Evaluation of low-cost phage-based Microbial Source Tracking tools for elucidating human fecal contamination pathways in Kolkata, India

Renuka Kapoor, James Ebdon, Ashutosh Wadhwa, Goutam Chowdhury, Yuke Wang, Suraja J. Raj, Casey Siesel, Sarah E. Durry, Wolfgang Mairinger, Asish K. Mukhopadhyay, Suman Kanungo, Shanta Dutta, Christine L. Moe

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Phages, such as those infecting Bacteroides spp., have been proven to be reliable indicators of human fecal contamination in microbial source tracking (MST) studies, and the efficacy of these MST markers found to vary geographically. This study reports the application and evaluation of candidate MST methods (phages infecting previously isolated B. fragilis strain GB-124 and recently isolated Kluyvera intermedia strain ASH-08), along with non-source specific somatic coliphages (SOMCPH infecting strain WG-5) and indicator bacteria (E. coli) for identifying fecal contamination pathways in Kolkata, India. Source specificity of the phage-based methods was first tested using 60 known non-human fecal samples from common animals, before being evaluated with 56 known human samples (municipal sewage) collected during both the rainy and dry season. SOMCPH were present in 40-90% of samples from different animal species and in 100% of sewage samples. Phages infecting GB-124 were not detected from the majority (95%) of animal samples (except in three porcine samples) and were present in 93% and 71% of the sewage samples in the rainy and dry season. Phages infecting ASH-08 were detected in 89% and 96% of the sewage samples in the rainy and dry season, respectively, and in all animal samples tested (except goats). GB-124 and SOMCPH were subsequently deployed within two low-income neighborhoods to determine the levels and origin of fecal contamination in 110 environmental samples. E. coli, SOMCPH, and phages of GB-124 were detected in 68, 42, and 28% of the samples, respectively. Analyses of 166 wastewater samples from shared community toilets and 21 samples from sewage pumping stations showed that SOMCPH were present in 100% and GB-124 phages in 31% of shared toilet samples (Median = 5.59 and <1 log10 PFU/100 mL, respectively), and both SOMCPH and GB-124 phages were detected in 95% of pumping station samples (Median = 5.82 and 4.04 log10 PFU/100 mL, respectively). Our findings suggest that GB-124 and SOMCPH have utility as low-cost fecal indicator tools which can facilitate environmental surveillance of enteric organisms, elucidate human and non-human fecal exposure pathways, and inform interventions to mitigate exposure to fecal contamination in the residential environment of Kolkata, India.
Original languageEnglish
Article number673604
JournalFrontiers in Microbiology
Publication statusAccepted/In press - 15 Apr 2021

Bibliographical note

© 2021 Kapoor, Ebdon, Wadhwa, CHOWDHURY, Wang, Raj, Siesel, Durry, Mairinger, Mukhopadhyay, Kanungo, Dutta and Moe. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.


  • fecal contamination
  • Environmental surveillance
  • Bacteriophage
  • GB-124
  • Exposure pathways
  • transmission
  • low-income

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