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

Research output: Contribution to journalArticlepeer-review


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, newly isolated Bacteroides strains (K10, K29, and K33) and recently isolated Kluyvera intermedia strain ASH-08), along with non-source specific somatic coliphages (SOMCPH infecting strain WG-5) and indicator bacteria (Escherichia 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 Bacteroides strain 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 (Mean = 1.42 and 1.83 log 10PFU/100mL, respectively), though at lower levels than SOMCPH (Mean = 3.27 and 3.02 log 10PFU/100mL, respectively). Phages infecting strain ASH-08 were detected in 89 and 96% of the sewage samples in the rainy and dry season, respectively, but were also present in all animal samples tested (except goats). Strains K10, K29, and K30 were not found to be useful MST markers due to low levels of phages and/or co-presence in non-human sources. 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 from the same districts showed that SOMCPH were present in 100% and GB-124 phages in 31% of shared toilet samples (Median = 5.59 and <1 log 10 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 log 10 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. Phages infecting Bacteroides fragilis strain GB-124 and non-source specific somatic coliphages (SOMCPH) were deployed for identification of fecal contamination pathways in Kolkata, India. Analyses of environmental samples representative of nine different exposure pathways, pooled sewage from shared community toilets and sewage from pumping stations showed the presence of both SOMCPH and GB-124 phages in all the sample types. (Figure presented.).

Original languageEnglish
Article number673604
Pages (from-to)1-14
Number of pages14
JournalFrontiers in Microbiology
Publication statusPublished - 20 May 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.

Funding Information: We are grateful for the efforts of NICED field and lab personnel in sample collection and analyses. The environmental sample collection was conducted by Suvankar Mandal, Biplap Jash, Buddhadeb Samaddar, Somnath Sarkar, Ashish Saha, Debabrata Maity, and Abhijit Guha. The lab analyses were conducted by Biswajit Sharma, Rinki Karmakar, Rajkumar, Sristi Biswas, Rajarshi Roy, Soma Banerjee, and Abhishek Das. Funding. This study was part of the SaniPath Typhoid Project funded by the Bill & Melinda Gates Foundation (Grant No. OPP1150697).


  • GB-124
  • bacteriophages
  • environmental surveillance
  • exposure pathways
  • fecal contamination
  • low-income
  • transmission


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