High diversity of coagulase negative staphylococci species in wild boars, with low antimicrobial resistance rates but detection of relevant resistance genes

Staphylococcus haemolyticus: An updated review on nosocomial infections, antimicrobial resistance, virulence, genetic traits, and strategies for combating this emerging opportunistic pathogen

Staphylococcus haemolyticus, a key species of the Staphylococcus genus, holds significant importance in healthcare-associated infections, due to its notable resistance to antimicrobials, like methicillin, and proficient biofilms-forming capabilities. This coagulase-negative bacterium poses a substantial challenge in the battle against nosocomial infections. Recent research has shed light on Staph. haemolyticus genomic plasticity, unveiling genetic elements responsible for antibiotic resistance and their widespread dissemination within the genus. This review presents an updated and comprehensive overview of the clinical significance and prevalence of Staph. haemolyticus, underscores its zoonotic potential and relevance in the one health framework, explores crucial virulence factors, and examines genetics features contributing to its success in causing emergent and challenging infections. Additionally, we scrutinize ongoing studies aimed at controlling spread and alternative approaches for combating it.

Staphylococcus aureus Carriage in the Nasotracheal Cavities of White Stork Nestlings (Ciconia ciconia) in Spain: Genetic Diversity, Resistomes and Virulence Factors

The molecular ecology of Staphylococcus aureus in migratory birds (such as white storks) is necessary to understand their relevance in the "One Health" ecosystems. This study determined the nasotracheal carriage rates of S. aureus from white storks in Southern Spain and genetically characterized the within-host diversity. A collection of 67 S. aureus strains, previously obtained from 87 white stork nestlings (52 nasal and 85 tracheal samples) fed by their parents with food foraged in natural and landfill habitats, were tested for their antimicrobial resistance (AMR) phenotypes. Moreover, the AMR genotypes, immune evasion cluster (IEC), virulence genes and the detection of CC398 lineage were studied by PCR. The spa types and multilocus-sequencing-typing (MLST) were also determined by PCR and sequencing. Staphylococcus aureus carriage was found in 31% of storks (36.5%/11.9% in nasal/tracheal samples). All isolates were methicillin-susceptible (MSSA) and 8.8% of them were also susceptible to all tested antibiotics. The AMR phenotype/percentage/genes detected were as follows: penicillin/79.1%/blaZ; erythromycin-clindamycin-inducible/19.1%/ermA, ermT; tetracycline/11.9%/tetK; clindamycin/4.5%/lnuA and ciprofloxacin/4.5%. Twenty-one different spa types, including 2 new ones (t7778-ST15-CC15 and t18009-ST26-CC25), were detected and ascribed to 11 clonal complexes (CCs). MSSA-CC398 (8.2%), MSSA-CC15 (7.1%) and MSSA-ST291 (5.9%) were the most prevalent lineages in storks. Moreover, tst-positive (MSSA-CC22-t223 and MSSA-CC30-t1654), eta-positive (MSSA-CC9-t209) and etb-positive strains (MSSA-CC45-t015) were detected in four storks. The 18.5% of storks harboured distinct MSSA strains (with different lineages and/or AMR genes). Nestlings of storks foraging in landfills (10 CCs) had more diverse S. aureus strains than those of parents foraging in natural habitats (3 CCs). Low level of AMR was demonstrated among S. aureus strains. The predominance of MSSA-CC398 (an emergent clade) and toxigenic MSSA strains in stork nestlings highlight the need for continuous surveillance of S. aureus in wild birds.

DISTRIBUTION AND ANTIMICROBIAL RESISTANCE OF STAPHYLOCOCCI ISOLATED FROM FREE-LIVING SOUTH AMERICAN COATI (NASUA NASUA) IN AN URBAN PARK IN MINAS GERAIS, BRAZIL

