Heavy metal and disinfectant resistance genes among livestock-associated methicillin-resistant Staphylococcus aureus isolates

Genomic Analyses of Methicillin-Resistant Staphylococcus pseudintermedius from Companion Animals Reveal Changing Clonal Populations, Multidrug Resistance, and Virulence

BACKGROUND/OBJECTIVES

Staphylococcus pseudintermedius is part of the normal microbiota in dogs. Since 2006, an increase in multidrug-resistant clones of methicillin-resistant S. pseudintermedius has been reported, as well as zoonotic transmission. Longitudinal investigations into clonal population structures, antibiotic resistance patterns, and the presence of resistance and virulence genes are important tools for gaining knowledge of the mechanisms behind the emergence of such clones.

METHODS

We investigated 87% of all non-repetitive MRSP isolates from dogs and cats in Sweden over a ten-year period (n = 356). All isolates were subjected to staphylococcal chromosomal cassette mec identification, whole-genome sequencing, multi-locus sequence typing, and analyses of genomic relatedness, as well as investigation of phenotypical resistance patterns and the presence of antibiotic resistance genes and virulence genes.

RESULTS

A considerable increase over time in the number of clonal lineages present was observed, indicating genomic diversification, and four clones became dominant: ST71, ST258, ST265, and ST551. In total, 96% of the isolates were multidrug-resistant. Statistically significant differences in resistance to several antibiotic classes between the four dominant clones were present. All isolates carried several virulence genes encoding factors associated with attachment, colonization, toxin synthesis, quorum sensing, antibiotic resistance, and immune evasion.

The genes mgtE and spoVG are involved in zinc tolerance of Staphylococcus aureus

Metals are essential for all living organisms, but the type of metal and its concentration determines its action. Even low concentrations of metals may have toxic effects on organisms and therefore exhibit antimicrobial activities. In this study, we investigate the evolutionary adaptation processes of Staphylococcus aureus to metals and common genes for metal tolerance. Laboratory and clinical isolates were treated with manganese, cobalt, zinc, or nickel metal salts to generate growth-adapted mutants. After growth in medium supplemented with zinc, whole-genome sequencing identified, among others, two genes, mgtE (SAUSA300_0910), a putative magnesium transporter and spoVG (SAUSA300_0475), a global transcriptional regulator, as hot spots for stress-induced single-nucleotide polymorphisms (SNPs). SNPs in mgtE were also detected in mutants treated with high levels of cobalt or nickel salts. To investigate the effect of these genes on metal tolerance, deletion mutants and complementation strains in an S. aureus USA300 LAC* laboratory strain were generated. Both, the mgtE and spoVG deletion strains were more tolerant to cobalt, manganese, and zinc. The mgtE mutant was also more tolerant to nickel exposure. Inductively coupled plasma mass spectrometry analysis demonstrated that the mgtE deletion mutant accumulated less intracellular zinc than the wild type, explaining increased tolerance. From these results, we conclude that mgtE gene inactivation increases zinc tolerance presumably due to reduced uptake of zinc. For the SpoVG mutant, no direct effect on the intracellular zinc concentration was detected, indicating toward different pathways to increase tolerance. Importantly, inactivation of these genes offers a growth advantage in environments containing certain metals, pointing toward a common tolerance mechanism.

IMPORTANCE

Staphylococcus aureus is an opportunistic pathogen causing tremendous public health burden and high mortality in invasive infections. Treatment is becoming increasingly difficult due to antimicrobial resistances. The use of metals in animal husbandry and aquaculture to reduce bacterial growth and subsequent acquisition of metal resistances has been shown to co-select for antimicrobial resistance. Therefore, understanding adaptive mechanisms that help S. aureus to survive metal exposure is essential. Using a screening approach, we were able to identify two genes encoding the transporter MgtE and the transcriptional regulator SpoVG, which conferred increased tolerance to specific metals such as zinc when inactivated. Further testing showed that the deletion of mgtE leads to reduced intracellular zinc levels, suggesting a role in zinc uptake. The accumulation of mutations in these genes when exposed to other metals suggests that inactivation of these genes could be a common mechanism for intrinsic tolerance to certain metals.

Decoupling livestock and poultry pollution emissions from industrial development: A step towards reducing environmental emissions

China has implemented policies like Leading areas for Agricultural Green Development (LAGD) to mitigate livestock and poultry farming pollution while promoting industry growth. However, it remains uncertain whether LAGDs have successfully balanced emission reduction with stable development. This study examines 165 LAGDs to analyze changes in emissions, assess the decoupling of emission reduction from output value, and identify influencing factors. Findings reveal that emissions from livestock and poultry in LAGDs initially increased and then decreased between 2010 and 2019. Cattle were responsible for over 40% of fecal emissions, and pigs for more than 20%. Additionally, pigs contributed to over 61% of urine emissions. From 2010 to 2014, increases in chemical oxygen demand were mainly due to pigs and cattle. Total nitrogen levels were significantly impacted by cattle, while pigs were affected by total phosphorus. From 2014 to 2019, reductions in emissions were largely attributed to a decrease in pig-related pollutants. The decoupling status shifted from strong to weak and then back to strong between 2014 and 2019. Production efficiency played a crucial role in reducing emissions, while changes in industrial structure moved from supporting to hindering this reduction. Economic development was a primary factor in driving these changes. Standard emissions in Chinese regions showed a rising and then declining trend from 2010 to 2019. The Northeast and Northwest regions of China demonstrated emission trends that were in sync with the growth in rural income. This study offers insights into the successes and challenges of LAGDs in achieving a balance between reduced emissions and development, using quantitative analysis. The findings are instrumental in informing policies for a sustainable livestock and poultry industry. Recommendations include evaluating coordinated approaches to pollution reduction and industrial growth, setting decoupling goals, designing policies based on influential factors, conducting regional assessments of livestock and poultry demand, and implementing region-specific strategies.

A Critical Review of AMR Risks Arising as a Consequence of Using Biocides and Certain Metals in Food Animal Production

The focus of this review was to assess what evidence exists on whether, and to what extent, the use of biocides (disinfectants and sanitizers) and certain metals (used in feed and other uses) in animal production (both land and aquatic) leads to the development and spread of AMR within the food chain. A comprehensive literature search identified 3434 publications, which after screening were reduced to 154 relevant publications from which some data were extracted to address the focus of the review. The review has shown that there is some evidence that biocides and metals used in food animal production may have an impact on the development of AMR. There is clear evidence that metals used in food animal production will persist, accumulate, and may impact on the development of AMR in primary animal and food production environments for many years. There is less evidence on the persistence and impact of biocides. There is also particularly little, if any, data on the impact of biocides/metal use in aquaculture on AMR. Although it is recognized that AMR from food animal production is a risk to human health there is not sufficient evidence to undertake an assessment of the impact of biocide or metal use on this risk and further focused in-field studies are needed provide the evidence required.

Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain

Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.

Antimicrobial resistance profiles and clonal diversity of Staphylococcus epidermidis isolates from pig farms, slaughterhouses, and retail pork

Livestock-associated coagulase-negative staphylococci (CoNS), such as Staphylococcus (S.) epidermidis, have emerged as a significant reservoir of antimicrobial resistance (AMR). In the current study, the AMR profiles and genetic diversity of S. epidermidis isolates obtained from pig farms, slaughterhouses, and retail pork were analyzed. A total of 89 S. epidermidis isolates, comprising 22 methicillin-resistant (MRSE) and 67 methicillin-susceptible S. epidermidis (MSSE) isolates, were assessed to determine (i) the clonal lineages of the isolates [multilocus sequence (MLST), agr, and staphylococcal cassette chromosome mec (SCCmec) types], (ii) the profiles of AMR phenotypes, and (iii) the carriage of genetic factors associated with major AMR phenotypes and zinc chloride resistance. Two dominant clonal lineages of S. epidermidis, ST100 and ST570, were observed on pig farms, especially in healthy pigs. In addition, potential transmission of pig-associated ST100 MRSE-SCCmec V and ST100 MSSE to farm workers was identified. The high prevalence of ST100 and ST570 isolates in pig farms was associated with high levels of AMR and zinc chloride resistance. In relation to resistance phenotypes, higher carriage rates of resistance genes, such as β-lactams (mecA), phenicols (fexA), and tetracyclines [tet(K), tet(L), tet(S), tet(M), and tet(O)], were identified in pig farm-associated isolates. Furthermore, cfr-mediated linezolid resistance was detected in 14 MSSE isolates from pig farms. This study is the first to provide important insights into the clonal structures and AMR profiles of S. epidermidis isolates collected from healthy pigs, carcass/pork samples, and human workers in Korea.

Biosecurity and Hygiene Procedures in Pig Farms: Effects of a Tailor-Made Approach as Monitored by Environmental Samples

In livestock, the importance of hygiene management is gaining importance within the context of biosecurity. The aim of this study was to monitor the implementation of biosecurity and hygiene procedures in 20 swine herds over a 12-month period, as driven by tailor-made plans, including training on-farm. The measure of adenosine triphosphate (ATP) environmental contents was used as an output biomarker. The presence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) and extended-spectrum β-lactamase producing Escherichia coli (ESBL-E. coli) was also investigated as sentinels of antibiotic resistance. A significant biosecurity improvement (p = 0.006) and a reduction in the ATP content in the sanitised environment (p = 0.039) were observed. A cluster including 6/20 farms greatly improved both biosecurity and ATP contents, while the remaining 14/20 farms ameliorated them only slightly. Even if the ESBL-E. coli prevalence (30.0%) after the hygiene procedures significantly decreased, the prevalence of LA-MRSA (22.5%) was unaffected. Despite the promising results supporting the adoption of tailor-made biosecurity plans and the measure of environmental ATP as an output biomarker, the high LA-MRSA prevalence still detected at the end of the study underlines the importance of improving even more biosecurity and farm hygiene in a one-health approach aimed to preserve also the pig workers health.

Genomic Islands Identified in Highly Resistant Serratia sp. HRI: A Pathway to Discover New Disinfectant Resistance Elements

Molecular insights into the mechanisms of resistance to disinfectants are severely limited, together with the roles of various mobile genetic elements. Genomic islands are a well-characterised molecular resistance element in antibiotic resistance, but it is unknown whether genomic islands play a role in disinfectant resistance. Through whole-genome sequencing and the bioinformatic analysis of Serratia sp. HRI, an isolate with high disinfectant resistance capabilities, nine resistance islands were predicted and annotated within the genome. Resistance genes active against several antimicrobials were annotated in these islands, most of which are multidrug efflux pumps belonging to the MFS, ABC and DMT efflux families. Antibiotic resistance islands containing genes encoding for multidrug resistance proteins ErmB (macrolide and erythromycin resistance) and biclomycin were also found. A metal fitness island harbouring 13 resistance and response genes to copper, silver, lead, cadmium, zinc, and mercury was identified. In the search for disinfectant resistance islands, two genomic islands were identified to harbour smr genes, notorious for conferring disinfectant resistance. This suggests that genomic islands are capable of conferring disinfectant resistance, a phenomenon that has not yet been observed in the study of biocide resistance and tolerance.

Farming Practice Influences Antimicrobial Resistance Burden of Non-Aureus Staphylococci in Pig Husbandries

Non-aureus staphylococci (NAS) are ubiquitous bacteria in livestock-associated environments where they may act as reservoirs of antimicrobial resistance (AMR) genes for pathogens such as Staphylococcus aureus. Here, we tested whether housing conditions in pig farms could influence the overall AMR-NAS burden. Two hundred and forty porcine commensal and environmental NAS isolates from three different farm types (conventional, alternative, and organic) were tested for phenotypic antimicrobial susceptibility and subjected to whole genome sequencing. Genomic data were analysed regarding species identity and AMR gene carriage. Seventeen different NAS species were identified across all farm types. In contrast to conventional farms, no AMR genes were detectable towards methicillin, aminoglycosides, and phenicols in organic farms. Additionally, AMR genes to macrolides and tetracycline were rare among NAS in organic farms, while such genes were common in conventional husbandries. No differences in AMR detection existed between farm types regarding fosfomycin, lincosamides, fusidic acid, and heavy metal resistance gene presence. The combined data show that husbandry conditions influence the occurrence of resistant and multidrug-resistant bacteria in livestock, suggesting that changing husbandry practices may be an appropriate means of limiting the spread of AMR bacteria on farms.

Copper Homeostatic Mechanisms and Their Role in the Virulence of Escherichia coli and Salmonella enterica

Copper is an essential micronutrient that also exerts toxic effects at high concentrations. This review summarizes the current state of knowledge on copper handling and homeostasis systems in Escherichia coli and Salmonella enterica. We describe the mechanisms by which transcriptional regulators, efflux pumps, detoxification enzymes, metallochaperones, and ancillary copper response systems orchestrate cellular response to copper stress. E. coli and S. enterica are important pathogens of humans and animals. We discuss the critical role of copper during killing of these pathogens by macrophages and in nutritional immunity at the bacterial-pathogen-host interface. In closing, we identify opportunities to advance our understanding of the biological roles of copper in these model enteric bacterial pathogens.

