Comparative Genome Analysis of Extended-Spectrum-β-Lactamase-ProducingEscherichia coliSequence Type 131 Strains from Nepal and Japan.
The global spread of extended-spectrum-β-lactamase (ESBL)-producingEscherichia coli(ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted whole-genome sequencing (WGS) of ESBL-E. coliST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data forE. coliST131 strains. Further, we conducted phylogenetic analysis of these isolates and all genome sequence data for ST131 strains to determine sequence diversity. One hundred five unique ESBL-E. coliisolates from Nepal (February 2013 to July 2013) and 76 isolates from Japan (October 2013 to September 2014) were included. Of these isolates, 54 (51%) isolates from Nepal and 11 (14%) isolates from Japan were identified as ST131 by WGS. Phylogenetic analysis based on WGS suggested that the majority of ESBL-E. coliST131 isolates from Nepal clustered together, whereas those from Japan were more diverse. Half of the ESBL-E. coliST131 isolates from Japan belonged to virotype C, whereas half of the isolates from Nepal belonged to a virotype other than virotype A, B, C, D, or E (A/B/C/D/E). The dominant sublineage ofE. coliST131 wasH30Rx, which was most prominent in ESBL-E. coliST131 isolates from Nepal. Our results revealed distinct phylogenetic characteristics of ESBL-E. coliST131 spread in the two geographical areas of Asia, indicating the involvement of multiple factors in its local spread in each region.IMPORTANCEThe global spread of ESBL-E. colihas been driven in large part by pandemic sequence type 131 (ST131). A recent study suggested that, withinE. coliST131, certain sublineages have disseminated worldwide with little association with their geographical origin, highlighting the complexity of the epidemiology of this pandemic clone. ST131 bacteria have also been classified into four virotypes based on the distribution of certain virulence genes. Information on virotype distribution in Asian ST131 strains is limited. We conducted whole-genome sequencing of ESBL-E. coliST131 strains collected in Nepal and Japan, two Asian countries with a high and low prevalence of ESBL-E. coli, respectively. We systematically compared these ST131 genomes with those reported from other regions to gain insights into the molecular epidemiology of their spread and found the distinct phylogenetic characteristics of the spread of ESBL-E. coliST131 in these two geographical areas of Asia.
Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
Tohru
T
Miyoshi-Akiyama
Department of Clinical Microbiology, Kathmandu University School of Medical Sciences, Dhulikhel, Nepal.
Jatan Bahadur
JB
Sherchan
Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
Yohei
Y
Doi
Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan; Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
Maki
M
Nagamatsu
Public Health Research Laboratory, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal.
Jeevan B
JB
Sherchand
Public Health Research Laboratory, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal.
Sarmila
S
Tandukar
Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan.
Norio
N
Ohmagari
Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
Teruo
T
Kirikae
Department of International Medical Cooperation, National Center for Global Health and Medicine, Tokyo, Japan.
Hiroshi
H
Ohara
Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan.
Kayoko
K
Hayakawa
CTX-M; Escherichia coli; ST131; antimicrobial resistance; extended-spectrum beta-lactamase; whole-genome sequence