Are host genetics the predominant determinant of persistent nasal Staphylococcus aureus carriage in humans?

Characterisation of PVL-Positive Staphylococcus argenteus from the United Arab Emirates

Staphylococcus argenteus is a recently described staphylococcal species that is related to Staphylococcus aureus but lacks the staphyloxanthin operon. It is able to acquire both resistance markers such as the SCCmec elements and mobile genetic elements carrying virulence-associated genes from S. aureus. This includes those encoding the Panton-Valentine leukocidin (PVL), which is associated mainly with severe and/or recurrent staphylococcal skin and soft tissue infections. Here, we describe the genome sequences of two PVL-positive, mecA-negative S. argenteus sequence type (ST) 2250 isolates from the United Arab Emirates in detail. The isolates were found in a dental clinic in the United Arab Emirates (UAE). Both were sequenced using Oxford Nanopore Technology (ONT). This demonstrated the presence of temperate bacteriophages in the staphylococcal genomes, including a PVL prophage. It was essentially identical to the published sequence of phiSa2wa_st78 (GenBank NC_055048), a PVL phage from an Australian S. aureus clonal complex (CC) 88 isolate. Besides the PVL prophage, one isolate carried another prophage and the second isolate carried two additional prophages, whereby the region between these two prophages was inverted. This "flipped" region comprised about 1,083,000 bp, or more than a third of the strain's genome, and it included the PVL prophage. Prophages were induced by Mitomycin C treatment and subjected to transmission electron microscopy (TEM). This yielded, in accordance to the sequencing results, one or, respectively, two distinct populations of icosahedral phages. It also showed prolate phages which presumptively might be identified as the PVL phage. This observation highlights the significance bacteriophages have as agents of horizontal gene transfer as well as the need for monitoring emerging staphylococcal strains, especially in cosmopolitan settings such as the UAE.

Prevalence of Staphylococcus argenteus among food handlers, kitchen utensils, and food samples in Japan

Staphylococcus argenteus has received increased attention from an aspect of food safety since several food poisoning outbreaks caused by the bacterium were reported in Japan. However, S. argenteus prevalence among food handlers and utensils has not yet been investigated. In this study, we investigated S. argenteus prevalence among a collection of coagulase-positive staphylococci (CPS) that were isolated during food sanitary inspections in Japan. Out of a total of 191 CPS isolates, 14 were identified as S. argenteus. One was isolated from shelled shrimp, nine were isolated from food handlers' hand swabs, and four were isolated from kitchen utensils. Whole-genome sequencing revealed that transmission of S. argenteus from human hands to utensils was possible. Though all 14 isolates were negative for the pvl and tst-1 genes, 6 harbored the seb gene. Only 21.4% of S. argenteus isolates were resistant to antibiotics, while 62.1% of the S. aureus isolates from the same sources were confirmed to be resistant. To the best of our knowledge, this is the first report to demonstrate possible transmission of S. argenteus from food handlers to utensils in food-processing environments.

Prevalence and Characteristics of Invasive Staphylococcus argenteus among Patients with Bacteremia in Hong Kong

Staphylococcus argenteus is a novel Staphylococcus species derived from Staphylococcus aureus. Information on the prevalence and genetic characteristics of invasive S. argenteus in Asia is limited. In this study, 275 invasive S. aureus complex strains were retrieved from blood culture specimens in Hong Kong and re-analyzed using MALDI-TOF mass spectrometry and an in-house multiplex real-time PCR for S. argenteus. The prevalence of invasive S. argenteus in Hong Kong was found to be 4.0% (11/275). These strains were primarily susceptible to commonly used antibiotics, except penicillin. Whole-genome sequencing revealed the circulation of three S. argenteus genotypes (ST-2250, ST-1223, and ST-2854) in Hong Kong, with ST-2250 and ST-1223 being the predominant genotypes. The local ST-2250 and ST-1223 strains showed close phylogenetic relationships with isolates from mainland China. Antimicrobial-resistant genes (fosB, tet-38, mepA, blaI, blaZ) could be found in nearly all local S. argenteus strains. The ST-1223 and ST-2250 genotypes carried multiple staphylococcal enterotoxin genes that could cause food poisoning and toxic shock syndrome. The CRISPR/Cas locus was observed only in the ST-2250 strains. This study provides the first report on the molecular epidemiology of invasive S. argenteus in Hong Kong, and further analysis is needed to understand its transmission reservoir.

Staphylococcus aureus and CA-MRSA Carriage among Brazilian Indians Living in Peri-Urban Areas and Remote Communities

The emergence of Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections among indigenous populations has been reported. Usually, indigenous communities live in extreme poverty and are at risk of acquiring infections. In Brazil, healthcare inequality is observed in this population. To date, there are no reports of CA-MRSA infections, and no active search for asymptomatic S. aureus carriage has been conducted among Brazilian Indians. The aim of this study was to investigate the prevalence of colonization with S. aureus and CA-MRSA among Brazilian Indians. We screened 400 Indians (from near urban areas and remote hamlets) for S. aureus and CA-MRSA colonization. The isolates were submitted to clonal profiling by pulsed-field gel electrophoresis (PFGE), and selected isolates were submitted to multilocus sequence typing (MLST). Among 931 specimens (nasal and oral) from different indigenous individuals in remote hamlets, S. aureus was cultured in 190 (47.6%). Furthermore, CA-MRSA was found in three isolates (0.7%), all SCCmec type IV. PFGE analysis identified 21 clusters among the S. aureus isolates, and MLST analysis showed a predominance of sequence type 5 among these isolates. Our study revealed a higher prevalence of S. aureus carriage among Shanenawa ethnicity individuals (41.1%). Therefore, ethnicity appears to be associated with the prevalence of S. aureus in these populations.

Multidrug-Resistant Bacteria: Their Mechanism of Action and Prophylaxis

In the present scenario, resistance to antibiotics is one of the crucial issues related to public health. Earlier, such resistance to antibiotics was limited to nosocomial infections, but it has now become a common phenomenon. Several factors, like extensive development, overexploitation of antibiotics, excessive application of broad-spectrum drugs, and a shortage of target-oriented antimicrobial drugs, could be attributed to this condition. Nowadays, there is a rise in the occurrence of these drug-resistant pathogens due to the availability of a small number of effective antimicrobial agents. It has been estimated that if new novel drugs are not discovered or formulated, there would be no effective antibiotic available to treat these deadly resistant pathogens by 2050. For this reason, we have to look for the formulation of some new novel drugs or other options or substitutes to treat such multidrug-resistant microorganisms (MDR). The current review focuses on the evolution of the most common multidrug-resistant bacteria and discusses how these bacteria escape the effects of targeted antibiotics and become multidrug resistant. In addition, we also discuss some alternative mechanisms to prevent their infection as well.

Staphylococcus aureus-induced immunosuppression mediated by IL-10 and IL-27 facilitates nasal colonisation

Staphylococcus aureus persistently colonises the anterior nares of a significant proportion of the healthy population, however the local immune response elicited during S. aureus nasal colonisation remains ill-defined. Local activation of IL-17/IL-22 producing T cells are critical for controlling bacterial clearance from the nasal cavity. However, recurrent and long-term colonisation is commonplace indicating efficient clearance does not invariably occur. Here we identify a central role for the regulatory cytokine IL-10 in facilitating bacterial persistence during S. aureus nasal colonisation in a murine model. IL-10 is produced rapidly within the nasal cavity following S. aureus colonisation, primarily by myeloid cells. Colonised IL-10^-/- mice demonstrate enhanced IL-17+ and IL-22+ T cell responses and more rapidly clear bacteria from the nasal tissues as compared with wild-type mice. S. aureus also induces the regulatory cytokine IL-27 within the nasal tissue, which acts upstream of IL-10 promoting its production. IL-27 blockade reduces IL-10 production within the nasal cavity and improves bacterial clearance. TLR2 signalling was confirmed to be central to controlling the IL-10 response. Our findings conclude that during nasal colonisation S. aureus creates an immunosuppressive microenvironment through the local induction of IL-27 and IL-10, to dampen protective T cell responses and facilitate its persistence.

