Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia

Water borne diarrheal pathogens might accumulate in river water and cause contamination of drinking and irrigation water. The La Paz River basin, including the Choqueyapu River, flows through La Paz city in Bolivia where it is receiving sewage, and residues from inhabitants, hospitals, and industry. Using quantitative real-time PCR (qPCR), we determined the quantity and occurrence of diarrheagenic Escherichia coli (DEC), Salmonella enterica, Klebsiella pneumoniae, Shigella spp. and total enterobacteria in river water, downstream agricultural soil, and irrigated crops, during one year of sampling. The most abundant and frequently detected genes were gapA and eltB, indicating presence of enterobacteria and enterotoxigenic E. coli (ETEC) carrying the heat labile toxin, respectively. Pathogen levels in the samples were significantly positively associated with high water conductivity and low water temperature. In addition, a set of bacterial isolates from water, soil and crops were analyzed by PCR for presence of the genes blaCTX-M, blaKPC, blaNDM, blaVIM and blaOXA-48. Four isolates were found to be positive for blaCTX-M genes and whole genome sequencing identified them as E. coli and one Enterobacter cloacae. The E. coli isolates belonged to the emerging, globally disseminated, multi-resistant E. coli lineages ST648, ST410 and ST162. The results indicate not only a high potential risk of transmission of diarrheal diseases by the consumption of contaminated water and vegetables but also the possibility of antibiotic resistance transfer from the environment to the community.水源性腹泻病原体可能在河水中蓄积，进而造成饮用水与灌溉用水的污染。拉巴斯河流域（含乔克亚普河）流经玻利维亚拉巴斯市，该流域接纳了居民、医院及工业产生的污水与废弃物。本研究在为期一年的采样周期中，采用实时荧光定量聚合酶链式反应（quantitative real-time PCR, qPCR），检测了河水、下游农田土壤以及灌溉作物中的致泻性大肠埃希氏菌（diarrheagenic Escherichia coli, DEC）、肠炎沙门氏菌（Salmonella enterica）、肺炎克雷伯菌（Klebsiella pneumoniae）、志贺氏菌属（Shigella spp.）以及肠杆菌科总菌的丰度与检出情况。检出丰度最高且检出频率最频繁的基因为gapA与eltB，分别对应肠杆菌科以及携带不耐热毒素的产肠毒素大肠埃希氏菌（enterotoxigenic E. coli, ETEC）。样本中的病原体载量与水体高电导率及低水温呈显著正相关。此外，本研究采用聚合酶链式反应（polymerase chain reaction, PCR），对取自水体、土壤与作物的一系列细菌分离株进行了blaCTX-M、blaKPC、blaNDM、blaVIM及blaOXA-48基因的检出分析。共检出4株blaCTX-M基因阳性分离株，经全基因组测序鉴定为大肠埃希氏菌（E. coli）与1株阴沟肠杆菌（Enterobacter cloacae）。该大肠埃希氏菌分离株分别属于全球传播的新型多重耐药大肠埃希氏菌谱系ST648、ST410与ST162。本研究结果表明，食用受污染的水体与蔬菜不仅存在较高的腹泻病传播风险，同时也存在抗生素耐药性从环境向社区传播的可能性。