TY - JOUR
T1 - Genomic Surveillance of Ceftriaxone-Resistant Escherichia coli in Western New York Suggests the Extended-Spectrum β-Lactamase blaCTX-M-27 Is Emerging on Distinct Plasmids in ST38
AU - Mostafa, Heba H.
AU - Cameron, Andrew
AU - Taffner, Samantha M.
AU - Wang, Jun
AU - Malek, Adel
AU - Dumyati, Ghinwa
AU - Hardy, Dwight J.
AU - Pecora, Nicole D.
N1 - Funding Information:
We thank UR Medicine Central Laboratory Clinical Microbiology for specimen collection and antimicrobial susceptibility testing. Ruichao Li and Chen Sheng (Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, PR China) provided technical advice for Nanopore sequencing. Dr. Steven Gill (URMC) and his group provided technical assistance with plasmid extractions. We also thank Dr. Paul Dunman (URMC) for critical reading of the manuscript. Funding. Funding from the Department of Pathology and Laboratory Medicine, University of Rochester Medical Center supported this study.
Publisher Copyright:
© Copyright © 2020 Mostafa, Cameron, Taffner, Wang, Malek, Dumyati, Hardy and Pecora.
PY - 2020/7/30
Y1 - 2020/7/30
N2 - Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae pose significant treatment and infection prevention challenges. Escherichia coli sequence type (ST) 131 associated with the blaCTX-M-15 gene has been the dominant lineage of ESBL-producing E. coli in the US and worldwide. In this study, our objective was to determine the β-lactamase profile, means of dissemination, prevalence, and the clonal identity of ESBL-producing E. coli in our region of Western New York. Whole-genome SNP-based phylogenomics was used to assess 89 ceftriaxone-resistant (CTR) E. coli. Isolates were collected from both inpatients and outpatients and from urine and sterile-sites over a 2 month period in 2017 or throughout the year, respectively. ST131 was the predominant ST (46.0%), followed by ST38 (15.7%). The blaCTX-M-15 gene was commonly found in 53.7% of ST131 isolates, whereas the blaCTX-M-27 gene was found in 26.8% of ST131, though was significantly associated with ST38, and was found in 71.4% of those strains. When compared to ST131, ST38 E. coli exhibited increased frequency of resistance to nitrofurantoin and decreased frequency of resistance to ciprofloxacin and ampicillin-sulbactam. Using Nanopore long-read sequencing technology, an analysis of the ESBL genetic context showed that the blaCTX-M-15 gene was chromosomal in 68.2% of ST131, whereas the blaCTX-M-27 gene was plasmid-borne in all ST131 and 90% of ST38 isolates. Notably, the blaCTX-M-27 gene in ST38 resided on highly-related (99.0–100.0% identity and 65.0–98.0% query coverage) conjugative IncF plasmids of distinct plasmid multi-locus sequence types (pMLSTs) from those in ST131. Furthermore, ST131 and ST38 were found to harbor different antibiotic resistance gene and virulence factor profiles. These findings raise the possibility of an emerging ESBL-producing E. coli lineage in our region.
AB - Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae pose significant treatment and infection prevention challenges. Escherichia coli sequence type (ST) 131 associated with the blaCTX-M-15 gene has been the dominant lineage of ESBL-producing E. coli in the US and worldwide. In this study, our objective was to determine the β-lactamase profile, means of dissemination, prevalence, and the clonal identity of ESBL-producing E. coli in our region of Western New York. Whole-genome SNP-based phylogenomics was used to assess 89 ceftriaxone-resistant (CTR) E. coli. Isolates were collected from both inpatients and outpatients and from urine and sterile-sites over a 2 month period in 2017 or throughout the year, respectively. ST131 was the predominant ST (46.0%), followed by ST38 (15.7%). The blaCTX-M-15 gene was commonly found in 53.7% of ST131 isolates, whereas the blaCTX-M-27 gene was found in 26.8% of ST131, though was significantly associated with ST38, and was found in 71.4% of those strains. When compared to ST131, ST38 E. coli exhibited increased frequency of resistance to nitrofurantoin and decreased frequency of resistance to ciprofloxacin and ampicillin-sulbactam. Using Nanopore long-read sequencing technology, an analysis of the ESBL genetic context showed that the blaCTX-M-15 gene was chromosomal in 68.2% of ST131, whereas the blaCTX-M-27 gene was plasmid-borne in all ST131 and 90% of ST38 isolates. Notably, the blaCTX-M-27 gene in ST38 resided on highly-related (99.0–100.0% identity and 65.0–98.0% query coverage) conjugative IncF plasmids of distinct plasmid multi-locus sequence types (pMLSTs) from those in ST131. Furthermore, ST131 and ST38 were found to harbor different antibiotic resistance gene and virulence factor profiles. These findings raise the possibility of an emerging ESBL-producing E. coli lineage in our region.
KW - Escherichia coli
KW - bacterial genomics
KW - ceftriaxone
KW - extended-spectrum beta lactamases
KW - mobile elements
KW - nitrofurantoin
KW - plasmids
UR - http://www.scopus.com/inward/record.url?scp=85089438405&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85089438405&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2020.01747
DO - 10.3389/fmicb.2020.01747
M3 - Article
C2 - 32849376
AN - SCOPUS:85089438405
SN - 1664-302X
VL - 11
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
M1 - 1747
ER -