Project description:Staphylococcus argenteus, a novel species of the genus Staphylococcus or a member of the S. aureus complex, is closely related to S. aureus and is usually misidentified. In this study, the presence of S. argenteus in isolated S. aureus was investigated in 67 rabbits with abscess lesions during 2014-2016. Among 19 S. aureus complex isolates, three were confirmed to be S. argenteus by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, nonribosomal peptide synthetase gene amplification, and multilocus sequence type. All S. aureus complex isolates, including the S. aureus isolates, were examined for their antimicrobial resistance phenotype by disk diffusion and for their resistance genotype by PCR assays. Among the S. argenteus isolates, one was susceptible to all antimicrobial drugs and the other two were resistant to penicillin and doxycycline. In contrast, most S. aureus isolates were resistant to penicillin (37.5%), and gentamicin (12.5%). Moreover, S. aureus isolates harbored the blaZ, mecA, aacA-aphD, and mrs(A) as well as mutations of gyrA and grlA, but S. argenteus isolates carried solely the blaZ. S. argenteus isolates were investigated for enterotoxin (sea-sed) and virulence genes by PCR. One isolate carried sea, sec, and sed, whereas the other two isolates carried only sea or sed. No isolate carried seb and see. All three S. argenteus isolates carried hla, hlb, and clfA, followed by pvl, whereas coa, spa (IgG-binding region), and spa (x region) were not detected in the three isolates. This paper presents the first identification of S. argenteus from rabbits in Thailand. S. argenteus might be pathogenic because the isolates carried virulence genes. Moreover, antimicrobial resistance was observed. Investigations of this new bacterial species should be conducted in other animal species as well as in humans.
Project description:Staphylococcus argenteus (S. argenteus) is a newly identified Staphylococcus species that has been misidentified as Staphylococcus aureus (S. aureus) and is clinically relevant. We identified 25 S. argenteus genomes in our collection of whole genome sequenced S. aureus. These genomes were compared to publicly available genomes and a phylogeny revealed seven clusters corresponding to seven clonal complexes. The genome of S. argenteus was found to be different from the genome of S. aureus and a core genome analysis showed that ~33% of the total gene pool was shared between the two species, at 90% homology level. An assessment of mobile elements shows flow of SCCmec cassettes, plasmids, phages, and pathogenicity islands, between S. argenteus and S. aureus. This dataset emphasizes that S. argenteus and S. aureus are two separate species that share genetic material.
Project description:Molecular typing of 246 Staphylococcus aureus isolates from unselected patients in Thailand showed that 10 (4.1%) were actually Staphylococcus argenteus. Contrary to the suggestion that S. argenteus is less virulent than S. aureus, we demonstrated comparable rates of morbidity, death, and health care-associated infection in patients infected with either of these two species.
Project description:Purpose:To further analyze a clinical isolate originally identified as methicillin-resistant Staphylococcus aureus (MRSA) using whole-genome sequencing and comparative genomics. Materials and methods:Classical diagnostic methods such as cultivation, biochemical tests, and PCR were supplemented with whole-genome sequencing and comparative genomics, to identify the isolate. Results:The isolate was phenotypically similar to MRSA. However, the presence of the nuc gene could not be confirmed using PCR, while it was positive for the mecA gene. Whole-genome sequencing correctly identified the isolate as Staphylococcus argenteus. The isolate possessed several resistance genes, such as mecA, blaZ (?-lactam antibiotics) and dfrG (trimethoprim). The nuc gene differed from that of MRSA. Six phylogenetic distinct clusters were identified by average nucleotide identity (ANI) analysis of all available S. argenteus whole-genome sequences. Our isolate, RK308, clustered with those isolated in Europe and Asia. Conclusion:Due to the invasive potential, the multi-drug resistance and the similarity to MRSA, S. argenteus should be included in the MRSA screening. Due to the divergent genome compared to MRSA, new PCR approaches have to be developed to avoid an unnoticed spreading of S. argenteus.
