The clinical impact of livestock-associated methicillin-resistant Staphylococcus aureus of the clonal complex 398 for humans

A look at staphylococci from the one health perspective

Staphylococcus aureus and other staphylococcal species are resident and transient multihost colonizers as well as conditional pathogens. Especially S. aureus represents an excellent model bacterium for the "One Health" concept because of its dynamics at the human-animal interface and versatility with respect to host adaptation. The development of antimicrobial resistance plays another integral part. This overview will focus on studies at the human-animal interface with respect to livestock farming and to companion animals, as well as on staphylococci in wildlife. In this context transmissions of staphylococci and of antimicrobial resistance genes between animals and humans are of particular significance.

Molecular characterization of MRSA collected during national surveillance between 2008 and 2019 in the Netherlands

BACKGROUND

Although the Netherlands is a country with a low endemic level, methicillin-resistant Staphylococcus aureus (MRSA) poses a significant health care problem. Therefore, high coverage national MRSA surveillance has been in place since 1989. To monitor possible changes in the type-distribution and emergence of resistance and virulence, MRSA isolates are molecularly characterized.

METHODS

All 43,321 isolates from 36,520 persons, collected 2008-2019, were typed by multiple-locus variable number tandem repeats analysis (MLVA) with simultaneous PCR detection of the mecA, mecC and lukF-PV genes, indicative for PVL. Next-generation sequencing data of 4991 isolates from 4798 persons were used for whole genome multi-locus sequence typing (wgMLST) and identification of resistance and virulence genes.

RESULTS

We show temporal change in the molecular characteristics of the MRSA population with the proportion of PVL-positive isolates increasing from 15% in 2008-2010 to 25% in 2017-2019. In livestock-associated MRSA obtained from humans, PVL-positivity increases to 6% in 2017-2019 with isolates predominantly from regions with few pig farms. wgMLST reveals the presence of 35 genogroups with distinct resistance, virulence gene profiles and specimen origin. Typing shows prolonged persistent MRSA carriage with a mean carriage period of 407 days. There is a clear spatial and a weak temporal relationship between isolates that clustered in wgMLST, indicative for regional spread of MRSA strains.

CONCLUSIONS

Using molecular characterization, this exceptionally large study shows genomic changes in the MRSA population at the national level. It reveals waxing and waning of types and genogroups and an increasing proportion of PVL-positive MRSA.

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.

Characterisation of a Staphylococcus aureus Isolate Carrying Phage-Borne Enterotoxin E from a European Badger (Meles meles)

Staphylococcus (S.) aureus colonizes up to 30% of all humans and can occasionally cause serious infections. It is not restricted to humans as it can also often be found in livestock and wildlife. Recent studies have shown that wildlife strains of S. aureus usually belong to other clonal complexes than human strains and that they might differ significantly with regard to the prevalence of genes encoding antimicrobial resistance properties and virulence factors. Here, we describe a strain of S. aureus isolated from a European badger (Meles meles). For molecular characterisation, DNA microarray-based technology was combined with various next-generation sequencing (NGS) methods. Bacteriophages from this isolate were induced with Mitomycin C and characterized in detail by transmission electron microscopy (TEM) and NGS. The S. aureus isolate belonged to ST425 and had a novel spa repeat sequence (t20845). It did not carry any resistance genes. The uncommon enterotoxin gene see was detected in one of its three temperate bacteriophages. It was possible to demonstrate the induction of all three prophages, although only one of them was expected to be capable of excision based on its carriage of the excisionase gene xis. All three bacteriophages belonged to the family Siphoviridae. Minor differences in size and shape of their heads were noted in TEM images. The results highlight the ability of S. aureus to colonize or infect different host species successfully, which can be attributed to a variety of virulence factors on mobile genetic elements, such as bacteriophages. As shown in the strain described herein, temperate bacteriophages not only contribute to the fitness of their staphylococcal host by transferring virulence factors, but also increase mobility among themselves by sharing genes for excision and mobilization with other prophages.

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.

A review of new emerging livestock-associated methicillin-resistant Staphylococcus aureus from pig farms

Methicillin-resistant Staphylococcus aureus (MRSA) is a S. aureus strain resistant to β-lactam antibiotics and is often associated with livestock, known as livestock-associated (LA)-MRSA. Using molecular typing with multi-locus sequence typing, MRSA clones have been classified in pigs, including clonal complex 398. Livestock-associated-methicillin-resistant S. aureus was first discovered in pigs in the Netherlands in 2005. Since then, it has been widely detected in pigs in other countries. Livestock-associated-methicillin-resistant S. aureus can be transmitted from pigs to pigs, pigs to humans (zoonosis), and humans to humans. This transmission is enabled by several risk factors involved in the pig trade, including the use of antibiotics and zinc, the size and type of the herd, and the pig pen management system. Although LA-MRSA has little impact on the pigs' health, it can be transmitted from pig to pig or from pig to human. This is a serious concern as people in direct contact with pigs are highly predisposed to acquiring LA-MRSA infection. The measures to control LA-MRSA spread in pig farms include conducting periodic LA-MRSA screening tests on pigs and avoiding certain antibiotics in pigs. This study aimed to review the emerging LA-MRSA strains in pig farms.

Methicillin-resistant and methicillin-sensitive Staphylococcus aureus isolates from skin and nares of Brazilian children with atopic dermatitis demonstrate high level of clonal diversity

BACKGROUND

Atopic dermatitis (AD) primarily affects the pediatric population, which is highly colonized by S. aureus. However, little is known about the genetic features of this microorganism and other staphylococcal species that colonize AD patients.

OBJECTIVE

This study aimed to characterize Staphylococcus spp. isolated from the nares and skin (with and without lesion) of 30 AD and 12 non-AD Brazilian children.

METHODS

Skin and nasal swabs were cultured onto mannitol salt agar, and bacterial colonies were counted and identified by matrix assisted laser desorption ionization time of flight mass spectrometry and polymerase chain reaction (PCR). Antimicrobial susceptibility was evaluated by phenotypic and genotypic tests. In S. aureus isolates, Panton-Valentine leukocidin genes were detected by PCR, and their clonality was assessed by pulsed-field gel electrophoresis and multilocus sequence typing.

RESULTS

S. aureus was more prevalent in the nares (P = 0.005) and lesional skin (P = 0.0002) of children with AD, while S. hominis was more frequent in the skin of non-AD children (P < 0.0001). All children in the study, except one from each group, were colonized by methicillin-resistant coagulase-negative Staphylococcus and 24% by methicillin-resistant S. aureus. Despite the great clonal diversity of S. aureus (18 sequence types identified), most AD children (74.1%) were colonized by the same genotype in both niches.

