Occurrence and distribution of Carbapenem-resistant Enterobacterales and carbapenemase genes along a highly polluted hydrographic basin

Pedro Teixeira; Marta Tacão; Isabel Henriques

doi:10.1016/j.envpol.2022.118958

Occurrence and distribution of Carbapenem-resistant Enterobacterales and carbapenemase genes along a highly polluted hydrographic basin

Environ Pollut. 2022 May 1:300:118958. doi: 10.1016/j.envpol.2022.118958. Epub 2022 Feb 4.

Authors

Pedro Teixeira¹, Marta Tacão², Isabel Henriques³

Affiliations

¹ Biology Department and CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal, University of Aveiro, Aveiro, Portugal.
² Biology Department and CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal, University of Aveiro, Aveiro, Portugal. Electronic address: martat@ua.pt.
³ University of Coimbra, Centre for Functional Ecology and Department of Life Sciences, Faculty of Science and Technology, Coimbra, Portugal.

PMID: 35131334
DOI: 10.1016/j.envpol.2022.118958

Abstract

We determined the distribution and temporal variation of Carbapenem Resistant Enterobacterales (CRE), carbapenemase-encoding genes and other antibiotic resistance genes (ARGs) in a highly polluted river (Lis River; Portugal), also assessing the potential influence of water quality to this distribution. Water samples were collected in two sampling campaigns performed one year apart (2018/2019) from fifteen sites and water quality was analyzed. CRE were isolated and characterized. The abundance of four ARGs (bla_NDM, bla_KPC, tetA, bla_CTX-M), two Microbial Source Tracking (MST) indicators (HF183 and Pig-2-Bac) and the class 1 integrase gene (IntI1) was measured by qPCR. RESULTS: confirmed the poor quality of the Lis River water, particularly in sites near pig farms. A collection of 23 CRE was obtained: Klebsiella (n = 19), Enterobacter (n = 2) and Raoultella (n = 2). PFGE analysis revealed a clonal relationship between isolates obtained in different sampling years and sites. All CRE isolates exhibited multidrug resistance profiles. Klebsiella and Raoultella isolates carried bla_KPC while Enterobacter harbored bla_NDM. Conjugation experiments were successful for only four Klebsiella isolates. All ARGs were detected by qPCR on both sampling campaigns. An increase in ARGs and IntI1 abundances was detected in sites located downstream of wastewater treatment plants. Strong correlations were observed between bla_CTX-M, IntI1 and the human-pollution marker HF183, and also between tetA and the pig-pollution marker Pig-2-bac, suggesting that both human- and animal-derived pollution in the Lis River are a potential source of ARGs. Plus, water quality parameters related to eutrophication and land use were significantly correlated with ARGs abundances. Our findings demonstrated that the Lis River encloses high levels of antibiotic resistant bacteria and ARGs, including CRE and carbapenemase-encoding genes. Overall, this study provides a better understanding on the impacts of water pollution resulting from human and animal activities on the resistome of natural aquatic systems.

Keywords: Antibiotic resistance; Carbapenem-resistant enterobacterales; Carbapenemases; Microbial source tracking; River; Water quality.

MeSH terms

Animals
Anti-Bacterial Agents / pharmacology
Bacterial Proteins / genetics
Carbapenems* / pharmacology
Swine
beta-Lactamases* / genetics

Substances

Anti-Bacterial Agents
Bacterial Proteins
Carbapenems
beta-Lactamases
carbapenemase