The scientific information regarding staphylococci in procyonids is scarce. Hence, the aim of this study was to evaluate the frequency, distribution, and pattern of antimicrobial resistance of staphylococcal species isolated from free-roaming coatis (Nasua nasua) in an urban park in Belo Horizonte, Minas Gerais, Brazil. Rectal swabs from 55 free-living coatis were plated onto mannitol salt agar for isolating staphylococci, and species were identified using matrix-assisted laser desorption/ionization-time of flight mass spectrometry, polymerase chain reaction (PCR) of nuc, and sequencing of 16S rRNA and rpoB when needed. Antimicrobial susceptibility was investigated using the disk diffusion method, and the presence of the mecA gene was investigated by PCR. A total of 72.7% of the animals tested positive for staphylococci. Nine different species were identified, and Staphylococcus intermedius (60.4%) and S. delphini (20.9%) were the most frequently isolated species. Most of the isolates were susceptible to most of the antimicrobials evaluated, with a resistance pattern seen for penicillin (13.9%). One isolate was multidrug-resistant (MDR). The present study suggests that coatis are natural hosts of S. intermedius and S. delphini and, despite living in a heavily anthropized environment, the Staphylococcus spp. isolates showed a low incidence of drug resistance.

Genomic Analysis of Bacteriocin-Producing Staphylococci: High Prevalence of Lanthipeptides and the Micrococcin P1 Biosynthetic Gene Clusters

Bacteriocins are antimicrobial peptides produced by bacteria. This study aimed to in silico analyze the presence of bacteriocin gene clusters (BGCs) among the genomes of 22 commensal Staphylococcus isolates from different origins (environment/human/food/pet/wild animals) previously identified as bacteriocin producers. The resistome and plasmidome were studied in all isolates. Five types of BGC were detected in 18 genomes of the 22 bacteriocin-producing staphylococci included in this study: class I (Lanthipeptides), class II, circular bacteriocins, the non-ribosomal-peptide lugdunin and the thiopeptide micrococcin P1 (MP1). A high frequency of lanthipeptides was detected in this collection: BGC variants of BSA, bacCH91, and epilancin15X were identified in two Staphylococcus aureus and one Staphylococcus warneri isolates from food and wild animals. Moreover, two potentially new lanthipeptide-like BGCs with no identity to database entries were found in Staphylococcus epidermidis and Staphylococcus simulans from food and wild animal, respectively. Interestingly, four isolates (one S. aureus and one Staphylococcus hominis, environmental origin; two Staphylococcus sciuri, food) carried the MP1 BGC with differences to those previously described. On the other hand, seven of the 22 genomes (~32%) lacked known genes related with antibiotic or disinfectant-acquired resistance mechanisms. Moreover, the potential carriage of plasmids was evaluated, and several Rep-proteins were identified (~73% of strains). In conclusion, a wide variety of BGCs has been observed among the 22 genomes, and an interesting relationship between related Staphylococcus species and the type of bacteriocin has been revealed. Therefore, bacteriocin-producing Staphylococcus and especially coagulase-negative staphylococci (CoNS) can be considered good candidates as a source of novel bacteriocins.

Comprehensive Approaches for the Search and Characterization of Staphylococcins

Novel and sustainable approaches are required to curb the increasing threat of antimicrobial resistance (AMR). Within the last decades, antimicrobial peptides, especially bacteriocins, have received increased attention and are being explored as suitable alternatives to antibiotics. Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria as a self-preservation method against competitors. Bacteriocins produced by Staphylococcus, also referred to as staphylococcins, have steadily shown great antimicrobial potential and are currently being considered promising candidates to mitigate the AMR menace. Moreover, several bacteriocin-producing Staphylococcus isolates of different species, especially coagulase-negative staphylococci (CoNS), have been described and are being targeted as a good alternative. This revision aims to help researchers in the search and characterization of staphylococcins, so we provide an up-to-date list of bacteriocin produced by Staphylococcus. Moreover, a universal nucleotide and amino acid-based phylogeny system of the well-characterized staphylococcins is proposed that could be of interest in the classification and search for these promising antimicrobials. Finally, we discuss the state of art of the staphylococcin applications and an overview of the emerging concerns.

