Whole Genome Sequence and Comparative Genomics Analysis of Multi-drug Resistant Environmental <i>Staphylococcus epidermidis</i> ST59

Xu, Zhen; Misra, Raju; Jamrozy, Dorota; Paterson, Gavin K.; Cutler, Ronald R.; Holmes, Mark A.; Gharbia, Saheer E.; Mkrtchyan, Hermine V.

doi:10.1534/g3.118.200314

Cited by 24 publications

(26 citation statements)

References 43 publications

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“…The presence of the sesJ gene in an MGE raises the possibility of its transfer to S. aureus. Another CWA protein, called Pls, has been reported in the J region of SCCmec type 1 and ⌿SCCpls in S. aureus and in an SCC element in S. epidermidis (25,42,43). In our study, we observed the presence of the sesJ gene in ACME IV and ACME V. Previous work by O'Connor et al on the prevalence of ACME in S. epidermidis also reported the presence of different CWA proteins in MGEs.…”

Section: Discussionsupporting

confidence: 76%

Staphylococcus epidermidis MSCRAMM SesJ Is Encoded in Composite Islands

Arora¹,

Hillhouse

et al. 2020

mBio

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Staphylococcus epidermidis is a leading cause of nosocomial infections in patients with a compromised immune system and/or an implanted medical device. Seventy to 90% of S. epidermidis clinical isolates are methicillin resistant and carry the mecA gene, present in a mobile genetic element (MGE) called the staphylococcal cassette chromosome mec (SCCmec) element. Along with the presence of antibiotic and heavy metal resistance genes, MGEs can also contain genes encoding secreted or cell wall-anchored virulence factors. In our earlier studies of S. epidermidis clinical isolates, we discovered S. epidermidis surface protein J (SesJ), a prototype of a recently discovered subfamily of the microbial surface component recognizing adhesive matrix molecule (MSCRAMM) group. MSCRAMMs are major virulence factors of pathogenic Gram-positive bacteria. Here, we report that the sesJ gene is always accompanied by two glycosyltransferase genes, gtfA and gtfB, and is present in two MGEs, called the arginine catabolic mobile element (ACME) and the staphylococcal cassette chromosome (SCC) element. The presence of the sesJ gene was associated with the left-hand direct repeat DR_B or DR_E. When inserted via DR_E, the sesJ gene was encoded in the SCC element. When inserted via DR_B, the sesJ gene was accompanied by the genes for the type 1 restriction modification system and was encoded in the ACME. Additionally, the SCC element and ACME carry different isoforms of the SesJ protein. To date, the genes encoding MSCRAMMs have been seen to be located in the bacterial core genome. Here, we report the presence of an MSCRAMM in an MGE in S. epidermidis clinical isolates. IMPORTANCE S. epidermidis is an opportunistic bacterium that has established itself as a successful nosocomial pathogen. The modern era of novel therapeutics and medical devices has extended the longevity of human life, but at the same time, we also witness the evolution of pathogens to adapt to newly available niches in the host. Increasing antibiotic resistance among pathogens provides an example of such pathogen adaptation. With limited opportunities to modify the core genome, most of the adaptation occurs by acquiring new genes, such as virulence factors and antibiotic resistance determinants present in MGEs. In this study, we describe that the sesJ gene, encoding a recently discovered cell wall-anchored protein in S. epidermidis, is present in both ACME and the SCC element. The presence of virulence factors in MGEs can influence the virulence potential of a specific strain. Therefore, it is critical to study the virulence factors found in MGEs in emerging pathogenic bacteria or strains to understand the mechanisms used by these bacteria to cause infections.

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Section: Discussionsupporting

confidence: 76%

Staphylococcus epidermidis MSCRAMM SesJ Is Encoded in Composite Islands

Arora¹,

Hillhouse

et al. 2020

mBio

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“…In recent years, more genomes of S. epidermidis from other sources were reported and analyzed. Apart from those isolated in clinical settings, analysis of a strain G6_2 isolated from the general public environment in London representing ST59 was described ( Xu et al, 2018 ). Comparative genomic analysis of this strain focused more on the antibiotic resistance and its virulence gene arsenal.…”

Section: Discussionmentioning

confidence: 99%

The Genome of Staphylococcus epidermidis O47

et al. 2020

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The skin colonizing coagulase-negative Staphylococcus epidermidis causes nosocomial infections and is an important opportunistic and highly adaptable pathogen. To gain more insight into this species, we sequenced the genome of the biofilm positive, methicillin susceptible S. epidermidis O47 strain (hereafter O47). This strain belongs to the most frequently isolated sequence type 2. In comparison to the RP62A strain, O47 can be transformed, which makes it a preferred strain for molecular studies. S. epidermidis O47's genome has a single chromosome of about 2.5 million base pairs and no plasmid. Its oriC sequence has the same directionality as S. epidermidis RP62A, S. carnosus, S. haemolyticus, S. saprophyticus and is inverted in comparison to Staphylococcus aureus and S. epidermidis ATCC 12228. A phylogenetic analysis based on all S. epidermidis genomes currently available at GenBank revealed that O47 is closest related to DAR1907. The genome of O47 contains genes for the typical global regulatory systems known in staphylococci. In addition, it contains most of the genes encoding for the typical virulence factors for S. epidermidis but not for S. aureus with the exception of a putative hemolysin III. O47 has the typical S. epidermidis genetic islands and several mobile genetic elements, which include staphylococcal cassette chromosome (SCC) of about 54 kb length and two prophages ϕO47A and ϕO47B. However, its genome has no transposons and the smallest number of insertion sequence (IS) elements compared to the other known S. epidermidis genomes. By sequencing and analyzing the genome of O47, we provide the basis for its utilization in genetic and molecular studies of biofilm formation.

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“…Our findings regarding virulence genetic determinants are concordant with those found in SE isolates from hospitals and commensal strains isolated worldwide. The most prominent features of these isolates are their ability to form biofilms, the presence of PMSs, and the multidrug resistance profile displayed (Otto, 2014; Xu et al, 2018). Employing a phylogenetic strategy using the ccrA, B, C recombinases, we conclude that most of the INPer SE strains carry the SCC mec type IV.…”

Section: Discussionmentioning

confidence: 99%

Genomic diversity of prevalentStaphylococcus epidermidismultidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey

Cabrera-Contreras

Santamaría

Bustos

et al. 2019

PeerJ

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Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.

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Whole Genome Sequence and Comparative Genomics Analysis of Multi-drug Resistant Environmental Staphylococcus epidermidis ST59

Cited by 24 publications

References 43 publications

Staphylococcus epidermidis MSCRAMM SesJ Is Encoded in Composite Islands

Staphylococcus epidermidis MSCRAMM SesJ Is Encoded in Composite Islands

The Genome of Staphylococcus epidermidis O47

Genomic diversity of prevalentStaphylococcus epidermidismultidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey

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