Whole genome sequencing of Escherichia coli isolates from aquatic environments in the context of the COVID-19 pandemic: A multicenter study conducted in Cameroon, Brazil and Madagascar

Introduction: The COVID-19 pandemic has brought attention to antimicrobial resistance (AMR), a major global health concern. The COVID-19 pandemic is increasing antimicrobial misuse and could have an impact on water microbial communities, and the likely interaction between SARS-CoV-2 and the aquatic microbial community has been less studied. In low- and middle-income countries, wastewater treatment plants are not available or do not function, so untreated wastewater is discharged directly into nearby water sources. The consortium Cameroon, Brazil, and Madagascar has set itself the goal of detecting and characterizing Escherichia coli isolates circulating in aquatic environment that have been influenced by the presence of SARV-CoV-2. Methods: Fom January to June 2022, wastewater samples were collected monthly in the cities of Yaounde, Antananarivo and Sao Paulo, in different points and nearby healthcare facilities receiving COVID-19 patients and in one control site and screened for the presence of ESBL and carbapenemase producing Escherichia coli on selective culture media. AMR patterns were determined according to CASFM guidelines, and Next Generation Sequencing (NGS) was performed to screen for (antimicrobial resistance genes) ARGs in the isolates. In addition, the presence of SARV-CoV-2 in water samples was investigated by RT-qPCR Results: A total of 41 strains of Escherichia coli predominantly ESBL phenotype (73,1%) were isolated with 10, 15 and 16 isolates respectively for Cameroon, Brazil and Madagascar, mainly in wastewater from hospitals receiving COVID-19 patients (82,9%). The pattern of multi-resistance to antimicrobials has been confirmed, observed in most isolates with the presence of a wide variety of variants of ARGs for most antimicrobial families and 26.8% of isolates with carbapenem ARGs. NGS showed a large diversity of ST and 04 strains of Madagascar belonged to ST-648 and present both at the hospital site and in surface waters at different months. SARS-CoV-2 RNA was detected in 34,14 % of sites where Escherichia coli was present and had no significant impact on its detection (p>0.05). Discussion: Escherichia coli is an AMR pathogen commonly found in water, and its prevalence in hospital sites may be due to the fact that conditions for AMR emergence are favorable there. The predominance of the ESBL phenotype on carbapenemases may be explained by the fact that carbapenems are considered a treatment option of last resort. The wide variety of ARGs presents a significant risk of therapeutic failure, and of potential acquisition of AMR by the bacterial community, as these genes are plasmid mediated. Conclusion: This study highlights high prevalence of Escherichia coli carrying ESBL and carbapenemases genes circulating in aquatic environments in the study countries, although no direct link could be found between the frequency of SARS-CoV-2. This study provides evidence to stakeholders to reinforce regulations on management of hospital and municipal wastewater.