CONCLUSION

High colonization by polyclonal S. aureus isolates was found among children with AD, while S. hominis was more frequent among non-AD children. The high prevalence of methicillin-resistant staphylococcal isolates highlights the importance of continued surveillance, especially when considering empiric antibiotic therapy for the treatment of skin infections in these patients.

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.

Staphylococcal Phages Adapt to New Hosts by Extensive Attachment Site Variability

Bacterial pathogens commonly carry prophages that express virulence factors, and human strains of Staphylococcus aureus carry Sa3int phages, which promote immune evasion. Recently, however, these phages have been found in livestock-associated, methicillin-resistant S. aureus (LA-MRSA). This is surprising, as LA-MRSA strains contain a mutated primary bacterial integration site, which likely explains why the rare integration events that do occur mostly happen at alternative locations. Using deep sequencing, we show that after initial integration at secondary sites, Sa3int phages adapt through nucleotide changes in their attachment sequences to increase homology with alternative bacterial attachment sites. Importantly, this homology significantly enhances integrations in new rounds of infections. We propose that promiscuity of the phage-encoded tyrosine recombinase is responsible for establishment of Sa3int phages in LA-MRSA. Our results demonstrate that phages can adopt extensive population heterogeneity, leading to establishment in strains lacking bona fide integration sites. Ultimately, their presence may increase virulence and zoonotic potential of pathogens with major implications for human health.

Protective Roles of Folic Acid in the Responses of Bovine Mammary Epithelial Cells to Different Virulent Staphylococcus aureus Strains

Mastitis caused by Staphylococcus aureus (S. aureus) infection is one of the most difficult diseases to treat in dairy cattle. Exploring the biological progression of S. aureus mastitis via the interaction between host, pathogen, and environment is the key to an effective and sustainable improvement of animal health. Here, two strains of S. aureus and a strain of MRSA (Methicillin-resistant Staphylococcus aureus) isolated from cows with different inflammation phenotypes were used to challenge Mac-T cells and to investigate their effects on the global transcriptome of the cells, then to explore the potential regulatory mechanisms of folic acid on S. aureus mastitis prevention. Differential gene expression or splicing analysis showed that different strains of S. aureus led to distinct transcriptional responses from the host immune system. Folic acid could protect host defense against the challenge of S. aureus and MRSA partially through activating cytoplasmic DNA sensing and tight junction pathway. ZBP1 at the upstream of cytoplasmic DNA sensing pathway was verified and related to anti-pathogen through RNA interference. Further enrichment analysis using these transcriptome data with cattle large-scale genome-wide association study (GWAS) data confirmed that ZBP1 gene is highly associated with bovine somatic cell score (SCS) trait. Our data shed light on the potential effect of FA through regulating key gene and then protect host cells' defense against S. aureus and MRSA.

Multiresistant Gram-Negative Pathogens—A Zoonotic Problem

BACKGROUND

Extended-spectrum-β-lactamase-producing, carbapenemase-producing, and colistin-resistant Enterobacteriaceae (ESBL-E, CPE, and Col-E) are multiresistant pathogens that are increasingly being encountered in both human and veterinary medicine. In this review, we discuss the frequency, sources, and significance of the zoonotic transmission of these pathogens between animals and human beings.

METHODS

This review is based on pertinent publications retrieved by a selective literature search. Findings for Germany are presented in the global context.

RESULTS

ESBL-E are common in Germany in both animals and human beings, with a 6-10% colonization rate in the general human population. A major source of ESBL-E is human-tohuman transmission, partly through travel. Some colonizations are of zoonotic origin (i.e., brought about by contact with animals or animal-derived food products); in the Netherlands, more than 20% of cases are thought to be of this type. CPE infections, on the other hand, are rare in Germany in both animals and human beings. Their main source in human beings is nosocomial transmission. Col-E, which bear mcr resistance genes, have been described in Germany mainly in food-producing animals and their meat. No representative data are available on Col-E in human beings in Germany; in Europe, the prevalence of colonization is less than 2%, with long-distance travel as a risk factor. The relevance of animals as a source of Col-E for human beings is not yet entirely clear.

CONCLUSION

Livestock farming and animal contact affect human colonization with the multiresistant Gram-negative pathogens CPE, ESBL-E and Col-E to differing extents. Improved prevention will require the joint efforts of human and veterinary medicine.

Emergence of livestock-associated MRSA ST398 from bulk tank milk, China

OBJECTIVES

To detect livestock-associated MRSA (LA-MRSA) ST398 from bulk tank milk in China and to determine the phenotypic and genomic characteristics of the strains.

METHODS

LA-MRSA ST398 strains were isolated from bulk tank milk samples in Shanghai and their susceptibilities to antimicrobials were determined using the broth dilution method. Genomic characterization of MRSA ST398 strains was performed by WGS and their evolutionary relationships were assessed by phylogenetic analysis.

RESULTS

Two LA-MRSA ST398 isolates were recovered from bulk tank milk samples in two geographically distant farms in China. Whole-genome analysis strongly suggested that the LA-MRSA ST398 strains were closely related to the highly virulent hospital-associated MRSA (HA-MRSA) ST398 strains in China.

CONCLUSIONS

The presence of LA-MRSA ST398 in bulk tank milk might be a serious threat to public health, highlighting the need for active surveillance of LA-MRSA in healthy cattle in China.

Prevalence and Genetic Characteristics of Staphylococcus aureus CC398 Isolates From Invasive Infections in Spanish Hospitals, Focusing on the Livestock-Independent CC398-MSSA Clade

Background

Livestock-associated (LA)-CC398-MRSA is closely related to pigs, being unfrequently detected in human invasive infections. CC398-MSSA is emerging in human invasive infections in some countries, but genetic and epidemiological characteristics are still scarcely reported.

Objectives

To determine the prevalence of Staphylococcus aureus (SA) CC398, both MRSA and MSSA, among blood cultures SA isolates recovered in Spanish hospitals located in regions with different pig-farming densities (PD) and characterize the recovered isolates.

Methods

One thousand twenty-two SA isolates (761 MSSA, 261 MRSA) recovered from blood cultures during 6–12 months in 17 Spanish hospitals (2018–2019) were studied. CC398 lineage identification, detection of spa-types, and antibiotic resistance, virulence and human immune evasion cluster (IEC) genes were analyzed by PCR/sequencing.

