Genetic characterization of antimicrobial resistant Escherichia coli isolated from a mixed-use watershed in northeast Georgia, USA

Authors: CHO, SOHYUN - University Of Georgia; NGUYEN, ANH - University Of Georgia; MCDONALD, JACOB - University Of Georgia; Woodley, Tiffanie; Hiott, Lari; Barrett, John; Jackson, Charlene; Frye, Jonathan

Submitted to: International Journal of Environmental Research and Public Health
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/4/2019
Publication Date: 10/7/2019
Citation: Cho, S., Nguyen, A., Mcdonald, J., Woodley, T.A., Hiott, L.M., Barrett, J.B., Jackson, C.R., Frye, J.G. 2019. Genetic characterization of antimicrobial resistant Escherichia coli isolated from a mixed-use watershed in northeast Georgia, USA. International Journal of Environmental Research and Public Health. https://doi.org/10.3390/ijerph16193761.
DOI: https://doi.org/10.3390/ijerph16193761

Interpretive Summary: Surface water may play a role in the development and spread of antibiotic resistant (AR) bacteria. To address this, 496 Escherichia coli were isolated in a 2015 to 2016 study of quarterly water samples from the upper Oconee watershed in Northeast Georgia. Of those isolates, 34 (6.85%) were resistant to one or more antibiotics. To help determine the source of these bacteria and their mechanisms of antibiotic resistance they were further characterized. The genotypes of the E. coli were determined by DNA finger printing and sequence typing (ST), while the AR genes were detected by PCR and DNA sequence analysis. Analysis identified the genes conferring resistance to azithromycin, ampicillin, chloramphenicol, streptomycin, sulfisoxazole, tetracycline, and trimethoprim/sulfamethoxazole. Five strains were also resistant to fluoroquinolones. Most of the isolates (n=28) also carried mobile genetic elements called plasmids that often encode AR genes. Eleven different plasmids were detected. Sequence typing identified 29 sequence types (ST), including the epidemic urinary tract infection-associated ST131. One of the three ST131 E. coli isolates produced an extended-spectrum beta (ß)-lactamase (ESBL) encoded by the blaCTX-M-15 gene. Bacteria expressing ESBLs are resistant to antibiotics like ceftriaxone used to treat dangerous infections. This is the first report of pathogenic ESBL-producing E. coli ST131 isolated from environmental water in the USA. AR mechanisms to commonly used antimicrobials were found in E. coli isolated from surface water, and they also often carried mobile genetic elements like plasmids, which may play a role in the transmission of AR genes among bacteria in the water environment. This study confirmed the presence of AR and pathogenic E. coli in recreational waters where there is a potential for human exposure.

Technical Abstract: Surface water may play a role in the development and spread of antibiotic resistant (AR) bacteria. To investigate this, surface water from the upper Oconee watershed in Northeast Georgia was collected for analysis. From 100 sites, 30 to 100 samples were taken each quarter of 2015 and 2016, for a total of 458 samples. Escherichia coli (n=496) were isolated from those samples and of those isolates, 34 (6.85%) were resistant to one or more of 14 antibiotics tested. These AR E. coli were characterized by pulsed-field gel electrophoresis (PFGE), AR gene detection, plasmid replicon typing, class I integron detection, and multi-locus sequence typing (MLST). Analysis identified AR genes conferring resistance to azithromycin (mph(A)), ß-lactams (blaCMY, blaCTX, blaTEM), chloramphenicol (floR), streptomycin (strA, strB), sulfisoxazole (sul1, sul2), tetracycline (tetA, tetB, tetC), and trimethoprim/sulfamethoxazole (dhfr5, dhfr12). There were five ciprofloxacin and/or nalidixic resistant isolates, which contained point mutations in gyrA with or without mutations in parC. Most of the isolates (n=28) carried plasmids with 11 replicon types detected, three of which were also positive for class I integrons. Of the 34 isolates, 29 sequence types (ST) were detected, including three epidemic urinary tract infection-associated ST131 isolates and two new STs. One of the three ST131 E. coli isolates exhibited an extended-spectrum beta (ß)-lactamase (ESBL) phenotype and carried genes blaCTX-M-15 and blaTEM-1. To our knowledge, this is the first study on the emergence of the uropathogenic ESBL-producing E. coli ST131 from environmental water in the USA. These E. coli carried antimicrobial resistance mechanisms to commonly used antibiotics and carried mobile genetic elements, which could play a role in transfer of AR genes among E. coli or other bacteria in the surface water environment. Pathogenic E. coli carrying AR genes including an ESBL were isolated from surface water potentially posing a risk to human health through recreational, agricultural, or municipal use of this natural resource.