Detection of antimicrobial producing Staphylococcus from migratory birds: Potential role in nasotracheal microbiota modulation

A collection of 259 staphylococci of 13 different species [212 coagulase-negative (CoNS) and 47 coagulase-positive (CoPS)] recovered from nasotracheal samples of 87 healthy nestling white storks was tested by the spot-on-lawn method for antimicrobial-activity (AA) against 14 indicator bacteria. Moreover, extracts of AP isolates were obtained [cell-free-supernatants (CFS) both crude and concentrated and butanol extracts] and tested against the 14 indicator bacteria. The microbiota modulation capacity of AP isolates was tested considering: (a) intra-sample AA, against all Gram-positive bacteria recovered in the same stork nasotracheal sample; (b) inter-sample AA against a selection of representative Gram-positive bacteria of the nasotracheal microbiota of all the storks (30 isolates of 29 different species and nine genera). In addition, enzymatic susceptibility test was carried out in selected AP isolates and bacteriocin encoding genes was studied by PCR/sequencing. In this respect, nine isolates (3.5%; seven CoNS and two CoPS) showed AA against at least one indicator bacteria and were considered antimicrobial-producing (AP) isolates. The AP isolates showed AA only for Gram-positive bacteria. Three of these AP isolates (S. hominis X3764, S. sciuri X4000, and S. chromogenes X4620) revealed AA on all extract conditions; other four AP isolates only showed activity in extracts after concentration; the remaining two AP isolates did not show AA in any of extract conditions. As for the microbiota modulation evaluation, three of the nine AP-isolates revealed intra-sample AA. It is to highlight the potent inter-sample AA of the X3764 isolate inhibiting 73% of the 29 representative Gram-positive species of the nasotracheal stork microbiota population. On the other hand, enzymatic analysis carried out in the two highest AP isolates (X3764 and X4000) verified the proteinaceous nature of the antimicrobial compound and PCR analysis revealed the presence of lantibiotic-like encoding genes in the nine AP isolates. In conclusion, these results show that nasotracheal staphylococci of healthy storks, and especially CoNS, produce antimicrobial substances that could be important in the modulations of their nasal microbiota.

Evaluation of the Occurrence of Staphylococcaceae with Reduced Susceptibility to Cefoxitin in Wild Ungulates in Brandenburg, Germany, Based on Land Use-Related Factors

Interactions between natural and human-used environments have a significant influence on the spread of antimicrobial resistance in wild ecosystems. Despite current knowledge, fundamental questions about the degree of impact of land use-related factors on the spread of antimicrobial-resistant staphylococci in European wild game animal populations have not yet been answered with certainty. In this study, we evaluated the occurrence of Staphylococcaceae showing reduced susceptibility to cefoxitin in nasal swabs of fallow deer (Dama dama), red deer (Cervus elaphus), roe deer (Capreolus capreolus), and wild boar (Sus scrofa) hunted in Brandenburg, Germany. Evaluations were focused on the use of open-source data regarding the extent as well as the degree of land use, especially for settlement or animal husbandry. Results showed that the detection rate of Staphylococcaceae showing a non-wild-type phenotype for cefoxitin differed between animal species of the studied hunting districts. Statistical analyses of results combined with data on land use features revealed that a high density of cattle or poultry in a county may be associated with an increased detection rate in roe deer or wild boar, respectively. Furthermore, positive correlations were determined between the prevalence of non-wild-type Staphylococcaceae in roe deer or fallow deer and the proportional extent of surface water bodies in the corresponding area. The presented approach establishes a general basis for a risk-oriented assessment of the effects of human activities on the epidemiology of transmissible microorganisms in the human-animal-environment interface, including antimicrobial-resistant bacteria. IMPORTANCE Intensive research regarding the impact of land use-related factors on the prevalence and distribution of antimicrobial-resistant Staphylococcaceae in game ungulate populations is necessary for adequately determining risks related to interactions between wild animals, domestic animals, and humans in common geographic locations. This systematic approach for the analysis of the observations in specific hunting districts of Brandenburg, Germany, adds an innovative value to the research strategy of antimicrobial resistance in wild game animals, which is in accordance with current recommendations worldwide. Thus, results and information obtained in this study build a relevant foundation for future risk assessment regarding the safety of game products. Furthermore, the data generated represent an important basis for improving existing guidelines in land use practices and hunting practices. The use of existing open source data collections provided by official governmental and nongovernmental entities increases not only the impact but also the applicability and comparability of information beyond the regional level.

Antimicrobial Resistance and Virulence Genes in Staphylococci Isolated from Aviary Capercaillies and Free-living Birds in South-eastern Poland

INTRODUCTION

The current study characterises Staphylococcus bacteria recovered from dead free-living birds and captive capercaillies kept in south-eastern Poland. The results provide novel information about the antimicrobial resistance phenotype/genotype and the virulence profile of these bacteria.