Heavy Metal Resistance in Salmonella Typhimurium and Its Association With Disinfectant and Antibiotic Resistance

Metals are widely used in animal feed for their growth-stimulating and antimicrobial effects, yet their use may potentially promote the proliferation of antibiotic resistance through co-selection. We studied the prevalence and associations of metal, antibiotic, and disinfectant resistances of 300 Salmonella Typhimurium isolates from pig meat, pig manure, chicken meat, poultry manure, and human stool from Sichuan, China. Seventy four percent of the 300 Salmonella Typhimurium isolates were considered resistant to Cu, almost 50% to Zn and Cr, over 25% to Mn and Cd, and almost 10% to Co. Most of the isolates carried at least one heavy metal resistance gene (HMRG). The Cr-Zn-Cd-resistance gene czcD was carried by 254 isolates and the Cu-resistance genes pcoR and pcoC by 196 and 179 isolates, respectively. Most of the isolates were resistant to at least one antibiotic and almost 80% were multidrug-resistant. The prevalence of resistance to six antibiotics was higher among the pig meat and manure isolates than among other isolates, and that of streptomycin and ampicillin were highest among the pig meat isolates and that of ciprofloxacin and ofloxacin among the pig manure isolates. From 55 to 79% of the isolates were considered resistant to disinfectants triclosan, trichloroisocyanuric acid, or benzalkonium chloride. The metal resistances and HMRGs were associated with resistance to antibiotics and disinfectants. Especially, Cu-resistance genes were associated with resistance to several antibiotics and disinfectants. The transfer of the Cr-Zn-Cd-resistance gene czcD, Cu-resistance gene pcoC, and Co-Ni-resistance gene cnrA into Escherichia coli and the increased Cu-resistance of the transconjugants implied that the resistance genes were located on conjugative plasmids. Thus, the excessive use of metals and disinfectants as feed additives and in animal care may have the potential to promote antibiotic resistance through co-selection and maintain and promote antibiotic resistance even in the absence of antibiotics.

MDR Salmonella enterica serovar Typhimurium ST34 carrying mcr-1 isolated from cases of bloodstream and intestinal infection in children in China

OBJECTIVES

Children are vulnerable to Salmonella infection due to their immature immune system. Cases of infection with mcr-1-harbouring Salmonella in child inpatients have not been reported in China before.

METHODS

Salmonella isolates from gastroenteritis and bacteraemia were screened using primers targeting mcr-1. Complete genome sequences of mcr-1-harbouring isolates were determined using the PacBio RS II platform. The transferability of mcr-1-harbouring plasmids was verified by conjugation.

RESULTS

We investigated two mcr-1-carrying polymyxin-resistant Salmonella enterica serovar Typhimurium ST34 isolates, S61394 and S44712, from bloodstream and intestinal Salmonella infection of two child inpatients, respectively. Both isolates were non-susceptible to commonly used antibiotics for children that compromised the success of clinical treatment and infection control. The mcr-1-harbouring plasmids pLS61394-MCR and pLS44712-MCR (from S61394 and S44712, respectively) were both conjugative pHNSHP45-2-like IncHI2-type epidemic plasmids carrying multiple resistance genes. Compared with pHNSHP45-2, a ∼33 kb insertion region encoding Tn7 transposition protein and heavy metal resistance proteins was identified in pLS61394-MCR, which might enhance adaptation of bacteria carrying this plasmid to various ecological niches. The phylogenetic tree of worldwide mcr-harbouring Salmonella indicated a host preference of mcr and a worldwide and cross-sectoral prevalence of the mcr-positive Salmonella ST34 clone.

CONCLUSIONS

To our knowledge, for the first time we report completed whole genomes of mcr-1-positive MDR Salmonella Typhimurium ST34 isolated from infected children in China, suggesting that improved surveillance is imperative for tackling the dissemination of mcr-harbouring MDR Salmonella Typhimurium ST34.

Profiles of coagulase-positive and -negative staphylococci in retail pork: prevalence, antimicrobial resistance, enterotoxigenicity, and virulence factors

Objective

The present study aimed to investigate the occurrence and species of coagulase-positive staphylococci (CoPS) and coagulase-negative staphylococci (CoNS) in retail pork meat samples collected during nationwide monitoring. The staphylococcal isolates were characterized for antimicrobial and zinc chloride resistance and enterotoxigenic potential.

Methods

A total of 260 pre-packaged pork meat samples were collected from 35 retail markets in 8 provinces in Korea for isolation of staphylococci. Antimicrobial and zinc chloride resistance phenotypes, and genes associated with the resistance phenotypes were determined on the isolates. Furthermore, the presence and distribution of 19 staphylococcal enterotoxin (SE) genes and enterotoxin-like genes among the pork-associated staphylococci were determined by multiplex polymerase chain reaction-based assays using the specific primer sets.

Results

A total of 29 staphylococcal strains (29/260, 11.1%) were isolated from samples of retail pork meat, 24 (83%) of which were CoNS. The four CoNS species identified were S. saprophyticus (n = 16, 55%), S. sciuri (n = 3, 10%), S. warneri (n = 3, 10%), and S. epidermidis (n = 2, 7%). Among the 29 isolates, four methicillin-resistant CoNS (MR-CoNS; three S. sciuri and one S. epidermidis) and one methicillin-resistant CoPS (MR-CoPS; one S. aureus) were identified. In addition, a relatively high level of tetracycline (TET) resistance (52%) was confirmed in CoNS, along with a predominant distribution of tet(K). The most prevalent SEs were sep (45%), and sen (28%), which were carried by 81% of S. saprophyticus.

Conclusion

These findings suggest that CoNS, especially S. saprophyticus strains, in raw pork meat could be a potential risk factor for staphylococcal food poisoning (SFP), and therefore, requires further investigation to elucidate the role of SEls in SFP and virulence of the pathogen. Our results also suggest that CoNS from raw pork meat may act as a source for transmission of antimicrobial resistance genes such as staphylococcal cassette chromosome mec and tet(K).

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 [...].

Dissemination and conservation of cadmium and arsenic resistance determinants in Listeria and other Gram-positive bacteria

Metal homeostasis in bacteria is a complex and delicate balance. While some metals such as iron and copper are essential for cellular functions, others such as cadmium and arsenic are inherently cytotoxic. While bacteria regularly encounter essential metals, exposure to high levels of toxic metals such as cadmium and arsenic is only experienced in a handful of special habitats. Nonetheless, Listeria and other Gram-positive bacteria have evolved an impressively diverse array of genetic tools for acquiring enhanced tolerance to such metals. Here, we summarize this fascinating collection of resistance determinants in Listeria, with special focus on resistance to cadmium and arsenic, as well as to biocides and antibiotics. We also provide a comparative description of such resistance determinants and adaptations in other Gram-positive bacteria. The complex coselection of heavy metal resistance and other types of resistance seems to be universal across the Gram-positive bacteria, while the type of coselected traits reflects the lifestyle of the specific microbe. The roles of heavy metal resistance genes in environmental adaptation and virulence appear to vary by genus, highlighting the need for further functional studies to explain the mystery behind the array of heavy metal resistance determinants dispersed and maintained among Gram-positive bacteria.

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.