Nasal colonisation by the bacterium Staphylococcus aureus is a very common occurrence in the human population. However there is a lack of knowledge on the immune response that controls nasal colonisation. It is known that a local pro-inflammatory immune response is important for bacterial clearance, however sustained colonisation is commonplace suggesting efficient clearance may not be occurring. Here we demonstrate for the first time that S. aureus is manipulating the host immune response by promoting immunosuppression in the nasal cavity which enables bacterial survival. We found that the regulatory proteins IL-10 and IL-27 are central to this suppressive response and result in reduced protective T cell responses. We also demonstrate that S. aureus is inducing IL-27 production to enhance IL-10 production in order to prolong bacterial colonisation. Our findings show that the host-pathogen interaction during nasal colonisation is more complex than previously described and that S. aureus is capable of manipulating the regulatory immune response of the host for its’ own benefit.

Worsening Glycemia Increases the Odds of Intermittent but Not Persistent Staphylococcus aureus Nasal Carriage in Two Cohorts of Mexican American Adults

Numerous host and environmental factors contribute to persistent and intermittent nasal Staphylococcus aureus carriage in humans. The effects of worsening glycemia on the odds of S. aureus intermittent and persistent nasal carriage was established in two cohorts from an adult Mexican American population living in Starr County, Texas. The anterior nares were sampled at two time points and the presence of S. aureus determined by laboratory culture and spa-typing. Persistent carriers were defined by the presence of S. aureus of the same spa-type at both time points, intermittent carriers were S. aureus-positive for 1 of 2 swabs, and noncarriers were negative for S. aureus at both time points. Diabetes status was obtained through personal interview and physical examination that included a blood draw for the determination of percent glycated hemoglobin A1c (%HbA1c), fasting plasma glucose, and other blood chemistry values. Using logistic regression and general estimating equations, the odds of persistent and intermittent nasal carriage compared to noncarriers across the glycemic spectrum was determined controlling for covariates. Increasing fasting plasma glucose and %HbA1c in the primary and replication cohort, respectively, were significantly associated with increasing odds of S. aureus intermittent, but not persistent nasal carriage. These data suggest that increasing dysglycemia is a risk factor for intermittent S. aureus nasal carriage potentially placing those with poorly controlled diabetes at an increased risk of acquiring an S. aureus infection. IMPORTANCE Factors affecting nasal S. aureus colonization have been studied primarily in the context of persistent carriage. In contrast, few studies have examined factors affecting intermittent nasal carriage with this pathogen. This study demonstrates that the odds of intermittent but not persistent nasal carriage of S. aureus significantly increases with worsening measures of dysglycemia. This is important in the context of poorly controlled diabetes since the risk of becoming colonized with one of the primary organisms associated with diabetic foot infections can lead to increased morbidity and mortality.

Antimicrobial Resistance and Molecular Epidemiology of Staphylococcus aureus from Hunters and Hunting Dogs

Several studies have showed that a dog-to-human transmission of Staphylococcus aureus occurs. Hunting dogs do not have as much contact with their owners as dogs that live in the same household as the owners; however, these dogs have contact with their owners during hunting activities as well as when hunting game; therefore, we aimed to isolate S. aureus from hunters and their hunting dogs to investigate a possible S. aureus transmission. Nose and mouth samples were collected from 30 hunters and their 78 hunting dogs for staphylococcal isolation. The species identification was performed using MALDI-TOF. The antimicrobial susceptibility profiles were accessed using the Kirby-Bauer method and respective antimicrobial resistance genes were investigated by PCR. Multilocus sequence typing (MLST) and spa- and agr-typing was performed in all S. aureus isolates. S. aureus were detected in 10 (30%) human samples and in 11 (15.4%) dog samples of which 11 and 5 were methicillin-resistant S. aureus (MRSA). Other staphylococci were identified, particularly, S. pseudintermedius. Most S. aureus isolates were resistant to penicillin, erythromycin, and tetracycline. Evidence of a possible transmission of S. aureus between human and dogs was detected in three hunters and their dogs. S. aureus isolates were ascribed to 10 STs and 9 spa-types. A moderate colonization of S. aureus in hunting dogs and their owners was detected in this study. A few dog-to-dog and dog-to-human possible transmissions were identified.

Evolutionary Divergence of the Novel Staphylococcal Species Staphylococcus argenteus

Currently, invasive infections caused by Staphylococcus argenteus, which is a recently named staphylococcal species, are increasingly reported worldwide. However, only a few genomic studies of S. argenteus have offered comprehensive information regarding its genetic diversity, epidemiological characteristics, antimicrobial resistance genes (ARGs), virulence genes and other profiles. Here, we describe a comparative genomic analysis by population structure, pangenome, panmobilome, region-specific accessory genes confer an adaptive advantage in 153 S. argenteus strains which comprised 24 strains sequenced in this study and 129 strains whose genome sequences were available from GenBank. As a result, the population of S. argenteus comprised seven genetically distinct clades, including two major clades (C1 and C2), with distinct isolation source patterns. Pangenome analysis revealed that S. argenteus has an open pangenome composed of 7,319 genes and a core genome composed of 1,508 genes. We further determined the distributions of 75 virulence factors (VFs) and 30 known ARGs and identified at least four types of plasmids and 93 complete or partial putative prophages. It indicate that S. argenteus may show a similar level of pathogenicity to that of S. aureus. This study also provides insights into the evolutionary divergence of this pathogen, indicating that the geographical distribution was a potential driving force behind the evolutionary divergence of S. argenteus. The preferential horizontal acquisition of particular elements, such as staphylococcal cassette chromosome mec elements and plasmids, was observed in specific regions, revealing potential gene exchange between S. argenteus strains and local S. aureus strains. Moreover, multiple specific genes related to environmental adaptation were identified in strains isolated from East Asia. However, these findings may help promote our understanding of the evolutionary divergence of this bacterium at a high genetic resolution by providing insights into the epidemiology of S. argenteus and may help combat its spread.