MATERIAL AND METHODS

Samples of internal organs were taken from dead birds. Staphylococcus strains were identified by matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry. Susceptibility to 13 antibiotics was tested using a standard disc diffusion method on Mueller-Hinton agar. All isolates were screened for the presence of antibiotic resistance genes and staphylococcal enterotoxins (A to E), toxic shock syndrome toxin 1, exfoliative toxins A and B and Panton-Valentine leukocidin.

RESULTS

A total of 129 bacterial strains belonging to 19 species of the Staphylococcus genus were isolated. A relatively high percentage of them resisted fluoroquinolones, tetracyclines, macrolides and β-lactams to a significant degree and harboured the tetK, tetM, ermC, mphC and mecA genes. Strains of the coagulase-negative S. sciuri, S. xylosus and S. cohnii were isolated with genes encoding enterotoxin A and toxic shock syndrome toxin.

CONCLUSION

Both coagulase-positive and coagulase-negative staphylococci isolated from aviary capercaillies and free-living birds have significant pathogenic potential, and greater attention must be paid to the coagulase-negative species, which are still often considered mere contaminants. Virulence factors associated with resistance to antimicrobials, this being multiple in some strains, seem most important because they can be easily transferred between animals, especially those living in a given area.

Bacteriocin-Like Inhibitory Substances in Staphylococci of Different Origins and Species With Activity Against Relevant Pathogens

Bacteriocins are antimicrobial peptides with relevance in the modulation of human and animal microbiota that have gained interest in biomedical and biotechnological applications. In this study, the production of bacteriocin-like inhibitory substances (BLIS) was tested among a collection of 890 staphylococci of different origins (humans, animals, food, and the environment) and species, both coagulase-positive (CoPS, 238 isolates of 3 species) and coagulase-negative staphylococci (CoNS, 652 isolates of 26 species). Of the 890 staphylococci, 60 (6.7%) showed antimicrobial activity by the spot-on-lawn method against at least one of the 25 indicator bacteria tested. BLIS-producer (BLIS⁺) isolates were detected in 8.8% of CoPS and 6.0% of CoNS. The staphylococcal species with the highest percentages of BLIS⁺ isolates were S. chromogenes (38.5%), S. pseudintermedius (26.7%), and S. warneri (23.1%). The production of BLIS was more frequently detected among isolates of pets, wild animals, and food. Moreover, 13 BLIS⁺ isolates showed wide antimicrobial activiy spectrum, and 7 of these isolates (of species S. aureus, S. pseudintermedius, S. sciuri, and S. hominis) demonstrated antimicrobial activity against more than 70% of the indicator bacteria tested. The genetic characterization (by PCR and sequencing) of the 60 BLIS⁺ isolates revealed the detection of (a) 11 CoNS and CoPS isolates carrying putative lantibiotic-like genes; (b) 3 S. pseudintermedius isolates harboring the genes of BacSp222 bacteriocin; and (c) 2 S. chromogenes isolates that presented the gene of a putative cyclic bacteriocin (uberolysin-like), being the first report in this CoNS species. Antimicrobial susceptibility testing was performed in BLIS⁺ isolates and one-third of the CoNS isolates showed susceptibility to all antibiotics tested, which also lacked the virulence genes studied. These BLIS⁺ CoNS are good candidates for further characterization studies.

A Preliminary Study on Antimicrobial Susceptibility of Staphylococcus spp. and Enterococcus spp. Grown on Mannitol Salt Agar in European Wild Boar (Sus scrofa) Hunted in Campania Region-Italy

Simple Summary

During the last decade, an increase in the European wild boar (Sus scrofa) population occurred; thus, over the years, wild boars have become an important potential carrier of pathogenic bacteria for both livestock animals and pets, but also for humans. Since antibiotic resistance has become one of the greatest challenges of global public health, the aim of the present study was to define the prevalence and the antibiotic resistance profiles of bacteria grown on the selective medium mannitol salt agar (MSA), isolated from nasal swabs of wild boars hunted in Campania Region (southern Italy). The most prevalent isolated bacteria were represented by the Staphylococcus spp. and Enterococcus spp. strains, which showed worrying antibiotic-resistant profiles. Consequently, constant surveillance of wild boars is strongly recommended, in order to assess their role as reservoirs of antibiotic resistant bacteria and as sentinels of a possible environmental contamination.