Local and Transboundary Transmissions of Methicillin-Resistant Staphylococcus aureus Sequence Type 398 through Pig Trading

Livestock-associated methicillin-resistant Staphylococcus aureus sequence type (ST) 398 (LA-MRSA ST398) is a genetic lineage for which pigs are regarded as the main reservoir. An increasing prevalence of LA-MRSA ST398 has been reported in areas with high livestock density throughout Europe. In this study, we investigated the drivers contributing to the introduction and spread of LA-MRSA ST398 through the pig farming system in southern Italy. Whole-genome sequencing (WGS) of LA-MRSA ST398 isolates collected in 2018 from pigs (n = 53) and employees (n = 14) from 10 farms in the Calabria region of Italy were comparatively analyzed with previously published WGS data from Italian ST398 isolates (n = 45), an international ST398 reference collection (n = 89), and isolates from Danish pig farms (n = 283), which are the main suppliers of pigs imported to Italy. Single-nucleotide polymorphisms (SNP) were used to infer isolate relatedness, and these data were used together with data from animal trading to identify factors contributing to LA-MRSA ST398 dissemination. The analyses support the existence of two concurrent pathways for the spread of LA-MRSA ST398 in southern Italy: (i) multiple introductions of LA-MRSA ST398 through the import of colonized pigs from other European countries, including Denmark and France, and (ii) the spread of distinct clones dependent on local trading of pigs between farms. Phylogenetically related Italian and Danish LA-MRSA ST398 isolates shared extensive similarities, including carriage of antimicrobial resistance genes. Our findings highlight the potential risk of transboundary transmission of antimicrobial-resistant bacterial clones with a high zoonotic potential during import of pigs from countries with high LA-MRSA prevalence.IMPORTANCE Over the past decade, livestock-associated methicillin-resistant Staphylococcus aureus sequence type 398 (LA-MRSA ST398) has spread among pig holdings throughout Europe, in parallel with the increased incidence of infections among humans, especially in intensive pig farming regions. Despite the growing prevalence of LA-MRSA ST398 in Italian pig farms, the transmission dynamics of this clone in Italy remains unclear. This work provides genome-based evidence to suggest transboundary LA-MRSA ST398 transmission through trading of colonized pigs between European countries and Italy, as well as between farms in the same Italian region. Our findings show that both international trading and local trading of colonized pigs are important factors contributing to the global spread of LA-MRSA ST398 and underscore the need for control measures on and off the farm to reduce the dissemination of this zoonotic pathogen.

Escherichia coli strains of chicken and human origin: Characterization of antibiotic and heavy-metal resistance profiles, phylogenetic grouping, and presence of virulence genetic markers

Multiple antibiotic-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) strains represent a serious health care problem both for poultry and humans. Recently isolates with combined resistance to both antibiotics and heavy metals have been increased worldwide, with growing concern for possible co-selection of antimicrobial resistant genes. In the present study we characterized, at a phenotypic and genetic level, 80 E. coli isolates: forty independent isolates were collected from manure samples of healthy chickens and 40 from independent human extra-intestinal infections (ExPEC strains). The results obtained indicated that i) compared to chicken, human isolates presented a broader spectrum of antibiotic resistance and virulence potentials; ii) although at a lower extent, ExPEC-associated virulence genes were also present in chicken isolates, suggesting they may be potentially pathogens; iii) that arsenic (As) and zinc (Zn) tolerance genetic determinants were significantly more prevalent among chicken and human isolates respectively, while those responsible for tolerance to cadmium (Cd), silver (Ag) and copper (Cu) were equally distributed among the two groups of strains; iv) a very strong correlation was found between chicken gentamicin (GM) resistance and cadmium (Cd) tolerance. Elucidating the role of heavy metals in the selection and spread of highly pathogenic E. coli strains (co-selection) is of primary importance to lower the potential risk of infections in poultry and humans. The control of bacterial zoonotic agents, that commonly occur in livestock and that may be transmitted, directly or via the food chain, to human populations, could be of relevant interest.

Prevalence and characteristics of livestock-associated methicillin-susceptible Staphylococcus aureus in the pork production chain in Korea

The emergence and prevalence of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) in livestock animals have become a worldwide public health concern. While the prevalence and genetic profiles of MRSA strains in pigs and pork meat have been actively studied, livestock-associated MSSA strains have only been characterized in a few small-scale studies. In this investigation, we assessed the nationwide prevalence of MSSA in the Korean pig production chain, including pig farms, slaughterhouses, and retail markets. Among the 41 MSSA strains, the predominant clonal lineages were sequence type (ST) 398 (n = 15, 37%) and ST5 (n = 13, 32%). Although the overall prevalence of MSSA (2.58%) was low and mostly restricted to pig farms, ST398 MSSA strains showed higher level of multidrug resistance phenotype versus non-ST398 MSSA strains. In addition to the MDR phenotype, all of the ST398 MSSA strains exhibited resistance to tetracycline as they harbored the tet(K), tet(L), and/or tet(M) genes. However, ST398 MSSA strains did not exhibit increased resistance to zinc compared with the non-ST398 strains. This study is the first to provide evidence of ST398 MSSA emergence in livestock animals in Korea. Further studies are necessary to elucidate the potential of ST398 MSSA strains for human transmission. Our findings suggest that the MDR phenotype and high levels of tetracycline resistance may have played an important role in the emergence and prevalence of ST398 MSSA in pig farms in Korea.

Characterization of Antibiotic and Biocide Resistance Genes and Virulence Factors of Staphylococcus Species Associated with Bovine Mastitis in Rwanda

The present study was conducted from July to August 2018 on milk samples taken at dairy farms in the Northern Province and Kigali District of Rwanda in order to identify Staphylococcus spp. associated with bovine intramammary infection. A total of 161 staphylococcal isolates originating from quarter milk samples of 112 crossbred dairy cattle were included in the study. Antimicrobial susceptibility testing was performed and isolates were examined for the presence of various resistance genes. Staphylococcus aureus isolates were also analyzed for the presence of virulence factors, genotyped by spa typing and further phenotypically subtyped for capsule expression using Fourier Transform Infrared (FTIR) spectroscopy. Selected S. aureus were characterized using DNA microarray technology, multi-locus sequence typing (MLST) and whole-genome sequencing. All mecA-positive staphylococci were further genotyped using dru typing. In total, 14 different staphylococcal species were detected, with S. aureus being most prevalent (26.7%), followed by S. xylosus (22.4%) and S. haemolyticus (14.9%). A high number of isolates was resistant to penicillin and tetracycline. Various antimicrobial and biocide resistance genes were detected. Among S. aureus, the Panton-Valentine leukocidin (PVL) genes, as well as bovine leukocidin (LukM/LukF-P83) genes, were detected in two and three isolates, respectively, of which two also carried the toxic shock syndrome toxin gene tsst-1 bovine variant. t1236 was the predominant spa type. FTIR-based capsule serotyping revealed a high prevalence of non-encapsulated S. aureus isolates (89.5%). The majority of the selected S. aureus isolates belonged to clonal complex (CC) 97 which was determined using DNA microarray based assignment. Three new MLST sequence types were detected.