Results

Forty-four CC398-MSSA isolates (4.3% of SA; 5.8% of MSSA) and 10 CC398-MRSA isolates (1% of SA; 3.8% of MRSA) were detected. Eleven spa-types were found among the CC398-MSSA isolates with t571 and t1451 the most frequent spa-types detected (75%). Most of CC398-MSSA isolates were Immune-Evasion-Cluster (IEC)-positive (88.6%), tetracycline-susceptible (95.5%) and erythromycin/clindamycin^–inducible-resistant/erm(T)-positive (75%). No statistical significance was detected when the CC398-MSSA/MSSA rate was correlated to PD (pigs/km²) (p = 0.108). On the contrary, CC398-MRSA isolates were all IEC-negative, predominately spa-t011 (70%), and the CC398-MRSA/MRSA rate was significantly associated to PD (p < 0.005).

Conclusion

CC398-MSSA is an emerging clade in invasive infections in Spanish hospitals. CC398-MRSA (mostly t011) and CC398-MSSA (mostly t571 and t1451) show important differences, possibly suggesting divergent steps in host-adaptation evolutionary processes. While CC398-MRSA is livestock-associated (lacking IEC-system), CC398-MSSA seems to be mostly livestock-independent, carrying human-adaptation markers.

Genomic Characterization of a New Biofilm-Forming and Adhesive ST398 Human-Adapted MSSA Lineage Causing Septic Knee Arthritis Following Surgical Reconstruction

Methicillin-susceptible (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) is a pathogen commonly found in bone and joint infections, including septic arthritis. S. aureus virulence and the frailty of affected patients can cause several complications; a prompt and specific antibiotic treatment can positively affect the outcome of patients. We carried out an in-depth genomic characterization by Illumina whole genome sequencing and bioinformatics of two biofilm-producing M1 and M2 ST398 MSSA causing septic knee arthritis not-responding to antimicrobial therapy. The strains were characterized for antibiotic resistance, biofilm and adhesive properties as well as genomics, single nucleotide polymorphism phylogeny, resistomics and virulomics. Our results showed that M1 and M2 MSSA were ST398-t1451-agrI-Cap5, susceptible to cefoxitin and resistant to erythromycin and clindamycin, traits consistent with the lack of the SCCmec-locus and the presence of the sole blaZ and ermT. Furthermore, M1 and M2 were biofilm-producing and largely potentially adhesive strains, as indicated by the adhesion gene profile. Our data characterized a new human-adapted ST398 MSSA lineage, representing a "fusion" between the human-animal independent ST398 and the Livestock Associated (LA) ST398 lineages, forming biofilm and genomically predicted high adhesive, characterized by different genomic adaptation conferring a great ability to adhere to the host's extracellular matrix causing septic knee arthritis.

Whole-Genome Analysis of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Strains Isolated From Patients With Bacteremia in China

Sequence type (ST) 398 is the most prevalent clone of livestock-associated methicillin-resistant Staphylococcus aureus (MRSA). To evaluate the molecular characteristics and phylogeny of Chinese ST398 isolates, 4 MRSA ST398 strains and 4 methicillin-susceptible S. aureus (MSSA) ST398 strains were collected from patients with bacteremia at 6 teaching hospitals in China between 1999 and 2016. Moreover, 689 ST398 genome sequences were downloaded from the GenBank database for comparison. The 4 MRSA ST398 strains were resistant to β-lactam antibiotics, and 2 strains were also resistant to erythromycin. Among the 4 MSSA ST398 strains, 2 strains displayed multidrug resistance (MDR) and were resistant to penicillin, erythromycin, tetracycline, and gentamicin. The accessory genome of MSSA ST398 was more diverse than that of MRSA ST398. All 4 MRSA ST398 strains carried type V staphylococcal cassette chromosome mec elements; however, MSSA ST398 carried more resistance genes than MRSA ST398. These 4 MRSA ST398 strains carried hemolysin, along with virulence genes associated with immune invasion and protease. Phylogenic analysis showed that the 4 MRSA ST398 strains clustered in 1 clade. The global ST398 phylogeny showed that ST398 was divided into an animal clade and a human clade, and the ST398 strains of this study clustered in the human clade. A small number of human strains were also present in the animal clade and vice versa, suggesting transmission of ST398 between animals and humans. In conclusion, livestock-associated MRSA ST398 has caused severe infections in Chinese hospitals, and it should therefore be paid more attention to and monitored.

The presence of antibiotic-resistant Staphylococcus spp. and Escherichia coli in smallholder pig farms in Uganda

BACKGROUND

The development of antimicrobial resistance is of global concern, and is commonly monitored by the analysis of certain bacteria. The aim of the present study was to study the antibiotic susceptibility in isolates of Staphylococcus spp. and Escherichia (E.) coli obtained from healthy pigs originating from nineteen herds enrolled in a study on herd health management in Lira district, northern Uganda. Skin and nasal swabs were analyzed for the presence of Staphylococcus spp., and selectively cultivated to investigate the presence of methicillin-resistant Staphylococcus (S.) aureus (MRSA), and rectal swabs were analyzed for the presence of E. coli. Antibiotic susceptibility was tested by broth micro-dilution. Information on the antibiotic usage and treatment regimens during the previous year was gathered using structured interviews and longitudinal data.

RESULTS

In Staphylococcus spp., resistance to penicillin (10/19 isolates; 53%), fusidic acid (42%) and tetracycline (37%) were most commonly found. In E. coli, resistance to sulfamethoxazole (46/52 isolates; 88%), tetracycline (54%) and trimethoprim (17%) was most frequent. Methicillin-resistant S. aureus was found in one sample (1/50; 2%). Multi-drug resistant isolates of Staphylococcus spp. and E. coli were found in 54 and 47% of the herds, respectively. At the herd level, no associations could be made between antibiotic resistance and herd size or treatment regimens for either of the bacteria.

CONCLUSION

In conclusion, resistance to important antibiotics frequently used in animals in Uganda was common, and the presence of MRSA was demonstrated, in Ugandan pig herds.

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 [...].

Linking antimicrobial resistance surveillance to antibiotic policy in healthcare settings: the COMBACTE-Magnet EPI-Net COACH project

OBJECTIVES

To systematically summarize the evidence on how to collect, analyse and report antimicrobial resistance (AMR) surveillance data to inform antimicrobial stewardship (AMS) teams providing guidance on empirical antibiotic treatment in healthcare settings.

METHODS

The research group identified 10 key questions about the link between AMR surveillance and AMS using a checklist of 9 elements for good practice in health research priority settings and a modified 3D combined approach matrix, and conducted a systematic review of published original studies and guidelines on the link between AMR surveillance and AMS.

RESULTS

The questions identified focused on AMS team composition; minimum infrastructure requirements for AMR surveillance; organisms, samples and susceptibility patterns to report; data stratification strategies; reporting frequency; resistance thresholds to drive empirical therapy; surveillance in high-risk hospital units, long-term care, outpatient and veterinary settings; and surveillance data from other countries. Twenty guidelines and seven original studies on the implementation of AMR surveillance as part of an AMS programme were included in the literature review.