Antimicrobial Resistance and Molecular Epidemiological Characteristics of Methicillin-Resistant and Susceptible Staphylococcal Isolates from Oral Cavity of Dental Patients and Staff in Northern Japan

The acquisition of drug resistance and virulence by staphylococcal species colonizing humans is a growing public health concern. The present study was conducted to investigate the prevalence, antimicrobial resistance and genetic characteristics of Staphylococcus isolates from the oral cavity and skin (hand) of systemically healthy subjects with dental disease and dental staff in northern Japan. Among a total of 133 subjects (91 patients and 42 staff), 87 coagulase-positive Staphylococcus (83 S. aureus/4 S. argenteus) and 162 coagulase-negative Staphylococcus (CoNS) isolates were recovered from 59 (44.4%) and 95 (71.4%) subjects, respectively. Three oral isolates were methicillin-resistant S. aureus (MRSA) (3.6%, 3/83) that were genotyped as ST8-SCCmec-IVl, ST4775(CC1)-SCCmec-IVa and ST6562(CC8)-SCCmec-IVa. Remarkably, the ST6562 isolate harbored PVL genes on ΦSa2usa and type I ACME (arginine catabolic mobile element). Four methicillin-susceptible isolates were identified as S. argenteus belonging to ST1223 and ST2250, which harbored enterotoxin genes egc-2 and sey, respectively. Among the fourteen CoNS species identified, methicillin-resistant (MR) isolates were detected in five species (11 isolates, 13.3% of CoNS), with S. saprophyticus and S. haemolyticus being the most common. ACME was prevalent in only S. epidermidis and S. capitis. These findings indicated the potential distribution of USA300 clone-like MRSA, toxigenic S. argenteus and MR-CoNS in the oral cavity of dental patients.

Comparison of Pharmaceutical Characteristics between Brand-Name Meropenem and Its Generics

This study aimed to provide comparative information of pharmaceutical properties, including particle morphology and distribution uniformity, solubility, presence of residual solvent and insoluble particles, and antimicrobial activities, between brand-name meropenem (Mepem^®, BNM) and its six generic products (GPs A-F) marketed in China. Particles of GP-A and -C in dry powder had similar diameters of BNM, while other GPs were larger. Only BNM and GP-A were completely dissolved within 100 s in the lab condition. No insoluble particles >25 μm in diameter were detected in BNM and GP-E. Regarding stability of GPs solutions evaluated by concentration of open-ring metabolites at 6 h and 8 h, BNM showed the lowest open-ringed metabolite concentrates. Residual solvent of acetone detected in one GP showed the maximum value, while ethanol and ethyl acetate were detected both in product E and product F. The concordance rates (%) of minimum inhibitory concentration (MIC) of each generic compared to BNM were 89.5, 85, 87.5, 88, 88.5, and 86.5, respectively, although no significant difference was reached in MIC. Pharmaceutical characteristic differences between the BNM and GPs identified in this study could provide insights into understanding the deviations in the drug manufacturing processes of generic drugs.

Infection outcome needs two to tango: human host and the pathogen

Infectious diseases are potential drivers for human evolution, through a complex, continuous and dynamic interaction between the host and the pathogen/s. It is this dynamic interaction that contributes toward the clinical outcome of a pathogenic disease. These are modulated by contributions from the human genetic variants, transcriptional response (including noncoding RNA) and the pathogen’s genome architecture. Modern genomic tools and techniques have been crucial for the detection and genomic characterization of pathogens with respect to the emerging infectious diseases. Aided by next-generation sequencing (NGS), risk stratification of host population/s allows for the identification of susceptible subgroups and better disease management. Nevertheless, many challenges to a general understanding of host–pathogen interactions remain. In this review, we elucidate how a better understanding of the human host-pathogen interplay can substantially enhance, and in turn benefit from, current and future applications of multi-omics based approaches in infectious and rare diseases. This includes the RNA-level response, which modulates the disease severity and outcome. The need to understand the role of human genetic variants in disease severity and clinical outcome has been further highlighted during the Coronavirus disease 2019 (COVID-19) pandemic. This would enhance and contribute toward our future pandemic preparedness.

Staphylococcal trafficking and infection - from 'nose to gut' and back

Staphylococcus aureus is an opportunistic human pathogen, which is a leading cause of infections worldwide. The challenge in treating S. aureus infection is linked to the development of multidrug-resistant strains and the mechanisms employed by this pathogen to evade the human immune defenses. In addition, S. aureus can hide asymptomatically in particular ‘protective’ niches of the human body for prolonged periods of time. In the present review, we highlight recently gained insights in the role of the human gut as an endogenous S. aureus reservoir next to the nasopharynx and oral cavity. In addition, we address the contribution of these ecological niches to staphylococcal transmission, including the roles of particular triggers as modulators of the bacterial dissemination. In this context, we present recent advances concerning the interactions between S. aureus and immune cells to understand their possible roles as vehicles of dissemination from the gut to other body sites. Lastly, we discuss the factors that contribute to the switch from colonization to infection. Altogether, we conclude that an important key to uncovering the pathogenesis of S. aureus infection lies hidden in the endogenous staphylococcal reservoirs, the trafficking of this bacterium through the human body and the subsequent immune responses.

Distribution of Virulence Factors and Resistance Determinants in Three Genotypes of Staphylococcus argenteus Clinical Isolates in Japan

Staphylococcus argenteus, a novel staphylococcal species independent of S. aureus, causes a wide spectrum of infectious diseases. As detection of this species from humans and animals has been increasingly reported worldwide, its growing virulence and drug resistance via external genetic determinants has become concerning. In this study, the prevalence and genetic characteristics of virulence factors and drug resistance determinants were investigated for 82 S. argenteus clinical isolates in Hokkaido, Japan, for a one-year period starting in August 2019. These S. argenteus isolates corresponded to 0.66% of the total number of S. aureus isolates collected in the same period. The most prevalent genotype was sequence type (ST) 2250 and staphylocoagulase (coa) genotype XId (45.1%, n = 37), followed by ST1223-coa XV (30.5%, n = 25) and ST2198-coa XIV (24.4%, n = 20). Panton-Valentine leukocidin genes (lukS-PV-lukF-PV) were identified in a single ST2250 isolate. Only ST1223 isolates had the enterotoxin gene cluster (egc-2), seb, and selw (detection rate; 100%, 60%, and 84%, respectively), while sec, sey, sel26-sel27, tst-1 were only detected in ST2250 isolates (detection rate; 10.8%, 100%, 67.6%, and 10.8%, respectively). ST2198 isolates harbored selx at a significantly higher rate (60%) than isolates of other STs. Although most of S. argenteus isolates were susceptible to antimicrobials examined, ST2198 showed higher resistance rates to penicillin, macrolides, and aminoglycosides than other STs, and it harbored various resistance genes such as blaZ, erm(C), msr(A), lnuA, and aac(6′)-Ie-aph(2″)-Ia. Only one ST2250 isolate possessed SCCmec-IVc, showing resistance to oxacillin. blaZ was the most prevalent determinant of resistance in the three STs and belonged to two plasmid groups and a chromosomal group, suggesting its diverse origin. lnu(A) in ST2198 isolates was assigned to a major cluster with various staphylococcal species. The present study indicates that the prevalence of virulence factors and drug resistance profile/determinants differ depending on the lineage (ST) of S. argenteus.

The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia

Much microbiome research has focused on populations that are predominantly of European descent, and from narrow demographics that do not capture the socio-economic and lifestyle differences which impact human health. Here we examined the airway microbiomes of the Orang Asli, the indigenous peoples of Malaysia. A total of 130 participants were recruited from two sites in the north-eastern state of Terengganu in Peninsular Malaysia. Using 16S rRNA sequencing, the nasal microbiome was significantly more diverse in those aged 5-17 years compared to 50+ years (p = 0.023) and clustered by age (PERMANOVA analysis of the Bray-Curtis distance, p = 0.001). Hierarchical clustering of Bray-Curtis dissimilarity scores revealed six microbiome clusters. The largest cluster (n = 28; 35.4%) had a marked abundance of Corynebacterium. In the oral microbiomes Streptococcus, Neisseria and Haemophilus were dominant. Using conventional microbiology, high levels of Staphylococcus aureus carriage were observed, particularly in the 18-65 age group (n = 17/36; 47.2% 95% CI: 30.9-63.5). The highest carriage of pneumococci was in the <5 and 5 to 17 year olds, with 57.1% (4/7) and 49.2% (30/61), respectively. Sixteen pneumococcal serotypes were identified, the most common being the nonvaccine-type 23A (14.6%) and the vaccine-type 6B (9.8%). The prevalence of pneumococcal serotypes covered by pneumococcal conjugate vaccines support introduction into a Malaysian national immunisation schedule. In addition, the dominance of Corynebacterium in the airway microbiomes is intriguing given their role as a potentially protective commensal with respect to acute infection and respiratory health.