Selection and dissemination of antimicrobial resistance in Agri-food production

Public unrest about the use of antimicrobial agents in farming practice is the leading cause of increasing and the emergences of Multi-drug Resistant Bacteria that have placed pressure on the agri-food industry to act. The usage of antimicrobials in food and agriculture have direct or indirect effects on the development of Antimicrobial resistance (AMR) by bacteria associated with animals and plants which may enter the food chain through consumption of meat, fish, vegetables or some other food sources. In addition to antimicrobials, recent reports have shown that AMR is associated with tolerance to heavy metals existing naturally or used in agri-food production. Besides, biocides including disinfectants, antiseptics and preservatives which are widely used in farms and slaughter houses may also contribute in the development of AMR. Though the direct transmission of AMR from food-animals and related environment to human is still vague and debatable, the risk should not be neglected. Therefore, combined global efforts are necessary for the proper use of antimicrobials, heavy metals and biocides in agri-food production to control the development of AMR. These collective measures will preserve the effectiveness of existing antimicrobials for future generations.

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

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

Bioaerosols Play a Major Role in the Nasopharyngeal Microbiota Content in Agricultural Environment

Background: Bioaerosols are a major concern for public health and sampling for exposure assessment purposes is challenging. The nasopharyngeal region could be a potent carrier of long-term bioaerosol exposure agents. This study aimed to evaluate the correlation between nasopharyngeal bacterial flora of swine workers and the swine barns bioaerosol biodiversity. Methods: Air samples from eight swine barns as well as nasopharyngeal swabs from pig workers (n = 25) and from a non-exposed control group (n = 29) were sequenced using 16S rRNA gene high-throughput sequencing. Wastewater treatment plants were used as the industrial, low-dust, non-agricultural environment control to validate the microbial link between the bioaerosol content (air) and the nasopharynxes of workers. Results: A multivariate analysis showed air samples and nasopharyngeal flora of pig workers cluster together, compared to the non-exposed control group. The significance was confirmed with the PERMANOVA statistical test (p-value of 0.0001). Unlike the farm environment, nasopharynx samples from wastewater workers did not cluster with air samples from wastewater treatment plants. The difference in the microbial community of nasopharynx of swine workers and a control group suggest that swine workers are carriers of germs found in bioaerosols. Conclusion: Nasopharynx sampling and microbiota could be used as a proxy of air sampling for exposure assessment studies or for the determination of exposure markers in highly contaminated agricultural environments.

Zinc phosphate-based nanoparticles as a novel antibacterial agent: in vivo study on rats after dietary exposure

Background

Development of new nanomaterials that inhibit or kill bacteria is an important and timely research topic. For example, financial losses due to infectious diseases, such as diarrhea, are a major concern in livestock productions around the world. Antimicrobial nanoparticles (NPs) represent a promising alternative to antibiotics and may lower antibiotic use and consequently spread of antibiotic resistance traits among bacteria, including pathogens.

Results

Four formulations of zinc nanoparticles (ZnA, ZnB, ZnC, and ZnD) based on phosphates with spherical (ZnA, ZnB) or irregular (ZnC, ZnD) morphology were prepared. The highest in vitro inhibitory effect of our NPs was observed against Staphylococcus aureus (inhibitory concentration values, IC₅₀, ranged from 0.5 to 1.6 mmol/L), followed by Escherichia coli (IC₅₀ 0.8-1.5 mmol/L). In contrast, methicillin resistant S. aureus (IC₅₀ 1.2-4.7 mmol/L) was least affected and this was similar to inhibitory patterns of commercial ZnO-based NPs and ZnO. After the successful in vitro testing, the in vivo study with rats based on dietary supplementation with zinc NPs was conducted. Four groups of rats were treated by 2,000 mg Zn/kg diet of ZnA, ZnB, ZnC, and ZnD, for comparison two groups were supplemented by 2,000 mg Zn/kg diet of ZnO-N and ZnO, and one group (control) was fed only by basal diet. The significantly higher (P < 0.05) Zn level in liver and kidney of all treated groups was found, nevertheless Zn NPs did not greatly influence antioxidant status of rats. However, the total aerobic and coliform bacterial population in rat feces significantly decreased (P < 0.05) in all zinc groups after 30 d of the treatment. Furthermore, when compared to the ZnO group, ZnA and ZnC nanoparticles reduced coliforms significantly more (P < 0.05).

Conclusions

Our results demonstrate that phosphate-based zinc nanoparticles have the potential to act as antibiotic agents.

The β-Lactamase Gene Profile and a Plasmid-Carrying Multiple Heavy Metal Resistance Genes of Enterobacter cloacae

In this work, by high-throughput sequencing, antibiotic resistance genes, including class A (bla_CTX-M, bla_Z, bla_TEM, bla_VEB, bla_KLUC, and bla_SFO), class C (bla_SHV, bla_DHA, bla_MIR, bla_AZECL-29, and bla_ACT), and class D (bla_OXA) β-lactamase genes, were identified among the pooled genomic DNA from 212 clinical Enterobacter cloacae isolates. Six bla_MIR-positive E. cloacae strains were identified, and pulsed-field gel electrophoresis (PFGE) showed that these strains were not clonally related. The complete genome of the bla_MIR-positive strain (Y546) consisted of both a chromosome (4.78 Mb) and a large plasmid pY546 (208.74 kb). The extended-spectrum β-lactamases (ESBLs) (bla_SHV-12 and bla_CTX-M-9a) and AmpC (bla_MIR) were encoded on the chromosome, and the pY546 plasmid contained several clusters of genes conferring resistance to metals, such as copper (pco), arsenic (ars), tellurite (ter), and tetrathionate (ttr), and genes encoding many divalent cation transporter proteins. The comparative genomic analyses of the whole plasmid sequence and of the heavy metal resistance gene-encoding regions revealed that the plasmid sequences of Klebsiella pneumoniae (such as pKPN-332, pKPN-3967, and pKPN-262) shared the highest similarity with those of pY546. It may be concluded that a variety of β-lactamase genes present in E. cloacae which confer resistance to β-lactam antibiotics and the emergence of plasmids carrying heavy metal resistance genes in clinical isolates are alarming and need further surveillance.

Resistance to Metals Used in Agricultural Production

Metals and metalloids have been used alongside antibiotics in livestock production for a long time. The potential and acute negative impact on the environment and human health of these livestock feed supplements has prompted lawmakers to ban or discourage the use of some or all of these supplements. This article provides an overview of current use in the European Union and the United States, detected metal resistance determinants, and the proteins and mechanisms responsible for conferring copper and zinc resistance in bacteria. A detailed description of the most common copper and zinc metal resistance determinants is given to illustrate not only the potential danger of coselecting antibiotic resistance genes but also the potential to generate bacterial strains with an increased potential to be pathogenic to humans. For example, the presence of a 20-gene copper pathogenicity island is highlighted since bacteria containing this gene cluster could be readily isolated from copper-fed pigs, and many pathogenic strains, including Escherichia coli O104:H4, contain this potential virulence factor, suggesting a potential link between copper supplements in livestock and the evolution of pathogens.