CONCLUSIONS

The evidence summarized in this review provides a useful basis for a more integrated process of developing procedures to report AMR surveillance data to drive AMS interventions. These procedures should be extended to settings outside the acute-care institutions, such as long-term care, outpatient and veterinary. Without proper AMR surveillance, implementation of AMS policies cannot contribute effectively to the fight against MDR pathogens and may even worsen the burden of adverse events from such interventions.

Acquisition Risk Factors of the SCCmec IX-Methicillin-Resistant Staphylococcus aureus in Swine Production Personnel in Chiang Mai and Lamphun Provinces, Thailand

Methicillin-resistant Staphylococcus aureus (MRSA) harboring the type-IX staphylococcal cassette chromosome mec (SCCmec) has been found in pigs and humans in Northern Thailand. However, knowledge of the prevalence and acquisition risk factors of this MRSA strain among swine production personnel (SPP) are needed. The nasal swab samples and data were collected from 202 voluntary SPP and 31 swine farms in Chiang Mai and Lamphun Provinces, Thailand in 2017. MRSA were screened and identified using mannitol salt agar, biochemical and antimicrobial susceptibility testing, multiplex PCR, and the SCCmec typing. The prevalence of MRSA was 7.9% (16/202) and 19.3% (6/31) among SPP and swine farms. All isolates were multidrug-resistant, and 55 of 59 isolates (93%) contained the type-IX SCCmec element. Data analysis indicated that education, working time, contact frequency, working solely with swine production, and personal hygiene were significantly related to MRSA acquisition (p < 0.05). The multivariate analysis revealed that pig farming experience, working days, and showering were good predictors for MRSA carriage among SPP (area under the curve (AUC) = 0.84). The biosecurity protocols and tetracycline use were significantly associated with MRSA detection in pig farms (p < 0.05). Hence, the active surveillance of MRSA and further development of local/national intervention for MRSA control are essential.

The first outbreak of methicillin-resistant Staphylococcus aureus in dairy cattle in Poland with evidence of on-farm and intrahousehold transmission

Staphylococcus aureus is a widely recognized pathogen responsible for many serious diseases in both humans and animals. It is also one of the major causative agents of bovine mastitis. Methicillin-resistant S. aureus (MRSA), although relatively rare in this pathology, has been increasingly reported in livestock animals, mainly in pigs, but also cattle, sheep, and poultry. The recent emergence of livestock-associated (LA-)MRSA is cause for an immediate public health concern due to the risk of zoonotic transmission to humans, and is of particular concern for people who work in animal husbandry or have prolonged contact with livestock animals. This study reports on the first LA-MRSA outbreak in dairy cattle and the first probable case of MRSA transmission between humans and cows in Poland. A single dairy farm located in Eastern Poland was monitored on a regular basis for the occurrence of mastitis. Over a 1-yr study period, 717 quarter-milk samples from 583 cows were collected and examined microbiologically. A total of 5 MRSA isolates from as many cows with subclinical mastitis were cultured. They all belonged to the same outbreak, given a 2-mo time window in which they were identified. During the outbreak, 24 oral and nasal swabs were voluntarily taken from 6 people: a milker, a veterinarian, and 4 members of the veterinarian's family. Eight swabs from a milker, veterinarian, and 2 family members yielded positive MRSA cultures. All MRSA isolates were genotyped with a combination of multiple-locus variable number tandem repeat analysis, multilocus sequence typing, and staphylococcal protein A gene (spa) typing. Eleven bovine (n = 5; 5 cases) and human (n = 6; 4 cases) isolates showed an identical drug-susceptibility profile and were indistinguishable upon multiple-locus variable number tandem repeat analysis (pattern A), multilocus sequence typing (ST398) and spa (t034) typing. The results of this study provide the evidence of transmission of MRSA between humans and cows, and between humans in the family setting. This work, despite being a preliminary investigation, underscores the risk of intra- and interspecies transmission of LA-MRSA and urges enhancement of the existing biosecurity measures aimed at preventing MRSA (and other milk pathogens) spread at both the farm- and household levels.

Risk of hospitalization and death within 2 years after methicillin-resistant Staphylococcus aureus (MRSA) diagnosis in persons colonized or infected with livestock and non-livestock-associated MRSA-A nationwide register-based cohort study

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) CC398 has emerged in humans throughout Europe and the USA during the last decade and is associated with the spread of LA-MRSA CC398 in production animals. In this study, we investigated the risk of subsequent hospitalization with an S. aureus-related diagnosis and death within the first 2 years after MRSA diagnosis. The study included 7,521 carriers of MRSA, an age-matched reference population of 376,041 individuals and 7,607 patients infected with MRSA. Hazard ratios (HR) for hospitalization with an S. aureus-related diagnosis were 4.09 (95% CI: 2.78-6.00) and for death 1.21 (95% CI: 0.80-1.83) in LA-MRSA CC398 carriers compared with the reference population. Comparing carriers of LA-MRSA CC398 and non-CC398 MRSA, HR for hospitalization was 0.61 (95% CI: 0.37-0.99) and death 0.25 (95% CI: 0.16-0.40), respectively. Patients initially diagnosed with LA-MRSA CC398 or non-CC398 MRSA infection differed from MRSA carriers in terms of older age, higher Charlson comorbidity index score and longer hospital stays. HR for subsequent hospitalization and death was similar regardless having infection with LA-MRSA CC398 or non-CC398 MRSA at the time of MRSA diagnosis. We established that MRSA CC398 carriers have a lower risk of hospitalization and death up to 2 years after MRSA diagnosis than non-CC398 MRSA carriers do. In contrast, MRSA carriage, regardless the MRSA strain is a burden in terms of hospitalization and death when compared to the background reference population. Further, we established that there are no differences in risk of subsequent hospitalization and death in patients initially diagnosed with MRSA CC398 or non-CC398 MRSA infection. We suggest that public health surveillance of MRSA clearly needs to distinguish between carriage and infection as well as strain type before any inference from number of cases to disease burden is made.

