Comparative Genome Analysis of Staphylococcus lugdunensis Shows Clonal Complex-Dependent Diversity of the Putative Virulence Factor, ess/Type VII Locus

Lebeurre, Jérémie; Dahyot, Sandrine; Diène, Seydina M.; Paulay, Amandine; Aubourg, Marion; Argemi, Xavier; Giard, Jean‐Christophe; Tournier, Isabelle; François, Patrice; Pestel-Caron, Martine

doi:10.3389/fmicb.2019.02479

Cited by 34 publications

(33 citation statements)

References 83 publications

(105 reference statements)

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“…In S. aureus , the capsule enhances virulence by impeding phagocytosis and stimulating colonization and persistence on mucosal surfaces ( Luong and Lee 2002 ; O’Riordan and Lee 2004 ). Capsule genes had been previously detected in S. lugdunensis ( Lebeurre et al 2019 ), and our results greatly expand the taxonomic distribution of cap8 genes. We detected four types of cap8 genes that were frequently found in S. sciuri, S. chromogenes, S. lugdunensis , and S. haemolyticus A genomes.…”

Section: Resultssupporting

confidence: 82%

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

Smith

Andam

2021

Genome Biology and Evolution

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

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Section: Resultssupporting

confidence: 82%

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

Smith

Andam

2021

Genome Biology and Evolution

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“…We further find that the number of repeats per gene can be large [>40 in one case ( 29 ); Fig. 6 ], spanning thousands of amino acids, and that variation in the number of stalk repeats can be extreme, increasing the length of the protein by an order of magnitude in some cases.…”

Section: Resultsmentioning

confidence: 95%

Periscope Proteins are variable-length regulators of bacterial cell surface interactions

Whelan

Lafita

Gilburt

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Changes at the cell surface enable bacteria to survive in dynamic environments, such as diverse niches of the human host. Here, we reveal “Periscope Proteins” as a widespread mechanism of bacterial surface alteration mediated through protein length variation. Tandem arrays of highly similar folded domains can form an elongated rod-like structure; thus, variation in the number of domains determines how far an N-terminal host ligand binding domain projects from the cell surface. Supported by newly available long-read genome sequencing data, we propose that this class could contain over 50 distinct proteins, including those implicated in host colonization and biofilm formation by human pathogens. In large multidomain proteins, sequence divergence between adjacent domains appears to reduce interdomain misfolding. Periscope Proteins break this “rule,” suggesting that their length variability plays an important role in regulating bacterial interactions with host surfaces, other bacteria, and the immune system.

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“…CC30 and CC22 were the only clones that were positive for exfoliative toxins etA , etB genes. These toxins are responsible for staphylococcal scalded skin syndrome [ 38 , 39 ]. The prevalence of these genes might be due to the specific geographic region.…”

Section: Discussionmentioning

confidence: 99%

Regulation of virulence and β-lactamase gene expression in Staphylococcus aureus isolates: cooperation of two-component systems in bloodstream superbugs

et al. 2021

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Background Methicillin-resistant Staphylococcus aureus (MRSA)-bloodstream infections (BSI) are predominantly seen in the hospital or healthcare-associated host. Nevertheless, the interactions of virulence factor (VFs) regulators and β-lactam resistance in MRSA-BSI are unclear. This study aims to characterize the molecular relationship of two-component systems of VFs and the expression of the β-lactamase gene in MRSA-BSI isolates. In this study, 639 samples were collected from BSI and identified by phenotypic methods. We performed extensive molecular characterization, including SCCmec type, agr type, VFs gene profiles determinations, and MLST on isolates. Also, a quantitative real-time PCR (q-RT PCR) assay was developed for identifying the gene expressions. Results Ninety-one (91) S. aureus and 61 MRSA (67.0%) strains were detected in BSI samples. The presence of VFs and SCCmec genes in MRSA isolates were as follows: tst (31.4%), etA (18.0%), etB (8.19%), lukS-PVL (31.4%), lukF-PV (18.0%), lukE-lukD (16.3%), edin (3.2%), hla (16.3%), hlb (18.0%), hld (14.7%), hlg (22.9%), SCCmecI (16.3%), SCCmecII (22.9%), SCCmecIII (36.0%), SCCmecIV (21.3%), and SCCmecV (16.3%). Quantitative real-time PCR showed overexpression of mecRI and mecI in the toxigenic isolates. Moreover, RNAIII and sarA genes were the highest expressions of MRSA strains. The multi-locus sequence typing data confirmed a high prevalence of CC5, CC8, and CC30. However, ST30, ST22, and ST5 were the most prevalent in the resistant and toxigenic strains. Conclusion We demonstrated that although regulation of β-lactamase gene expressions is a significant contributor to resistance development, two-component systems also influence antibiotic resistance development in MRSA-BSI isolates. This indicates that resistant strains might have pathogenic potential. We also confirmed that some MLST types are more successful colonizers with a potential for MRSA-BSI.

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Comparative Genome Analysis of Staphylococcus lugdunensis Shows Clonal Complex-Dependent Diversity of the Putative Virulence Factor, ess/Type VII Locus

Cited by 34 publications

References 83 publications

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

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

Periscope Proteins are variable-length regulators of bacterial cell surface interactions

Regulation of virulence and β-lactamase gene expression in Staphylococcus aureus isolates: cooperation of two-component systems in bloodstream superbugs

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