Evaluating biological plausibility in supporting evidence for action through systematic reviews in public health

OBJECTIVES

The objective of this research was to develop and test methods for accessing and evaluating information on the biological plausibility of observed associations between exposures or interventions and outcomes to generate scientific evidence for action consistent with practice in systematic reviews.

STUDY DESIGN

To undertake this research, we used the example of the observed associations between antimicrobial use in food animals and increased risks of human exposures to antimicrobial-resistant pathogens of zoonotic origin.

METHODS

We conducted a scoping search using terms related to biological plausibility or mechanism to identify key references. As recommended by these references, we also used expert consultation with researchers and a public health informationist. We used their recommendations, which included expert consultation, to identify mechanisms relevant to biological plausibility of the association we selected to test. We used the reviews conducted by the World Health Organization (WHO) Guidelines Development Group in support of reducing antimicrobial use in food animal production to populate our model for assessing biological plausibility.

RESULTS

We were able to develop a transparent model for biological plausibility based on the adverse outcome pathway used in toxicology and ecology. We were also able to populate this model using the WHO reviews.

CONCLUSIONS

This analysis of biological plausibility used transparent and validated methods to assess the evidence used in systematic reviews based on the observational studies accessed through searches of the scientific literature. Given the importance of this topic in systematic reviews and evidence-based decision-making, further research is needed to define and test the methodological approaches to access and properly evaluate information from the scientific literature.

Methicillin-resistant Staphylococcus aureus: livestock-associated, antimicrobial, and heavy metal resistance

Staphylococcus aureus is an opportunistic pathogen of human and other mammals that is of increasing clinical and veterinary importance due to its ability to rapidly develop antimicrobial resistance. The injudicious use of antibiotics has given rise to the emergence of antibiotic resistant S. aureus strains, most importantly methicillin-resistant Staphylococcus aureus (MRSA). The emergence of livestock-associated MRSA (LA-MRSA) has highlighted the importance of directed research toward its prevention, as well as the need for the discovery and development of more efficient treatment than is currently available. Furthermore, the treatment of MRSA is complicated by the co-selection of heavy metal and antibiotic resistance genes by microorganisms. Livestock and livestock production systems are large reservoirs of heavy metals due to their use in feed as well as environmental contaminant, which has allowed for the selection of LA-MRSA isolates with heavy metal resistance. The World Health Organization reported that Africa has the largest gaps in data on the prevalence of antimicrobial resistance, with no reports on rates for LA-MRSA harboring heavy metal resistance in South Africa. This review aimed to report the emergence of LA-MRSA in South Africa, specifically the most frequent sequence type ST398, globally. Furthermore, we aimed to highlight the importance of LA-MRSA in clinical and food security, as well as this research gap in South Africa. This review sheds light on the prevalence of heavy metals in livestock farms and abattoirs, and focuses on the phenomenon of the co-selection of heavy metal and antibiotic resistance genes in MRSA, emphasizing the importance of a focused direction for research in humans, animals as well as environment using one-health approach.

Heavy metal resistance in bacteria from animals

Resistance to metals and antimicrobials is a natural phenomenon that existed long before humans started to use these products for veterinary and human medicine. Bacteria carry diverse metal resistance genes, often harboured alongside antimicrobial resistance genes on plasmids or other mobile genetic elements. In this review we summarize the current knowledge about metal resistance genes in bacteria and we discuss their current use in the animal husbandry.

Augmented antibiotic resistance associated with cadmium induced alterations in Salmonella enterica serovar Typhi

In view of the reports on co-selection of metal and antibiotic resistance, recently we have reported that increased cadmium accumulation in Salmonella Typhi Ty2 leads to increased antibiotic resistance. In continuation, the present study was carried to substantiate this association in clinical isolates. Interestingly, the levels of cadmium were found to be more in the clinical isolates which co-related with their antibiotic sensitivity/resistance pattern. On cadmium accumulation, antibiotic(s) sensitive isolates were rendered resistant and the resistant isolates were rendered more resistant as per their minimum inhibitory concentration(s). Further, after subjecting the pathogen to cadmium accumulation, alterations occurring in the cells were assessed. Transgenerational cadmium exposure led to changes in growth response, morphology, proteome, elevated antioxidants other than SOD, increased biofilm formation, decreased intracellular macrophage killing coupled with upregulation of genes encoding metallothionein and metal transporters. Thus, these results indicate that cadmium, if acquired from the environment, being non-degradable can exert a long-lasting selective pressure on Salmonella in the host which may display antibiotic resistance later on, as a result of co-selection. Therefore, appropriate strategies need to be developed to inhibit such an enduring pressure of heavy metals, as these represent one of the factors for the emerging antibiotic resistance in pathogens.

Antimicrobial Resistance among Staphylococci of Animal Origin

Antimicrobial resistance among staphylococci of animal origin is based on a wide variety of resistance genes. These genes mediate resistance to many classes of antimicrobial agents approved for use in animals, such as penicillins, cephalosporins, tetracyclines, macrolides, lincosamides, phenicols, aminoglycosides, aminocyclitols, pleuromutilins, and diaminopyrimidines. In addition, numerous mutations have been identified that confer resistance to specific antimicrobial agents, such as ansamycins and fluoroquinolones. The gene products of some of these resistance genes confer resistance to only specific members of a class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents, including agents approved solely for human use. The resistance genes code for all three major resistance mechanisms: enzymatic inactivation, active efflux, and protection/modification/replacement of the cellular target sites of the antimicrobial agents. Mobile genetic elements, in particular plasmids and transposons, play a major role as carriers of antimicrobial resistance genes in animal staphylococci. They facilitate not only the exchange of resistance genes among members of the same and/or different staphylococcal species, but also between staphylococci and other Gram-positive bacteria. The observation that plasmids of staphylococci often harbor more than one resistance gene points toward coselection and persistence of resistance genes even without direct selective pressure by a specific antimicrobial agent. This chapter provides an overview of the resistance genes and resistance-mediating mutations known to occur in staphylococci of animal origin.