Livestock-associated methicillin-resistant Staphylococcus aureus in Korea: antimicrobial resistance and molecular characteristics of LA-MRSA strains isolated from pigs, pig farmers, and farm environment

The emergence of livestock-associated (LA)-methicillin-resistant Staphylococcus aureus (MRSA) in livestock animal has become a significant zoonotic concern. In the present study, we investigated nationwide prevalence of LA-MRSA across pork production chain including pig farms, slaughterhouses, and retail markets. A total of 40 MRSA strains were isolated during the investigation and the overall prevalence of MRSA was 3.4% (n = 37), 0.6% (n = 2), and 0.4% (n = 1) in pig farms, slaughterhouses, and retail markets, respectively. Multilocus sequence typing analyses revealed that the 2 most significant clonal lineages in pork production chain in Korea were ST398 (n = 25) and ST541 (n = 6). All of the 40 MRSA isolates were further characterized to investigate key genotypic and phenotypic correlates associated with the emergence and spread of clonal complex 398 (CC398; ST398, and ST541) LA-MRSA. Although the prevalence of swine-associated MRSA was still relatively low and mostly restricted to pig farms, multidrug-resistant CC398 LA-MRSA isolates with new spa types (t18102 and t18103) were identified as a major clonal lineage. The CC398 LA-MRSA strains tended to exhibit increased levels of multiple drug resistance (MDR) phenotype compared with non-CC398 MRSA strains. Of note, in comparison with non-CC398 MRSA isolates, CC398 LA-MRSA isolates exhibited significantly enhanced tetracycline (TET) and zinc resistance. These findings suggested that co-selection pressure associated with MDR phenotype, especially TET resistance, and zinc resistance may have played a significant role in the emergence and persistence of CC398 LA-MRSA in pig farms in Korea.

Molecular epidemiology of methicillin-resistant Staphylococcus aureus from dairy farms in North-eastern Italy

Transmission of Staphylococcus aureus along the dairy production chain is an emerging public health problem with human, veterinary, and food safety issues. The prevalence of multidrug-resistant, particularly methicillin-resistant S. aureus (MRSA), has steadily increased in several European countries. In this study, the prevalence of S. aureus in raw cow milk and farm workers was investigated, and the trajectories of MRSA transmission at the primary stage of the dairy chain were assessed. To this purpose, a longitudinal survey was conducted in 618 dairy farms in two contiguous regions with high livestock density in North-eastern Italy. S. aureus contamination of bulk tank milk (BTM) was observed in more than 80% of farms, while MRSA prevalence was 3.6% and 15.9% in BTM and farm workers, respectively. The majority of MRSA isolates from both BTM and farm workers were assigned to ST398, and showed a worrisome multidrug-resistant phenotype. Enterotoxin and Panton-Valentine leukocidin genes were detected in 11.5% and 4.9% of MRSA isolates from both sources. Nearly all MRSA isolates from workers belonged to the same epidemiological type as BTM isolates from the corresponding farm, denoting a bidirectional MRSA transmission pattern. A focus on the ST398 spa type t899 MRSA lineage in the Italian livestock system highlighted the presence of two major clusters whose dissemination was likely facilitated by the selective pressure imposed by antimicrobial use in animal farming. Our findings emphasize the need for continuous monitoring of MRSA along the dairy production chain, not only to avoid transmission between animals and exposed workers, but also to contain the risk of raw milk and dairy product contamination by multidrug resistant and toxigenic strain.

Risk of Antibiotic-Resistant Staphylococcus aureus Dispersion from Hog Farms: A Critical Review

The World Health Organization has declared antibiotic resistance "one of the biggest threats to global health." Mounting evidence suggests that antibiotic use in industrial-scale hog farming is contributing to the spread of antibiotic-resistant Staphylococcus aureus. To capture available evidence on these risks, we searched peer-reviewed studies published before June 2017 and conducted a meta-analysis of these studies' estimates of the prevalence of swine-associated, antibiotic-resistant S. aureus in animals, humans, and the environment. The 166 relevant studies revealed consistent evidence of livestock-associated methicillin-resistant S. aureus (MRSA) in hog herds (55.3%) raised with antibiotics. MRSA prevalence was also substantial in slaughterhouse pigs (30.4%), industrial hog operation workers (24.4%), and veterinarians (16.8%). The prevalence of swine-associated, multidrug-resistant S. aureus (MDRSA)-with resistance to three or more antibiotics-is not as well documented. Nonetheless, sufficient studies were available to estimate MDRSA pooled prevalence in conventional hog operation workers (15.0%), workers' household members (13.0%), and community members (5.37%). Evidence also suggests that antibiotic-resistant S. aureus can be present in air, soil, water, and household surface samples gathered in or near high-intensity hog operations. An important caveat is that prevalence estimates for humans reflect colonization, not active infection, and the health risks of colonization remain poorly understood. In addition, these pooled results may not represent risks in specific locations, due to wide geographic variation. Nonetheless, these results underscore the need for additional preventive action to stem the spread of antibiotic-resistant pathogens from livestock operations and a streamlined reporting system to track this risk.

Epidemiology of bacteria and viruses in the respiratory tract of humans and domestic pigs

Bacteria and viruses were analysed in the upper respiratory tract of symptomatic pig farmers and their domestic pigs. Eighty six human nasal and 495 (50 pools) porcine snout swabs were collected in Schleswig-Holstein, Germany. Staphylococcus (S.) aureus (62.8%, 54/86), human rhino- and coronaviruses (HRV, 29.1%, 25/86; HCoV, 16.3%, 14/86) were frequently detected in humans, while Haemophilus parasuis (90.0%, 45/50), Mycoplasma hyorhinis (78.6%, 11/14), Enterovirus G (EV-G, 56.0%, 28/50) and S. aureus (36.0%, 18/50), respectively, were highly prevalent in pigs. The detection of S. aureus in human follow-up samples indicates a carrier status. The methicillin-resistant phenotype (MRSA) was identified in 33.3% (18/54) of nasal swabs and in one of 18 (5.6%) pooled snout swabs that were tested positive for S. aureus. Strains were indicative of the livestock-associated clonal complex CC398, with t011 being the most common staphylococcal protein A type. Enterobacterales and non-fermenters were frequently isolated from swabs. Their detection in follow-up samples suggests a carrier status. All were classified as being non-multiresistant. There was no example for cross-species transmission of viruses. In contrast, transmission of S. aureus through occupational contact to pigs seems possible. The study contributes to the 'One Health' approach.

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.

Epidemiology and risk factors of Staphylococcus aureus CC398 bone and joint infections

Background

A particular ability of the Staphylococcus aureus clonal complex 398 (CC398) to cause bone and joint infections (BJI) remains questionable, since some studies have described high prevalence of MSSA CC398 in prosthetic joint infection (PJI) and diabetic foot ostemolyelitis (DFO). Here, we described the long-term epidemiology of CC398 among S. aureus isolated from BJI and identified risk factors associated with CC398.

Methods

We included all bone and joint samples with S. aureus-positive culture in our university hospital between January 2010 and December 2017. Logistic regression was used for univariate and multivariate analysis.

