Multiplex PCR for determining aetiology of infectious diarrhoea in rural and urban central Indian populations

Abstract

Introduction Infectious diarrhoea is a major cause of morbidity and mortality in Central India. There is an urgent unmet need to implement rapid point-of-care tests to deliver effective and targeted treatment plans. The aim of this exploratory study was to assess the performance of the FilmArray Gastrointestinal Panel for the detection of enteric pathogens directly from stool specimens collected from diarrhoeal and non-diarrhoeal control populations in Central India. Methods Faecal samples were collected from participants with and without acute diarrhoea presenting to an inpatient or outpatient setting in Nagpur city district and rural Melghat. Each stool sample was stored at 4°C and preserved in Cary-Blair enteric transport medium for multiplex PCR using the FilmArray GI Panel according to the manufacturer’s instructions. This panel allows for the simultaneous detection of 22 common diarrhoeal agents, including bacteria, viruses and protozoa. Baseline characteristics were also recorded and included: demographics, symptomatology, antibiotics exposure, duration of diarrhoea, hospitalisation status at recruitment, and duration, BMI, animal exposure, housing conditions, toilet access, and seasonality. Results 179 participants provided stool samples for analysis on the FilmArray GI Panel. 70 and 109 participants were from rural Melghat and Nagpur urban district, respectively. Of these, 138 were from mainly non-hospitalised participants with acute diarrhoea from urban (n=89) and rural areas (n=49). In the urban cohort, 81% (88/109) of all diarrhoeal and non-diarrhoeal samples tested positive for one (27%) or more (54%) pathogens. In the rural cohort, a striking 97% (68/70) of samples yielded positivity to one (14%) or multiple organisms (83%). The most prevalent pathogen detected in both the diarrhoeal and control cohorts was Enterohaemorrhagic E. coli (51% vs 59%, respectively). However, other pathotypes of diarrhoeagenic E. coli were highly prevalent in both cohorts, including ETEC, EPEC, Shigella/EIEC, and STEC. A higher proportion of diarrhoeal samples tested positive to Campylobacter (12%) compared to the non-diarrhoeal control group (5%). Unlike the diarrhoeal samples, no control samples yielded positivity to Vibrio cholerae, Cyclospora cayetanensis, Astrovirus, Rotavirus A or Sapovirus Conclusions Detection of high levels of polymicrobial enteric infections are prevalent in Central Indian symptomatic and asymptomatic populations. E. coli pathotypes predominate in both urban and rural settings. Further studies are required to understand the clinical significance of these mixed infections, as well as how best to manage them.