Characterization of peripheral blood mononuclear cells gene expression profiles of pediatric Staphylococcus aureus persistent and non-carriers using a targeted assay

Defects in innate immunity affect many different physiologic systems and several studies of patients with primary immunodeficiency disorders demonstrated the importance of innate immune system components in disease prevention or colonization of bacterial pathogens. To assess the role of the innate immune system on nasal colonization with Staphylococcus aureus, innate immune responses in pediatric S. aureus nasal persistent carriers (n = 14) and non-carriers (n = 15) were profiled by analyzing co-clustered gene sets (modules). We stimulated previously frozen peripheral blood mononuclear cells (PBMCs) from these subjects with i) a panel of TLR ligands, ii) live S. aureus (either a mixture of strains or stimulation with respective carriage isolates), or iii) heat-killed S. aureus. We found no difference in responses between carriers and non-carriers when PBMCs were stimulated with a panel of TLR ligands. However, PBMC gene expression profiles differed between persistent and non-S. aureus carriers following stimulation with either live or dead S. aureus. These observations suggest that individuals susceptible to persistent carriage with S. aureus may possess differences in their live/dead bacteria recognition pathway and that innate pathway signaling is different between persistent and non-carriers of S. aureus.

Staphylococcus argenteus isolated from retail foods in China: Incidence, antibiotic resistance, biofilm formation and toxin gene profile

Staphylococcus argenteus is a novel species of coagulase-positive staphylococci which was separated from Staphylococcus aureus in 2014. It can threaten human health like S. aureus but can not identify with conventional biochemical or other phenotypic testing. From 2011 to 2016, 1581 S. aureus strains were isolated from 4300 samples from retail foods covering most provincial capitals in China. According to multilocus sequence typing (MLST) and PCR confirmation, 7.2% of isolates (114/1581) were confirmed as S. argenteus. The pathogen was distributed in 22 of 39 sampled cities and all food types. Interestingly, most S. argenteus positive samples were collected from coastal cities in South China. MLST detected 8 different sequence types (STs), including five new STs. CC2250 was the predominant lineage of S. argenteus, followed by CC1223. To further characterize the isolates, their antibiotic resistance, virulence genes, biofilm formation and biofilm-related genes were examined. The pvl gene was not detected in S. argenteus, and only 1 isolate (0.9%) was positive for the tsst-1 gene. For 18 enterotoxin genes, 16.7% (19/114) of isolates harboured more than three genes, whereas 70.2% (80/114) of isolates had none of the investigated genes. Penicillin and ampicillin were the major antibiotics to which the S. argenteus isolates were resistant, followed by tetracycline, kanamycin and fusidic acid. A total of 94.7% of isolates had the ability to produce biofilms and all isolates harboured icaA, fnbA, and fib genes. Other biofilm-related genes, such as eno, clfB, fnbB, and icaC, were also found in 99.1%, 92.1%, 88.6%, and 74.6% of isolates, respectively. This study is the first systematic investigation of the prevalence of S. argenteus in retail foods in China and shows their ubiquity in food. We also provide comprehensive surveillance of the incidence of S. argenteus in retail foods and information to enable more accurate and effective treatment of infections of this new species.

Methicillin-resistant Staphylococcus argenteus misidentified as methicillin-resistant Staphylococcus aureus emerging in western Sweden

Two strains included in a whole-genome sequencing project for methicillin-resistant Staphylococcus aureus (MRSA) were identified as non-Staphylococcus aureus when the sequences were analysed using the bioinformatics software ALEX (www.1928diagnostics.com, Gothenburg, Sweden). Sequencing of the sodA gene of these strains identified them as Staphylococcus argenteus. The collection of MRSA in western Sweden was checked for additional strains of this species. A total of 18 strains of S. argenteus isolated between 2011 and December 2017 were identified.

Staphylococcus aureus Nasal Carriage and Autoimmune Diseases: From Pathogenic Mechanisms to Disease Susceptibility and Phenotype

The role of infective agents in autoimmune diseases (ADs) development has been historically investigated, but in the last years has been strongly reconsidered due to the interest in the link between the microbiome and ADs. Together with the gut, the skin microbiome is characterized by the presence of several microorganisms, potentially influencing innate and adaptive immune response. S. aureus is one of the most important components of the skin microbiome that can colonize anterior nares without clinical manifestations. Data from the literature demonstrates a significantly higher prevalence of nasal colonization in ADs patients in comparison with healthy subjects, suggesting a possible role in terms of disease development and phenotypes. Thus, in the present narrative review we focused on the mechanisms by which S. aureus could influence the immune response and on its relationship with ADs, in particular granulomatosis with polyangiitis, rheumatoid arthritis, and systemic lupus erythematosus.

Molecular Epidemiological Characterization of Staphylococcus argenteus Clinical Isolates in Japan: Identification of Three Clones (ST1223, ST2198, and ST2550) and a Novel Staphylocoagulase Genotype XV

Staphylococcus argenteus, a novel emerging species within Staphylococcus aureus complex (SAC), has been increasingly reported worldwide. In this study, prevalence of S. argenteus among human clinical isolates, and their clonal diversity and genetic characteristics of virulence factors were investigated in Hokkaido, the northern main island of Japan. During a four-month period starting from March 2019, twenty-four S. argenteus and 4330 S. aureus isolates were recovered from clinical specimens (the ratio of S. argenteus to S. aureus :0.0055). Half of S. argenteus isolates (n = 12) belonged to MLST sequence type (ST) 2250 and its single-locus variant, with staphylocoagulase genotype (coa-) XId, while the remaining isolates were assigned to ST2198/coa-XIV (n = 6), and ST1223 with a novel coa-XV identified in this study (n = 6). All the isolates were mecA-negative, and susceptible to all the antimicrobials tested, except for an ST2198 isolate with blaZ and an ST2250 isolate with tet(L) showing resistance to ampicillin and tetracyclines, respectively. Common virulence factors in the S. argenteus isolates were staphylococcal enterotoxin (-like) genes sey, selz, sel26, and sel27 in ST2250, selx in ST2198, and enterotoxin gene cluster (egc-1: seg-sei-sem-sen-seo) in ST1223 isolates, in addition to hemolysin genes (hla, hlb, and hld) distributed universally. Elastin binding protein gene (ebpS) and MSCRAMM family adhesin SdrE gene (sdrE) detected in all the isolates showed high sequence identity among them (> 97%), while relatively lower identity to those of S. aureus (78–92%). Phylogenetically, ebpS, sdrE, selx, sey, selw, sel26, and sel27 of S. argenteus formed clusters distinct from those of S. aureus, unlike sec, selz, tst-1, and staphylokinase gene (sak). The present study revealed the prevalence of S. argenteus among clinical isolates, and presence of three distinct S. argenteus clones (ST2250; ST2198 and ST1223) harboring different virulence factors in northern Japan. ST2198 S. argenteus, a minor clone (strain BN75-like) that had been rarely reported, was first identified in Japan as human isolates.

