Molecular epidemiology of extra-intestinal pathogenic Escherichia coli circulating in humans, animals, food, and the environment in Zimbabwe

Abstract

Antimicrobial resistance (AMR) in Enterobacterales is an emerging threat for human health globally, including in low-to-middle income countries (LMICs). The misuse of antibiotics has resulted in the establishment of various enzyme mediated AMR mechanisms, e.g. extended spectrum beta-lactamases (ESBLs), carbapenemases and colistin resistance, which are difficult to control. Developing countries like Zimbabwe are vulnerable to AMR due to poor pathogen surveillance, unhygienic and unregulated conditions of the agricultural and food production process, and poor sanitation. Limited information is available on the real burden of the extra-intestinal pathogenic Escherichia coli (ExPEC) and the population structure of such isolates in Zimbabwe. Active pathogen surveillance systems (One Health approach) in Zimbabwe’s healthcare setting is important for the continuous identification, tracking and control of the spread of circulating ExPEC clones. The aim of this study was to determine the molecular epidemiology of ExPEC isolates circulating in humans, animals, food, and the environment in Zimbabwe through phenotypic and genomic analysis. A total of 200 human urine isolates, 200 animal avian isolates and 50 environmental isolates were selected from the National Microbiology Reference Laboratory E. coli Biobank, which were collected over a 2-year period (2017-2019). All available demographic data was collected. No food product isolates were included in this study. This study utilised both phenotypic and molecular typing methods. The molecular typing methods included polymerase chain reaction (PCR) for identification of virulence genes (clinical urine isolates), Sequence type (ST)131, etc., real-time PCR for identifying clinical urine ExPEC clones, and whole genome sequencing (WGS) on ESBL positive isolates from human, animal, and environmental origin. Representative isolates from different geographical locations and time points were selected for WGS analysis based on ESBL prevalence. Among the 200 human isolates included for screening with the 7-SNP real time PCR method, 61% were confirmed ESBL positive. The isolates included for WGS analysis were recovered from the 200 human urine isolates (n= 48 ESBL positives), avian (n=21 ESBL positives), environment borehole (n =4 ESBL positives) and were multidrug resistant (MDR). Sequence type 131 (17/48, 35%) and ST410 (13/48, 27%) (in human isolates), and ST10 (7/21, 33%) (in animal isolates) were the most dominant clones detected in this study. No carbapenem resistant isolate was detected. One isolate (avian) harboured the mobilised colistin resistance (mcr)-1 gene. The majority of urine isolates produced cefotaximase-Munich (CTX-M)-15, CTX-M-14; and oxacillinase (OXA)-1. Avian isolates produced CTX-M-14, and Temoneira (TEM)-1, while the environmental isolates had sulfhydryl-variable (SHV), and TEM-1. The majority of isolates carried the incompatibility group (Inc) F plasmids depending on strain type. The use of a cost effective, rapid and reliable 7-Single Nucleotide Polymorphism real time PCR (7-SNP-PCR) typing method described the population structure of the clinical collection (urine) of ExPEC obtained in Zimbabwe. This technique was validated for human urine isolate only and hence was used for all the human isolates from this study. The presence of E. coli ST131 and ST410 shows that it has spread across various communities included in this study and poses complex challenges to infection control and prevention programs as well as to the planning of correct treatment regimens. This study provides baseline molecular data on the detection of specific lineages of ExPEC circulating in the Zimbabwean communities using both 7-SNP-PCR and WGS. The rapid identification of high-risk clones is critical to curb the dissemination and emergence of pandemic clones. Keywords: Escherichia coli, ExPEC, ESBL, ST131, ST410, ST10, Zimbabwe