Staphylococcus aureus in veterinary medicine

Virulence factors and biofilm forming ability of Staphyloccoccus species isolated from skeletal lesions of broiler chickens

Lameness in poultry is a significant issue in modern meat production that adversely affects both animal welfare and economic outcomes due to poor leg health, reduced locomotor function, increased feed conversion ratios, and poor performance. Fast-growing broilers are particularly susceptible to lameness, with Staphylococcus being a major bacterial cause of skeletal infections. The aim of this study was to identify Staphylococcus species isolated from skeletal lesions in broiler chickens and to characterize the factors that facilitate such infections. Bacterial strains were isolated from 25 commercial broiler flocks in eastern Poland. The median prevalence of Staphylococcus in birds per flock was 60%. In total, 47% of the examined chickens and 88% of the examined flocks tested positive for Staphylococcus. The main bone sites affected by staphylococci were the femur (56.7%), femoral head (necrosis) (34.3%), hock joints (9.0%), femoral head (transient necrosis) (9.0%), tibiotarsus (7.5%), foot pads (dermatitis) (3.0%), and stifle (knee) joints (1.5%). Of all 93 Staphylococcus strains, 59% (55/93) were isolated from the femora. Twelve staphylococcal species were identified, all coagulase-negative, where Staphylococcus cohnii (24.7%) was the most prevalent species, followed by S. epidermidis (16.1%), S. hominis (15.1%), S. lentus (10.8%), S. saprophyticus (9.7%), S. chromogenes (8.6%), S. arlettae (4.3%), S. sciuri (4.3%), S. haemolyticus (2.2%), S. xylosus (2.2%), S. carnosus (1.1%), and S. gallinarum (1.1%). Eleven and six different staphylococcal species were implicated in the pathogenesis of femoral and tibiotarsal lesions, respectively. More than one Staphylococcus species was isolated from 47.8% of all Staphylococcus-positive chickens. Nearly all (97.8%) of coagulase-negative staphylococci isolates had biofilm-forming ability, but most of them were categorized as weak biofilm producers. The highest biofilm production was observed in the strains that caused femoral head osteonecrosis and footpad dermatitis. Staphylococcus chromogenes, S. lentus, and S. epidermidis exhibited the highest DNase and/or gelatinase activity. Despite the low prevalence of certain adhesin genes, the eno gene encoding laminin-binding protein was highly represented in staphylococci (75.3%). The study highlights the complex nature of coagulase-negative staphylococcal infections in poultry and underscores the need for further research into their virulence mechanisms and control strategies.

Nutritional Stress Leads to Persistence and Persister-like Growth in Staphylococcus aureus

Staphylococcus aureus is a versatile zoonotic pathogen capable of causing a wide range of infections. Due to the organism's ability to persist, recalcitrant and recurring infections are a major concern for public and animal health. This study investigated the establishment of persistence using two S. aureus strains-ATCC 29740, a bovine mastitis isolate, and USA300, a human clinical isolate-under substrate depletion. This nutritional stress established a persistence phenotype where the strains remained persistent for >120 days at notable concentrations [>2 log10 CFU/mL] and developed persister-like growth, including small colony variant formations. With RT-qPCR, we found the cell density was higher than represented by the plate count while the intracellular ATP remained constant during the persistence phase. These findings indicate that S. aureus has complex survival strategies to support its persistent state, providing a host-specific perspective when addressing recurrent infections in human and animal infectious diseases.

HCAR2 Modulates the Crosstalk between Mammary Epithelial Cells and Macrophages to Mitigate Staphylococcus aureus Infection in the Mouse Mammary Gland

Staphylococcus aureus (S. aureus) is a major zoonotic pathogen, with mammary gland infections contributing to mastitis, a condition that poses significant health risks to lactating women and adversely affects the dairy industry. Therefore, understanding the immune mechanisms underlying mammary infections caused by S. aureus is essential for developing targeted therapeutic strategies against mastitis. This study identified hydroxycarboxylic acid receptor 2 (HCAR2) as a potential regulator of S. aureus infection in mammary glands. It is demonstrated that HCAR2 deficiency exacerbates the inflammatory response and disrupts the blood-milk barrier in the mammary gland during S. aureus infection, with NLRP3 inflammasome-mediated pyroptosis playing a central role. Activation of HCAR2, on the other hand, suppressed CMPK2 expression, thereby mitigating mitochondrial damage and pyroptosis in mouse mammary epithelial cells (mMECs) induced by S. aureus. Additionally, mitochondrial DNA (mtDNA) released from S. aureus-infected mMECs activates the cGAS/STING signaling pathway in macrophages, impairing their bactericidal activity. In conclusion, this study highlights the critical role of HCAR2 in S. aureus infection of the mammary gland and provides a theoretical basis for identifying potential therapeutic targets for such infections.

Understanding the bovine mastitis co-infections: Coexistence with Enterobacter alters S. aureus antibiotic susceptibility and virulence phenotype

The World Health Organization recently reported an alarming evolution and spread of antibiotic resistance, a global risk factor recognized as a One Health challenge. In veterinary, the general lack of clear treatment guidelines often leads to antibiotic misuse. Bovine mastitis is responsible for major economic losses and the main cause of antibiotic administration in the dairy industry, favoring the emergence of multi-resistant phenotypes. The complexity of inter-microbial and host-pathogen interactions in the mammary gland, demonstrated by culture-independent techniques, not only complicates the prediction of antibiotic treatment outcomes but also underscores the urgent need for further research in this field. This work evaluated the interactions between S. aureus L33 and Enterobacter sp. L34 obtained from an intramammary co-infection. The behavior of the dual-species culture resembled that of the Enterobacter monoculture in all the evaluated contexts. Most of the selected S. aureus virulence factors and the antibiotic susceptibility were altered by coexisting with Enterobacter. Under the protection of Enterobacter, S. aureus was able to survive upon exposure to concentrations of cloxacillin and other antibiotics that would be bactericidal for the monoculture. This could have serious implications for bacterial clearance of mastitis originating from the underestimated co-infections. These findings highlight the importance of broadening our knowledge of how microbial interactions in intramammary infections could contribute to antibiotic treatments failures. Moreover, they open new perspectives for the design of bovine mastitis therapies that consider the ecological context in order to optimize the antibiotic usage, improve the success rates and reduce antibiotic resistance.

Inferring Staphylococcus aureus host species and cross-species transmission from a genome-based model

BACKGROUND

Staphylococcus aureus is an important pathogen that can colonize humans and various animals. However, the host-associated determinants of S. aureus remain uncertain, which leads to difficulties in inferring its host species and cross-species transmission. We performed a 3-stage genome-wide association study (discovery, confirming, and validation) to compare genetic variation between pig and human S. aureus, aiming to elucidate the host-specific genetic elements (k-mers).

RESULTS

After 3-stage association analyses, we found a subset of 20 consensus-significant host-associated k-mers, which are significantly overrepresented in a specific host. Surprisingly for host prediction, both the final model with the top 5 k-mers and the simplest model with only the most important k-mer achieved a high classification accuracy of 98%, giving a simple target for predicting host species and cross-species transmission of S. aureus. The final classifier with the top 5 k-mers revealed that 97.5% of S. aureus isolates from livestock-exposed workers were predicted as pig origin, suggesting a high cross-species transmission risk. The time-based phylogeny inferred the cross-species transmission directions, indicating that ST9 can cross-species spread from animals to humans while ST59 can cross-species spread in the opposite direction.

CONCLUSION

Our findings provide novel insights into host-associated determinants and an accurate model for inferring S. aureus host species and cross-species transmission.

Sample-to-answer microfluidic device towards the point-of-need detection of Staphylococcus aureus enterotoxin genes in ruminant milk

Milk is commonly screened both for indicators of animal disease and health, but also for foodborne hazards. Included in these analyses is the detection of Staphylococcus aureus, that can produce an enterotoxin, causing staphylococcal food poisoning (SFP), which often leads to sudden onset of significant gastrointestinal symptoms in humans. Epidemiological data on SFP are limited, particularly in low- and middle-income countries. Many conventional assays for the detection of staphylococcal enterotoxins rely on the detection of the genes coding for them, either directly in food samples or after bacterial culture. Currently, many of the nucleic acid-based methods used require specific expertise and equipment, whilst bacterial culture takes 24-48 hours; both are contributory factors that limit efforts either during food safety emergencies or routine screening. Here we present the development of a "sample-to-answer" isothermal nucleic acid loop-mediated amplification (LAMP) assay in a microfluidic device for the detection of Staphylococcus aureus enterotoxin genes in ruminant milk. A multiplex LAMP assay targeting two of the most prevalent S. aureus enterotoxin-encoding genes (A and B) was integrated into a microfluidic device combining simple 1 : 10 dilution for sample preparation and a lateral flow assay for easy readout. We achieved a limit of detection of 104 colony forming units per ml in spiked cow and goat milk samples, an order of magnitude more sensitive than the European recommendation for the maximum allowable presence of coagulase-positive staphylococci in raw milk. The assay showed no cross-reactivity in detecting other tested non-enterotoxigenic S. aureus strains or associated foodborne pathogens. The test integrated the simplicity of use of microfluidic devices with the sensitivity, specificity and rapidity of a nucleic acid-based assay, and a simple lateral flow readout to provide an appropriate device to ensure the safety of milk for human consumption. To illustrate its potential for point-of-need practical applications, the test was performed in agricultural settings in rural Turkey in a limited feasibility exercise.