Implications of identifying the recently defined members of the Staphylococcus aureus complex S. argenteus and S. schweitzeri: a position paper of members of the ESCMID Study Group for Staphylococci and Staphylococcal Diseases (ESGS)

BACKGROUND

Staphylococcus argenteus and Staphylococcus schweitzeri, previously known as divergent Staphylococcus aureus clonal lineages, have been recently established as novel, difficult-to-delimit, coagulase-positive species within the S. aureus complex. Methicillin-resistant strains of S. argenteus are known from Australia and the UK. Knowledge of their epidemiology, medical significance and transmission risk is limited and partly contradictory, hampering definitive recommendations. There is mounting evidence that the pathogenicity of S. argenteus is similar to that of 'classical' S. aureus, while as yet no S. schweitzeri infections have been reported.

AIM

To provide decision support on whether and how to distinguish and report both species.

SOURCES

PubMed, searched for S. argenteus and S. schweitzeri.

CONTENT

This position paper reviews the main characteristics of both species and draws conclusions for microbiological diagnostics and surveillance as well as infection prevention and control measures.

IMPLICATIONS

We propose not distinguishing within the S. aureus complex for routine reporting purposes until there is evidence that pathogenicity or clinical outcome differ markedly between the different species. Primarily for research purposes, suitably equipped laboratories are encouraged to differentiate between S. argenteus and S. schweitzeri. Caution is urged if these novel species are explicitly reported. In such cases, a specific comment should be added (i.e. 'member of the S.aureus complex') to prevent confusion with less- or non-pathogenic staphylococci. Prioritizing aspects of patient safety, methicillin-resistant isolates should be handled as recommended for methicillin-resistant Staphylococcus aureus (MRSA). In these cases, the clinician responsible should be directly contacted and informed by the diagnosing microbiological laboratory, as they would be for MRSA. Research is warranted to clarify the epidemiology, clinical impact and implications for infection control of such isolates.

Antibiotic susceptibility profile and prevalence of mecA and lukS-PV/lukF-PV genes in Staphylococcus aureus isolated from nasal and pharyngeal sources of medical students in Ecuador

BACKGROUND

Staphylococcus aureus is a common nasal colonizer in 20-30% of the general population. When mucosal and cutaneous barriers are disrupted, S. aureus can cause severe infections. While MRSA nasal carriers have an increased risk of infections when compared to non-carriers, prolonged exposure to the hospital environment may cause an increase in carriage of MRSA.

MATERIALS AND METHODS

A survey questionnaire was filled for analyzing risk factors of colonization. Swab isolates were identified as S. aureus by traditional microbiological assays. Antibiotic susceptibility profiles were performed following the CLSI standard guidelines. Multiplex PCR was conducted to determine the presence of genes mecA and lukS-PV/lukF-PV. Chi-squared, univariate, and multivariate logistic regressions were applied to find statistically significant associations between risk factors and the presence of S. aureus and MRSA.

RESULTS

One hundred and eighty-six isolates were identified as S. aureus. The strains showed high resistance to penicillin, oxacillin, azithromycin, erythromycin, clindamycin (inducible), and tetracycline. The overall prevalence of MRSA in medical students was 45.9% [40.4-51.6] 95% CI. PCR showed a prevalence of mecA gene in MRSA isolates of 6.1% while lukS-PV/lukF-PV gene was present in 3.2% [1.2-6.9] 95% CI of the S. aureus samples. The risk factors frequency of antibiotic intake and repeated visits to hospitals demonstrated statistical significance.

CONCLUSION

S. aureus and MRSA isolates have a high prevalence of colonization, and antibiotic resistance in the population studied. MRSA resistance was not related to the presence of the mecA gene. The prevalence of PVL genes was low, but it could represent a risk because they are circulating in the community.

Genomic Evolution of Staphylococcus aureus During Artificial and Natural Colonization of the Human Nose

Staphylococcus aureus can colonize the human vestibulum nasi for many years. It is unknown whether and, how S. aureus adapts to this ecological niche during colonization. We determined the short (1 and 3 months) and mid-term (36 months) genomic evolution of S. aureus in natural carriers and artificially colonized volunteers. Eighty-five S. aureus strains were collected from 6 natural carriers during 3 years and 6 artificially colonized volunteers during 1 month. Multi-locus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis based on whole-genome sequencing (WGS) were carried out. Mutation frequencies within resident bacterial populations over time were quantified using core genome SNP counts (comparing groups of genomes) and pairwise SNP divergence assessment (comparing two genomes from strains originating from one host and sharing identical MLST). SNP counts (within 1–3 months) in all naturally colonizing strains varied from 0 to 757 (median 4). These strains showed random and independent patterns of pairwise SNP divergence (0 to 44 SNPs, median 7). When the different core genome SNP counts over a period of 3 years were considered, the median SNP count was 4 (range 0–26). Host-specific pairwise SNP divergence for the same period ranged from 9 to 57 SNPs (median 20). During short term artificial colonization the mutation frequency was even lower (0–7 SNPs, median 2) and the pairwise SNP distances were 0 to 5 SNPs (median 2). Quantifying mutation frequencies is important for the longitudinal follow-up of epidemics of infections and outbreak management. Random pattern of pairwise SNP divergence between the strains isolated from single carriers suggested that the WGS of multiple colonies is necessary in this context. Over periods up to 3 years, maximum median core genome SNP counts and SNP divergence for the strains studied were 4 and 20 SNPs or lower. During artificial colonization, where median core genome SNP and pairwise SNP distance scores were 2, there is no early stage selection of different genotypes. Therefore, we suggest an epidemiological cut off value of 20 SNPs as a marker of S. aureus strain identity during studies on nasal colonization and also outbreaks of infection.

Methicillin-Resistant Staphylococcus aureus Nasal Colonization among Healthcare Workers at Kampala International University Teaching Hospital, Southwestern Uganda

Whereas Staphylococcus aureus is a pathogen, it colonizes healthy people as normal flora without causing any symptoms or illness. Probably because of greater exposure, healthcare workers (HCWs) are more colonized, serving as reservoir for endogenous infections as well as dissemination. In developing countries including Uganda, there is scarcity of the literature on S. aureus carriage among HCWs, making infection control difficult. This study aimed at determining the nasal carriage rate and comparing the antimicrobial susceptibility profiles of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible Staphylococcus aureus (MSSA) isolates from HCWs of Kampala International University Teaching Hospital. Nasal swab specimens from HCWs were screened for MRSA using both phenotypic and genotypic methods. Antimicrobial susceptibility testing of the MRSA and MSSA isolates was performed using the Kirby–Bauer disc diffusion method. Out of the 97 participants, 28 (28.8%) participants were nasal carriers of S. aureus of which 13 (46.4%) were phenotypically MRSA (resistant to cefoxitin) and 8 (28.6%) were genotypically MRSA (had mecA gene). Only 6 isolates of the 13 isolates (46%) which showed resistance to cefoxitin had mecA gene detectable while 2 (13.3%) of the 15 cefoxitin susceptible isolates were found to carry mecA gene. The study thus shows that methicillin resistance in S. aureus may not only be determined by mecA gene.

