Underrated Staphylococcus species and their role in antimicrobial resistance spreading

Genomic analysis of multi-drug resistant coagulase-negative staphylococci from healthy humans and animals revealed unusual mechanisms of resistance and CRISPR-Cas system

BACKGROUND

Coagulase-negative staphylococci (CoNS) are evolving as major reservoirs and vectors of unusual and critical antimicrobial resistance (AMR) mechanisms.

MATERIALS AND METHODS

In this study, the genomic characterization of 26 multidrug-resistant (MDR)-CoNS (S. borealis, S. saprophyticus, S. sciuri, S. hominis, S. epidermidis, S. pasteuri, S. hyicus, S. simulans, S. haemolyticus, and S. arlettae) previously obtained from the nasal cavity of healthy nestling storks, humans who had no contact with animals, pigs, and pig farmers, as well as dogs and dog owners from Spain was performed. High-quality draft genomes obtained by Illumina sequencing technology were used to determine their resistome, virulome, mobile genetic elements, and CRISPR-Cas types. The relatedness of three CoNS species with publicly available genomes was assessed by core-genome single nucleotide polymorphisms (SNPs).

RESULTS

AMR genes to all classes of antibiotics in staphylococci were detected including unusual ones (mecC, ermT, and cfr), of which their corresponding genetic organizations were analyzed. About 96.1% of the MDR-CoNS strains harbored diverse adherence or immune evasion genes. Remarkably, one enterotoxin-C and -L-carrying S. epidermidis-ST595 strain from a nestling stork was detected. Moreover, various plasmid bound-biocide resistance genes (qacACGJ) were identified in 34.6% of the MDR-CoNS. Two genes that encode for cadmium and zinc resistance (cadD, czrC) were found, of which czrC predominated (42.3%). Complete CRISPR-Cas system was detected in 19.2% of the CoNS strains, of which cas-1, -2, and -9 predominated, especially in 75% of the S. borealis strains. The phylogenetic analysis identified clusters of related S. epidermidis lineages with those of other countries (SNP < 100). Also, highly related S. borealis isolates (SNP < 10) from pigs was confirmed for the first time in Spain.

CONCLUSION

These findings showed that various ecological niches harbor CoNS that presented MDR phenotypes mediated by multiple AMR genes carried by mobile genetic elements with relatively low frequency of intact CRISPR-Cas systems. Furthermore, the transmission of some CoNS species in humans and animals is strongly suggested.

Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale

Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.

Virulence determinants and antibiotic resistance in staphylococci isolated from the skin of captive bred reptiles

Knowledge of the composition and properties of skin microbiota in healthy reptiles is essential for preservation strategies and thus the prevention of skin dysbiosis leading to dermatological diseases. Despite the greatly increasing popularity of reptiles as pets, only a few studies have dealt with this topic. Therefore, the aim of this work was to analyse species composition of bacteria isolated from skin swabs of 40 reptiles (17 species) using MALDI-TOF spectrometry and to characterise the virulence properties of identified staphylococci (n = 51). The most common species were Staphylococcus xylosus and S. sciuri. Bacilli, enterococci, Escherichia coli, Salmonella sp. and Acinetobacter sp. were also common. The most frequent antimicrobial resistance in staphylococcal isolates was observed for ampicillin (100.0%) and cefoxitin (98.0%) with the blaZ gene being most prevalent (58.8%). In contrast, all staphylococci were susceptible to gentamicin, kanamycin and imipenem. Slime and biofilm production was observed in 86.3% and 76.5% of isolates, respectively. Gelatinase, DNase, protease and lipase activity was found more rarely (41.2%; 25.5%; 27.5% and 21.6%). Since reptiles are a reservoir of bacteria for their owners, common multi-drug resistance (84.3%, MAR index average 0.29 ± 0.09) and biofilm formation must be kept in mind, especially in the case of injury when handling reptiles.

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.

Pathogenic potential of meat-borne coagulase negative staphylococci strains from slaughterhouse to fork

This study aimed to determine the prevalence of coagulase-negative staphylococci (CoNS) in meat processing lines for their pathogenic potential associated with biofilm formation, staphylococcal toxin genes, and antibiotic resistance in obtained isolates. Out of 270 samples, 56 isolates were identified as staphylococcal with their species level, and their antimicrobial resistance profiles were also determined with the BD Phoenix™ system. Among these, CoNS were found in 32 isolates, including S. epidermidis (22%), S. warneri (22%), S. cohnii (9%), S. schleiferi (9%), S. capitis (6%), S. haemolyticus (6%), S. lugdunensis (6%), S. chromogenes (6%), S. kloosii (3%), S. sciuri (3%), S. lentus (3%), and S. caprae (3%). Biofilm formation was observed in 78.1% of CoNS isolates, with 56% being strong biofilm producers; and the frequency of the icaA, fnbA, and fnbB genes were 43.7% and 34.3%, and 9.3% in isolates, respectively. Twenty-five (78.1%) of these strains were resistant to at least one antimicrobial agent, 20 (80%) of which exhibited multidrug resistance (MDR). Regarding genotypic analyses, 15.6%, 22.2%, 87.5%, and 9% of isolates, were positive for blaZ, ermC, tetK, and aacA-aphD, respectively. In 8 (25%) of all isolates had one or more staphylococcal toxin genes: the sed gene was the most frequent (12.5%), followed by eta (9.3%), tst-1 (6.25%), and sea (3.1%). In conclusion, this study highlights meat; and meat products might be reservoirs for the biofilm-producing MDR-CoNS, which harbored several toxin genes. Hence, it should not be ignored that CoNS may be related to foodborne outbreaks.

Antimicrobial resistance and geographical distribution of Staphylococcus sp. isolated from whiting (Merlangius merlangus) and seawater in the English Channel and the North sea

Staphylococcus is a significant food safety hazard. The marine environment serves as a source of food for humans and is subject to various human-induced discharges, which may contain Staphylococcus strains associated with antimicrobial resistance (AMR). The aim of this study was to assess the occurrence and geographical distribution of AMR Staphylococcus isolates in seawater and whiting (Merlangius merlangus) samples collected from the English Channel and the North Sea. We isolated and identified 238 Staphylococcus strains, including 12 coagulase-positive (CoPs) and 226 coagulase-negative (CoNs) strains. All CoPs isolates exhibited resistance to at least one of the 16 antibiotics tested. Among the CoNs strains, 52% demonstrated resistance to at least one antibiotic, and 7 isolates were classified as multi-drug resistant (MDR). In these MDR strains, we identified AMR genes that confirmed the resistance phenotype, as well as other AMR genes, such as quaternary ammonium resistance. One CoNS strain carried 9 AMR genes, including both antibiotic and biocide resistance genes. By mapping the AMR phenotypes, we demonstrated that rivers had a local influence, particularly near the English coast, on the occurrence of AMR Staphylococcus. The analysis of marine environmental parameters revealed that turbidity and phosphate concentration were implicated in the occurrence of AMR Staphylococcus. Our findings underscore the crucial role of wild whiting and seawater in the dissemination of AMR Staphylococcus within the marine environment, thereby posing a risk to human health.

