistant Sequence Type 398 Staphylococcus aureus (MRSA) Harbor Mobile Genetic Elements Promoting Host Adaptation

Continuing introduction of multi-drug resistant, zoonotic pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) in horse clinics challenges the biosafety of employees and animal patients. This study was aimed to determine the occurrence of mobile genetic elements facilitating survival in the early stages of invasive infection in different host species, including humans and horses, in MRSA carried by equine patients admitted to a large horse clinic. A total of 341 equine patients were investigated for carriage of MRSA by hygiene screening directly at hospital admission. MRSA were further investigated by antimicrobial susceptibility testing, whole-genome sequencing and genomic composition, including virulence factors involved in immune evasion and host adaption. From a total of 340 validated specimens from equine nostrils, 3.5% yielded positive results for MRSA. All MRSA were found to be closely related belonging to sequence type (ST) 398_t011 with up to four additional antimicrobial resistances. All MRSA harbored a specific Staphylococcal Pathogenicity Island (SaPIbov5) involved in facilitating survival in ruminant and equine plasma. Moreover, a β-hemolysin (hlb) converting ΦSa3 phage encoding the human-specific Immune Evasion Cluster (IEC) was present in 72% of the isolates. An equid-specific leukotoxin encoded by a further temperate phage (Saeq1) was only rarely detected (22%). Despite the absence of β-hemolysin production for all IEC-positive ST398, a prominent hemolysis zone was demonstrable on sheep blood agar. Thus, IEC might remain undetected among the ST398 lineage, since the presence of IEC is commonly associated with reduction of hemolysis in S. aureus belonging to other genetic backgrounds. Here we describe MRSA-ST398 harboring different mobile genetic elements encoding variants of immune evasion factors and toxins previously shown to contribute to S. aureus invasive diseases in specific host species or ecologic niches. We suggest these combinations contribute to the adaptation of MRSA belonging to ST398 with respect to epidemic spread across different habitats and hosts, and may therefore confer a host “generalist” phenotype.

'Rothia nasisuis' sp. nov., 'Dermabacter porcinasus' sp. nov., 'Propionibacterium westphaliense' sp. nov. and 'Tessaracoccus nasisuum' sp. nov., isolated from porcine nasal swabs in the Münster region, Germany

We report the core features of 'Rothia nasisuis' strain 1a5R-CH16 sp. nov., 'Dermabacter porcinasus' strain 2a1I-BL09 sp. nov., 'Propionibacterium westphaliense' strain 1a7I-CH12an sp. nov. and 'Tessaracoccus nasisuum' strain 1a6R-CH11an sp. nov. In 2016, these isolates were cultured from porcine nasal swabs taken from healthy pigs from farms in the region around Münster, Germany.

Prevalence and Genomic Structure of Bacteriophage phi3 in Human-Derived Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates from 2000 to 2015

Whereas the emergence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex 398 (CC398) in animal husbandry and its transmission to humans are well documented, less is known about factors driving the epidemic spread of this zoonotic lineage within the human population. One factor could be the bacteriophage phi3, which is rarely detected in S. aureus isolates from animals but commonly found among isolates from humans, including those of the human-adapted methicillin-susceptible S. aureus (MSSA) CC398 clade. The proportion of phi3-carrying MRSA spa-CC011 isolates, which constitute presumptively LA-MRSA within the multilocus sequence type (MLST) clonal complex 398, was systematically assessed for a period of 16 years to investigate the role of phi3 in the adaptation process of LA-MRSA to the human host. For this purpose, 632 MRSA spa-CC011 isolates from patients of a university hospital located in a pig farming-dense area in Germany were analyzed. Livestock-associated acquisition of MRSA spa-CC011 was previously reported as having increased from 1.8% in 2000 to 29.4% in 2014 in MRSA-positive patients admitted to this hospital. However, in this study, the proportion of phi3-carrying isolates rose only from 1.1% (2000 to 2006) to 3.9% (2007 to 2015). Characterization of the phi3 genomes revealed 12 different phage types ranging in size from 40,712 kb up to 44,003 kb, with four hitherto unknown integration sites (genes or intergenic regions) and several modified bacterial attachment (attB) sites. In contrast to the MSSA CC398 clade, phi3 acquisition seems to be no major driver for the readaptation of MRSA spa-CC011 to the human host.

