title: Population structure of Japanese extraintestinal pathogenic Escherichia coli and its relationship with antimicrobial resistance.
abstract: To define the population structure of extraintestinal pathogenic Escherichia coli (ExPEC) in Japan and its relationship with antimicrobial resistance and the major resistance mechanisms for fluoroquinolones and β-lactams, we designed a multicentre prospective study.
  
  
  
  A total of 329 ExPEC isolates were collected at 10 Japanese acute-care hospitals during December 2014. We defined the clonal groups of ExPEC by fumC and fimH sequencing (CH typing). Antimicrobial susceptibility testing of 18 agents and the detection of mutations in quinolone resistance-determining regions (QRDRs) and β-lactamases were performed.
  
  
  
  Among the study isolates, 103 CH types were found, and CH40-30 (25%) and another 10 CH types (35% in total) constituted the major ExPEC population. Ciprofloxacin non-susceptibility, ESBLs and MDR phenotypes were found in 34%, 22% and 33%, respectively. CH40-30, corresponding to the C/H30 clade of the global pandemic ST131 clone, was associated with four QRDR mutations (100%) and bla CTX-M (60%) and was the most frequent type in 15 antimicrobial-non-susceptible populations (dominating 39%-75% of each population, the highest prevalence for ciprofloxacin), the ESBL producers (70%) and the MDR isolates (59%). Isolates that were non-susceptible to nalidixic acid and low-level resistant to ciprofloxacin with one or two QRDR mutations represented 16% of the study isolates and were distributed among the eight major and non-major CH types.
  
  
  
  More than half of the ExPEC population in Japan consisted of 11 major clones. Of these clones, the CH40-30-ST131-C/H30 clone was the predominant antimicrobial-resistant population. The presence of major clones with low-level ciprofloxacin resistance supports the potential future success of a non-ST131 fluoroquinolone-resistant clone.
authors.forename: Yasufumi
authors.initials: Y
authors.lastname: Matsumura
authors.forename: Taro
authors.initials: T
authors.lastname: Noguchi
authors.forename: Michio
authors.initials: M
authors.lastname: Tanaka
authors.forename: Toru
authors.initials: T
authors.lastname: Kanahashi
authors.forename: Masaki
authors.initials: M
authors.lastname: Yamamoto
authors.forename: Miki
authors.initials: M
authors.lastname: Nagao
authors.forename: Shunji
authors.initials: S
authors.lastname: Takakura
authors.forename: Satoshi
authors.initials: S
authors.lastname: Ichiyama
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D002648:Child; D002675:Child, Preschool; D024881:Drug Resistance, Bacterial; D004927:Escherichia coli Infections / Q000453:epidemiology / Q000382:microbiology*; D029968:Escherichia coli Proteins / Q000235:genetics; D000072282:Extraintestinal Pathogenic Escherichia coli / Q000145:classification* / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D006761:Hospitals; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007564:Japan / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D058889:Molecular Typing; D011446:Prospective Studies; D017422:Sequence Analysis, DNA; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D029968:Escherichia coli Proteins