Dataset Information

Draft Genome Sequence of Providencia rettgeri APW139_S1, an NDM-18-Producing Clinical Strain Originating from Hospital Effluent in South Africa.

ABSTRACT: Providencia rettgeri is an opportunistic pathogen implicated in various clinical infections. Here, we report the genome sequence of a Providencia rettgeri strain isolated from hospital effluent in South Africa, which harbors the New Delhi metallo-?-lactamase (NDM) variant 18 gene (bla NDM-18). The 4,835,047-bp genome encodes a resistome and virulome that are of cardinal importance to Providencia infections.

SUBMITTER: Ntshobeni NB

PROVIDER: S-EPMC6533383 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Draft Genome Sequence of Providencia rettgeri APW139_S1, an NDM-18-Producing Clinical Strain Originating from Hospital Effluent in South Africa.

Ntshobeni Noyise B NB Allam Mushal M Ismail Arshad A Amoako Daniel G DG Essack Sabiha Y SY Chenia Hafizah Y HY

Microbiology resource announcements 20190523 21

Providencia rettgeri is an opportunistic pathogen implicated in various clinical infections. Here, we report the genome sequence of a Providencia rettgeri strain isolated from hospital effluent in South Africa, which harbors the New Delhi metallo-β-lactamase (NDM) variant 18 gene (bla NDM-18). The 4,835,047-bp genome encodes a resistome and virulome that are of cardinal importance to Providencia infections. ...[more]

PMID: 31123013

Similar Datasets

Project description:BACKGROUND:Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-?-lactamase (NDM) and other ?-lactamases have been reported that reduce the efficiency of clinical antimicrobial treatments. In this study, we analyzed antibiotic resistance, the presence of resistance genes and the clonal relationship of two P. rettgeri isolates obtained from male patients admitted to the same hospital in Bogotá - Colombia, 2015. RESULTS:Antibiotic susceptibility profile evaluated by the Kirby-Bauer method revealed that both isolates were resistant to third-generation carbapenems and cephalosporins. Whole-genome sequencing (Illumina HiSeq) followed by SPAdes assembling, Prokka annotation in combination with an in-house Python program and resistance gene detection by ResFinder identified the same six ?-lactamase genes in both isolates: blaNDM-1, blaVIM-2, blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1. Additionally, various resistance genes associated with antibiotic target alteration (arnA, PmrE, PmrF, LpxA, LpxC, gyrB, folP, murA, rpoB, rpsL, tet34) were found and four efflux pumps (RosAB, EmrD, mdtH and cmlA). The additional resistance to gentamicin in one of the two isolates could be explained by a detected SNP in CpxA (Cys191Arg) which is involved in the stress response of the bacterial envelope. Genome BLAST comparison using CGView, the ANI value (99.99%) and the pangenome (using Roary) phylogenetic tree (same clade, small distance) showed high similarity between the isolates. The rMLST analysis indicated that both isolates were typed as rST-61,696, same as the RB151 isolate previously isolated in Bucaramanga, Colombia, 2013, and the FDAARGOS_330 isolate isolated in the USA, 2015. CONCLUSIONS:We report the coexistence of the carbapenemase genes blaNDM-1, and blaVIM-2, together with the ?-lactamase genes blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1, in P. rettgeri isolates from two patients in Colombia. Whole-genome sequence analysis indicated a circulation of P. rettgeri rST-61,696 strains in America that needs to be investigated further.

Dataset Information

Draft Genome Sequence of Providencia rettgeri APW139_S1, an NDM-18-Producing Clinical Strain Originating from Hospital Effluent in South Africa.

Publications

Draft Genome Sequence of Providencia rettgeri APW139_S1, an NDM-18-Producing Clinical Strain Originating from Hospital Effluent in South Africa.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure