Comparison of fecal indicators with pathogenic bacteria and rotavirus in rural Bangladesh groundwater

Groundwater is routinely analyzed for fecal indicators but direct comparisons of fecal indicators to the presence of bacterial and viral pathogens are rare. This study was conducted in rural Bangladesh where the human population density is high, sanitation is poor, and groundwater pumped from shallow tubewells is often contaminated with fecal bacteria. Five indicator microorganisms (E. coli, total coliform, F+RNA coliphage, Bacteroides and human-associated Bacteroides (HuBacteroides)) and various environmental parameters were compared to the direct detection of waterborne pathogens by quantitative PCR in groundwater pumped from 50 tubewells. Rotavirus was detected in groundwater filtrate from the largest proportion of tubewells (40%), followed by Shigella (10%), Vibrio (10%), and pathogenic E. coli (8%). Spearman rank correlations and sensitivity-specificity calculations indicate that some, but not all, combinations of indicators and environmental parameters can predict the presence of pathogens. Culture-dependent fecal indicator bacteria measured on a single date did not predict bacterial pathogens, but annually averaged monthly measurements of culturable E. coli did improve prediction for total bacterial pathogens. F+RNA coliphage were neither correlated nor sufficiently sensitive towards rotavirus, but were predictive of bacterial pathogens. A qPCR-based E. coli assay was the best indicator for the bacterial pathogens, rotavirus and all pathogens combined. Since groundwater cannot be excluded as a significant source of diarrheal disease in Bangladesh and neighboring countries with similar characteristics, the need to develop more effective methods for screening tubewells with respect to microbial contamination is necessary.人们通常会对地下水开展粪便指示物检测，但针对粪便指示物与细菌、病毒病原体检出情况之间的直接对比研究仍较为匮乏。本研究在孟加拉国农村地区开展，该区域人口密度较高、卫生条件简陋，且浅管井抽取的地下水常受粪便细菌污染。研究针对50口管井抽取的地下水，选取5种指示微生物（大肠杆菌（E. coli）、总大肠菌群、F+RNA噬菌体（F+RNA coliphage）、拟杆菌属（Bacteroides）以及人源拟杆菌（HuBacteroides））与多项环境参数，结合定量PCR（qPCR）直接检测水源性病原体的结果开展对比分析。结果显示，轮状病毒（Rotavirus）在检出率最高的管井滤液中被检出（占比40%），其次为志贺氏菌属（Shigella，10%）、弧菌属（Vibrio，10%）与致病性大肠杆菌（8%）。斯皮尔曼等级相关分析与灵敏度-特异性计算结果表明，部分（而非全部）指示物与环境参数的组合可用于预测病原体的存在。单次采样的培养依赖型粪便指示菌检测无法预测细菌病原体，但按月度采样并取年度平均值的大肠杆菌可培养检测结果可提升对总细菌病原体的预测能力。F+RNA噬菌体既未与轮状病毒呈现显著相关性，对轮状病毒的检测灵敏度也不足，但可用于预测细菌病原体。基于qPCR的大肠杆菌检测方法是针对细菌病原体、轮状病毒以及所有病原体综合情况的最优指示物。鉴于地下水无法被排除为孟加拉国及周边特征相似国家腹泻病的重要传染源，开发更有效的管井微生物污染筛查方法仍具有迫切必要性。