This study detected and characterized enteric pathogens (Salmonella, Shigella, E.coli and Vibrio cholerae) from an urban river in Johannesburg South Africa

The Jukskei River is a potential reservoir and vehicle for the transmission of enteric pathogens. It suffers from sewage pollution resulting from inflows of sewage from buildings with no sewage system and the informal settlements along the riverbanks. In South Africa, surveillance of enteric pathogens is limited to clinical specimens, and the presence of these pathogens in urban river water is poorly documented. The study aimed to isolate and characterize Escherichia coli, Shigella, and Vibrio cholerae in the Jukskei River. A total of 80 water samples collected from the Jukskei River were subjected to culture-based methods for the enumeration and isolation of the respective enteric pathogens. Real-time polymerase chain reaction assays targeting uidA, ipaH, and toxR genes, were used to detect the presence of E. coli, Shigella, and V. cholerae in the water samples and to confirm presumptive E. coli, Shigella, and V. cholerae, respectively. Confirmed isolates were sequenced using the MInION portable nanopore-sequencing device. Reference-based genome assemblies were constructed from the raw reads using the EPI2ME software followed by bioinformatics analysis using the Centre for Genomic Epidemiology website. Bacterial means counts ranged between 4.95 - 6.52 log10CFU/mL, 5.32 - 6.12 log10CFU/mL, and 2.02 - 4.4 log10CFU/mL for E.coli, Shigella and V. cholerae, respectively. The E.coli isolates were diverse and grouped into 23 different sequence types, the most abundant being ST1946. The 27 E. coli were further divided into seven different serotypes and 59% of the isolates were O16:H48. 44.4% of the isolates were enterotoxigenic E. coli, 3.7% were atypical enteropathogenic E. coli, and the remaining 51.9% were non-diarrheagenic E. coli. Antimicrobial-resistant genes were detected in 11.1% of the isolates displaying quinolone, macrolides, and aminoglycoside resistance. The 14 Shigella isolates were classified into Shigella flexneri (85.7%) Shigella boydii (7.1%), and Shigella sonnei (7.1%). Only one Shigella flexneri isolate harbored parC, varG, and gyrA resistance genes. All the V. cholerae isolates isolated from the Jukskei River were classified as non-O1/ non-O139. None of the isolates harbored the cholera toxin gene, ctxA. However, the isolates harbored other virulent genes including toxR, vspD, als, hlyA, makA, and rtxA. No diversity was observed among the 24 V. cholerae isolates as they all belong to ST741. Antimicrobial resistance genes (parC, varG, and gyrA) were detected in 83.3% of the V. cholerae isolates. This study unpacks the dangers of the Jukskei River to the communities along its riverbanks. Concerningly, the Jukskei River is known to flood during rainy seasons exposing communities along its banks to a host of deadly bacterial pathogens that can cause diarrheal diseases. Although V. cholerae non-O1/non-O139 are not associated with epidemic cholera they can still cause mild to life-threatening illnesses, especially in these already impoverished communities. Therefore, a one-health approach for the surveillance of enteric pathogens in the country is warranted in the fight against infectious pathogens.