Abstract

The importance of wild boar lies in its role as a bioindicator for the control of numerous zoonotic and non-zoonotic diseases, including antibiotic resistance. Mannitol Salt Agar (MSA) is a selective medium used for isolation, enumeration, and differentiation of pathogenic staphylococci. Other genera such as Enterococcus spp. are also salt tolerant and able to grow on MSA. The present study focused on the identification, by matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS), of bacteria grown on MSA isolated from the nasal cavities of 50 healthy wild boars hunted in Campania Region (southern Italy) in the year 2019. In addition, the antimicrobial resistance phenotype of the isolated strains was determined by disk diffusion method. Among genus Staphylococcus, coagulase-negative Staphylococcus (CoNS) were the most common isolated species, with Staphylococcus xylosus as the most prevalent species (33.3%). Furthermore, Enterococcus spp. strains were isolated, and Enterococcus faecalis was the species showing the highest frequency of isolation (93.8%). For staphylococci, high levels of resistance to oxacillin (93.3%) were recorded. Differently, they exhibited low frequencies of resistance to tested non-β-lactams antibiotics. Among enterococci, the highest resistances were observed for penicillin (93.7%), followed by ampicillin (75%), and ciprofloxacin (68.7%). Interestingly, 43.7% of the isolated strains were vancomycin-resistant. In conclusion, this study reports the phenotypic antibiotic resistance profiles of Staphylococcus spp. and Enterococcus spp. strains isolated from nasal cavities of wild boars hunted in Campania Region, highlighting that these wild animals are carriers of antibiotic resistant bacteria.

Extensive Horizontal Gene Transfer within and between Species of Coagulase-Negative Staphylococcus

Members of the gram-positive bacterial genus Staphylococcus have historically been classified into coagulase-positive Staphylococcus (CoPS) and coagulase-negative Staphylococcus (CoNS) based on the diagnostic presentation of the coagulase protein. Previous studies have noted the importance of horizontal gene transfer (HGT) and recombination in the more well-known CoPS species Staphylococcus aureus, yet little is known of the contributions of these processes in CoNS evolution. In this study, we aimed to elucidate the phylogenetic relationships, genomic characteristics, and frequencies of HGT in CoNS, which are now being recognized as major opportunistic pathogens of humans. We compiled a data set of 1,876 publicly available named CoNS genomes. These can be delineated into 55 species based on allele differences in 462 core genes and variation in accessory gene content. CoNS species are a reservoir of transferrable genes associated with resistance to diverse classes of antimicrobials. We also identified nine types of the mobile genetic element SCCmec, which carries the methicillin resistance determinant mecA. Other frequently transferred genes included those associated with resistance to heavy metals, surface-associated proteins related to virulence and biofilm formation, type VII secretion system, iron capture, recombination, and metabolic enzymes. The highest frequencies of receipt and donation of recombined DNA fragments were observed in Staphylococcus capitis, Staphylococcus caprae, Staphylococcus hominis, Staphylococcus haemolyticus, and members of the Saprophyticus species group. The variable rates of recombination and biases in transfer partners imply that certain CoNS species function as hubs of gene flow and major reservoir of genetic diversity for the entire genus.

Multiple Antimicrobial Resistance in Methicillin-Resistant Staphylococcus sciuri Group Isolates from Wild Ungulates in Spain

The aim of this study was to investigate the presence of methicillin-resistant Staphylococcus (MRS) strains in non-managed wild ungulates present in a typical Mediterranean forest in Spain. For this purpose, nasal swabs were obtained from 139 animals: 90 wild boar (Sus scrofa), 42 red deer (Cervus elaphus) and 7 fallow deer (Dama dama), which were subsequently pre-enriched in BHI+ NaCl (6.5%) (24 h/37 °C), and then seeded in Columbia blood agar (24 h/37 °C)). The presence of the mecA gene was investigated by PCR, first from the confluent and then from individual colonies. A total of 10 mecA+ colonies were obtained of which only seven showed phenotypic resistance to oxacillin/cefoxitin (methicillin resistance). All MRS strains belonged to the Staphylococcus sciuri group. Methicillin-resistant Staphylococcus aureus (MRSA) was not detected. In addition, a significant number of MRS strains showed resistance to other antimicrobials, mainly β-lactam (7/7), gentamicin (7/7), fusidic acid (6/7) and quinupristin-dalfopristin (6/7), showing an irregular correlation with their coding genes. The genetic profiles grouped the seven strains obtained according to the bacterial species but not in relation to the animal source or the geographical place of origin. The presence of SCCmec type III, common to animals and humans, has been detected in three of the strains obtained. In conclusion, the study reveals that the wild ungulates investigated play a role as potential reservoirs of multi-resistant strains of MRS. Such strains, due to their characteristics, can be easily transferred to other wild or domestic animal species and ultimately to humans through their products.

Antimicrobial Resistance Profiles of Coagulase-Negative Staphylococci in Community-Based Healthy Individuals in Germany

Coagulase-negative staphylococci (CoNS) are common opportunistic pathogens, but also ubiquitous human and animal commensals. Infection-associated CoNS from healthcare environments are typically characterized by pronounced antimicrobial resistance (AMR) including both methicillin- and multidrug-resistant isolates. Less is known about AMR patterns of CoNS colonizing the general population. Here we report on AMR in commensal CoNS recovered from 117 non-hospitalized volunteers in a region of Germany with a high livestock density. Among the 69 individuals colonized with CoNS, 29 had reported contacts to either companion or farm animals. CoNS were selectively cultivated from nasal swabs, followed by species definition by 16S rDNA sequencing and routine antibiotic susceptibility testing. Isolates displaying phenotypic AMR were further tested by PCR for presence of selected AMR genes. A total of 127 CoNS were isolated and Staphylococcus epidermidis (75%) was the most common CoNS species identified. Nine isolates (7%) were methicillin-resistant (MR) and carried the mecA gene, with seven individuals (10%) being colonized with at least one MR-CoNS isolate. While resistance against gentamicin, phenicols and spectinomycin was rare, high resistance rates were found against tetracycline (39%), erythromycin (33%) and fusidic acid (24%). In the majority of isolates, phenotypic resistance could be associated with corresponding AMR gene detection. Multidrug-resistance (MDR) was observed in 23% (29/127) of the isolates, with 33% (23/69) of the individuals being colonized with MDR-CoNS. The combined data suggest that MR- and MDR-CoNS are present in the community, with previous animal contact not significantly influencing the risk of becoming colonized with such isolates.

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).

The Use of Less Conventional Meats or Meat with High pH Can Lead to the Growth of Undesirable Microorganisms during Natural Meat Fermentation

The bacterial communities that are established during natural meat fermentation depend on the processing conditions and the type of meat substrate used. Six pork samples of variable quality (reflected in pH values) and six less conventional meats (beef, horse, hare, wild deer, wild duck, and wild boar) were naturally fermented under controlled conditions in model systems. The development of lactic acid bacteria (LAB), coagulase-negative staphylococci (CNS), and enterobacteria was followed using culture-dependent techniques and (GTG)₅-PCR fingerprinting of genomic DNA from the isolates obtained. Taken together, Latilactobacillus sakei was the most abundant LAB species, although Latilactobacillus curvatus was more manifest in high-pH pork. Within staphylococci, common species were encountered (i.e., Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus xylosus), although some atypical ones (i.e., Staphylococcus succinus) were also recovered. Within enterobacteria, Serratia spp. prevailed in more acidic pork batches and in beef, whereas Hafnia spp. prevailed in game meat fermentations. Enterobacterial counts were particularly high in fermentations with low acidity, namely for some pork batches, hare, wild duck, and wild boar. These findings should be considered when naturally fermented meat products are manufactured, as the use of game meat or meat with high pH can give rise to safety concerns.

Frequency and Characterization of Antimicrobial Resistance and Virulence Genes of Coagulase-Negative Staphylococci from Wild Birds in Spain. Detection of tst-Carrying S. sciuri Isolates