Therapeutic potential of low-molecular weight lignin model polymer fractions for treating skin lesions in animals: a pilot study

Bacterial infections and resistance to antibiotics are increasingly severe problems. In recent years, Staphylococcus species have emerged as important pathogens in animals and humans. Current therapeutic methods against these species have serious disadvantages; therefore new agents with antibacterial potential, such as plant-based substances, are very important in therapy. We report a pilot study with new method of fractioning the dehydrogenate polymer DHP obtained from coniferyl alcohol and application of the low-MW fractions of 200-3000 Da for antibacterial activity in healing animal lesions. In vivo experiments were conducted on the dogs having a skin lesion. Dogs were treated with the suspension containing the low-MW DHP fractions as the active ingredient, in combination with alginate for 7 days. Cytological smears and microbiological analyses of the affected area were performed. Staphylococcus spp. was isolated from lesions in all dogs from our research. The results show that the low-MW DHP suspension in alginate promotes skin healing and reduction of the infection of the lesions in the affected animals. Pharmaceutical composition containing the low-MW DHP fractions exerts a soothing effect on the subject in wound treatment. Reduction in the number of bacteria by 30% and more were noticed in 6 dogs, while in 4 dogs this percentage is above 50%. No side effects were noticed. Synthesized lignin oligomers may have a significant place as antimicrobial and skin healing agents, especially since an increasing number of multidrug-resistant staphylococci are found on the skin lesions in animals.

Topical antimicrobial formulations using medicinal plant-derived essential oils targeting methicillin resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) causes a variety of healthcare-associated and community-acquired infections. Due to limited availability of effective antimicrobials for treating MRSA infections, there is a growing need to explore alternative therapeutic approaches. Here, the antimicrobial activities of 19 oils, popularly used for their medicinal properties, were tested against MRSA USA300. Oils obtained from cinnamon, clove, tangerine, and coriander showed the most promising activities, demonstrating bactericidal, anti-adhesive and anti-biofilm activities, and synergistic properties with common antibiotics. Given that clove and cinnamon oils showed the best activities, they were incorporated into topical formulations. Not only did the formulations with oils maintain antimicrobial and anti-adhesive activities, but their anti-biofilm property was potentiated. Tests on Galleria mellonella larvae suggested that the formulation is non-toxic. The formulations proposed here are a great alternative for the decolonisation of surfaces containing MRSA and can help circumventing antimicrobial resistance, a growing threat in the hospital environment.

Nasal staphylococci microbiota and resistome in healthy adults in La Rioja, northern Spain: High frequency of toxigenic S. aureus and MSSA-CC398 subclade

This study determined the nasal staphylococci diversity and characterized their resistome, with a focus on the mobilome of methicillin-susceptible Staphylococcus aureus (MSSA)-CC398 subclade from healthy adults in La Rioja (northern Spain). Nasal staphylococci recovered from 57 healthy individuals (HI) were identified (MALDI-TOF-MS) and their antimicrobial resistance, virulence determinants and genetic lineages were studied. The relatedness of MSSA-CC398 isolates was assessed by core-genome single-nucleotide-polymorphisms (SNPs). One-hundred-forty-three non-repetitive staphylococci were obtained from most HI (98.2%), of which S. epidermidis (87.7%) and S. aureus (36.8%) were the predominant species. About 15% of the 27 S. aureus and 30.1% of the 116 coagulase-negative staphylococci (CoNS) isolates presented a multidrug resistance (MDR) phenotype. All S. aureus isolates were MSSA but 30.2% of CoNS isolates were mecA-positive and carried SCCmec types III, IV, and V. The highest non-beta-lactam resistance (frequency/genes) in S. aureus and CoNS were: erythromycin-clindamycin-inducible (25.9%/ermT, ermC) and mupirocin (30.1%/mupA), respectively. About 85% of S. aureus isolates carried relevant virulence genes. Eight clonal complexes (CCs) of MSSA were identified, of which CC398 was the predominant (33.3%). About 78% of the CC398 isolates harboured rep13-bound ermT gene, however, one carried a rep10-bound ermC gene. Only the ermT-positive MSSA-CC398 isolates were closely related (<50 SNPs) and carried the φSa3. Diverse MDR-S. epidermidis isolates were identified which included the lineages ST59 and ST210. The high rate of toxigenic S. aureus and of MSSA-CC398 subclade highlight the ability of HI to carry and transmit virulent isolates. Moreover, the high frequency of MDR-CoNS, often linked with SCCmec, needs to be monitored for their potential human health implications.

Methicillin-resistant Staphylococci in canine pyoderma in Thailand

Background and Aims

Methicillin-resistant Staphylococci (MRS) seriously threatens animal and human health. Repeated antibiotic use allows the bacteria to develop resistance to several antibiotic classes and become multidrug-resistant (MDR). Canine pyoderma, a common skin condition in dogs, is mainly caused by Staphylococci, including MRS. Detecting this infection in all canine populations is crucial to develop a proper preventive plan. This study estimated the prevalence, antibiogram, and risk factors of MRS in canine patients at a referral animal hospital in Khon Kaen, Thailand.

Materials and Methods

Skin swabs and relevant information were collected from 56 client-owned dogs that visited the hospital from September 2019 to September 2020. Staphylococci colonies were subjected to molecular identification and antibiotic susceptibility tests using an automated system (VITEK® 2). These colonies were also genetically identified using multiplex-polymerase chain reaction (PCR) and sequencing. The mecA gene, encoding methicillin resistance, was detected using simplex-PCR. The risk factors of MRS infection and their association with MRS infection were analyzed using logistic regression and the Chi-square test, respectively.

Results

The prevalence of MRS was found to be 35.7% (20/56 dogs). By species, methicillin-resistant Staphylococcus pseudintermedius was found in 24 of 104 isolates (23.1%), and all samples were MDR. Receiving systemic antibiotics in the past 6 months was a major risk factor associated with MRS infection (p < 0.05; odds ratio (OR) > 1). In addition to the MRS isolates, the mecA gene was also detected in methicillin-susceptible Staphylococci isolates. This might be because of the high expression of blaI, and mutations in c-di-AMP cyclase DacA, RelA, and Fem proteins.

Conclusion

A high prevalence of MRS and MDR was observed in the studied population, which might be potentially due to improper antibiotic use by the owners and horizontal transfer of drug-resistance genes.

