USING WHOLE GENOME SEQUENCING TO DETERMINE THE TRANSMISSION DYNAMICS AND ACQUISITION OF ANTIMICROBIAL RESISTANCE AT SELECTED REFERRAL HOSPITALS AND COMMUNITY SETTINGS IN UGANDA AND TANZANIA

Abstract

The recent comeback of multidrug resistant pathogens through persistent misapplication of antibiotics has aggravated their threat to worldwide human public health and well-being. Determining the scope of the antimicrobial resistance problem has been identified as an essential for formulating and monitoring effective response to antimicrobial resistance. The data generated from the study will contribute towards informing empirical patient treatment, epidemiological tracking of antimicrobial resistance (AMR), and formulation of improved infection control protocols in hospitals and community settings. This project therefore employed a mixed study design approach involving the application of traditional microbiology methods, social and behavioral sciences-based methods, together with Whole Genome Sequencing (WGS) to provide a deeper understanding of the local and global spread of antimicrobial resistance especially in hospitals and community settings. within Uganda and Tanzania. A command line-based bioinformatics workflow called the Rapid Microbial Analysis Pipeline (rMAP) was designed to analyze the WGS data obtained from the multi-drug resistant (MDR) isolates from Uganda and Tanzania. This software was designed to target ESKAPE group (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, and Enterobacter) pathogens with the ability to perform adapter trimming, quality control, genome assembly and annotation, variant calling, phylogenetic inference, antimicrobial element detection (AMR genes, multi-locus sequence typing, plasmid profiling and virulence factor determination), pangenome analysis, and insertion sequence detection. The source codes for the software are freely available via https://github.com/GunzIvan28/rMAP. With this tool, the genetic determinants like AMR genes, virulence factors, MLSTs, SNPs, and plasmids mediating AMR acquisition and transmission in East Africa were reported in comprehensive detail by this study. Data from the mother study standardized interviewer administered questionnaires on socio-demographics, behaviors/practices that influence the emergence and spread of drug resistant bacteria, bacterial culture, and sensitivity was analyzed to describe the emergence, epidemiology and transmission networks for these MDR pathogens. A very significant number of orthopedic patients, healthy community individuals and the inanimate environment in the wards located at the respective study sites were colonized vi with ESBL-producing K. Pneumoniae and E. coli bacteria as the most predominant organisms. Other bacteria like Enterobacter spp, Citrobacter spp and Acinetobacter baumannii were also found to colonize the study sites. This study further deduced that AMR acquisition and transmission occurred mostly via human-human interfaces both within and outside medical health care settings. Human practices like the rampant drug misuse, ineffective IPC, and treatment of animals and poultry with antibiotics exacerbate the AMR problem within our settings. This study re-emphasizes the dire need to implement and strengthen surveillance and monitoring systems for tracking AMR trends in East Africa by the respective stake holders and policy makers especially in ESBL-producing Gram-negative bacteria. The health ministries from Uganda and Tanzania should strengthen the mass sensitizations through utilizing the different media platforms to educate and inform people about the dangers of AMR. With the advent of bioinformatics tools like rMAP, we demonstrate the necessity of implementing technologies like WGS as routine diagnostic approaches alongside the conventional microbiology to guide clinical management plus decision making for patients, formulation of policies, and installation of surveillance systems for AMR.