scholarly journals Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8068 ◽  
Author(s):  
Roberto Cabrera-Contreras ◽  
Rosa I. Santamaría ◽  
Patricia Bustos ◽  
Irma Martínez-Flores ◽  
Enrique Meléndez-Herrada ◽  
...  
Keyword(s):  
Mexico City ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Multidrug Resistant ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Beta Lactams ◽  
Antibiotic Resistant ◽  
Transfer Rates ◽  
Health Care Unit

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.

scholarly journals Genomic analysis of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated during eight years in a single children hospital in México City.

2019 ◽  
Author(s):  
Roberto Cabrera-Contreras ◽  
Rosa I Santamaría ◽  
Patricia Bustos ◽  
Irma Martínez-Flores ◽  
Enrique Meléndez ◽  
...  
Keyword(s):  
Mexico City ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Antibiotic Resistant ◽  
Transfer Rates ◽  
Children Health ◽  
Health Care Unit

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 health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study. Resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides were included. 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 (MLST´s) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). However, half of the S. epidermidis analyzed lacked the icaoperon 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.

scholarly journals Genomic analysis of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated during eight years in a single children hospital in México City.

2019 ◽  
Author(s):  
Roberto Cabrera-Contreras ◽  
Rosa I Santamaría ◽  
Patricia Bustos ◽  
Irma Martínez-Flores ◽  
Enrique Meléndez ◽  
...  
Keyword(s):  
Mexico City ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Antibiotic Resistant ◽  
Transfer Rates ◽  
Children Health ◽  
Health Care Unit

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 health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study. Resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides were included. 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 (MLST´s) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). However, half of the S. epidermidis analyzed lacked the icaoperon 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.

scholarly journals Genomic diversity of antibiotic multi-resistant Staphylococcus epidermidis isolated from a tertiary care hospital in México City

2019 ◽  
Author(s):  
Roberto Cabrera-Contreras ◽  
Rosa I Santamaría ◽  
Patricia Bustos ◽  
Irma Martínez-Flores ◽  
Enrique Meléndez ◽  
...  
Keyword(s):  
Mexico City ◽  
Staphylococcus Epidermidis ◽  
Tertiary Care ◽  
Hospital Setting ◽  
Opportunistic Pathogen ◽  
Tertiary Hospital ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Care Hospital ◽  
Worldwide Distribution

Staphylococcus epidermidis is a human commensal and opportunistic pathogen worldwide distributed. To ascertain which pathogenic S. epidermidis clones are circulating in a local tertiary hospital setting, we sequenced the complete genomes of 17 S. epidermidis isolates obtained from neonatal infections at a Hospital Care Unit in México City. Genomic comparisons between S. epidermidis isolates revealed high pairwise whole genome nucleotide identities of about 97% to 99% and essentially a clonal structure. We inferred eight Multilocus Sequence Types (MLST´s), six of them of worldwide distribution, and two showing allelic variants, not in MLST databases. The profile of virulence includes genes involved in biofilm and modulin formation; most of the strains are multi-resistant to methicillin and several other beta-lactams, fluoroquinolones, and macrolides. 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 frequent than the mutation rate and affected the whole genome. Therefore, recombination properties shape the population structure of local nosocomial S. epidermidis strains, formed by pathogenic and probably, non-pathogenic clones.

scholarly journals Whole-Genome Sequencing Reveals a Prolonged and Persistent Intrahospital Transmission of Corynebacterium striatum, an Emerging Multidrug-Resistant Pathogen

2019 ◽  
Vol 57 (9) ◽  
Author(s):  
Xuebing Wang ◽  
Haijian Zhou ◽  
Dongke Chen ◽  
Pengcheng Du ◽  
Ruiting Lan ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Antimicrobial Agents ◽  
Chronically Ill ◽  
Multidrug Resistant ◽  
Resistance Rate ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Corynebacterium Striatum

ABSTRACT Corynebacterium striatum is an emerging multidrug-resistant (MDR) pathogen that occurs primarily among immunocompromised and chronically ill patients. However, little is known about the genomic diversity of C. striatum, which contributes to its long-term persistence and transmission in hospitals. In this study, a total of 192 C. striatum isolates obtained from 14 September 2017 to 29 March 2018 in a hospital in Beijing, China, were analyzed by antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing was conducted on 91 isolates. Nearly all isolates (96.3%, 183/190) were MDR. The highest resistance rate was observed for ciprofloxacin (99.0%, 190/192), followed by cefotaxime (90.6%, 174/192) and erythromycin (89.1%, 171/192). PFGE separated the 192 isolates into 79 pulsotypes, and differences in core genome single-nucleotide polymorphisms (SNPs) partitioned the 91 isolates sequenced into four clades. Isolates of the same pulsotype were identical or nearly identical at the genome level, with some exceptions. Two dominant subclones, clade 3a, and clade 4a, were responsible for the hospital-wide dissemination. Genomic analysis further revealed nine resistance genes mobilized by eight unique cassettes. PFGE and whole-genome sequencing revealed that the C. striatum isolates studied were the result mainly of predominant clones spreading in the hospital. C. striatum isolates in the hospital progressively acquired resistance to antimicrobial agents, demonstrating that isolates of C. striatum may adapt rapidly through the acquisition and accumulation of resistance genes and thus evolve into dominant and persistent clones. These insights will be useful for the prevention of C. striatum infection in hospitals.

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