Antimicrobial Susceptibility Profiles of Commensal Staphylococcus spp. Isolates from Chickens in Hungarian Poultry Farms Between 2022 and 2023

BACKGROUND

Antimicrobial resistance is one of the greatest challenges of our time, urging researchers in both veterinary and public health to engage in collaborative efforts, thereby fostering the One Health approach. Infections caused by Staphylococcus species can not only lead to significant diseases in poultry but also pose serious threats to human life, particularly in hospital (nosocomial) infections; therefore, it is crucial to identify their antimicrobial resistance.

METHODS

Our objective was to assess the susceptibility profile of commensal Staphylococcus aureus strains (n = 227) found in commercial chicken flocks in Hungary through the determination of minimum inhibitory concentration (MIC) values.

RESULTS

Based on our findings, resistance to tiamulin (82.8%; 95% CI: 77.4-87.2%) and doxycycline (74.4%; 95% CI: 68.5-79.7%) is the most critical. The 55.1% (95% CI: 48.8-61.3%) resistance rate to enrofloxacin, a critically important antimicrobial, is also concerning. The fact that 58.6% (95% CI: 52.4-64.5%) of the strains were resistant to amoxicillin and 35.7% (95% CI: 29.7-42.1) were resistant to amoxicillin-clavulanic acid suggests that a proportion of the strains produce β-lactamase. Comparing our results with the available human hospital data, it was found that resistance to macrolide antibiotics is similarly high in both cases.

CONCLUSIONS

Our findings highlight the necessity of conducting regular surveillance studies, which would allow the monitoring of future temporal trends. This information could benefit practitioners making clinical decisions to successfully treat infections. To uncover the underlying causes of multidrug resistance, next-generation sequencing can be employed to elucidate the genetic basis of phenotypic resistance.

Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis

Pathogens newly invading a host must compete with resident microbiota. This within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a natural microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but maintained its virulence across generations. Conversely, pathogen populations and microbiota passaged in isolation caused more host harm relative to their respective no-host controls. For the evolved pathogens, this increase in virulence was partly mediated by enhanced biofilm formation and expression of the global virulence regulator agr. Whole genome sequencing revealed shifts in the mode of selection from directional (on pathogens evolving in isolation) to fluctuating (on pathogens evolving in host microbiota). This approach also revealed that competitive interactions with the microbiota drove early pathogen genomic diversification. Metagenome sequencing of the passaged microbiota shows that evolution in pathogen-infected hosts caused a significant reduction in community stability (dysbiosis), along with restrictions on the co-existence of some species based on nutrient competition. Our study reveals how microbial competition during novel infection could determine the patterns and processes of evolution with major consequences for host health.

Impact of extracellular enzymes on Staphylococcus aureus host tissue adaptation and infection

Staphylococcus aureus is a multi-host pathogen that can colonize and infect both humans and livestock in a tissue-specific manner. This amazing feature of the pathogen is mainly facilitated by the surplus virulence agents produced upon necessity and favorable environmental factors. These factors are adept at damaging cellular barriers, manipulating host immune factors, and circumventing the host complement system. The delicate balance between the timely release of virulent factors and the regulation of their production underscores the significance of the exoenzyme network. Moreover, the intricate relationship between the pathogen and host tissue highlights the importance of understanding tissue-specific phenotypes for effective therapeutic strategies. Here, we provide a review on the diverse role played by the extracellular enzymes of S. aureus in tissue-specific infection and systemic colonization leading to distinctive diseased conditions. The article highlights the need to study the role of staphylococcal exoenzymes in various systemic invasions, their impact on the deterioration of host tissue, and the regulation of S. aureus virulence factors.

Environmental stressors and zoonoses in the Arctic: Learning from the past to prepare for the future

The risk of zoonotic disease transmission from animals to humans is elevated for people in close contact with domestic and wild animals. About three-quarters of all known human infectious diseases are zoonotic, and potential health impacts of these diseases are higher where infectious disease surveillance and access to health care and public health services are limited. This is especially the case for remote circumarctic regions, where drivers for endemic, emerging, and re-emerging zoonotic diseases include anthropogenic influences, such as pollution by long-range transport of industrial chemicals, climate change, loss of biodiversity and ecosystem alterations. In addition to these, indirect effects including natural changes in food web dynamics, appearance of invasive species and thawing permafrost also affect the risk of zoonotic disease spill-over. In other words, the Arctic represents a changing world where pollution, loss of biodiversity and habitat, and maritime activity are likely driving forward occurrence of infectious diseases. As a broad international consortium with a wide range of expertise, we here describe a selection of case studies highlighting the importance of a One Health approach to zoonoses in the circumarctic, encompassing human health, animal health, and environmental health aspects. The cases highlight critical gaps in monitoring and current knowledge, focusing on environmental stressors and lifestyle factors, and they are examples of current occurrences in the Arctic that inform on critically needed actions to prepare us for the future. Through these presentations, we recommend measures to enhance awareness and management of existing and emerging zoonoses with epidemic and pandemic potential while also focusing on the impacts of various environmental stressors and lifestyle factors on zoonoses in the Arctic.

Improved ability to utilize lactose and grow in milk as a potential explanation for emergence of the novel bovine Staphylococcus aureus ST5477

Staphyloccous aureus belonging to sequence type 5477 have recently been identified as a predominant clone causing bovine mastitis in Rwanda and Tanzania. We compared nine S. aureus ST5477 to 17 isolates belonging to other sequence types by their biochemical profile and ability to acidify milk and grow in minimum media containing lactose. We found that ST5477 isolates all were positive in ONPG (o-nitrophenyl-β-D-galactopyranoside) test and negative for mannitol fermentation potentially challenging the correct identification of this sequence type as S. aureus. In addition, ST5477 isolates were all much faster in acidifying milk and grew faster in minimal media with lactose compared to other strains suggesting an increased lactose utilization and thereby adaptation to the bovine udder environment as a possible reason for the recent successful emergence. Comparison of the lac gene region of the genome of a recently sequenced ST5477 and that of S. aureus reference genome showed that both strains contained the known lacABCD genes involved in the lactose degradation, but that ST5477 had a 12 amino-acid deletion and two amino-acid differences in the lac gene transcription regulator, suggesting that increased transcription might play a role. In conclusion, these preliminary data suggests that improved lactose utilization and the ability to grow faster in milk may have been a key feature for the recent success of ST5477 as a bovine adapted clone.

Characterizing Methicillin-Resistant Staphylococcus spp. and Extended-Spectrum Cephalosporin-Resistant Escherichia coli in Cattle

In the field of cattle medicine in Austria, to date, few studies have investigated the presence of methicillin-resistant Staphylococcus aureus and extended-spectrum β-lactamase-producing Escherichia coli in Austria. For this reason, milk and nasal samples were examined for the presence of methicillin-resistant Staphylococcus aureus as well as fecal samples for extended-spectrum cephalosporin-resistant Escherichia coli. The nasal and fecal swabs were collected during the veterinary treatment of calf pneumonia and calf diarrhea. For the milk samples, the first milk jets were milked into a pre-milking cup and then the teats were cleaned and disinfected before the samples were taken. The cows were selected during the veterinary visits to the farms when treatment was necessary due to mastitis. Depending on the severity of the mastitis (acute mastitis or subclinical mastitis), antibiotics and non-steroidal anti-inflammatory drugs were given immediately (acute disease) or after completion of the antibiogram (subclinical disease). Isolates were characterized by a polyphasic approach including susceptibility pheno- and genotyping and microarray-based assays. No methicillin-resistant Staphylococcus aureus was found in the milk samples, but one nasal swab was positive for methicillin-resistant Staphylococcus aureus. Twenty-two Escherichia coli isolates were detected among the fecal samples. All the Escherichia coli isolates were resistant to ceftazidime. In all the Escherichia coli isolates, genes from the blaCTX family were detected with other bla genes or alone; the most frequently observed β-lactamase gene was blaCTX-M-1/15 (n = 20). In total, 63.6% (n = 14) of the isolates exhibited a multidrug-resistant phenotype and one E. coli isolate (4.5%) harbored the AmpC gene. Precisely because the presence of data regarding extended-spectrum cephalosporin-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus in calves and cows in Austria is rare, this study further expands our understanding of antimicrobial resistance in Austrian cattle, which is highly relevant for successful antibiotic therapy in sick cattle.