Staphylococcus aureus Nasal Colonization: An Update on Mechanisms, Epidemiology, Risk Factors, and Subsequent Infections

Up to 30% of the human population are asymptomatically and permanently colonized with nasal Staphylococcus aureus. To successfully colonize human nares, S. aureus needs to establish solid interactions with human nasal epithelial cells and overcome host defense mechanisms. However, some factors like bacterial interactions in the human nose can influence S. aureus colonization and sometimes prevent colonization. On the other hand, certain host characteristics and environmental factors can predispose to colonization. Nasal colonization can cause opportunistic and sometimes life-threatening infections such as surgical site infections or other infections in non-surgical patients that increase morbidity, mortality as well as healthcare costs.

Accurate differentiation of novel Staphylococcus argenteus from Staphylococcus aureus using MALDI-TOF MS

Aim: We evaluated a Staphylococcus argenteus-specific diagnostic profile of matrix-assisted laser desorption/ionization time-of-flight mass spectrometer for accurate identification of this novel bacterium. Materials & methods: Staphylococcus argenteus was identified based on negative crtM gene and presence of specific sequence types. A classification model was generated by cluster analysis of matrix-assisted laser desorption/ionization time-of-flight mass spectrometer results and ClinProTools software for 25 S. argenteus and 25 methicillin-susceptible S. aureus (MSSA). The performance of the classification model was validated against 72 S. argenteus and 72 MSSA isolates. Results: With cluster analysis and classification model, differentiation of 72 S. argenteus from 72 MSSA had 100.0% accuracy by chemical extraction method and 87.5% sensitivity and 100.0% specificity by direct smear method. Conclusion: The classification model could accurately differentiate S. argenteus from MSSA.

Community-acquired methicillin-resistant Staphylococcus aureus can persist in the throat

Colonization by Staphylococcus aureus is an important factor in infections caused by this microorganism. Among the colonization niches of staphylococci are the nose, skin, intestinal tract, and, recently, the throat has been given relevance. Infections caused by community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) can be fatal. Persistence of S. aureus is an important process in the pathogenesis of this microorganism and must be studied. The aim of this study was to determine the persistence of S. aureus in the throat, and characterized the strains. We studied the persistence of S. aureus for 6 years in the throat of apparently healthy people. The isolated strains from the persistent carriers were characterized through PFGE, spa-typing, SCCmec typing, resistance to methicillin, presence of virulence genes (adhesins and toxins), and the formation of biofilm. We found persistent and intermittent carriers of S. aureus in the throat, with methicillin-sensitive (MSSA), methicillin-resistant (MRSA) strains, and confirmed for the first time that CA-MRSA colonizes this niche. These strains can colonize persistently the throat for four years or more. Typification of strains through PFGE and spa-typing revealed that some carriers present the same strain, whereas others present different strains along the period of persistence. Almost all strains induced a strong biofilm formation. All strains presented adhesin and toxin genes, but no shared genotype was found. We conclude that S. aureus, including CA-MRSA strains, can remain persistently in the throat, finding a wide variability among the persistent strains.

Human Genetic Susceptibility to Native Valve Staphylococcus aureus Endocarditis in Patients With S. aureus Bacteremia: Genome-Wide Association Study

Staphylococcus aureus infective endocarditis (SaIE) is a severe complication of S. aureus bacteremia (SAB) occurring in up to 22% of patients. Bacterial genetic factors and host conditions for SaIE have been intensely studied before; however, to date no study has focused on predisposing host genetic factors to SaIE. The present study aimed to identify genetic polymorphisms associated with SaIE by a Genome-Wide Association Study (GWAS) of 67 patients with definite native valve SaIE (cases) and 72 matched native valve patients with SAB but without IE (controls). All patients were enrolled in the VIRSTA cohort (Le Moing et al., 2015) study. Four single nucleotide polymorphisms (SNPs) located on chromosome 3 were associated with SaIE (P < 1 × 10^-5) without reaching conventional genome-wide significance. For all, the frequency of the minor allele was lower in cases than in controls, suggesting a protective effect of the minor allele against SaIE. The same association was observed using an independent Danish verification cohort of SAB with (n = 57) and without (n = 123) IE. Ex vivo analysis of aortic valve tissues revealed that SaIE associated SNPs mentioned above were associated with significantly higher mRNA expression levels of SLC7A14, a predicted cationic amino acid transporter protein. Taken together, our results suggest an IE-protective effect of SNPs on chromosome 3 during the course of SAB. The effects of protective minor alleles may be mediated by increasing expression levels of SLC7A14 in valve tissues. We conclude that occurrence of SaIE may be the combination of a well-adapted bacterial genotype to a susceptible host.

Distribution of the Most Prevalent Spa Types among Clinical Isolates of Methicillin-Resistant and -Susceptible Staphylococcus aureus around the World: A Review

Background:Staphylococcus aureus, a leading cause of community-acquired and nosocomial infections, remains a major health problem worldwide. Molecular typing methods, such as spa typing, are vital for the control and, when typing can be made more timely, prevention of S. aureus spread around healthcare settings. The current study aims to review the literature to report the most common clinical spa types around the world, which is important for epidemiological surveys and nosocomial infection control policies.

Methods: A search via PubMed, Google Scholar, Web of Science, Embase, the Cochrane library, and Scopus was conducted for original articles reporting the most prevalent spa types among S. aureus isolates. The search terms were “Staphylococcus aureus, spa typing.”

Results: The most prevalent spa types were t032, t008 and t002 in Europe; t037 and t002 in Asia; t008, t002, and t242 in America; t037, t084, and t064 in Africa; and t020 in Australia. In Europe, all the isolates related to spa type t032 were MRSA. In addition, spa type t037 in Africa and t037and t437 in Australia also consisted exclusively of MRSA isolates. Given the fact that more than 95% of the papers we studied originated in the past decade there was no option to study the dynamics of regional clone emergence.

Conclusion: This review documents the presence of the most prevalent spa types in countries, continents and worldwide and shows big local differences in clonal distribution.

Staphylococcus aureus and Methicillin-Resistant Staphylococcus aureus in Workers in the Food Industry

Staphylococcus aureus is part of the common flora on the skin and mucous membranes of mammals and approximately 20–30% of humans are persistently colonized, mainly by mostly susceptible human-adapted isolates. In contrast, colonization with methicillin-resistant S. aureus is rare (approximately 1%), predominantly transient and associated with prior contact to the health care system. Additionally, in recent years livestock-associated S. aureus clones contributed to colonization in humans, especially in those working in close contact to farm animals. A considerable percentage of colonizing S. aureus isolates is equipped with enterotoxin genes. Humans carrying enterotoxigenic isolates represent a contamination source when handling food, thus generating a continuous risk of S. aureus food intoxication. Molecular characterization of isolates colonizing humans and obtained from food, respectively, enables the tracing of food-related outbreaks back to the source of food intoxication. We will summarize current knowledge about the S. aureus population colonizing humans, including those in close contact to animals and food, respectively. Additionally, we will review data on the molecular characterization of S. aureus isolates related to staphylococcal foodborne disease and the elucidation of staphylococcal foodborne outbreaks. Staphylococcal food poisoning is a common foodborne disease, mediated by the ingestion of enterotoxins produced by enterotoxigenic strains of S. aureus. For several outbreaks of foodborne S. aureus disease, colonized personnel could be identified as the source of food contamination. However, because of the widespread occurrence of enterotoxigenic strains as human colonizers and the often transient nature of colonization, the source of contamination cannot always be identified unambiguously. Therefore, compliance with hygiene measures is the most important requirement to prevent food contamination by both human colonization and environmental S. aureus reservoirs.