Dynamics of antimicrobial resistance and virulence of staphylococcal species isolated from foods traded in the Cape Coast metropolitan and Elmina municipality of Ghana

The impact of staphylococci on food poisoning and infections could be higher than previously reported. In this study, we characterised the occurrence and coexistence of antimicrobial resistance and virulence genes of staphylococci isolates in foods. Staphylococci were isolated from 236 samples of selected street-vended foods and identified. The pattern of antimicrobial resistance and virulence genes in the staphylococci were assessed using disc diffusion, PCR and analysis of next-generation sequencing data. The food samples (70.76 %) showed a high prevalence of staphylococci and differed among the food categories. Forty-five Staphylococcus species were identified and comprised coagulase-negative and positive species. Staphylococcus sciuri (now Mammaliicoccus sciuri), S. aureus, S. kloosii, S. xylosus, S. saprophyticus, S. haemolyticus and S. succinus were the most abundant species. The staphylococcal isolates exhibited resistance to tetracycline, levofloxacin, ciprofloxacin, norfloxacin, gentamicin and amikacin and susceptibility to nitrofurantoin. Antimicrobial susceptibilities were also reported for cefoperazone, ceftriaxone, cefotaxime, nalidixic acid and piperacillin-tazobactam. The antimicrobial resistance and virulence genes commonly detected consisted of tet, arl, macB, van, gyr, nor, optrA, bcrA, blaZ, taeA and S. aureus lmrS. The isolates frequently exhibited multiple resistance (30.42 %) of up to eight antimicrobial drug classes. The isolates predominantly harboured genes that express efflux pump proteins (50.53 %) for antibiotic resistance compared with inactivation (10.05 %), target alteration (26.72 %), protection (7.67 %) and replacement (3.17 %). The virulence determinants comprised genes of pyrogenic toxin superantigens (eta, etb, tst), adhesions (clf, fnbA, fnbB, cna, map, ebp, spA, vWbp, coa) and genes that express exoproteins (nuclease, metalloprotease, γ-hemolysin, hyaluronate lyase). There was a statistically significant difference in the prevalence of staphylococci isolates and their antimicrobial resistance and virulence profile as revealed by the phenotypic, PCR and next-generation sequencing techniques. The findings suggest a higher health risk for consumers. We recommend a critical need for awareness and antimicrobial susceptibility and anti-virulence strategies to ensure food safety and counteract the spread of this clinically relevant genus.

Within-Host Diversity of Coagulase-Negative Staphylococci Resistome from Healthy Pigs and Pig Farmers, with the Detection of cfr-Carrying Strains and MDR-S. borealis

The ecology and diversity of resistome in coagulase-negative staphylococci (CoNS) from healthy pigs and pig farmers are rarely available as most studies focused on the livestock-associated methicillin-resistant S. aureus. This study aims to characterize the antimicrobial resistance (AMR) mechanisms, intra-host species diversity (more than one species in a host), and intra-species AMR diversity (same species with more than one AMR profile) in CoNS recovered from the nasal cavities of healthy pigs and pig farmers. One-hundred-and-one CoNS strains previously recovered from 40 pigs and 10 pig farmers from four Spanish pig farms were tested to determine their AMR profiles. Non-repetitive strains were selected (n = 75) and their AMR genes, SCCmec types, and genetic lineages were analyzed by PCR/sequencing. Of the non-repetitive strains, 92% showed a multidrug resistance (MDR) phenotype, and 52% were mecA-positive, which were associated with SCCmec types V (46.2%), IVb (20.5%), and IVc (5.1%). A total of 28% of the pigs and pig farmers had intra-host species diversity, while 26% had intra-species AMR diversity. High repertoires of AMR genes were detected, including unusual ones such as tetO, ermT, erm43, and cfr. Most important was the detection of cfr (in S. saprophyticus and S. epidermidis-ST16) in pigs and pig farmers; whereas MDR-S. borealis strains were identified in pig farmers. Pig-to-pig transmission of CoNS with similar AMR genes and SCCmec types was detected in 42.5% of pigs. The high level of multidrug, within-host, and intra-species resistome diversity in the nasal CoNS highlights their ability to be AMR gene reservoirs in healthy pigs and pig farmers. The detection of MDR-S. borealis and linezolid-resistant strains underscore the need for comprehensive and continuous surveillance of MDR-CoNS at the pig farm level.

ANTIMICROBIAL SUSCEPTIBILITY OF STAPHYLOCOCCUS SPP. ISOLATED FROM FELIDS AND CANIDS IN BELO HORIZONTE ZOO, BRAZIL

The epidemiology of Staphylococcus spp. has become a major concern among humans and animals due to increasing antimicrobial resistance and frequent reports of infection. Despite the importance of animals as reservoirs for staphylococci, little is known about the epidemiology of Staphylococcus spp. in most nondomestic species, including canids and felids. This study evaluated the frequency, distribution, and patterns of antimicrobial resistance of staphylococcal species isolated from captive felids and canids from Belo Horizonte Zoo, Brazil. Rectal, oral, and nasal swabs from apparently healthy maned wolves (Chrysocyon brachyurus, n= 7), a lion (Panthera leo, n = 1), jaguars (Panthera onca, n = 3), and one swab of a cougar (Puma concolor) with an ear infection were streaked onto mannitol salt agar. Colonies identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry, polymerase chain reaction for the Staphylococcus intermedius group (SIG), and 16S rRNA gene sequencing. Isolates were subjected to antimicrobial susceptibility tests and Staphylococcus pseudintermedius strains were subjected to multilocus sequence typing. Staphylococcus species were isolated from 24 of the 34 samples (70.6%). Among the isolated strains, S. pseudintermedius and Staphylococcus felis were the most frequent species (41.7 and 25%, respectively). Five novel sequence types were identified among the S. pseudintermedius isolates. Resistance to tetracycline (7/24, 29.2%) or penicillin (6/23, 26.1%) was significantly higher than the other antimicrobial agents tested (P < 0.05). One isolate, Staphylococcus nepalensis, was positive for mecA and resistant to five antimicrobials, and was thus classified as multidrug-resistant. The present work suggests that maned wolves are natural hosts of SIG and also reports the isolation of S. felis in sick and healthy, captive, nondomestic carnivores. The isolated staphylococci were susceptible to most classes of antimicrobials tested. However, the multidrug-resistance capability of an S. nepalensis strain reinforces the hypothesis that felids and canids act as reservoirs of pathogens with antimicrobial resistance.