Novel sequence types and low levels of antimicrobial resistance associated with clinical mastitis in sheep flocks across Scotland

This research paper aimed to demonstrate that mammary secretions provided by sheep farmers across Scotland from cases of clinical mastitis are free from environmental contamination, as well as to provide information on the major bacterial causes of disease and levels of antimicrobial resistance. Mastitis represents one of most significant diseases of small ruminant production worldwide. Staphylococcus aureus, Mannheimia haemolytica, Streptococcus uberis and coagulase-negative Staphylococcal species are common pathogens isolated from cases of sheep mastitis. Sampling kits supplied to 23 farms provided 33 samples for bacteriology, antimicrobial susceptibility testing and genetic analysis. Of the bacterial isolates identified, 60% were S. aureus, 23% M. haemolytica and 7% coagulase-negative staphylococci. Low levels of antimicrobial resistance were identified in the S. aureus isolates which provided novel multi-locus sequence types. In conclusion, this proof-of-concept survey demonstrated that mammary secretions free from environmental contamination may be provided by sheep farmers. It also provided data on the prevalence of antimicrobial resistance associated with clinical mastitis in sheep and will inform on the scale required for larger surveys aiming to improve current strategies for mastitis control in sheep flocks across the UK.

Unravelling the complexity of bovine milk microbiome: insights into mastitis through enterotyping using full-length 16S-metabarcoding

BACKGROUND

Mastitis, inflammation of the mammary gland, is a major disease of dairy cattle and the main cause for antimicrobial use. Although mainly caused by bacterial infections, the aetiological agent often remains unidentified by conventional microbiological culture methods. The aim of this study was to test whether shifts in the bovine mammary gland microbiota can result in initiation or progression of mastitis.

METHODS

Oxford-Nanopore long-read sequencing was used to generate full-length 16S rRNA gene reads (16S-metabarcoding) to characterise the microbial population of milk from healthy and diseased udder of cows classified into five groups based on their mastitis history and parity.

RESULTS

Samples were classified into six enterotypes, each characterised by a marker genus and several differentially-abundant genera. Two enterotypes were exclusively composed of clinical mastitis samples and displayed a marked dysbiosis, with a single pathogenic genus predominating and displacing the endogenous bacterial population. Other mastitis samples (all subclinical and half of the clinical) clustered with those from healthy animals into three enterotypes, probably reflecting intermediate states between health and disease. After an episode of clinical mastitis, clinical recovery and microbiome reconstitution do not always occur in parallel, indicating that the clinical definition of the udder health status does not consistently reflect the microbial profile.

CONCLUSIONS

These results show that mastitis is a dynamic process in which the udder microbiota constantly changes, highlighting the complexity of defining a unique microbiota profile indicative of mastitis.

The interplay between mobilome and resistome in Staphylococcus aureus

Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.

Staphylococcal Enterotoxins: Description and Importance in Food

Staphylococcus aureus stands out as one of the most virulent pathogens in the genus Staphylococcus. This characteristic is due to its ability to produce a wide variety of staphylococcal enterotoxins (SEs) and exotoxins, which in turn can cause staphylococcal food poisoning (SFP), clinical syndromes such as skin infections, inflammation, pneumonia, and sepsis, in addition to being associated with the development of inflammation in the mammary glands of dairy cattle, which results in chronic mastitis and cell necrosis. SEs are small globular proteins that combine superantigenic and emetic activities; they are resistant to heat, low temperatures, and proteolytic enzymes and are tolerant to a wide pH range. More than 24 SE genes have been well described (SEA-SEE, SEG, SEH, SEI, SEJ, SElK, SElL, SElM, SElN, SElO, SElP, SElQ, SElR, SElS, SElT, SElU, SElV, SElW, SElX, SElY, and SElZ), being a part of different SFP outbreaks, clinical cases, and isolated animal strains. In recent years, new genes (sel26, sel27, sel28, sel31, sel32, and sel33) from SEs have been described, as well as two variants (seh-2p and ses-3p) resulting in a total of thirty-three genes from Ses, including the nine variants that are still in the process of genetic and molecular structure evaluation. SEs are encoded by genes that are located in mobile genetic elements, such as plasmids, prophages, pathogenicity islands, and the enterotoxin gene cluster (egc), and housed in the genomic island of S. aureus. Both classical SEs and SE-like toxins (SEls) share phylogenetic relationships, structure, function, and sequence homology, which are characteristics for the production of new SEs through recombination processes. Due to the epidemiological importance of SEs, their rapid assessment and detection have been crucial for food security and public health; for this reason, different methods of identification of SEs have been developed, such as liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS), molecular methods, and whole-genome sequencing; providing the diagnosis of SEs and a better understanding of the occurrence, spread, and eradication of SEs. This review provides scientific information on the enterotoxins produced by S. aureus, such as structural characteristics, genetic organization, regulatory mechanisms, superantigen activity, mechanisms of action used by SEs at the time of interaction with the immune system, methods of detection of SEs, and recent biocontrol techniques used in food.

Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing

Outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) are well described in the neonatal intensive care unit (NICU) setting. Genomics has revolutionized the investigation of such outbreaks; however, to date, this has largely been completed retrospectively and has typically relied on short-read platforms. In 2022, our laboratory established a prospective genomic surveillance system using Oxford Nanopore Technologies sequencing for rapid outbreak detection. Herein, using this system, we describe the detection and control of an outbreak of sequence-type (ST)97 MRSA in our NICU. The outbreak was identified 13 days after the first MRSA-positive culture and at a point where there were only two known cases. Ward screening rapidly defined the extent of the outbreak, with six other infants found to be colonized. There was minimal transmission once the outbreak had been detected and appropriate infection control measures had been instituted; only two further ST97 cases were detected, along with three unrelated non-ST97 MRSA cases. To contextualize the outbreak, core-genome single-nucleotide variants were identified for phylogenetic analysis after de novo assembly of nanopore data. Comparisons with global (n=45) and national surveillance (n=35) ST97 genomes revealed the stepwise evolution of methicillin resistance within this ST97 subset. A distinct cluster comprising nine of the ten ST97-IVa genomes from the NICU was identified, with strains from 2020 to 2022 national surveillance serving as outgroups to this cluster. One ST97-IVa genome presumed to be part of the outbreak formed an outgroup and was retrospectively excluded. A second phylogeny was created using Illumina sequencing, which considerably reduced the branch lengths of the NICU isolates on the phylogenetic tree. However, the overall tree topology and conclusions were unchanged, with the exception of the NICU outbreak cluster, where differences in branch lengths were observed. This analysis demonstrated the ability of a nanopore-only prospective genomic surveillance system to rapidly identify and contextualize an outbreak of MRSA in a NICU.

Phenotypic and Genotypic Characterization of Staphylococcus aureus Isolated from Nasal Samples of Healthy Dairy Goats in Algeria

The present study aimed to determine the phenotypic and genotypic characteristics of S. aureus isolates from the nasal swabs of goats. A total of 232 nasal samples (one per animal) were collected from goats on 13 farms located in two regions of Algeria and were analyzed for the presence of S. aureus. The detection of virulence factors was carried out using PCR. The antibiotic susceptibility of the recovered isolates was assessed using the disc diffusion method. The biofilm formation ability was assessed by the Congo red agar method and a microtiter plate assay, and the molecular characterization of isolates was carried out by spa-typing, and for selected isolates also by multilocus sequence typing (MLST). Overall, 36 out of 232 nasal swabs (15.5%) contained S. aureus, and 62 isolates were recovered. Regarding the virulence factors, at least one staphylococcal enterotoxin gene was detected in 30 (48.4%) isolates. The gene tst encoding the toxic shock syndrome toxin was detected in fifteen isolates (24.2%), but none of the isolates harbored the gene of Panton-Valentine leukocidin (lukF/S-PV). Nine different spa-types were identified, including the detection of a new one (t21230). The recovered isolates were assigned to three clonal complexes, with CC5 (51.8%) being the most common lineage. Two isolates were methicillin-resistant (MRSA) and belonged to ST5 (CC5) and to spa-types t450 and t688. Moreover, 27 (43.5%) of the S. aureus isolates were found to be slime producers in Congo red agar, and all of the recovered isolates could produce biofilms in the microtiter plate assay. Our study showed that the nares of healthy goats could be a reservoir of toxigenic and antibiotic-resistant strains of S. aureus isolates, including MRSA, which could have implications for public health.

Distribution and prevalence of enterotoxigenic Staphylococcus aureus and staphylococcal enterotoxins in raw ruminants' milk: A systematic review

Enterotoxins produced by Staphylococcus aureus are a common cause of food poisoning, leading to significant gastrointestinal symptoms and even hospitalization. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we searched three electronic databases for studies on detection of staphylococcal enterotoxins or enterotoxigenic S. aureus in raw ruminant milk. The 128 studies included in this systematic review showed a worldwide distribution of studies on staphylococcal enterotoxins and enterotoxigenic S. aureus, with an increase in the number from 1980 to 2021, a shift in detection methods from enterotoxins to enterotoxin genes, and a preponderance of studies from Europe and South America. Most studies focused on milk from individual animals with mastitis, especially cattle. Based on 24 studies, the within-herd prevalence of enterotoxigenic S. aureus in raw milk samples was 11.6%. Many studies failed to report the health status of sampled animals, or the numerator and denominator data needed for prevalence calculation. Cultural and legislative differences, economic status, diagnostic capabilities, and public awareness are all likely factors contributing to the observed distribution of studies. Our review highlighted a significant gap in quality and completeness of data reporting, which limits full assessment of prevalence and distribution of hazards posed by raw milk.

A look at staphylococci from the one health perspective

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

Occurrence and Antimicrobial Resistance of Staphylococcus aureus Isolated from Healthy Pet Rabbits

Background: Staphylococcus aureus is a ubiquitous microorganism and an opportunistic pathogen responsible for numerous diseases in humans and animals, characterized by different clinical pictures with acute or subacute course. S. aureus, due to its great adaptability and versatility in terms of infections and hosts, can be considered a relevant pathogen because of the harmful effects on animal health and its potential for transmission from animals to humans and vice versa. In recent years, a marked increase in multidrug-resistant S. aureus has been reported, posing a serious threat for disease management, food safety, and animal and human health as they limit available therapeutic options. In light of a growing interest of the scientific community for this micro- organism and considering the limited data availability on the prevalence of this pathogen in pet rabbits, the purpose of this research was to evaluate the presence of S. aureus in pet rabbits. Materials and Methods: From November 2021 to December 2022, nasal swabs were collected from 50 pet rabbits from private households in the Campania Region, southern Italy, and underwent analysis for S. aureus detection. Samples were enriched in broth, then inoculated onto nutrient and selective media, including Blood agar base supplemented with 7% sheep blood and Baird-Parker Agar Base, following standard laboratory protocols. Incubations in aerobic conditions at 37°C were performed for 24/48h for colony identification. Antimicrobial susceptibility testing for all S. aureus isolates was conducted using the disc diffusion method. Results: Our results reported the presence of S. aureus in 16/50 (32%) rabbits examined, showing high levels of phenotypic resistance to different antibiotics, in particular penicillin 10U (81.2%) and erythromycin 15 μg (62.5%). Conclusion: The study demonstrated that pet rabbits represent a significant reservoir of S. aureus and contributes to the knowledge on the phenotypic antimicrobial resistance of these bacteria in rabbits raised in a domestic environment.

Is Galleria mellonella model a good alternative to study virulence in Staphylococcus aureus from bovine mastitis?

Staphylococcus aureus is one of the agents of bovine mastitis of hardest control due to a complex pathogenesis comprising a variety of virulence factors, which ensures its persistence in the mammary gland, causing significant health and economic losses. Therefore, understanding the pathogenesis of this agent is imperative. Galleria mellonella has stood out as an invertebrate animal model for the study of infectious diseases that affect several hosts. This work aimed to evaluate G. mellonella larvae as an experimental model for the study of virulence phenotypes in an S. aureus population isolated from bovine mastitis. Thirty genetically divergent S. aureus strains were chosen based on PFGE analysis. After experimental infection, larvae survival rates, bacterial growth in hemolymph, melanization intensity of the dorsal vessel, and histological characteristics of the infected tissues were evaluated. The G. mellonella model showed a clear diversity in the S. aureus pathogenicity pattern, allowing the differentiation of strains with virulence phenotypes ranging from high to low degrees. Histological analysis confirmed that the strains tested were capable of inducing the formation of nodules and melanization spots in the dorsal vessels of the larvae in different magnitudes. The strains 16S-717, 19C-828, and 31S-1443 presented the highest virulence intensity among the bacteria tested and will be used further for the generation of S. aureus mutant populations to prospect genetic targets aimed to develop control strategies of bovine mastitis. Altogether, our results suggest that G. mellonella is an attractive and low-cost animal model for characterizing virulence phenotypes of large S. aureus populations.

Anti-staphylococcal activity of soilless cultivated cannabis across the whole vegetation cycle under various nutritional treatments in relation to cannabinoid content

Antibiotic resistance in staphylococcal strains and its impact on public health and agriculture are global problems. The development of new anti-staphylococcal agents is an effective strategy for addressing the increasing incidence of bacterial resistance. In this study, ethanolic extracts of Cannabis sativa L. made from plant parts harvested during the whole vegetation cycle under various nutritional treatments were assessed for in vitro anti-staphylococcal effects. The results showed that all the cannabis extracts tested exhibited a certain degree of growth inhibition against bacterial strains of Staphylococcus aureus, including antibiotic-resistant and antibiotic-sensitive forms. The highest antibacterial activity of the extracts was observed from the 5th to the 13th week of plant growth across all the nutritional treatments tested, with minimum inhibitory concentrations ranging from 32 to 64 µg/mL. Using HPLC, Δ9-tetrahydrocannabinolic acid (THCA) was identified as the most abundant cannabinoid in the ethanolic extracts. A homolog of THCA, tetrahydrocannabivarinic acid (THCVA), reduced bacterial growth by 74%. These findings suggest that the cannabis extracts tested in this study can be used for the development of new anti-staphylococcal compounds with improved efficacy.

Use of Essential Oils to Counteract the Phenomena of Antimicrobial Resistance in Livestock Species

Antimicrobial resistance is an increasingly widespread phenomenon that is of particular concern because of the possible consequences in the years to come. The dynamics leading to the resistance of microbial strains are diverse, but certainly include the incorrect use of veterinary drugs both in terms of dosage and timing of administration. Moreover, the drug is often administered in the absence of a diagnosis. Many active ingredients in pharmaceutical formulations are, therefore, losing their efficacy. In this situation, it is imperative to seek alternative treatment solutions. Essential oils are mixtures of compounds with different pharmacological properties. They have been shown to possess the antibacterial, anti-parasitic, antiviral, and regulatory properties of numerous metabolic processes. The abundance of molecules they contain makes it difficult for treated microbial species to develop pharmacological resistance. Given their natural origin, they are environmentally friendly and show little or no toxicity to higher animals. There are several published studies on the use of essential oils as antimicrobials, but the present literature has not been adequately summarized in a manuscript. This review aims to shed light on the results achieved by the scientific community regarding the use of essential oils to treat the main agents of bacterial infection of veterinary interest in livestock. The Google Scholar, PubMed, SciELO, and SCOPUS databases were used for the search and selection of studies. The manuscript aims to lay the foundations for a new strategy of veterinary drug use that is more environmentally friendly and less prone to the emergence of drug resistance phenomena.

Antimicrobial Resistance Profiles of Staphylococcus Isolated from Cows with Subclinical Mastitis: Do Strains from the Environment and from Humans Contribute to the Dissemination of Resistance among Bacteria on Dairy Farms in Colombia?

Staphylococcus is a very prevalent etiologic agent of bovine mastitis, and antibiotic resistance contributes to the successful colonization and dissemination of these bacteria in different environments and hosts on dairy farms. This study aimed to identify the antimicrobial resistance (AMR) genotypes and phenotypes of Staphylococcus spp. isolates from different sources on dairy farms and their relationship with the use of antibiotics. An antimicrobial susceptibility test was performed on 349 Staphylococcus strains (S. aureus, n = 152; non-aureus staphylococci (NAS), n = 197) isolated from quarter milk samples (QMSs) from cows with subclinical mastitis (176), the teats of cows (116), the milking parlor environment (32), and the nasal cavities of milk workers (25). Resistance and multidrug resistance percentages found for S. aureus and NAS were (S. aureus = 63.2%, NAS = 55.8%) and (S. aureus = 4.6%, NAS = 11.7%), respectively. S. aureus and NAS isolates showed resistance mainly to penicillin (10 IU) (54.1% and 32.4%) and ampicillin (10 mg) (50.3% and 27.0%) drugs. The prevalence of AMR Staphylococcus was higher in environmental samples (81.3%) compared to other sources (52.6-76.0%). In S. aureus isolates, the identification of the blaZ (83.9%), aacAaphD (48.6%), ermC (23.5%), tetK (12.9%), and mecA (12.1%) genes did not entirely agree with the AMR phenotype. We conclude that the use of β-lactam antibiotics influences the expression of AMR in Staphylococcus circulating on dairy farms and that S. aureus isolates from the environment and humans may be reservoirs of AMR for other bacteria on dairy farms.

Absence of Staphylococcus aureus in Wild Populations of Fish Supports a Spillover Hypothesis

Staphylococcus aureus is a human commensal and opportunistic pathogen that also infects other animals. In humans and livestock, where S. aureus is most studied, strains are specialized for different host species. Recent studies have also found S. aureus in diverse wild animals. However, it remains unclear whether these isolates are also specialized for their hosts or whether their presence is due to repeated spillovers from source populations. This study focuses on S. aureus in fish, testing the spillover hypothesis in two ways. First, we examined 12 S. aureus isolates obtained from the internal and external organs of a farmed fish. While all isolates were from clonal complex 45, genomic diversity indicates repeated acquisition. The presence of a φSa3 prophage containing human immune evasion genes suggests that the source was originally human. Second, we tested for S. aureus in wild fish that were isolated from likely sources. In particular, we sampled 123 brown trout and their environment at 16 sites in the remote Scottish Highlands with variable levels of exposure to humans, birds, and livestock. This screen found no S. aureus infection in any of the wild populations or their environment. Together, these results support that the presence of S. aureus in fish and aquaculture is due to spillover from humans rather than specialization. Given the trends of increasing fish consumption, a better understanding of the dynamics of S. aureus spillover in aquaculture will mitigate future risks to fish and human health. IMPORTANCE Staphylococcus aureus is a human and livestock commensal but also an important pathogen responsible for high human mortality rates and economic losses in farming. Recent studies show that S. aureus is common in wild animals, including fish. However, we do not know whether these animals are part of the normal host range of S. aureus or whether infection is due to repeated spillover events from true S. aureus hosts. Answering this question has implications for public health and conservation. We find support for the spillover hypothesis by combining genome sequencing of S. aureus isolates from farmed fish and screens for S. aureus in isolated wild populations. The results imply that fish are unlikely to be a source of novel emergent S. aureus strains but highlight the prominence of the spillover of antibiotic-resistant bacteria from humans and livestock. This may affect both future fish disease potential and the risk of human food poisoning.

Analysis of Retrospective Laboratory Data on the Burden of Bacterial Pathogens Isolated at the National Veterinary Research Institute Nigeria, 2018-2021

Farm animals harbour bacterial pathogens, which are often viewed as important indicators of animal health and determinants of food safety. To better understand the prevalence and inform treatment, we audited laboratory data at the Bacteriology Laboratory of the NVRI from 2018-2021. Antibiotics were classified into seven basic classes: quinolones, tetracyclines, beta-lactams, aminoglycosides, macrolides, nitrofuran, and cephalosporins. Trends were analysed using a generalised linear model with a log link function for the Poisson distribution, comparing proportions between years with an offset to account for the variability in the total number of organisms per year. Avian (73.18%) samples were higher than any other sample. The major isolates identified were Escherichia. coli, Salmonella spp., Klebsiella spp., Staphylococcus spp., Proteus spp., and Pseudomonas spp. We found that antimicrobial resistance to baseline antibiotics increased over the years. Of particular concern was the increasing resistance of Klebsiella spp. to cephalosporins, an important second-generation antibiotic. This finding underscores the importance of farm animals as reservoirs of pathogens harbouring antimicrobial resistance. Effective biosecurity, surveillance, and frugal use of antibiotics in farms are needed because the health of humans and animals is intricately connected.

Genetic diversity, antibiotic resistance, and virulence characteristics of Staphylococcus aureus from raw milk over 10 years in Shanghai

Staphylococcus aureus (S. aureus) is a major cause of foodborne infections and its persistence in raw milk is a multifaceted phenomenon that poses a considerable public health challenge. Our study investigated the prevalence, virulence genes, antibiotic resistance, and genetic characterization of S. aureus in raw milk in six Shanghai districts from 2013 to 2022. At 18 dairy farms, a total of 704 S. aureus strains were isolated from 1799 samples tested for drug sensitivity. The highest rates of antibiotic resistance were ampicillin (96.7 %), sulfamethoxazole (65 %), and erythromycin (21.6 %). Between 2018 and 2022, there was a significant decrease in the resistance rates of ceftiofur, ofloxacin, tilmicosin, erythromycin, clindamycin, amoxicillin-clavulanic acid, and sulfamethoxazole in comparison to the period from 2013 to 2017. There were 205 S. aureus strains chosen for whole genome sequencing (WGS), with no more than 2 strains of the same resistance phenotype from each farm per year. The prevalence of mecA-positive strains was 14.15 %, while other antibiotic resistance-associated genes were observed as follows: blaI (70.21 %), lnu(B) (5.85 %), lsa(E) (5.75 %), fexA (6.83 %), erm(C) (4.39 %), tet(L) (9.27 %), and dfrG (5.85 %). Isolates harboring the immune evasion cluster (IEC) genes (scn, chp, and sak) were predominantly categorized as sequence types (STs) 7, 188, 15, 59, and 398. The predominant cluster complexes were CC97, CC1, CC398, and CC1651. In 2017-2022, there was a transition in CC1 from the highly antibiotic-resistant ST9 strain that emerged between 2013 and 2018 to the low-resistant but highly virulent ST1 strain. Retrospective phylogenetic analysis elucidated the evolutionary history of the isolates and demonstrated that the human-animal host transition of S. aureus was linked to the genesis of MRSA CC398. The implementation of extended surveillance will aid in the development of innovative strategies to avoid the transmission of S. aureus along the dairy food chain and the occurrence of public health events.

Crystal Structure of Staphopain C from Staphylococcus aureus

Staphylococcus aureus is a common opportunistic pathogen of humans and livestock that causes a wide variety of infections. The success of S. aureus as a pathogen depends on the production of an array of virulence factors including cysteine proteases (staphopains)-major secreted proteases of certain strains of the bacterium. Here, we report the three-dimensional structure of staphopain C (ScpA2) of S. aureus, which shows the typical papain-like fold and uncovers a detailed molecular description of the active site. Because the protein is involved in the pathogenesis of a chicken disease, our work provides the foundation for inhibitor design and potential antimicrobial strategies against this pathogen.

Prevalence and characteristics of foodborne pathogens from slaughtered pig carcasses in Korea

The introduction of bacteria into slaughterhouses can lead to microbial contamination in carcasses during slaughter, and the initial level of bacteria in carcasses is important because it directly affects spoilage and the shelf life. This study was conducted to investigate the microbiological quality, and the prevalence of foodborne pathogens in 200 carcasses from 20 pig slaughterhouses across Korea. Distribution of microbial counts were significantly higher for aerobic bacteria at 3.01–4.00 log10 CFU/cm2 (42.0%) and 2.01–3.00 log10 CFU/cm2 (28.5%), whereas most of Escherichia coli showed the counts under 1.00 log10 CFU/cm2 (87.0%) (P < 0.05). The most common pathogen isolated from 200 carcasses was Staphylococcus aureus (11.5%), followed by Yersinia enterocolitica (7.0%). In total, 17 S. aureus isolates from four slaughterhouses were divided into six pulsotypes and seven spa types, and showed the same or different types depending on the slaughterhouses. Interestingly, isolates from two slaughterhouses carried only LukED associated with the promotion of bacterial virulence, whereas, isolates from two other slaughterhouses carried one or more toxin genes associated with enterotoxins including sen. In total, 14 Y. enterocolitica isolates from six slaughterhouses were divided into nine pulsotypes, 13 isolates belonging to biotype 1A or 2 carried only ystB, whereas one isolate belonging to bio-serotype 4/O:3 carried both ail and ystA. This is the first study to investigate microbial quality and the prevalence of foodborne pathogens in carcasses from slaughterhouses nationally, and the findings support the need for ongoing slaughterhouse monitoring to improve the microbiological safety of pig carcasses.

Effective Treatment of Staphylococcus aureus Intramammary Infection in a Murine Model Using the Bacteriophage Cocktail StaphLyse™

Staphylococcus aureus causes intramammary infections (IMIs), which are refractory to antibiotic treatment and frequently result in chronic mastitis. IMIs are the leading cause of conventional antibiotic use in dairy farms. Phage therapy represents an alternative to antibiotics to help better manage mastitis in cows, reducing the global spread of resistance. A mouse mastitis model of S. aureus IMI was used to study the efficacy of a new cocktail of five lytic S. aureus-specific phages (StaphLyse™), administered either via the intramammary (IMAM) route or intravenously (IV). The StaphLyse™ phage cocktail was stable in milk for up to one day at 37 °C and up to one week at 4 °C. The phage cocktail was bactericidal in vitro against S. aureus in a dose-dependent manner. A single IMAM injection of this cocktail given 8 h after infection reduced the bacterial load in the mammary glands of lactating mice infected with S. aureus, and as expected, a two-dose regimen was more effective. Prophylactic use (4 h pre-challenge) of the phage cocktail was also effective, reducing S. aureus levels by 4 log10 CFU per gram of mammary gland. These results suggest that phage therapy may be a viable alternative to traditional antibiotics for the control of S. aureus IMIs.

Prevalence and Molecular Characterization of Methicillin-Resistant Staphylococci (MRS) and Mammaliicocci (MRM) in Dromedary Camels from Algeria: First Detection of SCCmec-mecC Hybrid in Methicillin-Resistant Mammaliicoccus lentus

Dromedary camels are an important source of food and income in many countries. However, it has been largely overlooked that they can also transmit antibiotic-resistant bacteria. The aim of this study was to identify the Staphylococcaceae bacteria composition of the nasal flora in dromedary camels and evaluate the presence of methicillin-resistant Mammaliicoccus (MRM) and methicillin-resistant Staphylococcus (MRS) in dromedary camels in Algeria. Nasal swabs were collected from 46 camels from seven farms located in two different regions of Algeria (M'sila and Ouargla). We used non-selective media to determine the nasal flora, and antibiotic-supplemented media to isolate MRS and MRM. The staphylococcal isolates were identified using an Autoflex Biotyper Mass Spectrometer (MALDI-TOF MS). The mecA and mecC genes were detected by PCR. Methicillin-resistant strains were further analysed by long-read whole genome sequencing (WGS). Thirteen known Staphylococcus and Mammaliicoccus species were identified in the nasal flora, of which half (49.2%) were coagulase-positive staphylococci. The results showed that four out of seven farms were positive for MRS and/or MRM, with a total of 16 isolates from 13 dromedary camels. The predominant species were M. lentus, S. epidermidis, and S. aureus. Three methicillin-resistant S. aureus (MRSA) were found to be ST6 and spa type t304. Among methicillin-resistant S. epidermidis (MRSE), ST61 was the predominant ST identified. Phylogenetic analysis showed clonal relatedness among M. lentus strains, while S. epidermidis strains were not closely related. Resistance genes were detected, including mecA, mecC, ermB, tet(K), and blaZ. An SCCmec type VIII element was found in a methicillin-resistant S. hominis (MRSH) belonging to the ST1 strain. An SCCmec-mecC hybrid element was detected in M. lentus, similar to what was previously detected in M. sciuri. This study highlights that dromedary camels may be a reservoir for MRS and MRM, and that they contain a specific set of SCCmec elements. This emphasizes the need for further research in this ecological niche from a One Health perspective.

Genomic Characterization of Staphylococcus aureus in Wildlife

Staphylococcus aureus is an opportunistic multi-host pathogen that threatens both human and animal health. Animals can act as a reservoir of S. aureus for humans, but very little is known about wild animals’ epidemiological role. Therefore, in this study, we performed a genomic characterization of S. aureus isolates from wildlife, hunters, and their auxiliary hunting animals of Eastern Spain. Of 20 different species, 242 wild animals were examined, of which 28.1% were S. aureus carriers. The common genet, the Iberian ibex, and the European hedgehog were the species with the highest S. aureus carriage. We identified 30 different sequence types (STs), including lineages associated with wild animals such as ST49 and ST581, multispecies lineages such as ST130, ST398, and ST425, and lineages commonly isolated from humans, including ST1 and ST5. The hunters and the single positive ferret shared ST5, ST398, or ST425 with wild animals. In wildlife isolates, the highest resistance levels were found for penicillin (32.8%). For virulence factors, 26.2% of them carried superantigens, while 14.8% harbored the immune evasion cluster (IEC), which indicates probable human origin. Our findings suggest that wild animals are a reservoir of clinically relevant genes and lineages that could have the potential to be transmitted to humans. These data support the notion that wildlife surveillance is necessary to better understand the epidemiology of S. aureus as a pathogen that circulates among humans, animals, and the environment.

Genome sequencing and comparative genomic analysis of bovine mastitis-associated Staphylococcus aureus strains from India

BACKGROUND

Bovine mastitis accounts for significant economic losses to the dairy industry worldwide. Staphylococcus aureus is the most common causative agent of bovine mastitis. Investigating the prevalence of virulence factors and antimicrobial resistance would provide insight into the molecular epidemiology of mastitis-associated S. aureus strains. The present study is focused on the whole genome sequencing and comparative genomic analysis of 41 mastitis-associated S. aureus strains isolated from India.

RESULTS

The results elucidate explicit knowledge of 15 diverse sequence types (STs) and five clonal complexes (CCs). The clonal complexes CC8 and CC97 were found to be the predominant genotypes comprising 21 and 10 isolates, respectively. The mean genome size was 2.7 Mbp with a 32.7% average GC content. The pan-genome of the Indian strains of mastitis-associated S. aureus is almost closed. The genome-wide SNP-based phylogenetic analysis differentiated 41 strains into six major clades. Sixteen different spa types were identified, and eight isolates were untypeable. The cgMLST analysis of all S. aureus genome sequences reported from India revealed that S. aureus strain MUF256, isolated from wound fluids of a diabetic patient, was the common ancestor. Further, we observed that all the Indian mastitis-associated S. aureus isolates belonging to the CC97 are mastitis-associated. We identified 17 different antimicrobial resistance (AMR) genes among these isolates, and all the isolates used in this study were susceptible to methicillin. We also identified 108 virulence-associated genes and discuss their associations with different genotypes.

CONCLUSION

This is the first study presenting a comprehensive whole genome analysis of bovine mastitis-associated S. aureus isolates from India. Comparative genomic analysis revealed the genome diversity, major genotypes, antimicrobial resistome, and virulome of clinical and subclinical mastitis-associated S. aureus strains.

Molecular Basis of Methicillin and Vancomycin Resistance in Staphylococcus aureus from Cattle, Sheep Carcasses and Slaughterhouse Workers

Staphylococcus aureus (S. aureus) is a serious infection-causing pathogen in humans and animal. In particular, methicillin-resistant S. aureus (MRSA) is considered one of the major life-threatening pathogens due to its rapid resistance to several antibiotics in clinical practice. MRSA strains have recently been isolated in a number of animals utilized in food production processes, and these species are thought to be the important sources of the spread of infection and disease in both humans and animals. The main objective of the current study was to assess the prevalence of drug-resistant S. aureus, particularly vancomycin-resistant S. aureus (VRSA) and MRSA, by molecular methods. To address this issue, a total of three hundred samples (200 meat samples from cattle and sheep carcasses (100 of each), 50 hand swabs, and 50 stool samples from abattoir workers) were obtained from slaughterhouses in Egypt provinces. In total, 19% S. aureus was isolated by standard culture techniques, and the antibiotic resistance was confirmed genotypically by amplification nucA gen. Characteristic resistance genes were identified by PCR with incidence of 31.5%, 19.3%, 8.7%, and 7% for the mecA, VanA, ermA, and tet L genes, respectively, while the aac6-aph gene was not found in any of the isolates. In this study, the virulence genes responsible for S. aureus' resistance to antibiotics had the highest potential for infection or disease transmission to animal carcasses, slaughterhouse workers, and meat products.

Bovine Staphylococcus aureus: a European study of contagiousness and antimicrobial resistance

In dairy herds managements, mastitis is the leading cause of economic losses. One of the most important pathogens responsible for intra-mammary infections is Staphylococcus aureus. The genetic properties of S. aureus have a strong influence on its pathogenicity and contagiousness. In this study, we aimed to obtain a comprehensive overview of the key bovine S. aureus clinical properties, such as contagiousness and antimicrobial resistance, present in European strains. For this, 211 bovine S. aureus strains from ten European countries that were used in a previous study were used in this study. Contagiousness was assessed using qPCR for the detection of the marker gene adlb. Antimicrobial resistance was evaluated using a broth microdilution assay and mPCR for the detection of genes involved in penicillin resistance (blaI, blaR1, and blaZ). It was found that adlb was present in CC8/CLB strains; however, in Germany, it was found in CC97/CLI and in an unknown CC/CLR strains. CC705/CLC strains from all countries were found to be susceptible to all tested antibiotics. Major resistance to penicillin/ampicillin, chloramphenicol, clindamycin and tetracycline was detected. Resistance to oxacillin, trimethoprim/sulfamethoxazole and cephalosporins was rarely observed. In addition, contagiousness and antibiotic resistance seem to correlate with different CCs and genotypic clusters. Hence, it is recommended that multilocus sequence typing or genotyping be utilized as a clinical instrument to identify the most appropriate antibiotic to use in mastitis treatment. Actualization of the breakpoints of veterinary strains is necessary to address the existing antibiotic resistance of the bacteria involved in veterinary mastitis.

