A Longitudinal Survey of Antibiotic-Resistant Enterobacterales in the Irish Environment, 2019-2020

Brigid Hooban; Kelly Fitzhenry; Louise O'Connor; Georgios Miliotis; Aoife Joyce; Alexandra Chueiri; Maeve Louise Farrell; Niall DeLappe; Alma Tuohy; Martin Cormican; Dearbháile Morris

doi:10.1016/j.scitotenv.2022.154488

A Longitudinal Survey of Antibiotic-Resistant Enterobacterales in the Irish Environment, 2019-2020

Sci Total Environ. 2022 Jul 1:828:154488. doi: 10.1016/j.scitotenv.2022.154488. Epub 2022 Mar 10.

Affiliations

¹ Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland. Electronic address: b.hooban1@nuigalway.ie.
² Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland.
³ National Salmonella, Shigella and Listeria Reference Laboratory, Galway University Hospitals, Galway, Ireland.
⁴ Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland; National Salmonella, Shigella and Listeria Reference Laboratory, Galway University Hospitals, Galway, Ireland; Health Service Executive, Ireland.

PMID: 35278563
DOI: 10.1016/j.scitotenv.2022.154488

Abstract

The natural environment represents a complex reservoir of antibiotic-resistant bacteria as a consequence of different wastewater discharges including anthropogenic and agricultural. Therefore, the aim of this study was to examine sewage and waters across Ireland for the presence of antibiotic-resistant Enterobacterales. Samples were collected from the West, East and South of Ireland. Two periods of sampling took place between July 2019 and November 2020, during which 118 water (30 L) and 36 sewage samples (200 mL) were collected. Waters were filtered using the CapE method, followed by enrichment and culturing. Sewage samples were directly cultured on selective agars. Isolates were identified by MALDI-TOF and antibiotic susceptibility testing was performed in accordance with EUCAST criteria. Selected isolates were examined for bla_CTX-M, bla_VIM, bla_IMP, bla_OXA-48, bla_NDM, and bla_KPC by real time PCR and whole genome sequencing (n = 146). A total of 419 Enterobacterales (348 water, 71 sewage) were isolated from all samples. Hospital sewage isolates displayed the highest percentage resistance to many beta-lactam and aminoglycoside antibiotics. Extended-spectrum beta-lactamase-producers were identified in 78% of water and 50% of sewage samples. One or more carbapenemase-producing Enterobacterales were identified at 23 individual sampling sites (18 water, 5 sewage). This included the detection of bla_OXA-48 (n = 18), bla_NDM (n = 14), bla_KPC (n = 4) and bla_OXA-484 (n = 1). All NDM-producing isolates harbored the ble-MBL bleomycin resistance gene. Commonly detected sequence types included Klebsiella ST323, ST17, and ST405 as well as E. coli ST131, ST38 and ST10. Core genome MLST comparisons detected identical E. coli isolates from wastewater treatment plant (WWTP) influent and nursing home sewage, and the surrounding waters. Similarly, one Klebsiella pneumoniae isolated from WWTP influent and the surrounding estuarine water were identical. These results highlight the need for regular monitoring of the aquatic environment for the presence of antibiotic-resistant organisms to adequately inform public health policies.

Keywords: Antibiotic resistance; Aquatic environment; Carbapenemase; Extended-spectrum beta-lactamase; Wastewater.

MeSH terms

Anti-Bacterial Agents* / pharmacology
Bacterial Proteins / genetics
Escherichia coli* / genetics
Microbial Sensitivity Tests
Multilocus Sequence Typing
Sewage
Water
beta-Lactamases / genetics

Substances

Anti-Bacterial Agents
Bacterial Proteins
Sewage
Water
beta-Lactamases