A mechanistic model for spread of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) within a pig herd

Before an efficient control strategy for livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) in pigs can be decided upon, it is necessary to obtain a better understanding of how LA-MRSA spreads and persists within a pig herd, once it is introduced. We here present a mechanistic stochastic discrete-event simulation model for spread of LA-MRSA within a farrow-to-finish sow herd to aid in this. The model was individual-based and included three different disease compartments: susceptible, intermittent or persistent shedder of MRSA. The model was used for studying transmission dynamics and within-farm prevalence after different introductions of LA-MRSA into a farm. The spread of LA-MRSA throughout the farm mainly followed the movement of pigs. After spread of LA-MRSA had reached equilibrium, the prevalence of LA-MRSA shedders was predicted to be highest in the farrowing unit, independent of how LA-MRSA was introduced. LA-MRSA took longer to spread to the whole herd if introduced in the finisher stable, rather than by gilts in the mating stable. The more LA-MRSA positive animals introduced, the shorter time before the prevalence in the herd stabilised. Introduction of a low number of intermittently shedding pigs was predicted to frequently result in LA-MRSA fading out. The model is a potential decision support tool for assessments of short and long term consequences of proposed intervention strategies or surveillance options for LA-MRSA within pig herds.

Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus

Background

Staphylococcus argenteus and S. schweitzeri, were recently proposed as novel species within S. aureus complex (SAC). S. argenteus has been reported in many countries and can threaten human health. S. schweitzeri has not been associated with human infections, but has been isolated from non-human primates. Questions regarding the evolution of pathogenicity of these two species will remain elusive until an exploratory evolutionary framework is established.

Results

We present genomic comparison analysis among members of SAC based on a pan-genome definition, which included 15 S. argenteus genomes (five newly sequenced), six S. schweitzeri genomes and 30 divergent S. aureus genomes. The three species had divergent core genomes and rare interspecific recombination was observed among the core genes. However, some subtypes of staphylococcal cassette chromosome mec (SCCmec) elements and prophages were present in different species. Of 111 tested virulence genes of S. aureus, 85 and 86 homologous genes were found in S. argenteus and S. schweitzeri, respectively. There was no difference in virulence gene content among the three species, but the sequence of most core virulence genes was divergent. Analysis of the agr locus and the genes in the capsular polysaccharides biosynthetic operon revealed that they both diverged before the speciation of SAC members. Furthermore, the widespread geographic distribution of S. argenteus, sequence type 2250, showed ambiguous biogeographical structure among geographically isolated populations, demonstrating an international spread of this pathogen.

Conclusions

S. argenteus has spread among several countries, and invasive infections and persistent carriage may be not limited to currently reported regions. S. argenteus probably had undergone a recent host adaption and can cause human infections with a similar pathogenic potential.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4149-9) contains supplementary material, which is available to authorized users.

Multidrug-Resistant Bacteria in the Community: Trends and Lessons Learned

Multidrug resistant (MDR) bacteria are one of the most important threats to public health. Typically, MDR bacteria are associated with nosocomial infections. However, some MDR bacteria have become prevalent causes of community-acquired infections. The spread of MDR bacteria into the community is a crucial development, and is associated with increased morbidity, mortality, health care costs, and antibiotic use. Factors associated with community dissemination of MDR bacteria overlap but are distinct from those associated with nosocomial spread. Prevention of further community spread of MDR bacteria is of the utmost importance, and requires a multidisciplinary approach involving all stakeholders.

Evolution of the Staphylococcus argenteus ST2250 Clone in Northeastern Thailand Is Linked with the Acquisition of Livestock-Associated Staphylococcal Genes

Staphylococcus argenteus is a newly named species previously described as a divergent lineage of Staphylococcus aureus that has recently been shown to have a global distribution. Despite growing evidence of the clinical importance of this species, knowledge about its population epidemiology and genomic architecture is limited. We used whole-genome sequencing to evaluate and compare S. aureus (n = 251) and S. argenteus (n = 68) isolates from adults with staphylococcal sepsis at several hospitals in northeastern Thailand between 2006 and 2013. The majority (82%) of the S. argenteus isolates were of multilocus sequence type 2250 (ST2250). S. aureus was more diverse, although 43% of the isolates belonged to ST121. Bayesian analysis suggested an S. argenteus ST2250 substitution rate of 4.66 (95% confidence interval [CI], 3.12 to 6.38) mutations per genome per year, which was comparable to the S. aureus ST121 substitution rate of 4.07 (95% CI, 2.61 to 5.55). S. argenteus ST2250 emerged in Thailand an estimated 15 years ago, which contrasts with the S. aureus ST1, ST88, and ST121 clades that emerged around 100 to 150 years ago. Comparison of S. argenteus ST2250 genomes from Thailand and a global collection indicated a single introduction into Thailand, followed by transmission to local and more distant countries in Southeast Asia and further afield. S. argenteus and S. aureus shared around half of their core gene repertoire, indicating a high level of divergence and providing strong support for their classification as separate species. Several gene clusters were present in ST2250 isolates but absent from the other S. argenteus and S. aureus study isolates. These included multiple exotoxins and antibiotic resistance genes that have been linked previously with livestock-associated S. aureus, consistent with a livestock reservoir for S. argenteus. These genes appeared to be associated with plasmids and mobile genetic elements and may have contributed to the biological success of ST2250.

In this study, we used whole-genome sequencing to understand the genome evolution and population structure of a systematic collection of ST2250 S. argenteus isolates. A newly identified ancestral species of S. aureus, S. argenteus has become increasingly known as a clinically important species that has been reported recently across various countries. Our results indicate that S. argenteus has spread at a relatively rapid pace over the past 2 decades across northeastern Thailand and acquired multiple exotoxin and antibiotic resistance genes that have been linked previously with livestock-associated S. aureus. Our findings highlight the clinical importance and potential pathogenicity of S. argenteus as a recently emerging pathogen.

Staphylococcus aureus nasal colonization among HIV-infected adults in Botswana: prevalence and risk factors

We sought to determine the clinical and epidemiologic determinants of Staphylococcus aureus nasal colonization in HIV-infected individuals at two outpatient centers in southern Botswana. Standard microbiologic techniques were used to identify S. aureus and methicillin-resistant S. aureus (MRSA). In a sample of 404 HIV-infected adults, prevalence of S. aureus nasal carriage was 36.9% (n = 152) and was associated with domestic overcrowding and lower CD4 cell count. MRSA prevalence was low (n = 13, 3.2%), but more common among individuals with asthma and eczema. The implications of these findings for HIV management are discussed.

Differentiation of Staphylococcus argenteus (formerly: Staphylococcus aureus clonal complex 75) by mass spectrometry from S. aureus using the first strain isolated from a wild African great ape

The species Staphylococcus argenteus was separated recently from Staphylococcus aureus (Tong S.Y., F. Schaumburg, M.J. Ellington, J. Corander, B. Pichon, F. Leendertz, S.D. Bentley, J. Parkhill, D.C. Holt, G. Peters, and P.M. Giffard, 2015). The objective of this work was to characterise the genome of a non-human S. argenteus strain, which had been isolated from the faeces of a wild-living western lowland gorilla in Gabon, and analyse the spectrum of this species in matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The full genome sequence revealed a scarcity of virulence genes and absence of resistance genes, indicating a decreased virulence potential compared to S. aureus and the human methicillin-resistant S. argenteus isolate MSHR1132^T. Spectra obtained by MALDI-TOF MS and the analysis of available sequences in the genome databases identified several MALDI-TOF MS signals that clearly differentiate S. argenteus, the closely related Staphylococcus schweitzeri and S. aureus. In conclusion, in the absence of biochemical tests that identify the three species, mass spectrometry should be employed as method of choice.