Results

We identified 124 CC398 isolates among the 958 BJI-associated S. aureus. The proportion of CC398 among S. aureus increased steadily from 4% in 2010 to 26% in 2017. Only 4 isolates of CC398 were resistant to methicillin. The distribution of BJI types due to CC398 and non CC398 isolates was similar. In multivariate analysis, age (p = 0.034, OR = 3.9), McCabe score (p = 0.005, OR = 5) and inoculation mechanism (p = 0.020, OR = 3.7) were associated with PJI-related CC398. The year of infection (p < 0.001, OR = 1.6), Charlson’s score (p = 0.001, OR = 1.5) and grade 4 (severe) of the International Working Group of the Diabetic Foot classification (p < 0.001, OR = 8.5) were associated with DFO-related CC398.

Conclusion

We highlighted here the emergence and spread of CC398-MSSA in BJI. Patients with comorbidities are at high risk of CC398 MSSA PJI and DFO. The spread of CC398 in the community and hospital settings remains unclear and further epidemiological studies are needed to identify the determinants of its success.

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.

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.

Unidirectional animal-to-human transmission of methicillin-resistant Staphylococcus aureus ST398 in pig farming; evidence from a surveillance study in southern Italy

Background

Livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) belonging to clonal complex 398 is recognized as an occupational hazard for workers employed in intensive animal husbandry, especially in the swine-breeding chain. In this study, we compared the prevalence and epidemiological type of MRSA isolates from swine and farm workers in a large area of southern Italy.

Methods

Between January and March 2018, 88 workers from 32 farms where we had previously performed a survey for MRSA colonization of farmed pigs, were sampled by nasal swabbing. A follow-up investigation was conducted on seven workers 1 year after primary screening. MRSA isolates were characterized by MLST, spa and SCCmec typing, and tested for susceptibility to 15 antimicrobials. Epidemiological correlations between human and swine MRSA isolates were supported by Rep-MP3 and RAPD PCR fingerprinting, and whole-genome sequencing.

Results

The overall colonization rate of MRSA in swine farm workers was 21.6%, being significantly higher in intensive farms and in workers with direct animal contact. All human MRSA isolates were multi-drug resistant, belonged to the ST398 livestock clade, and did not carry Panton-Valentine leukocidin and enterotoxin genes. Notably, 94.1% of human MRSA isolates belonged to the same epidemiological type as swine MRSA isolates from the corresponding farm. Persistent MRSA carriage was documented in some workers 1 year after primary sampling.

Conclusions

We report a high prevalence of MRSA among swine farm workers, with higher colonization rates associated with intensive breeding and animal exposure. Our findings suggest unidirectional animal-to-human transmission of LA-MRSA and denote the high zoonotic transmissibility of the ST398 livestock clade.

Livestock-Associated Methicillin-Resistant Staphylococcus aureus From Animals and Animal Products in the UK

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an emerging problem in many parts of the world. Although animal-adapted LA-MRSA has been known for many years, recent reports suggest a possible increasing trend in the zoonotic transmission of LA-MRSA in Europe. Since its emergence in the early 2000's, several investigations have indicated that persons in prolonged, repeated contact with affected livestock are at a higher risk of becoming colonized with LA-MRSA. LA-MRSA monitoring in livestock is voluntary under current EU legislation, and not all member states, including the UK, participate. UK LA-MRSA isolates have been detected through scanning surveillance, where samples are submitted from clinically diseased livestock for diagnostic investigation, and research studies. Surveys conducted on retail beef, pig and poultry meat on sale in the UK have also detected LA-MRSA. Taken together these results suggest that LA-MRSA is present in the UK, possibly at low prevalence level, as suggested by available evidence. In this review, we examine the data available from UK livestock and animal products, and make recommendations for future. We also review the findings from whole genome sequencing (WGS) of the possible lineage of some UK livestock isolates.

MRSA diversity and the emergence of LA-MRSA in a large teaching hospital in Slovenia

The methicillin-resistant Staphylococcus aureus (MRSA) is one of the major causes of a variety of infections in hospitals and the community. One of the most prominent changes in the MRSA epidemiology is the emergence of livestock-associated MRSA (LA-MRSA) strains in the human population. The aim of this study was to follow the MRSA epidemiology in a large teaching hospital during an 8-year time period (2006-2013). Altogether 519 MRSA, cultured from screening or clinical samples, were distributed into 77 spa types, of which three (t003 and t001, associated with CC5; and t015; associated with CC45) were the most common. LA-MRSA-associated spa types (t011, t034, t108, t899; associated with CC398) started to emerge in the year 2009 and continued to be found annually at a frequency from 3.9% to 12.7% of all MRSA strains examined. Only 6 of 27 LA-MRSA strains were associated with infections.

Antimicrobial Resistance on Farms: A Review Including Biosecurity and the Potential Role of Disinfectants in Resistance Selection

Resistance to therapeutic antimicrobial agents is recognized as a growing problem for both human and veterinary medicine, and the need to address the issue in both of these linked domains is a current priority in public policy. Efforts to limit antimicrobial resistance (AMR) on farms have so far focused on control of the supply and use of antimicrobial drugs, plus husbandry measures to reduce infectious disease. In the United Kingdom and some other countries, substantial progress has been made recently against targets on agricultural antimicrobial drug use. However, evidence suggests that resistant pathogenic and commensal bacteria can persist and spread within and between premises despite declining or zero antimicrobial drug use. Reasons for this are likely complex and varied but may include: bacterial adaptations to ameliorate fitness costs associated with maintenance and replication of resistance genes and associated proteins, horizontal transmission of genetic resistance determinants between bacteria, physical transfer of bacteria via movement (of animals, workers, and equipment), ineffective cleaning and disinfection, and co-selection of resistance to certain drugs by use of other antimicrobials, heavy metals, or biocides. Areas of particular concern for public health include extended-spectrum cephalosporinases and fluoroquinolone resistance among Enterobacteriaceae, livestock-associated methicillin-resistant Staphylococcus aureus, and the emergence of transmissible colistin resistance. Aspects of biosecurity have repeatedly been identified as risk factors for the presence of AMR on farm premises, but there are large gaps in our understanding of the most important risk factors and the most effective interventions. The present review aims to summarize the present state of knowledge in this area, from a European perspective.

