Genomic analysis of multidrug resistant Escherichia coli from surface water in Northeast Georgia, USA: Presence of a ST131 epidemic strain containing blaCTX-M-15 on a phage-like plasmid

Authors: CHO, SOHYUN - University Of Georgia; GUPTA, SUSHIM - Orise Fellow; MCMILLAN, ELIZABETH - University Of Georgia; SHARMA, POONAM - Orise Fellow; RAMADAN, HAZEM - Mansoura University; JOVE, THOMAS - Inserm University Of Limoges; Jackson, Charlene; Frye, Jonathan

Submitted to: Microbial Drug Resistance
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2019
Publication Date: 11/14/2019
Citation: Cho, S., Gupta, S., Mcmillan, E., Sharma, P., Ramadan, H., Jove, T., Jackson, C.R., Frye, J.G. 2019. Whole genome sequencing of multidrug resistant E. coli from surface water in northeast Georgia, USA, including a ST131 epidemic strain with a blaCTX-M-15 extended spectrum beta-lactamase gene encoded on a phage-like plasmid. Microbial Drug Resistance. https://doi.org/10.1089/mdr.2019.0306.
DOI: https://doi.org/10.1089/mdr.2019.0306

Interpretive Summary: Surface waters such as streams, lakes, and rivers can be contaminated with bacteria, including bacteria that are antibiotic resistant (AR). Contaminated water could be responsible for spreading AR bacteria, including potential pathogens, to humans through drinking untreated water, recreational contact, or irrigation of fresh fruits or vegetables. To investigate this, water samples were taken from streams in the Upper Oconee watershed near Athens, GA, from 2015-2017. Escherichia coli, a bacteria that can be a harmless resident of the human gut or in some cases can be a human pathogen were isolated from these samples. Almost 500 E. coli were isolated, out of which 34 (6.9%) were AR. Six isolates that were resistant to multiple antibiotics were investigated by whole genome sequencing. Analysis of their sequences identified mobile genetic elements (MGEs) and genes encoding AR. One of the E. coli isolates was a pathogenic strain and carried the blaCTX-M-15 gene. This gene encodes resistance to extended spectrum beta-lactams (e.g. ceftriaxone) which are used to treat invasive E. coli infections. This gene was located on a MGE that is a very rarely found phage-like plasmid. The discovery of a blaCTX-M-15-containing phage-like plasmid suggests it may be a new emerging mechanism of AR gene transmission.

Technical Abstract: Surface water is suspected of playing a role in the development and spread of antimicrobial resistant (AR) bacteria, including human pathogens. To investigate this phenomenon, a total of 496 Escherichia coli isolates were recovered from water samples collected over a two year period from streams near Athens in the Upper Oconee watershed, GA, out of which 34 (6.9%) were AR isolates. Of these, six isolates were selected based on the multidrug resistance (MDR) phenotypes, the presence of mobile genetic elements (MGEs), and their pathogenic potential and subjected to whole genome sequence (WGS) analysis for the current study to enhance our understanding of environmental MDR E. coli isolates. This study is the first report on genomic characterization of MDR E. coli from environmental water in the USA through a WGS approach. The sequences of the six MDR E. coli isolates were analyzed and the locations of their AR genes were identified. One of the E. coli isolates, which produced an extended-spectrum ß-lactamase (ESBL), carried the blaCTX-M-15 gene on a plasmid that is likely a member of a very rarely reported family of phage-like plasmids. This is the first time an in-depth sequence analysis has been done on a blaCTX-M-15- containing phage-like plasmid, the presence of which suggests a new emerging mechanism of AR gene transmission.