Molecular Epidemiology of Staphylococcus aureus in the General Population in Northeast Germany: Results of the Study of Health in Pomerania (SHIP-TREND-0)

Population-based studies on Staphylococcus aureus nasal colonization are scarce. We examined the prevalence, resistance, and molecular diversity of S. aureus in the general population in Northeast Germany. Nasal swabs were obtained from 3,891 adults in the large-scale population-based Study of Health in Pomerania (SHIP-TREND). Isolates were characterized using spa genotyping, as well as antibiotic resistance and virulence gene profiling. We observed an S. aureus prevalence of 27.2%. Nasal S. aureus carriage was associated with male sex and inversely correlated with age. Methicillin-resistant S. aureus (MRSA) accounted for 0.95% of the colonizing S. aureus strains. MRSA carriage was associated with frequent visits to hospitals, nursing homes, or retirement homes within the previous 24 months. All MRSA strains were resistant to multiple antibiotics. Most MRSA isolates belonged to the pandemic European hospital-acquired MRSA sequence type 22 (HA-MRSA-ST22) lineage. We also detected one livestock-associated MRSA ST398 (LA-MRSA-ST398) isolate, as well as six livestock-associated methicillin-susceptible S. aureus (LA-MSSA) isolates (clonal complex 1 [CC1], CC97, and CC398). spa typing revealed a diverse but also highly clonal S. aureus population structure. We identified a total of 357 spa types, which were grouped into 30 CCs or sequence types. The major seven CCs (CC30, CC45, CC15, CC8, CC7, CC22, and CC25) included 75% of all isolates. Virulence gene patterns were strongly linked to the clonal background. In conclusion, MSSA and MRSA prevalences and the molecular diversity of S. aureus in Northeast Germany are consistent with those of other European countries. The detection of HA-MRSA and LA-MRSA within the general population indicates possible transmission from hospitals and livestock, respectively, and should be closely monitored.

Identification of Staphylococcus argenteus in Eastern China based on a nonribosomal peptide synthetase (NRPS) gene

AIM

To investigate whether the Staphylococcus argenteus is present in Eastern China and to verify the utility of a new screening process.

MATERIALS & METHODS

Phenotype observation, PCR assay targeting a hypothetical nonribosomal peptide synthetase (NRPS) gene, phylogenetic analysis of rpoB and multilocus sequence typing were used to screen and identify strains of S. argenteus from 839 presumptive S. aureus isolates.

RESULTS

Eighty-nine (89/839, 10.6%) of the presumptive S. aureus isolates produced white colonies on tryptone soya agar plates. Of the white-colony isolates, six (6/89, 7%) were S. argenteus, 75 (75/89, 84%) were S. aureus and eight (8/89, 9%) were other bacteria.

CONCLUSION

The PCR-based method targeting the NRPS gene can simultaneously identify and distinguish S. argenteus and S. aureus. All representative sequences of rpoB generated in this study were deposited in GenBank under accession numbers SJTU F20002, KT767581; SJTU F20269, KT767582; SJTU F20419, KT767583; SJTU F20420, KT767584; SJTU F20124, KT767585; SJTU F21164, KT767586; SJTU F21285, KT767587; SJTU F21224, KT767588; SJTU F21155, KT767589; SJTU F21294, KT767590; SJTU F20030, KT767591; SJTU F20044, KT767592; SJTU F20135, KT767593; SJTU F20123, KT767594; SJTU F21319, KT767595, respectively. All the new sequence types (STs) were submitted to a multilocus sequence typing database and the assigned ST numbers are ST3261 (151-469-20-101-145-150-131), ST3262 (12-3-1-1-4-4-410) and ST3267 (2-471-2-2-6-3-2).

Host-Bacterial Crosstalk Determines Staphylococcus aureus Nasal Colonization

Staphylococcus aureus persistently colonizes the anterior nares of approximately one fifth of the population and nasal carriage is a significant risk factor for infection. Recent advances have significantly refined our understanding of S. aureus-host communication during nasal colonization. Novel bacterial adherence mechanisms in the nasal epithelium have been identified, and novel roles for both the innate and the adaptive immune response in controlling S. aureus nasal colonization have been defined, through the use of both human and rodent models. It is clear that S. aureus maintains a unique, complex relationship with the host immune system and that S. aureus nasal colonization is overall a multifactorial process which is as yet incompletely understood.

Novel pandemic influenza A (H1N1) and community-associated methicillin-resistant Staphylococcus aureus pneumonia

Postinfluenza bacterial pneumonia is a leading cause of influenza-associated death, and Staphylococcus aureus and Streptococcus pneumoniae have been important pathogens that have caused pneumonia since the influenza pandemic in 1919. Emergence of novel influenza A (H1N1) pdm09 and the concomitant global spread of community-associated methicillin-resistant S. aureus (CA-MRSA) have led to increasing prevalence of CA-MRSA pneumonia following influenza infection. Such an epidemiologic change poses a therapeutic challenge due to a high risk of inappropriate empiric antimicrobial therapy and poor clinical outcomes. Early diagnosis and initiation of appropriate antimicrobial therapy for post-influenza bacterial pneumonia have become even more important in the era of CA-MRSA. Therefore, novel molecular diagnostic techniques should be applied to more readily diagnose MRSA pneumonia.

Low occurrence of the new species Staphylococcus argenteus in a Staphylococcus aureus collection of human isolates from Belgium

Staphylococcus argenteus is a novel Staphylococcus species closely related to Staphylococcus aureus that has been recently described. In this study, we investigated the proportion and the characteristics of S. argenteus recovered from humans in Belgium. S. aureus. human isolates collected in Belgium from 2006 to 2015 (n = 1,903) were retrospectively characterised via the presence of non-pigmented colonies on chocolate agar, spa typing and rpoB sequencing to determine if some of them were in fact S. argenteus. Out of 73 strains non-pigmented on chocolate plates, 3 isolates (0.16 %) showed rpoB sequences, in addition to spa and sequence types (ST2250/t5787, ST2250/t6675, ST3240/t6675), related to S. argenteus. Two of them were methicillin-resistant, harbouring a SCCmec type IV. The three S. argenteus isolates carried genes (sak, scn) of the immune evasion cluster. This first Belgian nationwide analysis showed a low occurrence of S. argenteus. Further studies should be conducted to identify the distribution range and the clinical impact of this new species.

Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates

Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control.

A multifaceted 'omics' approach for addressing the challenge of antimicrobial resistance

The inappropriate use of antibiotics has severe global health and economic consequences, including the emergence of antibiotic-resistant bacteria. A major driver of antibiotic misuse is the inability to accurately distinguish between bacterial and viral infections based on currently available diagnostic solutions. A multifaceted 'omics' approach that integrates personalized patient data such as genetic predisposition to infections (genomics), natural microbiota composition and immune response to infection (proteomics and transcriptomics) together with comprehensive pathogen profiling has the potential to help physicians improve their antimicrobial prescribing practices. In this respect, the EU has funded a multidisciplinary project (TAILORED-Treatment) that will develop novel omics-based personalized treatment schemes that have the potential to reduce antibiotic consumption, and help limiting the spread of antibiotic resistance.