Vancomycin Resistance in Enterococcus and Staphylococcus aureus

Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.

Review on skeletal disorders caused by Staphylococcus spp. in poultry

Lameness or leg weakness is the main cause of poor poultry welfare and serious economic losses in meat-type poultry production worldwide. Disorders related to the legs are often associated with multifactorial aetiology which makes diagnosis and proper treatment difficult. Among the infectious agents, bacteria of genus Staphylococcus are one of the most common causes of bone infections in poultry and are some of the oldest bacterial infections described in poultry. Staphylococci readily infect bones and joints and are associated with bacterial chondronecrosis with osteomyelitis (BCO), spondylitis, arthritis, tendinitis, tenosynovitis, osteomyelitis, turkey osteomyelitis complex (TOC), bumblefoot, dyschondroplasia with osteomyelitis and amyloid arthropathy. Overall, 61 staphylococcal species have been described so far, and 56% of them (34/61) have been isolated from clinical cases in poultry. Although Staphylococcus aureus is the principal cause of poultry staphylococcosis, other Staphylococcus species, such as S. agnetis, S. cohnii, S. epidermidis, S. hyicus, S. simulans, have also been isolated from skeletal lesions. Antimicrobial treatment of staphylococcosis is usually ineffective due to the location and type of lesion, as well as the possible occurrence of multidrug-resistant strains. Increasing demand for antibiotic-free farming has contributed to the use of alternatives to antibiotics. Other prevention methods, such as better management strategies, early feed restriction or use of slow growing broilers should be implemented to avoid rapid growth rate, which is associated with locomotor problems. This review aims to summarise and address current knowledge on skeletal disorders associated with Staphylococcus spp. infection in poultry.

Bavachin Suppresses Alpha-Hemolysin Expression and Protects Mice from Pneumonia Infection by Staphylococcus aureus

Staphylococcus aureus (S. aureus) infection causes dramatic harm to human health as well as to livestock development. As an important virulence factor, alpha-hemolysin (hla) is critical in the process of S. aureus infection. In this report, we found that bavachin, a natural flavonoid, not only efficiently inhibited the hemolytic activity of hla, but was also capable of inhibiting it on transcriptional and translational levels. Moreover, further data revealed that bavachin had no neutralizing activity on hla, which did not affect the formation of hla heptamers and exhibited no effects on the hla thermal stability. In vitro assays showed that bavachin was able to reduce the S. aureus-induced damage of A549 cells. Thus, bavachin repressed the lethality of pneumonia infection, lung bacterial load and lung tissue inflammation in mice, providing potent protection to mice models in vivo. Our results indicated that bavachin has the potential for development as a candidate hla inhibitor against S. aureus.

Characterization of Staphylococcus aureus Isolates from Bovine Mastitis and Bulk Tank Milk: First Isolation of Methicillin-Susceptible Staphylococcus aureus in Japan

Staphylococcus aureus is one of the most important pathogens in humans as well as in livestock. Particularly, bovine mastitis caused by S. aureus is a serious issue in dairy farms due to disease recurrence. Here, cases of S. aureus-mediated intramammary infection occurring in the Miyagi Prefecture in Japan were monitored from May 2015 to August 2019; a total of 59 strains (49 from bovine milk and 10 from bulk milk) were obtained from 15 dairy farms and analyzed via sequence-based typing methods and antibiotic susceptibility tests. Two pairs of isolates were determined as recurrence cases from the same cows in distinct farms. The sequence type (ST), spa type, and coa type of each pair were the same: one pair showed ST705, t529, and VIb and the other showed ST352, t267, and VIc. In addition, the possession of toxin genes analyzed of each pair was exactly the same. Furthermore, seven oxacillin-sensitive clonal complex 398 isolates were obtained from a single farm. This is the first confirmed case of a Methicillin-Sensitive SA (MSSA) ST398 strain isolated from mastitis-containing cows in Japan. Our findings suggest that nationwide surveillance of the distribution of ST398 strains in dairy farms is important for managing human and animal health.

Virulence Potential of Biofilm-Producing Staphylococcus pseudintermedius, Staphylococcus aureus and Staphylococcus coagulans Causing Skin Infections in Companion Animals

Coagulase-positive staphylococci (CoPS) account for most bacteria-related pyoderma in companion animals. Emergence of methicillin-resistant strains of Staphylococcus pseudintermedius (MRSP), Staphylococcus aureus (MRSA) or Staphylococcus coagulans (MRSC), often with multidrug-resistant (MDR) phenotypes, is a public health concern. The study collection comprised 237 staphylococci (S. pseudintermedius (n = 155), S. aureus (n = 55) and S. coagulans (n = 27)) collected from companion animals, previously characterized regarding resistance patterns and clonal lineages. Biofilm production was detected for 51.0% (79/155), 94.6% (52/55) and 88.9% (24/27) of the S. pseudintermedius, S. aureus and S. coagulans, respectively, and was a frequent trait of the predominant S. pseudintermedius and S. aureus clonal lineages. The production of biofilm varied with NaCl supplementation of the growth media. All S. pseudintermedius and S. aureus strains carried icaADB. Kaplan–Meier survival analysis of Galleria mellonella infected with different CoPS revealed a higher virulence potential of S. aureus when compared with other CoPS. Our study highlights a high frequency of biofilm production by prevalent antimicrobial-resistant clonal lineages of CoPS associated with animal pyoderma, potentially related with a higher virulence potential and persistent or recurrent infections.

Prevalence and molecular characteristics of Staphylococcus aureus in raw milk and milk products in Ethiopia: a systematic review and meta-analysis

Background

Staphylococcus aureus is an important opportunistic pathogen of raw milk and milk products, and the enterotoxins cause food poisoning. Milk and milk products are important reservoirs of enterotoxin-producing S. aureus. The aims of this systematic review were to estimate the pooled prevalence of S. aureus, including methicillin-resistant Staphylococcus aureus (MRSA), and to summarize their molecular characteristics, assess the potential sources of S. aureus contamination in bulk milk and analyse the antimicrobial resistance patterns of the isolates.

Methods

Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we searched publicly available scientific online databases and search engines: PubMed, Research for Life, African Journal Online (AJOL), and Google Scholar. In addition, the reference lists of the identified studies were manually checked for relevant literature. A random effects model using the DerSimonian method was used to compute pooled prevalence estimates, and the data were transformed using variance stabilizing Freeman-Tukey double arcsine transformation.

Results

A total of 38 studies were included in this systematic review. The pooled prevalence of S. aureus was highest in raw cow milk (30.7%), followed by camel milk (19.3%), goat milk (13.6%) and pasteurized milk (3.8%). The pooled prevalence of S. aureus in locally produced soft cheese (ayib) and traditional fermented milk (ergo) was 18.6% and 14.9%, respectively. The pooled prevalence of MRSA in milk and milk products was 0.73%. In this study, 58.9% of S. aureus isolates recovered from milk and milk products harbored at least one type of enterotoxin gene. Raw milk of the three species (cow, goat and camel) showed the highest S. aureus pooled prevalence rate at processing plants (50.3%), followed by milk collection centers (MCCs) (47.1%), selling points (34.5%), farm bulk milk (25.8%), milking buckets (24.8%) and udder milk (20.3%). Water for washing milking utensils (39.3%) was more contaminated than swab samples from farm workers’ nares (31.5%), milkers’ hands (25.9%), MCCs containers (23.8%), bulk tanks (20.4%), udders (15.6%), milking buckets (14.2%) and towels (10%). S. aureus isolates were highly resistant to penicillin G (92%), followed by ampicillin (82%) and amoxicillin (62.6%). The pooled multidrug resistance (MDR) was high (62.1%).

Conclusion

This systematic review revealed a high and increasing level of S. aureus contamination of raw milk from udder to MCCs or processing plants. Enterotoxin genes and MRSA were reported in milk, milk products and samples from farm workers. S. aureus showed resistance to different antimicrobial agents, with β-lactams showing the highest pooled antimicrobial resistance and the level of MDR was high. The results of this study indicated that the consumption of raw milk and milk products may predispose consumers to staphylococcal food poisoning. Application of good hygiene and handling practices across the dairy value chain starting from farm, udder health, milk cooling, heat treatment of milk before drinking and rational use of antibiotics in veterinary medicine can reduce the potential health risks from S. aureus and MRSA contamination of milk and milk products.