Occurrence of antimicrobial-resistant Staphylococcus aureus in a Brazilian veterinary hospital environment

Antimicrobial resistance is a threat to public health. The emergence of antibiotic-resistant Staphylococcus aureus represents a priority for the implementation of preventive measures. The objective was to isolate S. aureus in humans, animals, and animal health care environment, and to characterize the genotypic and phenotypic profile of antimicrobial resistance in these isolates. We isolated S. aureus from staff, animals, and environment of a veterinary hospital, and identified their antimicrobial resistance profiles. Samples were collected from 20 humans, 13 animals, 14 surfaces, 8 mobile phones, and 7 veterinarians' stethoscopes by using sterile swabs. S. aureus was isolated by culturing on mannitol salt agar and preliminary identification was done by Gram staining and catalase test. Subsequently, a polymerase chain reaction was performed for species confirmation and investigating their antimicrobial-resistant genotypic profiles. Phenotypic profiles of resistant isolates were determined using the disk-diffusion technique. Ten S. aureus isolates were recovered from 5/20 humans (25%), it was also recovered from 2/13 animals (15.38%), including 1 dog and 1 cat, and from 1/14 of surfaces (7.14%). The oxacillin-susceptible mecA-positive Staphylococcus aureus phenotype was identified in a feline. Most of the isolates carried at least two resistance genes of different antimicrobial classes, with 90% (9/10) presenting the gene blaZ, with 10% (1/10) presenting the gene mecA, 20% (2/10) presenting tet38, 10% (1/10) presenting tetM, 90% (9/10) presenting norA, 50% (5/10) presenting norC, 10% (1/10) presenting ermA, and 60% (6/10) presenting ermB. In antibiograms, resistance to penicillin was identified in all the isolates, resistance to erythromycin was identified in 80% (8/10), and all the isolate's resistance to erythromycin presented erythromycin-induced resistance to clindamycin. Antimicrobial resistance in the veterinary hospital requires attention due to the risk of interspecies transmission, gene transfer between bacteria that colonize companion animals and humans and, can make antimicrobial therapy difficult.

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

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

Unusual carriage of virulence genes sasX/sesI/shsA by nosocomial Staphylococcus haemolyticus from Brazil

Background: Staphylococcus haemolyticus is an emerging threat in the nosocomial environment but only some virulence factors are known. Materials & methods: The frequency of the sasX gene (or orthologues sesI/shsA), encoding an invasiveness-related surface-associated protein, in S. haemolyticus was detected in different hospitals in Rio de Janeiro. Results: 9.4% of strains were sasX/sesI/shsA-positive, some were in the context of the ΦSPβ-like prophage and devoid of CRISPR systems, indicating potential transferability of their virulence genes. Gene sequencing evidenced that Brazilian S. haemolyticus harbored sesI, instead of the usual sasX, while S. epidermidis had sasX instead of sesI, suggesting horizontal acquisition. Conclusion: The contexts of Brazilian sasX/sesI/shsA favor transfer, which is alarming given the difficulty in treating infections caused by S. haemolyticus.

The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia

Methicillin-resistant Staphylococcus aureus (MRSA) is a priority nosocomial pathogen with plasmids playing a crucial role in its genetic adaptability, particularly in the acquisition and spread of antimicrobial resistance. In this study, the genome sequences of 79 MSRA clinical isolates from Terengganu, Malaysia, (obtained between 2016 and 2020) along with an additional 15 Malaysian MRSA genomes from GenBank were analyzed for their plasmid content. The majority (90%, 85/94) of the Malaysian MRSA isolates harbored 1-4 plasmids each. In total, 189 plasmid sequences were identified ranging in size from 2.3 kb to ca. 58 kb, spanning all seven distinctive plasmid replication initiator (replicase) types. Resistance genes (either to antimicrobials, heavy metals, and/or biocides) were found in 74% (140/189) of these plasmids. Small plasmids (<5 kb) were predominant (63.5%, 120/189) with a RepL replicase plasmid harboring the ermC gene that confers resistance to macrolides, lincosamides, and streptogramin B (MLS_B) identified in 63 MRSA isolates. A low carriage of conjugative plasmids was observed (n = 2), but the majority (64.5%, 122/189) of the non-conjugative plasmids have mobilizable potential. The results obtained enabled us to gain a rare view of the plasmidomic landscape of Malaysian MRSA isolates and reinforces their importance in the evolution of this pathogen.

Staphylococcus spp. Causatives of Infections and Carrier of blaZ, femA, and mecA Genes Associated with Resistance

Staphylococcus spp. have been associated with cases of healthcare associated infections due to their high incidence in isolates from the hospital environment and their ability to cause infections in immunocompromised patients; synthesize biofilms on medical instruments, in the case of negative coagulase species; and change in genetic material, thus making it possible to disseminate genes that code for the acquisition of resistance mechanisms against the action of antibiotics. This study evaluated the presence of blaZ, femA, and mecA chromosomal and plasmid genes of Staphylococcus spp. using the qPCR technique. The results were associated with the phenotypic expression of resistance to oxacillin and penicillin G. We found that the chromosomal femA gene was present in a greater proportion in S. intermedius when compared with the other species analyzed, while the plasmid-borne mecA gene was prevalent in the S. aureus samples. The binary logistic regression performed to verify the association among the expression of the genes analyzed and the acquisition of resistance to oxacillin and penicillin G were not significant in any of the analyses, p > 0.05.

Dispersion and persistence of antimicrobial resistance genes among Staphylococcus spp. and Mammaliicoccus spp. isolated along a swine manure treatment plant

Staphylococcus spp. and Mammaliicoccus spp. colonize the skin and mucosa of humans and other animals and are responsible for several opportunistic infections. Staphylococci antibiotic resistance may be present in the environment due to the spread of treated and untreated manure from the livestock industry due to antibiotic use to disease control or growth promoter. In this work, we analyzed the species distribution and antimicrobial susceptibility of Staphylococcus and Mammaliicoccus species along different sites of a swine manure treatment plant from Southeastern Brazil. Bacterial colonies were obtained on mannitol salt agar, selected after catalase test and Gram staining, and finally identified by mass spectrometry and sequencing of the tuf gene. According to the results, S.cohnii and S. simulans were the most prevalent species. Antibiotic resistance test revealed that several strains were resistant to multiple drugs, with high levels of chloramphenicol resistance (98%), followed by erythromycin (79%), tetracycline (73%), gentamicin (46%), ciprofloxacin (42%), cefoxitin (18%), sulfamethoxazole + trimethoprim (12%), and linezolid (4%). In addition, gene detection by PCR showed that all strains carried at least 2 resistance genes and one of them carried all 11 genes investigated. Using the GTG₅-PCR approach, a high genetic similarity was observed between some strains that were isolated from different points of the treatment plant. Although some were seemingly identical, differences in their resistance phenotype and genotype suggest horizontal gene transfer. The presence of resistant bacteria and resistance genes along the treatment system highlights the potential risk of contamination by people in direct contact with these animals and the soil since the effluent is used as a biofertilizer in the surrounding environment.

Current Limitations of Staph Infection Diagnostics, and the Role for VOCs in Achieving Culture-Independent Detection

Staphylococci are broadly adaptable and their ability to grow in unique environments has been widely established, but the most common and clinically relevant staphylococcal niche is the skin and mucous membranes of mammals and birds. S. aureus causes severe infections in mammalian tissues and organs, with high morbidities, mortalities, and treatment costs. S. epidermidis is an important human commensal but is also capable of deadly infections. Gold-standard diagnostic methods for staph infections currently rely upon retrieval and characterization of the infectious agent through various culture-based methods. Yet, obtaining a viable bacterial sample for in vitro identification of infection etiology remains a significant barrier in clinical diagnostics. The development of volatile organic compound (VOC) profiles for the detection and identification of pathogens is an area of intensive research, with significant efforts toward establishing breath tests for infections. This review describes the limitations of existing infection diagnostics, reviews the principles and advantages of VOC-based diagnostics, summarizes the analytical tools for VOC discovery and clinical detection, and highlights examples of how VOC biomarkers have been applied to diagnosing human and animal staph infections.

