Genomic Surveillance of Antimicrobial Resistance in Wastewater Sources.pptx

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1. Genomic Surveillance of Antimicrobial Resistance in Wastewater Sources

2. Background The release of untreated or poorly treated wastewater into the environment is being increasingly recognized as the major factor driving the spread of clinically relevant antimicrobial resistant (AMR) bacteria and genes (ARB and ARGs) in low- and middle-income countries (LMIC), through the environment into healthcare facilities and community settings E nvironmental AMR surveillance from the culture-based techniques to also include advanced molecular methods is paramount to understand and mitigate the spread of ARG in the future U sing the One Health approach, this proposed research project will employ advanced molecular techniques to assess the risks associated with AMR in three different wastewater types, namely hospital, slaughterhouse, and municipal wastewaters in Owerri, southeast Nigeria, with Nigeria serving as a model LMIC.

3. Statement of Problem Wastewaters occupy a critical crossover point for the spread of AMR from the environment to the clinics. However, this domain remains poorly surveyed in the low and middle income countries (LMICs) unlike in the high-income settings where state-of-the-art techniques are currently being used for the surveillance of antimicrobial resistant bacteria and genes in the environment Wastewater surveillance (WWS) of ARB and ARGs provides composite samples for an entire population, with easy access to the mixed community microbiome This concept is emerging rapidly, but the clinical utility, sensitivity, and uniformity of WWS of ARB remains poorly understood especially in LMICs where the burden of AMR is high and advanced molecular methods are rarely used. Therefore , there is a clear need to explore how and if molecular WWS for AMR can be applied in LMICs to evaluate the risks associated with the release of these wastewaters and if detected AMR loads can be related to clinical cases and outcomes in the local communities

4. Research questions What is the role of wastewaters as drivers of the environmental spread and evolution of AMR in LMICs using Nigeria as a model LMIC?   How do the microbiome and resistome structure and the resistance gene mobility from different types of Nigerian wastewaters differ?   What are the associated risks for the transfer of these ARGs from environmental isolates to clinical pathogens?   To what extent can molecular and non-culture-based methods be used for generating accurate and reliable data on the epidemiology and burden of AMR from environmental settings in Nigeria?

5. Objectives of the study The main aim of this project is to perform molecular method-based surveillance of AMR from hospital, slaughterhouse, and municipal wastewater sources in Owerri, southeast Nigeria as a model LMIC settings to assess the relative abundance and mobility potential of ARGs from these environmental sources.   To elucidate the genetic determinants sustaining AMR in MDR isolates and complex microbial communities from different Nigerian wastewater types and compare them to German wastewaters.   To determine the virulence of the environmental MDR isolates and their ability to spread ARGs to human pathogens   To ascertain the mobility potential of ARGs in the complex microbial communities from the three different types of wastewater to support risk assessment of possible transmission to human pathogens.   To identify molecular methods that are transferable to LMIC settings to support local AMR surveillance

6. Research Plan and Methodology WP1 – Sampling of wastewaters and isolation and phenotypic characterization of MDR Enterobacterales WP 1.1. The Nigerian sampling campaign of three types of wastewaters WP 1.2. The German sampling campaign WP2 - Molecular analysis of isolate libraries. W hole genome sequence (WGS) analysis WP 2.1 Phylogeny/Epidemiology WP 2.2 Screening for antibiotic resistance genes WP 2.3 Analysis of Mobile genetic elements WP 2.4 Determining Virulence factors WP3 - Whole-community microbiome, resistome and ARG mobility analysis WP3.1 16SrRNA based amplicon sequencing and High-throughput qPCR analysis of ARGs WP 3.2 Mobility analysis of selected ARGs based on sequencing results from isolates WP4 – Defining indicators for future AMR analysis suitable for application in LMIC