The objective of this study was to determine the prevalence and diversity of coagulase-negative staphylococci (CoNS) species from wild birds in Spain, as well as to analyze the antimicrobial resistance phenotype/genotype and the virulence gene content. During 2015–2016, tracheal samples of 242 wild birds were collected in different regions of Spain for staphylococci recovery. The species identification was performed using MALDI-TOF. The antimicrobial resistance phenotype and genotype was investigated by the disk diffusion method and by PCR, respectively. The presence of the virulence genes lukF/S-PV, tst, eta, etb, etd and scn was investigated by PCR. Moreover, CoNS carrying the mecA gene were subjected to SCCmec typing. Of the tested animals, 60% were CoNS-carriers, and 173 CoNS isolates were recovered from the 146 positive animals, which belonged to 11 species, with predominance of S. sciuri (n = 118) and S. lentus (n = 25). A total of 34% of CoNS isolates showed a multidrug resistance phenotype, and 42 mecA-positive methicillin-resistant CoNS (MRCoNS) were detected. The isolates showed resistance to the following antimicrobials (percentage of resistant isolates/antimicrobial resistance genes detected): penicillin (49/ blaZ, mecA), cefoxitin (24/ mecA), erythromycin and/or clindamycin (92/ erm(B), erm(C), erm(43), msr(A), mph(C), lnu(A), lsa(B), vga(A) and sal(A)), gentamicin and/or tobramycin (5/ aac(6′)-Ie-aph(2″)-Ia, ant(4′)-Ia), streptomycin (12/str), tetracycline (17/ tet(K), tet(L), tet(M)), ciprofloxacin (4), chloramphenicol (1/ fexA), fusidic acid (86/ fusB, fusD) and trimethoprim–sulfamethoxazole (1/ dfrK). None of the isolates harbored the lukF/S-PV, eta, etb, etd and scn genes, but two S. sciuri isolates (1%) carried the tst gene. Wild birds are frequently colonized by CoNS species, especially S. sciuri. We identified scavenging on intensively produced livestock and feeding on landfills as risk factors for CoNS carriage. High proportions of MRCoNS and multidrug resistant CoNS were detected, which coupled with the presence of important virulence genes is of concern.

Diversity of methicillin-resistant staphylococci among wild Lepus granatensis: first detection of mecA-MRSA in hares

MRSA in humans, pets and livestock have been widely investigated, nevertheless, there is still little information of MRSA in wild animals. Therefore, this study aimed to investigate the occurrence and antimicrobial resistance profiles of methicillin-resistant staphylococci (MRS) in wild Iberian hares and to characterize their genetic lineages. Samples from 83 wild hares (Lepus granatensis) were collected during the hunting season. Isolation of MRS was accomplish using Oxacillin Resistant Screening Agar medium with 2 mg/L of oxacillin. The susceptibility of the isolates was tested by the Kirby-Bauer disc diffusion method. The presence of resistance and virulence genes was studied by PCR. S. aureus strains were further characterized by multilocus sequence typing, agr, spa and SCCmec typing. From the 83 samples, 12 (14.45%) coagulase-negative staphylococci and 3 (3.6%) MRSA strains were isolated. Nine coagulase-negative isolates showed resistance to at least one antibiotic. One MRSA isolate showed a multidrug-resistant profile with resistances to ß-lactams, aminoglycosides, macrolides and lincosamides. All MRSA strains were ascribed to ST2855, t1190 and SCCmec type III. The frequency of MRSA strains in wild hares was low, nevertheless, the presence of MRSA in game animals is considered a public health problem and may represent a route of transmission between animals and humans.

Antimicrobial Resistance, Virulence, and Genetic Lineages of Staphylococci from Horses Destined for Human Consumption: High Detection of S. aureus Isolates of Lineage ST1640 and Those Carrying the lukPQ Gene

Simple Summary

Staphylococci are opportunistic pathogens which colonize humans and animals. Zoonotic transfer of staphylococcal species between domestic animals and humans is common and can occur through direct contact, the environment, and animal-derived food processing, implying a risk of the spread of antimicrobial resistance mechanisms and virulence factors into different ecosystems. Our work aimed at studying the diversity of staphylococcal species in nasal and faecal samples of healthy horses intended for human consumption and their resistance and virulence determinants. Staphylococci were detected in 90% and 66% of nasal and faecal samples tested, respectively. Eight staphylococcal species were detected, with the most prevalent ones being Staphylococcus aureus (all isolates were methicillin-susceptible), Staphylococcus delphini, and Staphylococcus sciuri. The predominant S. aureus lineage, ST1640, is associated with horses for the first time in this study. S. aureus isolates, except those of lineage ST1640, produced equid-adapted leukocidin (LukPQ) and blocker of equine complement system activation (eqSCIN). The toxic shock syndrome toxin-encoding gene was also detected in some S. aureus isolates. Multidrug resistance was observed among S. sciuri isolates, but not among S. aureus. Measures of hygiene and control should be implemented during horse slaughter and meat processing.