Methicillin-resistant Staphylococcus aureus

Since the 1960s, methicillin-resistant Staphylococcus aureus (MRSA) has emerged, disseminated globally and become a leading cause of bacterial infections in both health-care and community settings. However, there is marked geographical variation in MRSA burden owing to several factors, including differences in local infection control practices and pathogen-specific characteristics of the circulating clones. Different MRSA clones have resulted from the independent acquisition of staphylococcal cassette chromosome mec (SCCmec), which contains genes encoding proteins that render the bacterium resistant to most β-lactam antibiotics (such as methicillin), by several S. aureus clones. The success of MRSA is a consequence of the extensive arsenal of virulence factors produced by S. aureus combined with β-lactam resistance and, for most clones, resistance to other antibiotic classes. Clinical manifestations of MRSA range from asymptomatic colonization of the nasal mucosa to mild skin and soft tissue infections to fulminant invasive disease with high mortality. Although treatment options for MRSA are limited, several new antimicrobials are under development. An understanding of colonization dynamics, routes of transmission, risk factors for progression to infection and conditions that promote the emergence of resistance will enable optimization of strategies to effectively control MRSA. Vaccine candidates are also under development and could become an effective prevention measure.

The Novel Phage-Derived Antimicrobial Agent HY-133 Is Active against Livestock-Associated Methicillin-Resistant Staphylococcus aureus

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) isolates are increasingly migrating from livestock into human and animal health care settings. Alternative substances are needed to overcome the drawbacks of currently available drugs used for MRSA eradication. The recombinant bacteriophage endolysin HY-133 has proved to be an active agent against S. aureus Here, the in vitro activity of HY-133 was studied against a large collection of genetically diverse LA-MRSA isolates revealing its high activity against mecA-, mecB-, and mecC-positive LA-MRSA.

Livestock-associated meticillin-resistant Staphylococcus aureus (MRSA) among human MRSA isolates, European Union/European Economic Area countries, 2013

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

Survival of LA-MRSA in Dust from Swine Farms

Dust is suspected to be an important factor in transmission of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) between pigs and pig farmers and their families. The aim of this study was to determine the rate of decay for Staphylococcus aureus and LA-MRSA in dust from swine farms. Electrostatic dust fall collectors (EDCs) were used for passive sampling of settling airborne dust in 11 stable sections from six swine farms. Extraction, plating, identification, and enumeration of cultivable S. aureus and LA-MRSA from the EDCs were performed after storage for 0-30 days postsampling. The survival of S. aureus was measured in 196 dust samples from all farms, and data were used to estimate the decay constant λ according to a model for exponential decay: N(t) = N0 × e-λt. The number of S. aureus colonies was up to 600-fold higher than the number of LA-MRSA colonies on MRSA selective agar. The data showed a good fit to the model (λ = 0.13, r2 = 0.86) even with a large difference in initial concentrations of S. aureus between stables. The loads of S. aureus and LA-MRSA in the dust were significantly reduced by storage time, and the half-life was 5 days for both S. aureus and LA-MRSA. In dust samples with high initial concentrations, LA-MRSA and S. aureus could still be cultivated 30 days after sampling. On all farms MRSA isolates belonged to the clonal complex (CC) 398, and at one farm some isolates also belonged to CC30. A screening for other Staphylococcus species in the farm dust revealed 13 different species numerically dominated by Staphylococcus equorum. Based on the exponential decay model, S. equorum had a half-life of 4 days. In conclusion, the presence of MRSA in airborne dust from five of six farms indicates that dust might be an important vehicle for transmission of LA-MRSA. LA-MRSA and S. aureus was found to survive well in farm dust with half-lives of 5 days, and dependent on the initial concentration they could be found in farm dust for weeks. The 99.9% die-off rate was 66 days for LA-MRSA. Thus, farm dust can pose an exposure risk for humans in the farm environment, but also when transported to other environments. On the other hand, the risk will decrease by time. These results provide important knowledge to diminish spread from farm environments to other environments on, e.g., tools or clothing, and in relation to cleaning of emptied LA-MRSA-positive stables.

Increase of zinc resistance in German human derived livestock-associated MRSA between 2000 and 2014

PROBLEM ADDRESSED

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA), particularly of the clonal complex (CC) 398, emerged as zoonotic pathogens predominantly among humans with direct or indirect livestock contact, but also in healthcare settings. The factors contributing to the success of LA-MRSA are only poorly understood.

OBJECTIVE

During the past years, the use of heavy metal compounds as feed-supplements was found to influence the co-selection of LA-MRSA in pig herds. This study aimed to determine the prevalence of zinc resistance among MRSA CC398 isolated from patients of a German university hospital located in a pig farming-dense area.

METHODS AND APPROACH

In comparison to concurrent healthcare-associated MRSA (HA-MRSA), LA-MRSA CC398 comprising isolates from their first appearance in 2000 to recent isolates from 2014 were included.

RESULTS

Among MRSA CC398, the overall resistance rate towards zinc chloride was 57% compared to only 3% among concurrently isolated HA-MRSA. Zinc resistance correlated with the presence of the czrC gene in 100% of the MRSA CC398 and in 67% of the HA-MRSA.