Staphylococcus aureus and MRSA in Livestock: Antimicrobial Resistance and Genetic Lineages

Animal production is associated with the frequent use of antimicrobial agents for growth promotion and for the prevention, treatment, and control of animal diseases, thus maintaining animal health and productivity. Staphylococcus aureus, in particular methicillin-resistant S. aureus (MRSA), can cause a variety of infections from superficial skin and soft tissue infections to life-threatening septicaemia. S. aureus represents a serious public health problem in hospital and community settings, as well as an economic and animal welfare problem. Livestock-associated MRSA (LA-MRSA) was first described associated with the sequence (ST) 398 that was grouped within the clonal complex (CC) 398. Initially, LA-MRSA strains were restricted to CC398, but over the years it has become clear that its diversity is much greater and that it is constantly changing, a trend increasingly associated with multidrug resistance. Therefore, in this review, we aimed to describe the main clonal lineages associated with different production animals, such as swine, cattle, rabbits, and poultry, as well as verify the multidrug resistance associated with each animal species and clonal lineage. Overall, S. aureus ST398 still remains the most common clone among livestock and was reported in rabbits, goats, cattle, pigs, and birds, often together with spa-type t011. Nevertheless, a wide diversity of clonal lineages was reported worldwide in livestock.

Genetic Diversity among Methicillin-Resistant Staphylococcus aureus in Malaysia (2002-2020)

1.

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) is a common organism seen in both healthcare-associated and community-associated infections worldwide and in Malaysia over the past two decades. The aim of this review is to provide a firsthand documentation of all MRSA strains prevalent in the Malaysian population from 2002 to present and briefly describe the changing patterns. 2.

METHODS

Electronic and manual intensive literature searches were conducted between 2002 and 2020, addressing issues directly related to patients and published in the English language were selected. 3.

RESULTS

The literature search retrieved a total of 2217 articles and abstracts of 27 articles. The search yielded a total of 24 articles on genotyping of MRSA in Malaysia. The study found that MRSA strains were mostly genetically related and resulted in the predominant MRSA clones that caused active infections. Thirty-six different sequence types (ST) were recorded. The highest rates of STs detected were ST239 (52.6%), ST1 (47.4%), and ST22 (42.1%). The majority of studies showed that both SCCmec types III and IV were the most common SCCm type in Malaysia, followed by SCCmec type V (57.9%). 4.

CONCLUSIONS

Both Brazilian (ST 239 IIIA) and Hungarian (ST 239-III) MRSA strains were detected in Malaysia. PFGE remains the best method for comparing MRSA strains. However, whole-genome sequencing has a promising chance to replace PFGE in the future.

Diversity of endophytic bacterial and fungal microbiota associated with the medicinal lichen Usnea longissima at high altitudes

Endophytic microbial communities of lichen are emerging as novel microbial resources and for exploration of potential biotechnological applications. Here, we focused on a medicinal lichen Usnea longissima, and investigated its bacterial and fungal endophytes. Using PacBio 16S rRNA and ITS amplicon sequencing, we explored the diversity and composition of endophytic bacteria and fungi in U. longissima collected from Tibet at five altitudes ranging from 2,989 to 4,048 m. A total of 6 phyla, 12 classes, 44 genera, and 13 species of the bacterial community have been identified in U. longissima. Most members belong to Alphaproteobacteria (42.59%), Betaproteobacteria (33.84%), Clostridia (13.59%), Acidobacteria (7%), and Bacilli (1.69%). As for the fungal community, excluding the obligate fungus sequences, we identified 2 phyla, 15 classes, 65 genera, and 19 species. Lichen-related fungi of U. longissima mainly came from Ascomycota (95%), Basidiomycota (2.69%), and unidentified phyla (2.5%). The presence of the sequences that have not been characterized before suggests the novelty of the microbiota. Of particular interest is the detection of sequences related to lactic acid bacteria and budding yeast. In addition, the possible existence of harmful bacteria was also discussed. To our best knowledge, this is the first relatively detailed study on the endophytic microbiota associated with U. longissima. The results here provide the basis for further exploration of the microbial diversity in lichen and promote biotechnological applications of lichen-associated microbial strains.

Novel Organization of the Staphylococcal Cassette Chromosome mec Composite Island in Clinical Staphylococcus haemolyticus and Staphylococcus hominis Subspecies hominis Isolates from Dogs

Staphylococcus haemolyticus and Staphylococcus hominis subsp. hominis are common coagulase-negative staphylococcus opportunistic pathogens. In Thailand, the clinical strains S. haemolyticus 1864 and 48 and S. hominis subsp. hominis 384 and 371 have been recovered from sick dogs. These strains were methicillin resistant with the nontypeable staphylococcal cassette chromosome mec (NT-SCCmec). The SCCmec element distribution in the clinical isolates from dogs was analyzed using whole-genome sequencing, which revealed the presence of different SCCmec composite islands (CIs) and gene structure. The SCCmec-CIs of ψSCCmec1864 (13 kb) and ψSCC1864 (11 kb) with a class C1 mec complex but no ccr gene were discovered in S. haemolyticus 1864. The CIs of ψSCCmec48 with a C1 mec complex (28 kb), SCC48 with ccrA4B4 (23 kb), and ψSCC48 (2.6 kb) were discovered in S. haemolyticus 48. In SCC48, insertion sequence IS256 contained an aminoglycoside-resistant gene [aph(2″)-Ia]. Two copies of IS431 containing the tetracycline-resistant gene tet(K) were found downstream of ψSCC48. In S. hominis subsp. hominis, the SCCmec-CI in strain 384 had two separate sections: ψSCCmec384 (20 kb) and SCCars (23 kb). ψSCCmec384 lacked the ccr gene complex but carried the class A mec complex. Trimethoprim-resistant dihydrofolate reductase (dfrC) was discovered on ψSCCmec384 between two copies of IS257. In strain 371, SCCmec VIII (4A) (37 kb) lacking a direct repeat at the chromosomal end was identified. This study found SCCmec elements in clinical isolates from dogs that were structurally complex and varied in their genetic content, with novel organization. IMPORTANCE In Thailand, the staphylococcal cassette chromosome mec (SCCmec) element, which causes methicillin resistance through acquisition of the mec gene, has been studied in clinical coagulase-negative Staphylococcus isolates from various companion animals, and Staphylococcus haemolyticus and Staphylococcus hominis subsp. hominis were found to have the most nontypeable (NT)-SCCmec elements. These species are more prone to causing illness and more resistant to a variety of antimicrobials than other coagulase-negative staphylococci. However, full characterization of NT-SCCmec in clinical S. haemolyticus and S. hominis subsp. hominis isolates from such animals has been limited. Our findings support the use of full nucleotide sequencing rather than PCR designed for Staphylococcus aureus in further research of novel SCCmec elements. Moreover, several antimicrobial resistance and heavy metal resistance genes were identified on the SCCmec elements; these are important as they could limit the therapeutic options available in veterinary medicine.

A Peek into the Bacterial Microbiome of the Eurasian Red Squirrel (Sciurus vulgaris)

Sciurus vulgaris (the Eurasian red squirrel) is native to Europe and Asia, but due to habitat destruction or fragmentation, interspecific competition, and infectious diseases, especially in European island areas the species finds itself at the brink of extinction. The repopulation of such bare habitats requires healthy squirrel specimens, either translocated from other wild habitats or reintroduced to the wilderness following captive breeding. Captivity, nonetheless, has shown an immense capacity to reshape the structure of wild species’ microbiota, adapting it to the less diverse diet and fewer environmental challenges. Therefore, assessing the differences between “wild” and “captive” microbiota in this species could elucidate if special living conditions are needed in order to augment the survival rate of specimens reintroduced into the wild. Furthermore, the microflora profile of the normal flora of healthy red squirrels raised in captivity could support clinicians in addressing infectious diseases episodes and also raise awareness on the zoonotic risk. Hence, this study aimed at documenting the bacterial species carried by S. vulgaris, disclosing overall similarities and variability patterns of the microbiota identified in individuals from two different living environments. We anticipated that the bacterial community would be less diverse in individuals raised in captivity, owing to their restrictive diet and to unchanging conditions in the enclosure. We also hypothesized that there would be a higher prevalence of zoonotic microorganisms in the captive animals, due to the proximity of humans and of other domestic species. To test this, samples (n = 100) were taken from five body regions of 20 red squirrels, both free-ranging and bred in captivity, processed by classical microbiology techniques, and further identified by biochemical assay (VITEK®2 Compact System). A relatively poor bacterial community, comprising 62 bacterial strains belonging to 18 species and 8 different genera, was identified. Most of these microorganisms were reported for the first time in S. vulgaris. With no discrimination between living environments, the highest prevalence (p < 0.001), was registered in Staphylococcus sciuri (60%; 12/20), followed by Escherichia coli (45%; 9/20) and Bacillus cereus (35%; 7/20). The results suggest unremarkable differences in diversity and richness of the resident aerobic microbiota of S. vulgaris, in relation to the living environment.

Interspecies transfer of plasmid-borne gentamicin resistance between Staphylococcus isolated from domestic dogs to Staphylococcus aureus

As preconized by the One Health concept, the intimate relationship between pets and owners is a common source for the trade of microorganisms with zoonotic potential, and with them, antimicrobial resistance genes. In this work, we evaluated the presence of antimicrobial resistance genes, that are usually within mobile genetic elements, in a laboratory collection of 79 canine Staphylococcus strains, mostly Staphylococcus pseudintermedius and Staphylococcus coagulans. Resistance to tetracycline was observed in 34% of the strains, followed by resistance to erythromycin (21%) and gentamicin (19%). These phenotypes were partially correlated with the presence of the tetracycline resistance genes tet(M) and tet(K) in 64% and 44% of all strains, respectively; erythromycin resistance genes erm(A) and erm(C) in 53% and 23%; and gentamicin resistance gene aac(6')-aph(2″) in 26% of the strains. At least 45% of the strains harbored high- and/or low-molecular weight plasmids, whose transfer may be facilitated by their widespread biofilm-forming capacity, and absence of restrictive CRISPR systems. We selected eight plasmid-bearing and multidrug resistant strains, which were submitted to plasmid curing by stress with SDS. No strain lost resistance during stressing cultivation but, by conjugation experiments, the S. pseudintermedius strain 27 transferred its plasmid-borne resistance to gentamicin, conferred by the aac(6')-aph(2″) gene, to Staphylococcus aureus. The frequent empirical use of gentamicin to treat skin and ear infections in domestic dogs is likely to select resistant strains. Also, as demonstrated by our study, these strains can serve as gene reservoirs for human pathogens, such as S. aureus.

Co-occurrence of cfr-mediated linezolid-resistance in ST398 LA-MRSA and non-aureus staphylococci isolated from a pig farm

Linezolid resistance, mediated by the cfr gene, which confers resistant phenotypes to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A antimicrobials, has emerged in S. aureus and non-aureus staphylococci (NAS). Moreover, due to the transferable potential via plasmids, the spread of cfr among staphylococci is of great concern. In the present study, we investigated the prevalence of cfr-mediated linezolid resistance in ST398 methicillin-resistant S. aureus (MRSA) and NAS strains isolated from a pig farm. Among the 26 staphylococci isolates collected from a pig farm, 14 cfr-harboring ST398 MRSA and NAS (S. epidermidis, S. pasteuri, S. cohnii, and S. rostri) strains were resistant to linezolid and also carried the fexA gene. Comparative genome analysis of cfr-carrying linezolid-resistant ST398 MRSA and NAS (S. pasteuri, S. cohnii, and S. epidermidis) strains revealed that the segments harboring cfr in different staphylococcal strains showed ≥ 99 % sequence identity and the corresponding region containing the cfr, fexA, and Tn558 elements were located in a 38-kb plasmid, designated pSA12 of ST398 MRSA. These observations indicate that the cfr-carrying plasmids and/or fragments may be disseminated among staphylococci in a pig farm and possibly transmitted to staphylococci of human origin, subsequently posing a threat to public health. This is the first report of the co-existence of cfr in linezolid-resistant ST398 MRSA and NAS isolated from a pig farm in South Korea.

Wild Animals Are Reservoirs and Sentinels of Staphylococcus aureus and MRSA Clones: A Problem with "One Health" Concern

Background: The availability of comprehensive data on the ecology and molecular epidemiology of Staphylococcus aureus/MRSA in wild animals is necessary to understand their relevance in the "One Health" domain. Objective: In this study, we determined the pooled prevalence of nasal, tracheal and/or oral (NTO) Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA) carriage in wild animals, with a special focus on mecA and mecC genes as well as the frequency of MRSA and methicillin susceptible S. aureus (MSSA) of the lineages CC398 and CC130 in wild animals. Methodology: This systematic review was executed on cross-sectional studies that reported S. aureus and MRSA in the NTO cavities of wild animals distributed in four groups: non-human primates (NHP), wild mammals (WM, excluding rodents and NHP), wild birds (WB) and wild rodents (WR). Appropriate and eligible articles published (in English) between 1 January 2011 to 30 August 2021 were searched for from PubMed, Scopus, Google Scholar, SciElo and Web of Science. Results: Of the 33 eligible and analysed studies, the pooled prevalence of NTO S. aureus and MRSA carriage was 18.5% (range: 0-100%) and 2.1% (range: 0.0-63.9%), respectively. The pooled prevalence of S. aureus/MRSA in WM, NHP, WB and WR groups was 15.8/1.6, 32.9/2.0, 10.3/3.4 and 24.2/3.4%, respectively. The prevalence of mecC-MRSA among WM/NHP/WB/WR was 1.64/0.0/2.1/0.59%, respectively, representing 89.9/0.0/59.1/25.0% of total MRSA detected in these groups of animals.The MRSA-CC398 and MRSA-CC130 lineages were most prevalent in wild birds (0.64 and 2.07%, respectively); none of these lineages were reported in NHP studies. The MRSA-CC398 (mainly of spa-type t011, 53%), MRSA-CC130 (mainly of spa types t843 and t1535, 73%), MSSA-CC398 (spa-types t571, t1451, t6606 and t034) and MSSA-CC130 (spa types t843, t1535, t3625 and t3256) lineages were mostly reported. Conclusion: Although the global prevalence of MRSA is low in wild animals, mecC-mediated resistance was particularly prevalent among MRSA isolates, especially among WM and WB. Considering the genetic diversity of MRSA in wild animals, they need to be monitored for effective control of the spread of antimicrobial resistance.