Nasal Colonization of Humans with Occupational Exposure to Raw Meat and to Raw Meat Products with Methicillin-Susceptible and Methicillin-Resistant Staphylococcus aureus

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is widely disseminated as a nasal colonizer of conventionally raised livestock and of humans subjected to occupational exposure. Reports on contamination of raw meat raise the question as to whether occupationally exposed food handlers are at particular risk of nasal colonization by LA-MRSA. Here, we report the results from a cross-sectional study on nasal S. aureus/MRSA colonization of butchers, meat sellers, and cooks in Germany. We sampled 286 butchers and meat sellers in 26 butcheries and 319 cooks handling meat in 16 professional canteen kitchens. Swabs were processed on both blood agar plates and MRSA-selective plates. MRSA were confirmed by PCR for mec genes and by broth microdilution. All isolates were subjected to molecular typing. PCR for markers useful to differentiate human-adapted and animal-adapted subpopulations was performed due to the presence of clonal complexes known to occur in both livestock and humans (CC5, CC7, CC8, CC9, and CC398). Only two participants (0.33%) were colonized by MRSA (Hospital-associated MRSA ST22). Nasal colonization by methicillin-susceptible S. aureus (MSSA) was detected in 16.6% of cooks and in 26.2% of butchers and meat sellers. Among 16 of the isolates attributed to CC7, three were negative for the immune evasion gene cluster, suggesting an animal origin. Isolates attributed to CC5, CC8, and CC398 were negative for markers typical of animal-adapted subpopulations. The occupational handling of raw meat and raw meat products was not associated with nasal colonization by LA-MRSA.

Plasmid-Encoded Transferable mecB-Mediated Methicillin Resistance in Staphylococcus aureus

During cefoxitin-based nasal screening, phenotypically categorized methicillin-resistant Staphylococcus aureus (MRSA) was isolated and tested negative for the presence of the mecA and mecC genes as well as for the SCCmec-orfX junction region. The isolate was found to carry a mecB gene previously described for Macrococcus caseolyticus but not for staphylococcal species. The gene is flanked by β-lactam regulatory genes similar to mecR, mecI, and blaZ and is part of an 84.6-kb multidrug-resistance plasmid that harbors genes encoding additional resistances to aminoglycosides (aacA-aphD, aphA, and aadK) as well as macrolides (ermB) and tetracyclines (tetS). This further plasmidborne β-lactam resistance mechanism harbors the putative risk of acceleration or reacceleration of MRSA spread, resulting in broad ineffectiveness of β-lactams as a main therapeutic application against staphylococcal infections.

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.

Comparative Secretome Analyses of Human and Zoonotic Staphylococcus aureus Isolates CC8, CC22, and CC398

The spread of methicillin-resistant Staphylococcus aureus (MRSA) in the community, hospitals and in livestock is mediated by highly diverse virulence factors that include secreted toxins, superantigens, enzymes and surface-associated adhesins allowing host adaptation and colonization. Here, we combined proteogenomics, secretome and phenotype analyses to compare the secreted virulence factors in selected S. aureus isolates of the dominant human- and livestock-associated genetic lineages CC8, CC22, and CC398. The proteogenomic comparison revealed 2181 core genes and 1306 accessory genes in 18 S. aureus isolates reflecting the high genome diversity. Using secretome analysis, we identified 869 secreted proteins with 538 commons in eight isolates of CC8, CC22, and CC398. These include 64 predicted extracellular and 37 cell surface proteins that account for 82.4% of total secretome abundance. Among the top 10 most abundantly secreted virulence factors are the major autolysins (Atl, IsaA, Sle1, SAUPAN006375000), lipases and lipoteichoic acid hydrolases (Lip, Geh, LtaS), cytolytic toxins (Hla, Hlb, PSMβ1) and proteases (SspB). The CC398 isolates showed lower secretion of cell wall proteins, but higher secretion of α- and β-hemolysins (Hla, Hlb) which correlated with an increased Agr activity and strong hemolysis. CC398 strains were further characterized by lower biofilm formation and staphyloxanthin levels because of decreased SigB activity. Overall, comparative secretome analyses revealed CC8- or CC22-specific enterotoxin and Spl protease secretion as well as Agr- and SigB-controlled differences in exotoxin and surface protein secretion between human-specific and zoonotic lineages of S. aureus.

High prevalence of spa type t571 among methicillin-susceptible Staphylococcus aureus from bacteremic patients in a French University Hospital

Staphylococcus aureus bacteremia is one of the most frequent severe bacterial infections worldwide, with an associated mortality of about 20–40% in developed countries. In 2013, we noted an increase in this infection in the teaching hospital in Grenoble, France, compared to 2012. The mean incidence of S. aureus bacteremia was 0.28 per 1,000 patient-days in 2012 and 0.35 per 1,000 patient-days in 2013. This trend was confirmed in 2014 (0.35 per 1,000 patient-days). In the present work we aimed to study the population of patients presenting with S. aureus bacteremia in 2013 and to genotype the corresponding S. aureus strains in order to identify a successful and/or virulent genotype to design a specific infection control program. One hundred ninety-one S. aureus isolates (including 9 methicillin-resistant) out of 199 corresponding cases of bacteremia were characterized with the spa typing method. Among 108 spa types, t571, t002, t008 and t084 were the most prevalent. Although not widely prevalent, t571 was the most frequently identified clone (8.4% of all isolates). Spa type t571 has been described in previous studies as belonging to the clonal complex CC398, which is consistent with the recent emergence of methicillin-susceptible S. aureus CC398 reported in blood cultures in Europe.

Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology

Staphylococcus aureus, a major human pathogen, has a collection of virulence factors and the ability to acquire resistance to most antibiotics. This ability is further augmented by constant emergence of new clones, making S. aureus a "superbug." Clinical use of methicillin has led to the appearance of methicillin-resistant S. aureus (MRSA). The past few decades have witnessed the existence of new MRSA clones. Unlike traditional MRSA residing in hospitals, the new clones can invade community settings and infect people without predisposing risk factors. This evolution continues with the buildup of the MRSA reservoir in companion and food animals. This review focuses on imparting a better understanding of MRSA evolution and its molecular characterization and epidemiology. We first describe the origin of MRSA, with emphasis on the diverse nature of staphylococcal cassette chromosome mec (SCCmec). mecA and its new homologues (mecB, mecC, and mecD), SCCmec types (13 SCCmec types have been discovered to date), and their classification criteria are discussed. The review then describes various typing methods applied to study the molecular epidemiology and evolutionary nature of MRSA. Starting with the historical methods and continuing to the advanced whole-genome approaches, typing of collections of MRSA has shed light on the origin, spread, and evolutionary pathways of MRSA clones.

'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.

Antimicrobial Resistance Distribution Differs Among Methicillin Resistant Staphylococcus aureus Sequence Type (ST) 5 Isolates From Health Care and Agricultural Sources

Antimicrobial resistance (AMR) is an expanding public health concern and methicillin resistant Staphylococcus aureus (MRSA) is a notable example. Since the discovery of livestock associated MRSA (LA-MRSA), public health concerns have arisen surrounding the potential of LA-MRSA isolates to serve as a reservoir for AMR determinants. In this study, we compare swine associated LA-MRSA ST5 and human clinical MRSA ST5 isolates for phenotypic antimicrobial susceptibilities determined via broth microdilution and genotypic determinants of AMR using whole genome sequencing and comparative genomic analysis to identify AMR elements. Swine associated LA-MRSA ST5 isolates exhibited phenotypic resistance to fewer antibiotics than clinical MRSA ST5 isolates from humans with no swine contact. Distinct genomic AMR elements were harbored by each subgroup, with little overlap in shared AMR genes between swine associated LA-MRSA ST5 and clinical MRSA ST5 isolates. Our results demonstrate that phenotypic antimicrobial susceptibilities and genotypic determinants of AMR among swine associated LA-MRSA ST5 and clinical MRSA ST5 isolates are separate and distinct.

