1. Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases
- Author
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Adriana Piza-Buitrago, María Teresa Reguero, John C Donato, Verónica Rincón, Emiliano Barreto-Hernández, Sandra Yamile Saavedra, Carolina Duarte, Jaime Morero, and Laurent Falquet
- Subjects
Microbiology (medical) ,Male ,Sequence analysis ,medicine.drug_class ,Cephalosporin ,lcsh:QR1-502 ,Microbial Sensitivity Tests ,Providencia ,Biology ,Colombia ,Microbiology ,lcsh:Microbiology ,beta-Lactam Resistance ,beta-Lactamases ,bla OXA-10 ,03 medical and health sciences ,Antibiotic resistance ,Bacterial Proteins ,Drug Resistance, Multiple, Bacterial ,medicine ,Humans ,030304 developmental biology ,And bla TEM-1 ,Whole genome sequencing ,0303 health sciences ,Whole-genome sequencing ,030306 microbiology ,Enterobacteriaceae Infections ,Providencia rettgeri ,biochemical phenomena, metabolism, and nutrition ,bacterial infections and mycoses ,biology.organism_classification ,rpoB ,Anti-Bacterial Agents ,bla CTX-M-15 ,And blaTEM-1 ,bla CMY-2 ,Parasitology ,Gentamicin ,Genome, Bacterial ,medicine.drug ,Research Article - Abstract
BackgroundProvidencia rettgeriis a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) and other β-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 twoP. rettgeriisolates obtained from male patients admitted to the same hospital in Bogotá – Colombia, 2015.ResultsAntibiotic 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 β-lactamase genes in both isolates:blaNDM-1, blaVIM-2, blaCTX-M-15, blaOXA-10, blaCMY-2andblaTEM-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 andcmlA).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.ConclusionsWe report the coexistence of the carbapenemase genesblaNDM-1, andblaVIM-2, together with the β-lactamase genesblaCTX-M-15, blaOXA-10, blaCMY-2andblaTEM-1, inP. rettgeriisolates from two patients in Colombia. Whole-genome sequence analysis indicated a circulationof P. rettgerirST-61,696 strains in America that needs to be investigated further.
- Published
- 2020