Genomic Characterization of Nonclonal mcr-1-Positive Multidrug-Resistant Klebsiella pneumoniae from Clinical Samples in Thailand

Abstract

Multidrug-resistant Klebsiella pneumoniae strains are one of the most prevalent causes of nosocomial infections and pose an increasingly dangerous public health threat. The lack of remaining treatment options has resulted in the utilization of older drug classes, including colistin. As a drug of last resort, the discovery of plasmid-mediated colistin resistance by mcr-1 denotes the potential development of pandrug-resistant bacterial pathogens. To address the emergence of the mcr-1 gene, 118 gram-negative Enterobacteriaceae isolated from clinical samples collected at Queen Sirikit Naval Hospital in Chonburi, Thailand were screened for colistin resistance using automated antimicrobial susceptibility testing and conventional PCR screening. Two K. pneumoniae strains, QS17-0029 and QS17-0161, were positive for mcr-1, and both isolates were sequenced to closure using short- and long-read whole-genome sequencing. QS17-0029 carried 16 antibiotic resistance genes in addition to mcr-1, including 2 carbapenemases, blaNDM-1 and blaOXA-232. QS17-0161 carried 13 antibiotic resistance genes in addition to mcr-1, including the extended-spectrum β-lactamase blaCTX-M-55. Both isolates carried multiple plasmids, but mcr-1 was located alone on highly similar 33.9 Kb IncX4 plasmids in both isolates. The IncX4 plasmid shared considerable homology to other mcr-1-containing IncX4 plasmids. This is the first report of a clinical K. pneumoniae strain from Thailand carrying mcr-1 as well as the first strain to simultaneously carry mcr-1 and multiple carbapenemase genes (QS17-0029). The identification and characterization of these isolates serves to highlight the urgent need for continued surveillance and intervention in Southeast Asia, where extensively drug-resistant pathogens are being increasingly identified in hospital-associated infections.

Genomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15, and OXA-232

“…The bla CTX-M-15 gene was localized in the chromosome of the three KL8, KL11, and KL29 strains, flanked by the insertion sequence ISEcp1 and the truncated transposon DTn2, integrated in the metaldependent hydrolase tRNA synthetase gene (MH523447). The same structure and integration site was also found in the chromosome of QS17-0029 [11] (between positions 2449972 and 2452365 in CP024038), while it was absent in the chromosome of FDAAR-GOS_440. However, QS17-0029 (CP024040) and FDAARGOS_440 (CP023922) and strains from Sweden (CP029588) and France (LT994840) carried a plasmid copy of the bla CTX-M-15 gene located on IncFIIk.…”

“…The cgMLST analysis [9,10] showed that there were between 13 and 85 out of 629 core genome locus differences among ST16 genomes. KL11 showed 13, 15, 24, and 85 locus differences compared with QS17-0029 (CP024038.1) from Thailand, positive to bla OXA-232 , bla NDM-1 , bla CTX-M-15 , and mcr-1 [11], FDAARGOS_440 (CP023919.1) isolated in Canada positive to bla NDM-1 , bla OXA-232 , and bla CTX-M-15 , UCLAOXA232KP (CP012568) from the USA, positive to bla OXA-232 and bla CTX-M-15 , and AR_0087 (CP029738) identified in the USA, negative for carbapenemase and ESBL genes, respectively. KL29, the ST16 isolated in Italy in 2016, differed for 32 and 43 loci from outbreak strains KL11 and KL8, respectively.…”

Resistencia a colistín mediado por el gen mcr-1 identificado en cepas de Escherichia coli y Klebsiella pneumoniae. Primeros reportes en el Perú

“…En los resultados obtenidos todos los aislamientos presentan halos ≤11mm lo que los categoriza como resistentes 11 , a excepción de la cepa 22964 que presenta como resultado 16mm. En cuanto a los resultados de microdilución en caldo, todos los aislamientos presentaron MIC ≥4µg/mL que los posiciona en la categoría resistente 23,24 .…”

“…Concluimos que de 326 uroculti vos positi vo, se obtuvieron 7 aislamientos de Escherichia coli resistentes a colistí n y con expresión del gen mcr-1. Si bien este ti po de resistencia ya había sido identi fi cado en países lejanos 24,27,28 e incluso vecinos al nuestro 19 , estos representan los primeros aislamientos confi rmados en enterobacterias en el Perú asociados a la presencia del gen mcr-1. Recomendamos conti nuar el estudio para la búsqueda de aislamientos con esta resistencia e implementar pruebas en los laboratorios para su detección temprana 30 , con la fi nalidad de generar fuentes de información para detectar la presencia de este gen y sus variantes 23,24 .…”

Novel IncR/IncP6 Hybrid Plasmid pCRE3-KPC Recovered from a Clinical KPC-2-Producing Citrobacter braakii Isolate

“…Plasmid pCRE3-KPC was extracted from the cells using a Qiagen Plasmid Midi kit (Qiagen, Germany). The plasmid conjugal transfer and electroporation tests were performed as described previously (40,41).…”