Staphylococcus-Induced Bacteriospermia In Vitro: Consequences on the Bovine Spermatozoa Quality, Extracellular Calcium and Magnesium Content

Simple Summary

Livestock semen is often contaminated by opportunistic bacterial pathogens originating from an intrinsic environment of the urogenital tract. Particularly, species classified in the Staphylococcus genus are predominantly represented in bovine ejaculates. Until recently, it was believed that these are a negligible part of the bovine ejaculate; however, recent studies revealed their potentially adverse effects on the sperm quality. Hereby, we simulated staphylococcal infection of bovine semen under laboratory conditions and analyzed its consequences on the sperm quality.

Abstract

Bacterial contamination of bovine ejaculates intended for artificial insemination may be reflected in a significant economic loss due to unsuccessful fertilization as well as health issues of the recipients. The Staphylococcus genus represents a large part of bacteriocenosis of bovine ejaculates. Therefore, this study aims to get a closer look on the effects of Staphylococcus-induced bacteriospermia under in vitro conditions on bovine sperm quality. Prior to inducing bacteriospermia, spermatozoa were separated from each ejaculate using Percoll^® Plus gradient medium in order to limit the effects only to the selected bacterial species. Seven Staphylococcus species previously isolated from bovine semen were used for our experiments at a turbidity of 0.5 McFarland (equivalent to 1.5 × 10⁸ colony-forming units per mL). The contaminated semen samples were incubated at 37 °C and at times of 0, 2, and 4 h, motility, mitochondrial membrane potential, reactive oxygen species (ROS) generation, sperm DNA fragmentation, and magnesium (Mg) and calcium (Ca) extracellular concentration were analyzed and compared with the control group (uncontaminated). The results showed no significant changes at the initial measurement. However, significant adverse effects were observed after 2 h and 4 h of incubation. Most notably, the presence of S. aureus, S. warneri, S. kloosii, and S. cohnii caused a significantly increased ROS production, leading to sperm DNA fragmentation, changes in the mitochondrial membrane potential, and a decreased sperm motility. Furthermore, the presence of Staphylococcus species led to lower extracellular concentrations of Mg and Ca. In conclusion, the overgrowth of Staphylococcus bacteria in bovine semen may contribute to oxidative stress resulting in sperm DNA fragmentation, altered mitochondrial membrane potential, and diminished sperm motility.

Genomic epidemiology of the opportunistic pathogen Staphylococcus coagulans from companion dogs

Introduction

Staphylococcus coagulans (formerly Staphylococcus schleiferi subsp. coagulans) is a common commensal and opportunistic pathogen of companion dogs. It carries a range of antimicrobial resistance genes and is an occasional zoonotic pathogen.

Hypothesis/Gap Statement

Despite the potential insight offered by genome sequencing into the biology of S. coagulans, few genomes are currently available for study.

Aim

To sequence and analyse S. coagulans genomes to improve understanding of this organism’s molecular epidemiology, antimicrobial resistance and bacterium–host interactions.

Methodology

Twenty-five genomes of clinical isolates collected at a veterinary referral hospital in Scotland, UK, were sequenced with Illumina technology. These genomes were analysed by a series of bioinformatics tools along with 16 previously sequenced genomes.

Results

Phylogenetic comparison of the 41 genomes shows that the current S. coagulans phylogeny is dominated by clades of closely related isolates, at least one of which has spread internationally. Ten of the 11 methicillin-resistant S. coagulans genomes in this collection of 41 encoded the mecA promoter and gene mutations that are predicted to render the isolates susceptible to penicillins in the presence of clavulanic acid, a feature only described to date in methicillin-resistant Staphylococcus aureus. Seven such isolates were from the current study and, in line with the genome-based prediction, all were susceptible to amoxicillin/clavulanic acid in vitro. S. coagulans shared very few highly conserved virulence-associated genes with Staphylococcus pseudintermedius, another common commensal and opportunistic canine pathogen.

Conclusion

The availability of a further 25 genome sequences from clinical S. coagulans isolates will aid in better understanding the epidemiology, bacterial–host interactions and antimicrobial resistance of this opportunistic pathogen.

Characterization of biofilms and antimicrobial resistance of coagulase-negative Staphylococcus species involved with subclinical mastitis

Biofilm formation is a central feature to guarantee staphylococcal persistence in hosts and is associated with several diseases that are difficult to treat. In this research paper, biofilm formation and antimicrobial susceptibility were investigated in staphylococcal strains belonging to several species. These strains were isolated from the milk of cows with subclinical mastitis and most of them were coagulase-negative, with the prevalence of Staphylococcus chromogenes. High genetic diversity was observed among the strains by pulsed field gel electrophoresis. Antimicrobial resistance was assessed by disk diffusion and more than 50% of the strains were resistant to ampicillin and penicillin G, with multi-resistance profiles (13.6%) also being observed. Most strains (65.9%) formed biofilms when cultivated in BHI supplemented with 1% glucose. Most strains (72.7%) carried the intercellular adhesion gene (icaA), while less than half (36.3%) carried the biofilm-associated protein gene (bap). Concentrations of up to 10xMIC of erythromycin and tetracycline were not sufficient to suppress cell viability in preformed biofilms. Our results revealed that a genetically diverse group of biofilm-forming Staphylococcus species can be involved in subclinical mastitis. Since high antimicrobial concentrations cannot eradicate biofilm cells in vitro, their use in dairy animals may be ineffective in controlling infections, while supporting selection of resistant microorganisms. These data reinforce the need for alternative therapies aiming at disrupting biofilms for effective disease control.

Draft Genome Sequences of Three Multidrug-Resistant Staphylococcus spp. Isolated from Hospital Wastewater in Malaysia

Staphylococcus spp. are Gram-positive bacteria that reside within the normal microbiota of humans and animals but pose a health threat as reservoirs of antimicrobial resistance genes. Here, we present the draft genome sequences of three Staphylococcus sp. strains isolated from hospital wastewater in Malaysia that demonstrated resistance to multiple antibiotics.