Complete Genomic Analysis of a Salmonella enterica Serovar Typhimurium Isolate Cultured From Ready-to-Eat Pork in China Carrying One Large Plasmid Containing mcr-1

One mcr-1-carrying ST34-type Salmonella Typhimurium WW012 was cultured from 3,200 ready-to-eat (RTE) pork samples in 2014 in China. Broth dilution method was applied to obtain the antimicrobial susceptibility of Salmonella Typhimurium WW012. Broth matting assays were carried out to detect transferability of this phenotype and whole-genome sequencing was performed to analyze its genomic characteristic. Thirty out of 3,200 RTE samples were positive for Salmonella and the three most frequent serotypes were identified as S. Derby (n = 8), S. Typhimurium (n = 6), and S. Enteritidis (n = 6). One S. Typhimurium isolate (S. Typhimurium WW012) cultured from RTE prepared pork was found to contain the mcr-1 gene. S. Typhimurium WW012 expressed a level of high resistance to seven different antimicrobial compounds in addition to colistin (MIC = 8 mg/L). A single plasmid, pWW012 (151,609-bp) was identified and found to be of an IncHI2/HI2A type that encoded a mcr-1 gene along with six additional antimicrobial resistance genes. Plasmid pWW012 contained an IS30-mcr-1-orf-orf-IS30 composite transposon that can be successfully transferred to Escherichia coli J53. When assessed further, the latter demonstrated considerable similarity to three plasmids pHYEC7-mcr-1, pSCC4, and pHNSHP45-2, respectively. Furthermore, plasmid pWW012 also contained a multidrug resistance (MDR) genetic structure IS26-aadA2-cmlA2-aadA1-IS406-sul3-IS26-dfrA12-aadA2-IS26, which showed high similarity to two plasmids, pHNLDF400 and pHNSHP45-2, respectively. Moreover, genes mapping to the chromosome (4,991,167-bp) were found to carry 28 mutations, related to two component regulatory systems (pmrAB, phoPQ) leading to modifications of lipid A component of the lipopolysaccharide structure. Additionally, one mutation (D87N) in the quinolone resistance determining region (QRDR) gene of gyrA was identified in this mcr-1 harboring S. Typhimurium. In addition, various virulence factors and heavy metal resistance-encoding genes were also identified on the genome of S. Typhimurium WW012. This is the first report of the complete nucleotide sequence of mcr-1-carrying MDR S. Typhimurium strain from RTE pork in China.

Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain

Antimicrobial resistance is a major health care problem, with the intensive use of heavy metals and biocides recently identified as a potential factor contributing to the aggravation of this situation. The present study investigated heavy metal susceptibility and genetic resistance determinants in Escherichia coli isolated from clinical urine samples from Sweden, Germany, and Spain. A total of 186 isolates were tested for their sodium arsenite, silver nitrate, and copper(II) sulfate MICs. In addition, 88 of these isolates were subjected to whole-genome sequencing for characterization of their genetic resistance determinants and epidemiology. For sodium arsenite, the isolates could be categorized into a resistant and a nonresistant group based on MIC values. Isolates of the resistant group exhibited the chromosomal ars operon and belonged to non-B2 phylogenetic groups; in contrast, within the B2 phylogroup, no ars operon was found, and the isolates were susceptible to sodium arsenite. Two isolates also harbored the silver/copper resistance determinant pco/sil, and they belonged to sequence types ST10 (phylogroup A) and ST295 (phylogroup C). The ST295 isolate had a silver nitrate MIC of ≥512 mg/liter and additionally produced extended-spectrum beta-lactamases. To our knowledge, this is the first study to describe the distribution of the arsenic resistance ars operon within phylogroups of E. coli strains isolated from patients with urinary tract infections. The arsenic resistance ars operon was present only in all non-B2 clades, which have previously been associated with the environment and commensalism in both humans and animals, while B2 clades lacked the ars operon.

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.

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.

Clonal diversity and geographic distribution of methicillin-resistant Staphylococcus pseudintermedius from Australian animals: Discovery of novel sequence types

Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an increasingly prevalent pathogen in veterinary medicine. This study examined the molecular epidemiology of clinical MRSP isolated from Australian animals. Clinical staphylococci submitted to all Australian veterinary diagnostic laboratories were collected during 2013 and identified using traditional phenotypic tests and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Phenotypic antimicrobial resistance was determined using broth microdilution and disk diffusion. MRSP isolates were characterized by whole genome sequencing which included identification of the mecA gene. Phylogenetic relationships were inferred by comparison of single nucleotide polymorphisms. Of the 669 S. pseudintermedius isolates collected from dogs, cats and cattle, 77 (11.5%) were MRSP. Nineteen multilocus sequence types (STs) were identified, with most isolates belonging to one of five STs (ST71, ST497, ST316, ST496 and ST45). Phylogenetic analysis revealed that Australian ST71 appears closely related to ST71 from overseas. ST497 and ST496 represented novel sequence types, not previously reported outside Australia. Most other STs were novel and only distantly related to each other. Geographical clustering of STs was observed. All isolates belonging to the five main STs were multi- to extensively- drug resistant while isolates from singleton STs generally had lower levels of antimicrobial resistance. The frequency of ciprofloxacin, trimethoprim-sulfamethoxazole, gentamicin, chloramphenicol and tetracycline resistance varied significantly between STs (p<0.01). Australian MRSP isolates are phylogenetically diverse, with a mix of previously unreported and well known international MRSP clones that demonstrate geographic clustering and exhibit both multidrug-resistant and extensively drug-resistant phenotypes.

Anti-microbial coating innovations to prevent infectious diseases (AMiCI): Cost action ca15114

Worldwide, millions of patients are affected annually by healthcare-associated infection (HCAI), impacting up to 80,000 patients in European Hospitals on any given day. This represents not only public health risk, but also an economic burden. Complementing routine hand hygiene practices, cleaning and disinfection, antimicrobial coatings hold promise based, in essence, on the application of materials and chemicals with persistent bactericidal or -static properties onto surfaces or in textiles used in healthcare environments. The focus of considerable commercial investment and academic research energies, such antimicrobial coating-based approaches are widely believed to have potential in reduction of microbial numbers on surfaces in clinical settings. This belief exists despite definitive evidence as to their efficacy and is based somewhat on positive studies involving, for example, copper, silver or gold ions, titanium or organosilane, albeit under laboratory conditions. The literature describes successful delay and/or prevention of recontamination following conventional cleaning and disinfection by problematic microbes such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant enterococci (VRE), among others. However, there is a scarcity of studies assessing antimicrobial surfaces other than copper in the clinical environment, and a complete lack of published data regarding the successful implementation of these materials on clinically significant outcomes (including HCAI). Through its Cooperation in Science and Technology program (COST), the European Commission has funded a 4-year initiative to establish a network of stakeholders involved in development, regulation and use of novel anti-microbial coatings for prevention of HCAI. The network (AMiCI) comprises participants of more than 60 universities, research institutes and companies across 29 European countries and, to-date, represents the most comprehensive consortium targeting use of these emergent technologies in healthcare settings. More specifically, the network will prioritise coordinated research on the effects (both positive and negative) of antimicrobial coatings in healthcare sectors; know-how regarding availability and mechanisms of action of (nano)-coatings; possible adverse effects of such materials (e.g., potential emergence of microbial resistance or emission of toxic agents into the environment); standardised performance assessments for antimicrobial coatings; identification and dissemination of best practices by hospitals, other clinical facilities, regulators and manufacturers.