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.

Bactericidal Activity and Synergy Studies of Peptide AP-CECT7121 Against Multi-resistant Bacteria Isolated from Human and Animal Soft Tissue Infections

AP-CECT7121 is an antimicrobial peptide, produced by Enterococcus faecalis CECT7121, with bactericidal activity against Gram-positive bacteria. The aim of this study was to evaluate the bactericidal activity of AP-CECT7121, alone and with gentamicin, against multi-resistant bacteria isolated from human and animals with soft tissue infections. During the period 2014-2015, bacterial strains producing human and animal soft tissue infections were studied. Samples from patients attended at a general hospital and cattle from four dairies in the Province of Buenos Aires (Argentina) were included. Twenty-two methicillin-resistant Staphylococcus aureus (11, human blood samples; 11, cow milk) and five vancomycin-resistant Ent. faecium strains isolated from four mastitic dairy cows were tested. AP-CECT7121 (12 mg/L) potency was assessed by time-kill curves alone or with sub-inhibitory concentrations of gentamicin. All staphylococcal strains were susceptible to gentamicin; enterococci did not show high-level gentamicin resistance. Colony counts were carried out at 0, 2, 4, 8, and 24 h of incubation. AP-CECT7121 showed bactericidal activity against all the enterococcal strains. In addition, AP-CECT7121 had a bactericidal effect on most staphylococci (16/22). Early AP-CECT7121/gentamicin synergy (4-8 h) for all staphylococci was detected. At 24 h, synergy (19/22) and indifference (3/22) were observed. Synergy with gentamicin was detected for staphylococci. AP-CECT7121 constitutes an attractive candidate for its use as a natural therapeutic tool for the treatment of infections produced by multi-resistant Staph. aureus and vancomycin-resistant Ent. faecium isolated from humans and animals.

Persistent and Transient Airborne MRSA Colonization of Piglets in a Newly Established Animal Model

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) was first found in 2005 and is up to date widespread in animal husbandry reservoir – focusing on pig farming. The regular detectability of MRSA in the air of pigsties as well as in exhaust air of pig farms (mean count: 10² cfu/m³) poses the question whether an airborne spread and, therefore, a MRSA colonization of animals via the airborne route exists. To answer this question, we exposed three groups of nine MRSA-negative tested piglets each to a defined airborne MRSA concentration (10², 10⁴, and 10⁶ cfu/m³) in our aerosol chamber for 24 h. In the following observation period of 21 days, the MRSA status of the piglets was monitored by taking different swab samples (nasal, pharyngeal, skin, conjunctival, and rectal swab). At the end of the experiment, we euthanized the piglets and investigated different tissues and organs for the spread of MRSA. The data of our study imply the presence of an airborne MRSA colonization route: the animals exposed to 10⁶ cfu/m³ MRSA in the air were persistent colonized. The piglets exposed to an airborne MRSA concentration of 10⁴ cfu/m³ were transient, and the piglets exposed to an airborne MRSA concentration of 10² cfu/m³ were not colonized. Consequently, a colonization via the airborne route was proven.

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.

Carbapenem-resistant Enterobacteriaceae in wildlife, food-producing, and companion animals: a systematic review

OBJECTIVES

The spread of carbapenem-resistant Enterobacteriaceae (CRE) in healthcare settings challenges clinicians worldwide. However, little is known about dissemination of CRE in livestock, food, and companion animals and potential transmission to humans.

METHODS

We performed a systematic review of all studies published in the PubMed database between 1980 and 2017 and included those reporting the occurrence of CRE in samples from food-producing and companion animals, wildlife, and exposed humans. The primary outcome was the occurrence of CRE in samples from these animals; secondary outcomes included the prevalence of CRE, carbapenemase types, CRE genotypes, and antimicrobial susceptibilities.

RESULTS

We identified 68 articles describing CRE among pigs, poultry, cattle, seafood, dogs, cats, horses, pet birds, swallows, wild boars, wild stork, gulls, and black kites in Africa, America, Asia, Australia, and Europe. The following carbapenemases have been detected (predominantly affecting the genera Escherichia and Klebsiella): VIM, KPC, NDM, OXA, and IMP. Two studies found that 33-67% of exposed humans on poultry farms carried carbapenemase-producing CRE closely related to isolates from the farm environment. Twenty-seven studies selectively screened samples for CRE and found a prevalence of <1% among livestock and companion animals in Europe, 2-26% in Africa, and 1-15% in Asia. Wildlife (gulls) in Australia and Europe carried CRE in 16-19%.

CONCLUSIONS

The occurrence of CRE in livestock, seafood, wildlife, pets, and directly exposed humans poses a risk for public health. Prospective prevalence studies using molecular and cultural microbiological methods are needed to better define the scope and transmission of CRE.

Variability of SCCmec elements in livestock-associated CC398 MRSA

The most common livestock-associated lineage of methicillin-resistant Staphylococcus aureus (MRSA) in Western Europe is currently clonal complex (CC) 398. CC398-MRSA spread extensively across livestock populations in several Western European countries, and livestock-derived CC398-MRSA strains can also be detected in humans. Based on their SCCmec elements, different CC398 strains can be distinguished. SCCmec elements of 100 veterinary and human CC398-MRSA isolates from Germany and Austria were examined using DNA microarray-based assays. In addition, 589 published SCC and/or genome sequences of CC398-MRSA (including both, fully finished and partially assembled sequences) were analysed by mapping them to the probe sequences of the microarrays. Several isolates and sequences showed an insertion of a large fragment of CC9 genomic DNA into the CC398 chromosome. Fifteen subtypes of SCCmec elements were detected among the 100 CC398 isolates and 41 subtypes could be discerned among the published CC398 sequences. Eleven of these were also experimentally detected within our strain collection, while four subtypes identified in the isolates where not found among the sequences. A high prevalence of heavy metal resistance genes, especially of czrC, was observed among CC398-MRSA. A possible co-selection of resistances to antibiotics and zinc/copper supplements in animal feed as well as a spill-over of SCCmec elements that have evolved in CC398-MRSA to other, possibly more virulent and/or medically relevant S. aureus lineages might pose public health problems in future.