Project description:Staphylococcus argenteus is a novel staphylococcal species (also considered as a part of Staphylococcus aureus complex) that is infrequently reported on, and clinical S. argenteus infections are largely unstudied. Here, we report a persistent and recurrent hip joint infection case in which a S. argenteus strain and its small colony variants (SCVs) strain were successively isolated. We present features of the two S. argenteus strains and case details of their pathogenicity, explore factors that induce S. argenteus SCVs formation in the course of anti-infection therapy, and reveal potential genetic mechanisms for S. argenteus SCVs formation. S. argenteus strains were identified using phenotypic and genotypic methods. The S. argenteus strain XNO62 and SCV strain XNO106 were characterized using different models. S. argenteus SCVs were induced by the administration of amikacin and by chronic infection course based on the clinical case details. The genomes of both strains were sequenced and aligned in a pair-wise fashion using Mauve. The case details gave us important insights on the characteristics and therapeutic strategies for infections caused by S. argenteus and its SCVs. We found that strain XNO62 and SCV strain XNO106 are genetically-related sequential clones, the SCV strain exhibits reduced virulence but enhanced intracellular persistence compared to strain XNO62, thus promoting persistent infection. The induction experiments for S. argenteus SCVs demonstrated that high concentrations of amikacin greatly induce S. argenteus XNO62 to form SCVs, while a chronic infection of S. argenteus XNO62 slightly induces SCVs formation. Potential genetic mechanisms for S. argenteus SCVs formation were revealed and discussed based on genomic alignments. In conclusion, we report the first case of infection caused by S. argenteus and its SCVs strain. More attention should be paid to infections caused by S. argenteus and its SCVs, as they constitute a challenge to current therapeutic strategies. The problem of S. argenteus SCVs should be noticed, in particular when amikacin is used or in the case of a chronic S. argenteus infection.
Project description:Staphylococcus argenteus TWCC 58113 was isolated from a specimen from a 12-year-old boy with purulent lymphadenitis. The S. argenteus TWCC 58113 genome was completely sequenced. The TWCC 58113 chromosome was 2,761,442?bp in size with a GC content of 32.44%. S. argenteus TWCC 58113 was found to harbor two plasmids.
Project description:Many countries using sensitive screening methods for detection of carriage of methicillin-resistant Staphylococcus aureus (MRSA) have a sustained low incidence of MRSA infections. For diagnostic laboratories with high sample volumes, MRSA screening requires stability, low maintenance and high performance at a low cost. Herein we designed oligonucleotides for a new nuc targeted hydrolysis probe PCR to replace the standard in-house nuc SybrGreen PCR assay. This new, more time-efficient, PCR assay resulted in a 40% increase in daily sample capacity, with maintained high specificity and sensitivity. The assay was also able to detect Staphylococcus aureus clonal cluster 75 (CC75) lineage strains, recently re-classified as Staphylococcus argenteus, with a sensitivity considerably increased compared to our previous assay. While awaiting consensus if the CC75 lineage of S. aureus should be considered as S. argenteus, and whether methicillin-resistant S. argenteus should be included in the MRSA definition, many diagnostic laboratories need to update their MRSA assay sensitivity/specificity towards this lineage/species. The MRSA screening assay presented in this manuscript is comprised of nuc oligonucleotides separately targeting S. aureus and CC75 lineage strains/S. argenteus, thus providing high user flexibility for the detection of CC75 lineage strains/S. argenteus.
Project description:This report presents a case of prosthetic hip infection caused by Staphylococcus argenteus, a potentially overlooked etiology of prosthetic joint infections (PJIs). Whole-genome sequencing showed that the S. argenteus isolate was an ST2250 and clustered within other CC2250 isolates, the largest clonal group of S. argenteus. This sequence type is prevalent and may be associated with invasive infections. The present isolate was phenotypically fully susceptible to all tested antimicrobial agents and genome analysis did not detect any resistance genes, nor were any staphylococcal cassette chromosome residues detected. Despite initial appropriate management with debridement and biofilm-active antibiotics, the outcome was unfavorable with recurrence and a persistent infection treated with suppressive antibiotics. Regarding the repertoire of genomic traits for virulence in S. argenteus, PJIs caused by this bacterium should be treated accordingly as Staphylococcus aureus PJIs.
Project description:We report a rare case of Staphylococcus argenteus bone and joint infection in a 9-year-old boy in France. His finger arthritis was complicated by osteitis 5 weeks later, which resulted in a secondary intervention. This case indicates the virulence of S. argenteus, an emerging pathogen whose clinical effects are poorly described.
Project description:Currently, invasive infections caused by <i>Staphylococcus argenteus</i>, which is a recently named staphylococcal species, are increasingly reported worldwide. However, only a few genomic studies of <i>S</i>. <i>argenteus</i> 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 <i>S</i>. <i>argenteus</i> 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 <i>S</i>. <i>argenteus</i> comprised seven genetically distinct clades, including two major clades (C1 and C2), with distinct isolation source patterns. Pangenome analysis revealed that <i>S</i>. <i>argenteus</i> 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 <i>S</i>. <i>argenteus</i> may show a similar level of pathogenicity to that of <i>S</i>. <i>aureus</i>. 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 <i>S</i>. <i>argenteus</i>. The preferential horizontal acquisition of particular elements, such as staphylococcal cassette chromosome <i>mec</i> elements and plasmids, was observed in specific regions, revealing potential gene exchange between <i>S</i>. <i>argenteus</i> strains and local <i>S</i>. <i>aureus</i> 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 <i>S</i>. <i>argenteus</i> and may help combat its spread.