Dataset Information

Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children's Hospital in Mexico City in an eight-years survey.

ABSTRACT: 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.

SUBMITTER: Cabrera-Contreras R

PROVIDER: S-EPMC6874853 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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

Cabrera-Contreras Roberto R Santamaría Rosa I RI Bustos Patricia P Martínez-Flores Irma I Meléndez-Herrada Enrique E Morelos-Ramírez Rubén R Barbosa-Amezcua Martín M González-Covarrubias Vanessa V Silva-Herzog Eugenia E Soberón Xavier X González Víctor V

PeerJ 20191120

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 e ...[more]

PMID: 31768302

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Project description:Homicide is without doubt one of Mexico's most important security problems, with data showing that this dismal kind of violence sky-rocketed shortly after the war on drugs was declared in 2007. Since then, violent war-like zones have appeared and disappeared throughout Mexico, causing unfathomable human, social and economic losses. One of the most emblematic of these zones is the Monterrey metropolitan area (MMA), a central scenario in the narco-war. Being an important metropolitan area in Mexico and a business hub, MMA has counted hundreds to thousands of casualties. In spite of several approaches being developed to understand and analyze crime in general, and homicide in particular, the lack of accurate spatio-temporal homicide data results in incomplete descriptions. In order to describe the manner in which violence has evolved and spread in time and space through the city, here we propose a network-based approach. For this purpose, we define a homicide network where nodes are geographical entities that are connected through spatial and temporal relationships. We analyzed the time series of homicides in different municipalities and neighborhoods of the MMA, to observe whether or not a global correlation appeared. We studied the spatial correlation between neighborhoods where homicides took place, to observe whether distance is a factor of influence in the frequency of homicides. We constructed yearly co-occurrence networks, by correlating neighborhoods with homicides happening within a same week, and counting the co-occurrences of these neighborhood pairs in 1 year. We also constructed a crime network by aggregating all data of homicides, eliminating the temporal correlation, in order to observe whether homicide clusters appeared, and what those clusters were distributed geographically. Finally, we correlated the location and frequency of homicides with roads, freeways and highways, to observe if a trend in the homicidal violence appeared. Our network approach in the homicide evolution of MMA allows us to identify that (1) analyzing the whole 86-month period, we observed a correlation between close cities, which decreases in distant places. (2) at neighborhood level, correlations are not distance-dependent, on the contrary, highest co-occurrences appeared between distant neighborhoods and a polygon formed by close neighborhoods in downtown Monterrey. Moreover, (3) An elevated number of homicides occur close to the 85th freeway, which connects MMA with the US border. (4) Some socioeconomic barriers determine the presence of homicide violence. Finally, (5) we show a relation between homicidal crime and the urban landscape by studying the distance of safe and violent neighborhoods to the closest highway and by studying the evolution of highway and crime distance over the cartel-related years and the following period. With this approach, we are able to describe the spatial and temporal evolution of homicidal crime in a metropolitan area.

Dataset Information

Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children's Hospital in Mexico City in an eight-years survey.

Publications

Genomic diversity of prevalent <i>Staphylococcus epidermidis</i> multidrug-resistant strains isolated from a Children's Hospital in México City in an eight-years survey.

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