CONCLUSIONS

The zinc resistance rate in MRSA CC398 significantly increased from 2009 to 2014 with a maximum in 2014. Alarmingly, zinc resistance has become a frequent phenotype of human LA-MRSA in Germany potentially facilitating co-selection of antibiotic resistance genes.

Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an emerging problem in many parts of the world. LA-MRSA has been isolated previously from animals and humans in the United Kingdom (UK), but the prevalence is unknown. The aim of this study was to determine the prevalence and to describe the molecular epidemiology of LA-MRSA isolated in the East of England (broadly Cambridge and the surrounding area). We accessed whole genome sequence data for 2,283 MRSA isolates from 1,465 people identified during a 12-month prospective study between 2012 and 2013 conducted in the East of England, United Kingdom. This laboratory serves four hospitals and 75 general practices. We screened the collection for multilocus sequence types (STs) and for host specific resistance and virulence factors previously associated with LA-MRSA. We identified 13 putative LA-MRSA isolates from 12 individuals, giving an estimated prevalence of 0.82% (95% CI 0.47% to 1.43%). Twelve isolates were mecC-MRSA (ten CC130, one ST425 and one ST1943) and single isolate was ST398. Our data demonstrate a low burden of LA-MRSA in the East of England, but the detection of mecC-MRSA and ST398 indicates the need for vigilance. Genomic surveillance provides a mechanism to detect and track the emergence and spread of MRSA clones of human importance.

Healthy Bovines as Reservoirs of Major Pathogenic Lineages of Staphylococcus aureus in Portugal

The nosocomial prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Portugal is close to 50% and remains one of the highest in Europe. MRSA reservoirs in the animal setting in Portugal have been very poorly investigated, namely among animal husbandry. A total of 52 samples (nasal, inguinal region, and milk) were obtained from bovine animals and analyzed for the presence of S. aureus. The isolates were characterized by pulsed-field gel electrophoresis (PFGE), spa typing, SCCmec typing, and multilocus sequence typing and tested for antimicrobial susceptibility, presence of mecA and mecC genes, and virulence determinants. Overall, 54% of the screened animals were colonized with S. aureus in at least one body site. Notably, S. aureus nasal carriage followed an increasing trend with animal age (p = 0.0006). None of the isolates harbored the mecA or mecC genes. Resistance to penicillin, rifampicin, and tetracycline was observed in 24%, 18%, and 6% of the isolates, respectively. The isolates were distributed into three clonal lineages: PFGE type A, spa type t1166, ST1247-CC133 (43%), PFGE B-t267-ST352-CC97 (30%), and PFGE C-t091-ST7-CC7 (27%). CC133 was associated to older animals (p = 0.0025), whereas CC97 was isolated from calves (p = 0.0016). Virulence determinants commonly found in mastitis were widely detected in carriage isolates: lukDE and hlgv (100%), hlb (76%), and lukM (35%). Although healthy bovines do not represent a MRSA reservoir in Portugal, they are mainly colonized with S. aureus pathogenic lineages associated to mastitis in cattle (CC97 and CC133).

Frequent isolation of methicillin resistant Staphylococcus aureus (MRSA) ST398 among healthy pigs in Portugal

Background

Although livestock-associated ST398 methicillin-resistant Staphylococcus aureus (MRSA) has been widely reported in different geographic regions, MRSA carriage studies among healthy pigs in Portugal are very limited.

Methods and findings

In total, 101 swine nasal samples from two Portuguese farms were screened for MRSA. In addition five swine workers (including one veterinary and one engineer) and four household members were nasally screened. The isolates were characterized by spa typing, SCCmec typing and MLST. All isolates were tested for antimicrobial susceptibility, presence of mecA and mecC genes, and virulence determinants.

MRSA prevalence in swine was 99% (100/101), 80% (4/5) in swine workers and 25% (1/4) in household members. All isolates belonged to ST398 distributed over two spa types–t011 (57%) and t108 (42%). SCCmec type V was present in most of the isolates (n = 95; 82%) while 21 isolates amplified the mecA gene only and were classified as nontypeable. The majority of the isolates were resistant to tetracycline (100%), clindamycin (97%), erythromycin (96%), chloramphenicol (84%) and gentamycin (69%). Notably, 12% showed resistance to quinupristin-dalfopristin (MICs 3–8 μg/mL). Beta-hemolysin (81%) and gamma-hemolysin (74%) were the unique virulence determinants detected. None of the isolates harboured PVL or mecC gene.

Conclusions

This study showed a massive occurrence of ST398-MRSA in two independent swine farms, highlighting its establishment among healthy pigs in Portugal.