The Arsenic Resistance-Associated Listeria Genomic Island LGI2 Exhibits Sequence and Integration Site Diversity and a Propensity for Three Listeria monocytogenes Clones with Enhanced Virulence

In the foodborne pathogen Listeria monocytogenes, arsenic resistance is encountered primarily in serotype 4b clones considered to have enhanced virulence and is associated with an arsenic resistance gene cluster within a 35-kb chromosomal region, Listeria genomic island 2 (LGI2). LGI2 was first identified in strain Scott A and includes genes putatively involved in arsenic and cadmium resistance, DNA integration, conjugation, and pathogenicity. However, the genomic localization and sequence content of LGI2 remain poorly characterized. Here we investigated 85 arsenic-resistant L. monocytogenes strains, mostly of serotype 4b. All but one of the 70 serotype 4b strains belonged to clonal complex 1 (CC1), CC2, and CC4, three major clones associated with enhanced virulence. PCR analysis suggested that 53 strains (62.4%) harbored an island highly similar to LGI2 of Scott A, frequently (42/53) in the same location as Scott A (LMOf2365_2257 homolog). Random-primed PCR and whole-genome sequencing revealed seven novel insertion sites, mostly internal to chromosomal coding sequences, among strains harboring LGI2 outside the LMOf2365_2257 homolog. Interestingly, many CC1 strains harbored a noticeably diversified LGI2 (LGI2-1) in a unique location (LMOf2365_0902 homolog) and with a novel additional gene. With few exceptions, the tested LGI2 genes were not detected in arsenic-resistant strains of serogroup 1/2, which instead often harbored a Tn554-associated arsenic resistance determinant not encountered in serotype 4b. These findings indicate that in L. monocytogenes, LGI2 has a propensity for certain serotype 4b clones, exhibits content diversity, and is highly promiscuous, suggesting an ability to mobilize various accessory genes into diverse chromosomal loci.IMPORTANCEListeria monocytogenes is widely distributed in the environment and causes listeriosis, a foodborne disease with high mortality and morbidity. Arsenic and other heavy metals can powerfully shape the populations of human pathogens with pronounced environmental lifestyles such as L. monocytogenes Arsenic resistance is encountered primarily in certain serotype 4b clones considered to have enhanced virulence and is associated with a large chromosomal island, Listeria genomic island 2 (LGI2). LGI2 also harbors a cadmium resistance cassette and genes putatively involved in DNA integration, conjugation, and pathogenicity. Our findings indicate that LGI2 exhibits pronounced content plasticity and is capable of transferring various accessory genes into diverse chromosomal locations. LGI2 may serve as a paradigm on how exposure to a potent environmental toxicant such as arsenic may have dynamically selected for arsenic-resistant subpopulations in certain clones of L. monocytogenes which also contribute significantly to disease.

Antibiotic Resistance in Salmonella from Retail Foods of Animal Origin and Its Association with Disinfectant and Heavy Metal Resistance

This study aims to demonstrate the antibiotic resistance and its association with disinfectant and heavy metal resistance in 152 Salmonella isolates recovered from retail foods of animal origins. Susceptibility testing demonstrated that 92.8% isolates were resistant to at least one antibiotic, and the resistance was highest to oxytetracycline (80.9%), followed by trimethoprim (64.5%), amoxicillin (28.9%), ampicillin (28.3%), levofloxacin (21.7%), ciprofloxacin (16.4%), and gentamicin (10.5%), respectively. The bla_TEM and tetA genes (44.7%) were commonly present. The qacF and qacEΔ1 genes were detected in 18.4% and 8.6% of all isolates. The Cu-resistance genes pcoR, pcoC, and pcoA were the most prevalent (20.4-40.8%), followed by Hg-resistance gene merA (17.8%) and As-resistance genes arsB (6.6%). The antibiotic resistance was highly associated with disinfectant or certain heavy metal resistance genes. Most notably, the association among Cu-resistance genes (pcoC, pcoR), disinfectant resistance genes (qacF, qacEΔ1), and tetracycline and sulfonamide resistance genes (tet, sul) was significant (p < 0.05). Pulsed-field gel electrophoresis revealed that Salmonella isolates was associated with supermarkets indicating the possibility of crosscontamination in farms or processing environment. This study indicated that retail meats may be a reservoir for the dissemination of antibiotic-resistant Salmonella and using disinfectants for decontamination or metals in livestock may provide a pressure for coselecting strains with acquired resistance to other antimicrobials.

Bacteria from Animals as a Pool of Antimicrobial Resistance Genes

Antimicrobial agents are used in both veterinary and human medicine. The intensive use of antimicrobials in animals may promote the fixation of antimicrobial resistance genes in bacteria, which may be zoonotic or capable to transfer these genes to human-adapted pathogens or to human gut microbiota via direct contact, food or the environment. This review summarizes the current knowledge of the use of antimicrobial agents in animal health and explores the role of bacteria from animals as a pool of antimicrobial resistance genes for human bacteria. This review focused in relevant examples within the ESC(K)APE (Enterococcus faecium, Staphylococcus aureus, Clostridium difficile (Klebsiella pneumoniae), Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae) group of bacterial pathogens that are the leading cause of nosocomial infections throughout the world.

At the Nexus of Antibiotics and Metals: The Impact of Cu and Zn on Antibiotic Activity and Resistance

Environmental influences on antibiotic activity and resistance can wreak havoc with in vivo antibiotic efficacy and, ultimately, antimicrobial chemotherapy. In nature, bacteria encounter a variety of metal ions, particularly copper (Cu) and zinc (Zn), as contaminants in soil and water, as feed additives in agriculture, as clinically-used antimicrobials, and as components of human antibacterial responses. Importantly, there is a growing body of evidence for Cu/Zn driving antibiotic resistance development in metal-exposed bacteria, owing to metal selection of genetic elements harbouring both metal and antibiotic resistance genes, and metal recruitment of antibiotic resistance mechanisms. Many classes of antibiotics also form complexes with metal cations, including Cu and Zn, and this can hinder (or enhance) antibiotic activity. This review highlights the ways in which Cu/Zn influence antibiotic resistance development and antibiotic activity, and in so doing impact in vivo antibiotic efficacy.

Proactive Approach for Safe Use of Antimicrobial Coatings in Healthcare Settings: Opinion of the COST Action Network AMiCI

Infections and infectious diseases are considered a major challenge to human health in healthcare units worldwide. This opinion paper was initiated by EU COST Action network AMiCI (AntiMicrobial Coating Innovations) and focuses on scientific information essential for weighing the risks and benefits of antimicrobial surfaces in healthcare settings. Particular attention is drawn on nanomaterial-based antimicrobial surfaces in frequently-touched areas in healthcare settings and the potential of these nano-enabled coatings to induce (eco)toxicological hazard and antimicrobial resistance. Possibilities to minimize those risks e.g., at the level of safe-by-design are demonstrated.