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High-Throughput DNA Microarray Detection of Pathogenic Bacteria in Shallow Well Groundwater in the Kathmandu Valley, Nepal

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Abstract

Because of heavy dependence on groundwater for drinking water and other domestic use, microbial contamination of groundwater is a serious problem in the Kathmandu Valley, Nepal. This study investigated comprehensively the occurrence of pathogenic bacteria in shallow well groundwater in the Kathmandu Valley by applying DNA microarray analysis targeting 941 pathogenic bacterial species/groups. Water quality measurements found significant coliform (fecal) contamination in 10 of the 11 investigated groundwater samples and significant nitrogen contamination in some samples. The results of DNA microarray analysis revealed the presence of 1–37 pathogen species/groups, including 1–27 biosafety level 2 ones, in 9 of the 11 groundwater samples. While the detected pathogens included several feces- and animal-related ones, those belonging to Legionella and Arthrobacter, which were considered not to be directly associated with feces, were detected prevalently. This study could provide a rough picture of overall pathogenic bacterial contamination in the Kathmandu Valley, and demonstrated the usefulness of DNA microarray analysis as a comprehensive screening tool of a wide variety of pathogenic bacteria.

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Acknowledgments

This work was partly supported by the Global COE Program and by Grant-in-Aids for Scientific Research (C) (No. 23560641) and for Challenging Exploratory Research (No. 25630226), all of which were sponsored by the Japan Society for the Promotion of Science (JSPS), and by the Science and Technology Research Partnership for Sustainable Development (SATREPS) program, which was sponsored by the Japan Science and Technology Agency (JST) and Japan International Cooperation Agency (JICA).

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Authors and Affiliations

  1. Department of Health Science, School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan

    Daisuke Inoue, Noriko Suzuki & Kazunari Sei

  2. Environment and Medical Sciences Course, Graduate School of Medical Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan

    Daisuke Inoue, Takuji Hinoura & Kazunari Sei

  3. Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan

    Junqin Pang & Michihiko Ike

  4. Center of Research for Environment Energy and Water (CREEW), Baluwatar, GPO Box 25563, Kathmandu, Nepal

    Rabin Malla & Saroj Kumar Chapagain

  5. Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan

    Sadhana Shrestha & Yasuhiro Tanaka

  6. International Research Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan

    Hiroaki Matsuzawa, Takashi Nakamura & Kei Nishida

Authors
  1. Daisuke Inoue
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  2. Takuji Hinoura
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  3. Noriko Suzuki
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  4. Junqin Pang
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  5. Rabin Malla
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  6. Sadhana Shrestha
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  7. Saroj Kumar Chapagain
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  8. Hiroaki Matsuzawa
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  9. Takashi Nakamura
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  10. Yasuhiro Tanaka
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  11. Michihiko Ike
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  12. Kei Nishida
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  13. Kazunari Sei
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Corresponding author

Correspondence to Daisuke Inoue.

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Inoue, D., Hinoura, T., Suzuki, N. et al. High-Throughput DNA Microarray Detection of Pathogenic Bacteria in Shallow Well Groundwater in the Kathmandu Valley, Nepal. Curr Microbiol 70, 43–50 (2015). https://doi.org/10.1007/s00284-014-0681-x

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  • DOI: https://doi.org/10.1007/s00284-014-0681-x

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