Staphylococcus spp. are Gram-positive bacteria that reside within the normal microbiota of humans and animals but pose a health threat as reservoirs of antimicrobial resistance genes. Here, we present the draft genome sequences of three Staphylococcus sp. strains isolated from hospital wastewater in Malaysia that demonstrated resistance to multiple antibiotics.

Protective efficacy of Hla-MntC-SACOL0723 fusion protein adjuvanted in alum and MPL against Staphylococcus aureus sepsis infection in mice

To develop a suitable and effective vaccine against Staphylococcus aureus (S. aureus), we selected the Hla-MntC-SACOL0723 (HMS) recombinant protein with two different formulations of alum and Monophosphoryl lipid A (MPL) adjuvants. In this study, we aimed to evaluate the potentials of alum and MPL adjuvants in stimulating the immune response of HMS vaccine candidate against S. aureus. To evaluate the type of induced immune response, anti-HMS total IgG, IgG1, IgG2a, and IFN-γ, IL-2, IL-4, and IL-17 cytokines were determined after vaccination of mice with HMS-alum, HMS-MPL candidates. Mice were challenged with Methicillin-resistant Staphylococcus aureus (MRSA) was isolated from pressure sores and evaluated for bacterial load in the kidney homogenates and survival rate. It was observed that total IgG and isotypes (IgG1 and IgG2a), IL-4, and IL-17 were significantly increased in the group that received HMS-alum vaccine compared with the group that received HMS-MPL formulation. On the other hand, the levels of IFN-γ and IL-2 cytokines in the group that received HMS-MPL were higher than the group that received HMS-alum formulation. Bacterial load in the mice who received HMS protein formulated with alum adjuvant was reduced more than the mice who received HMS protein formulated with MPL adjuvant. Histopathological analysis showed more pathological changes in kidney tissues of the group received of HMS-MPL compared with the HMS-alum formulation. The survival rate was equal in both groups of immunized with HMS-alum and HMS-MPL formulations. Finally, it could be concluded that both adjuvants of alum and MPL are suitable immune response enhancers to HMS vaccine candidate.

Draft genome sequence of the producer strain of aureocin 4181, an antimicrobial peptide with antagonistic activity against multidrug-resistant staphylococci

OBJECTIVES

The present study reports the draft genome sequence of Staphylococcus aureus 4181, a strain involved in bovine mastitis that produces aureocin 4181, a broad-spectrum antimicrobial peptide (AMP). Inhibition of multidrug-resistant (MDR) staphylococci involved in human infections by S. aureus 4181 was also investigated.

METHODS

A sequencing library was constructed using a Nextera XT DNA Library Preparation Kit (Illumina). Whole-genome shotgun sequencing was performed using an Illumina MiSeq System. The A5-miseq pipeline was employed for de novo genome assembly. Genome annotation was performed by the RAST server. The online automated tools BAGEL4 and antiSMASH v.5.0 were used for mining gene clusters encoding AMP production. The virulence potential of the strain was investigated employing online tools. Its inhibitory activity toward MDR staphylococcal isolates associated with human infections was tested by the deferred antagonism assay on brain-heart infusion agar medium.

RESULTS

The total scaffold size was determined to be 2 719 949 bp, with a G + C content of 32.7%. Genome analyses revealed 2504 protein-coding sequences and 74 RNA-coding sequences as well as several genes encoding drug resistance and a single AMP gene cluster coding for aureocin 4181. Staphylococcus aureus 4181 exhibited a pathogenic potential and inhibited all MDR staphylococcal isolates tested as a target.

CONCLUSIONS

This study describes the main features of the draft genome of S. aureus 4181, a strain that produces the third four-component bacteriocin described in the literature, namely aureocin 4181. This bacteriocin is a potential alternative drug to control MDR staphylococcal isolates involved in human infections.

Staphylococcins: an update on antimicrobial peptides produced by staphylococci and their diverse potential applications

Staphylococcins are antimicrobial peptides or proteins produced by staphylococci. They can be separated into different classes, depending on their amino acid composition, structural complexity, and steps involved in their production. In this review, an overview of the current knowledge on staphylococcins will be presented with emphasis on the information collected in the last decade, including a brief description of new peptides. Most staphylococcins characterized to date are either lantibiotics or linear class II bacteriocins. Recently, gene clusters coding for production of circular bacteriocins, sactipeptides, and thiopeptides have been mined from the genome of staphylococcal isolates. In contrast to class II bacteriocins, lantibiotics, sactipeptides, and thiopeptides undergo post-translational modifications that can be quite extensive, depending on the peptide. Few staphylococcins inhibit only some staphylococcal species, but most of them have proven to target pathogens belonging to different genera and involved in a variety of infectious diseases of clinical or agronomic importance. Therefore, these peptides exhibit potential application as anti-infective drugs in different areas. This review will also cover this diverse and remarkable potential. To be commercialized, however, staphylococcin production should be cost-effective and result in high bacteriocin yields, which are not generally achieved from the culture supernatant of their native producers. Such low yields make their production quite costly and not suitable at large industrial scale. Efforts already made to overcome this limitation, minimizing costs and time of production of some staphylococcins and employing either chemical synthesis or in vivo biosynthesis, will be addressed in this review as well. KEY POINTS: • Staphylococci produce a variety of antimicrobial peptides known as staphylococcins. • Most staphylococcins are post-translationally modified peptides. • Staphylococcins exhibit potential biotechnological applications. Graphical abstract.

Staphylococcus nepalensis, a commensal of the oral microbiota of domestic cats, is a reservoir of transferrable antimicrobial resistance

Staphylococcus nepalensis is a commensal bacterium from the oral microbiota of domestic cats, with a still obscure clinical importance. In this work, we analysed the ability of feline strains of S. nepalensis to transfer antimicrobial resistance genes to Staphylococcus aureus isolated from humans through plasmids. To this end, we first analysed all publicly available genomes from cat staphylococci using computational methods to build a pan-resistome. Genes that encode resistance to erythromycin, gentamicin, mupirocin and tetracycline, common to human and cat staphylococci and previously described to be located in mobile genetic elements, were chosen for the next analyses. We studied 15 strains of S. nepalensis, which were shown to be genetically different by GTG₅-PCR. As observed by disc diffusion, resistance to tetracycline was widespread (80 %), followed by resistance to erythromycin (40 %), gentamicin (27 %) and mupirocin (7 %). The strains were positive for several antimicrobial resistance genes and more than half of them harboured plasmids. The loss of plasmids and resistance genes in some strains were induced by stress with SDS. Through conjugation experiments, we observed that these plasmids can be transferred to S. aureus, thus increasing its potential to resist drug therapy. Our findings show that S. nepalensis, an underestimated inhabitant of the cat microbiota, can be a reservoir of antimicrobial resistance genes for S. aureus and, like many other staphylococci, be an overlooked and silent threat to their animal hosts and humans living with them.