Impact of Environmental Conditions on the Protein Content of Staphylococcus aureus and Its Derived Extracellular Vesicles

Staphylococcus aureus, a major opportunistic pathogen in humans, produces extracellular vesicles (EVs) that are involved in cellular communication, the delivery of virulence factors, and modulation of the host immune system response. However, to date, the impact of culture conditions on the physicochemical and functional properties of S. aureus EVs is still largely unexplored. Here, we use a proteomic approach to provide a complete protein characterization of S. aureus HG003, a NCTC8325 derivative strain and its derived EVs under four growth conditions: early- and late-stationary growth phases, and in the absence and presence of a sub-inhibitory concentration of vancomycin. The HG003 EV protein composition in terms of subcellular localization, COG and KEGG categories, as well as their relative abundance are modulated by the environment and differs from that of whole-cell (WC). Moreover, the environmental conditions that were tested had a more pronounced impact on the EV protein composition when compared to the WC, supporting the existence of mechanisms for the selective packing of EV cargo. This study provides the first general picture of the impact of different growth conditions in the proteome of S. aureus EVs and its producing-cells and paves the way for future studies to understand better S. aureus EV production, composition, and roles.

Combination Treatment for Inhibition of the Growth of Staphylococcus aureus with Recombinant SAP8 Endolysin and Nisin

Staphylococcus aureus, a pathogenic species of genus Staphylococcus involved in foodborne illness always remain among the top priorities of the world major concerns. In the present study, we have used recombinant SAP8 endolysin from the bacteriophage SAP8 and commercial nisin to inhibit the viability of pathogenic S. aureus KCTC 3881 cells; however, the approach was not identified as cost-effective. A gradual decrease in the viable S. aureus KCTC 3881 cell counts was observed with an increase in the concentrations of recombinant SAP8 endolysin and nisin. However, combined treatment with recombinant SAP8 endolysin and nisin decreased the viable S. aureus KCTC 3881 cell counts in a significant manner. The combination of 0.01 µM of recombinant SAP8 endolysin with 9 IU/mL and 18 IU/mL of nisin demonstrated a promising decrease in the viable cell counts of the strain. Under the scanning electron microscope, the combination treatment with 0.01 µM of recombinant SAP8 endolysin and 18 IU/mL of nisin showed complete cellular destruction of S. aureus KCTC 3881. We propose that a combination of recombinant SAP8 endolysin and nisin could be a strong alternative to antibiotics to control the growth of S. aureus including MRSA.

Survey of Staphylococcus aureus carriage by free-living red deer (Cervus elaphus): Evidence of human and domestic animal lineages

Staphylococcus aureus is a pathogen that can affect multiple host species. Evidence of transmission between humans and animals and among different animal species has been reported in recent years. In this study, we investigated 284 free-living red deer (Cervus elaphus) in the Central Italian Alps to assess the prevalence and molecular characteristics of S. aureus in nasal and intestinal samples in relation to host features and environmental factors. A prevalence of 90%, 26.2% and 10.7% of S. aureus was detected in nasal rectal swabs and faeces, respectively. Calves had a higher probability of being S. aureus intestinal carriers than adults, especially in females when considering faecal samples. Clonal complex (CC) 425 was the most prevalent lineage (61.5%). This is a lineage known to be widespread in both domestic and free-living animals. It was followed by CC2671 (15.4%) and CC350 (6.4%). A high rate of the phage-borne virulence factor lukM/lukF-P83 was detected in CC425 and CC350. Further lineages, which are known to occur in both humans and animals, were detected sporadically in red deer faeces only, that is, CC7, CC9, CC121 and CC707, harbouring the genes of the penicillinase operon and a gene for macrolide resistance (CC9 and CC121). Methicillin resistance genes mecA and mecC were not found. Our results suggest that free-living red deer may be reservoir for S. aureus in Alpine habitats.

Usefulness of molecular typing methods for epidemiological and evolutionary studies of Staphylococcus aureus isolated from bovine intramammary infections

In cattle, Staphylococcus aureus is a major pathogen of increasing importance due to its association with intramammary infections (IMIs), which are a primary cause of antibiotic use on farms and thus of the rise in antibiotic resistance. Methicillin-resistant S. aureus (MRSA), which are frequently isolated from cases of bovine mastitis, represent a public health problem worldwide. Understanding the epidemiology and the evolution of these strains relies on typing methods. Such methods were phenotypic at first, but more recently, molecular methods have been increasingly utilized. Multiple-locus variable number tandem repeat analysis (MLVA), a high-throughput molecular method for determining genetic diversity and the emergence of host- or udder-adapted clones, appears to be the most useful PCR-based method. Despite the difficulties present in reproducibility, interlaboratory reliability, and hard work, it is agreed that pulsed-field gel electrophoresis (PFGE) remains the gold standard, particularly for short-term surveillance. Multilocus sequence typing (MLST) is a good typing method for long-term and global epidemiological investigations, but it is not suitable for outbreak investigations. Staphylococcal protein A (spa) typing is the most widely used method today for first-line typing in the study of molecular evolution, and outbreaks investigations. Staphylococcal cassette chromosome mec (SCCmec) typing has gained popularity for the evolutionary analysis of MRSA strains. Whole-genome sequencing (WGS) and DNA microarrays that represent relatively new DNA-based technologies, provide more information for tracking antibioresistant and virulent outbreak strains. They offer a higher discriminatory power, but are not suitable for routine use in clinical veterinary medicine at this time. Descriptions of the evolution of these methods, their advantages, and limitations are given in this review.

Role of milk and milk products in the spread of methicillin-resistant Staphylococcus aureus in the dairy production chain

Milk and milk products can harbor a multiple varieties of microorganisms. Therefore, they can be an important source of foodborne pathogens, including multidrug-resistant bacteria. Methicillin-resistant Staphylococcus aureus (MRSA) causes a wide spectrum of infections both in animals and humans. Over the last two decades, the presence of MRSA in foods and food-producing animals, including milk and milk products, has been frequently reported worldwide, raising public health concerns. In order to monitor and prevent foodborne MRSA contamination, it is necessary to understand their sources, the pheno/genotypic characteristics of the strains, and their transmission dynamics. In this review, studies conducted worldwide were summarized in order to assess the prevalence and diversity of MRSA circulating in milk and milk products. The risk factors for the occurrence of MRSA in milk and milk products were also discussed with preventive and control measures to avoid MRSA contamination in the dairy food chain.

Staphylococcus aureus Causing Skin and Soft Tissue Infections in Companion Animals: Antimicrobial Resistance Profiles and Clonal Lineages

Staphylococcus aureus is a relevant agent of skin and soft tissue infections (SSTIs) in animals. Fifty-five S. aureus comprising all SSTI-related isolates in companion animals, collected between 1999 and 2018 (Lab 1) or 2017 and 2018 (Lab 2), were characterized regarding susceptibility to antibiotics and heavy metals and carriage of antimicrobial resistance determinants. Clonal lineages were established by PFGE, MLST and agr typing. Over half of the isolates (56.4%, 31/55) were methicillin-resistant S. aureus (MRSA), and 14.5% showed a multidrug resistance (MDR) phenotype. Resistance was most frequently observed for beta-lactams (81.8%, related to blaZ and/or mecA), fluoroquinolones (56.4%) and macrolides/lincosamides (14.5%, related to erm(A) or erm(C)). The distributions of heavy-metal MICs allowed the detection of non-wild-type populations associated with several resistance genes. The collection showed genetic diversity, with prevalence of clonal lineage ST22-agrI (45.5%, 25/55), comprising only MRSA isolates, and several less frequently detected clones, including ST5-agrII (14.6%, 8/55), ST398-agrI (9.1%, 5/55) and ST72-agrI (7.3%, 4/55). This work highlights the high frequency of SSTI-related MRSA strains that reflect the clonal lineages circulating both in companion animals and humans in Portugal, reinforcing the need for a One Health approach when studying staphylococci causing infections in companion animals.

Diversity and pathogenesis of Staphylococcus aureus from bovine mastitis: current understanding and future perspectives

Staphylococcus aureus is a leading cause of bovine mastitis worldwide. Despite some improved understanding of disease pathogenesis, progress towards new methods for the control of intramammary infections (IMI) has been limited, particularly in the field of vaccination. Although herd management programs have helped to reduce the number of clinical cases, S. aureus mastitis remains a major disease burden. This review summarizes the past 16 years of research on bovine S. aureus population genetics, and molecular pathogenesis that have been conducted worldwide. We describe the diversity of S. aureus associated with bovine mastitis and the geographical distribution of S. aureus clones in different continents. We also describe studies investigating the evolution of bovine S. aureus and the importance of host-adaptation in its emergence as a mastitis pathogen. The available information on the prevalence of virulence determinants and their functional relevance during the pathogenesis of bovine mastitis are also discussed. Although traits such as biofilm formation and innate immune evasion are critical for the persistence of bacteria, the current understanding of the key host-pathogen interactions that determine the outcome of S. aureus IMI is very limited. We suggest that greater investment in research into the genetic and molecular basis of bovine S. aureus pathogenesis is essential for the identification of novel therapeutic and vaccine targets.