Abstract

This work aimed to determine the frequency and diversity of Staphylococcus species carriage in horses intended for human consumption, as well as their resistance and virulence determinants. Eighty samples (30 nasal; 50 faecal) were recovered from 73 healthy horses in a Spanish slaughterhouse. The samples were cultured for staphylococci and methicillin-resistant staphylococci (MRS) recovery. The phenotype/genotype of antimicrobial resistance was analysed for all isolates. The spa-type and sequence-type (ST) were determined in Staphylococcus aureus strains; moreover, the presence of virulence and host-adaptation genes (tst, eta, etb, pvl, lukPQ, scn-eq, and scn) was studied by PCR. Staphylococcus species were detected in 27/30 (90%) and 33/50 (66%) of nasal and faecal samples, respectively. Ninety isolates belonging to eight species were recovered, with predominance of S. aureus (n = 34), Staphylococcus delphini (n = 19), and Staphylococcus sciuri (n = 19). S. aureus strains were all methicillin-susceptible (MSSA), 28/34 were susceptible to all the antibiotics tested, and the remaining six showed resistance to (gene-detected) streptomycin (ant (6)-Ia), penicillin (blaZ), and trimetroprim/sulphametoxazole (SXT) (dfrA, dfrG). The lineage ST1640/t2559 was predominant (n = 21). The genes lukPQ and scn-eq were present in all but the ST1640 isolates. Three S. sciuri isolates were multidrug-resistant. Healthy horses in Spain seem to be a reservoir for virulent MSSA and the lineage ST1640, although the presence of the latter in horses is described for the first time in this study. Moreover, the equine-adapted leukocidin gene lukPQ is frequent among S. aureus strains. A large variety of staphylococcal species with low antibiotic resistance rate were also observed.

Diversity of staphylococcal species in food producing animals in Spain, with detection of PVL-positive MRSA ST8 (USA300)

This work aimed to determine the prevalence, diversity, antibiotic-resistance phenotype/genotype and virulence factors in staphylococci of farm-animals. Nasal samples of 117 farm-animals (calve: 72; lamb: 37; goat: 8) were collected from one slaughterhouse in La Rioja/Spain and cultured for staphylococci and methicillin-resistant Staphylococcus (MRS) recovery. Identification was performed by MALDI-TOF. Antimicrobial resistance phenotype/genotype was determined by susceptibility testing and specific PCRs. Molecular typing (spa-typing, multilocus-sequence-typing, agr-typing, SCCmec), and detection of 12 virulence genes and human Immune-evasive-cluster (IEC) genes were performed by PCR/sequencing in S. aureus. Two marker genes of arginine catabolic mobile element (ACME) were determined by PCR (USA300-MRSA detection). Staphylococci were identified in 50%, 54% and 21% of goat, lamb and calve samples, respectively. Among the 13 S. aureus isolates recovered, 11 were susceptible to all antimicrobials tested, and two were multidrug-resistant-MRSA [beta-lactams (blaZ, mecA), macrolides [(msr(A)/msr(B)] and fluoroquinolones]. The MSSA harboured either tst or enterotoxin genes, while the MRSA harboured the lukF/lukS-PV genes. Five sequence-types were detected. The two MRSA strains (from lamb and goat) were typed as t5173/ST8/agr-I/SCCmec-IVa/ACME-positive, corresponding to USA300 clone, and were IEC-B-positive. Among the 47 coagulase-negative staphylococci (CoNS), six species were identified, predominating S. simulans (n = 25) and S. sciuri (n = 11). Fifty-three percent of CoNS showed resistance to at least one antimicrobial agent (six multidrug-resistant strains), and the following resistance phenotypes/genotypes were detected: streptomycin [27.6%; ant(6)-Ia, str], tetracycline [23.4%; tet(M), tet(L), tet(K)], clindamycin [19.1%; lnu(A), vgaA], erythromycin [10.6%; erm(C), msr(A)/msr(B)], chloramphenicol (8.5%; fexA), tobramycin (6.4%), penicillin-cefoxitin (4.3%; blaZ, mecA), and SXT (2.1%). The detection of the MRSA-USA300 lineage in food animals is worrisome and should be further monitored.