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

Current Microbiology

Volumn 70, Issue 1, 2015, Pages 43-50

  Inoue, Daisuke ^a   Hinoura, Takuji ^a   Suzuki, Noriko ^a   Pang, Junqin ^b   Malla, Rabin ^c   Shrestha, Sadhana ^d   Chapagain, Saroj Kumar ^c   Matsuzawa, Hiroaki ^d   Nakamura, Takashi ^d   Tanaka, Yasuhiro ^d   Ike, Michihiko ^b   Nishida, Kei ^d   Sei, Kazunari ^a  

^a KITASATO UNIVERSITY   (Japan)

^b OSAKA UNIVERSITY   (Japan)

^c Center of Research for Environment Energy and Water CREEW   (Nepal)

^d UNIVERSITY OF YAMANASHI   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DRINKING WATER; GROUND WATER; NITROGEN;

ARTHROBACTER; ARTICLE; BACTERIA; BACTERIUM CONTAMINATION; BIOSAFETY; CONTROLLED STUDY; FECES; HIGH THROUGHPUT DNA MICROARRAY ANALYSIS; HUMAN; LEGIONELLA; MEASUREMENT; MICROARRAY ANALYSIS; NEPAL; NONHUMAN; PATHOGENIC BACTERIA; PRIORITY JOURNAL; WATER QUALITY; BACTERIUM; CLASSIFICATION; DNA MICROARRAY; EVALUATION STUDY; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PROCEDURES;

ANIMALIA; ARTHROBACTER; BACTERIA (MICROORGANISMS); LEGIONELLA;

BACTERIA; DRINKING WATER; FECES; GROUNDWATER; NEPAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 84921414740     PISSN: 03438651     EISSN: 14320991     Source Type: Journal    
DOI: 10.1007/s00284-014-0681-x     Document Type: Article

References (32)

1. Asian Development Bank (2010) Project Rationale: Need and Demand. In: 2010 Kathmandu Valley water supply and wastewater system improvement (Project feasibility study: Final report). Government of Nepal, Ministry of Physical Planning & Works, Kathmandu Upatyaka Khanepani Limited, pp. 21–32
2. Aydın E, Taştan E, Yücel M, Aydoğan F, Karakoş E, Arslan N, Kantekin Y, Demirci M (2012) Concurrent assay for four bacterial species including Alloiococcus otitidis in middle ear, nasopharynx and tonsils of children with otitis media with effusion: a preliminary report. Clin Exp Otorhinolaryngol 5:81–85
3. Brooks T, Osicki RA, Springthorpe VS, Sattar SA, Filion L, Abrial D, Riffard S (2004) Detection and identification of Legionella species from groundwaters. J Toxicol Environ Health A 67:1845–1859
4. 15N to identify nitrate contamination of groundwater in a wastewater irrigated field near the city of Shijizhuang, China. J Hydrol 326:367–378
5. Costa J, Tiago I, da Costa MS, Veríssimo A (2005) Presence and persistence of Legionella spp. in groundwater. Appl Environ Microbiol 71:663–671
6. DeAngelis KM, Wu CH, Beller HR, Brodie EL, Chakraborty R, DeSantis TZ, Fortney JL, Hazen TC, Osman SR, Singer ME, Tom LM, Andersen GL (2011) PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip. Appl Environ Microbiol 77:6313–6322
7. Fields BS, Benson RF, Besser RE (2002) Legionella and Legionnaires’ disease: 25 years of investigation. Clin Microbiol Rev 15:506–526
8. Government of Nepal (2012) Environment statistics of Nepal 2011. http://cbs.gov.np/wp-content/uploads/2012/03/environment_book_final.pdf. Accessed 5 Mar 2014
9. Haramoto E, Yamada K, Nishida K (2011) Prevalence of protozoa, viruses, coliphages and indicator bacteria in groundwater and river water in the Kathmandu Valley, Nepal. Trans R Soc Trop Med Hyg 105:711–716
10. Hariyama A, Takada R, Hendolin PH, Fujii N, Ylikoski J, Himi T (2006) High incidence of Alloiococcus otitidis in children with otitis media, despite treatment with antibiotics. J Clin Microbiol 44:946–949
11. He Z, Deng Y, Van Nostrand JD, Tu Q, Xu M, Hemme CL, Li X, Wu L, Gentry TJ, Yin Y, Liebich J, Hazen TC, Zhou J (2010) GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J 4:1167–1179
12. Inoue D, Inaba M, Upadhye RR, Sei K, Ike M (2009) Multiple detection of occurrence of bacterial pathogens in two rivers in the Kinki district of Japan with a DNA microarray. Jpn J Water Treat Biol 45:31–43
13. Lee DY, Lauder H, Cruwys H, Falletta P, Beaudette LA (2008) Development and application of an oligonucleotide microarray and real-time quantitative PCR for detection of wastewater bacterial pathogens. Sci Total Environ 398:203–211
14. Lee MR, Huang YT, Liao CH, Chuang TY, Wang WJ, Lee SW, Lee LN (2012) Clinical and microbiological characteristics of bacteremia caused by Eggerthella, Paraeggerthella, and Eubacterium species at a university hospital in Taiwan from 2001 to 2010. J Clin Microbial 50:2053–2055
15. Lu Z, He Z, Parisi VA, Kang S, Deng Y, Van Nostrand JD, Masoner JR, Cozzarelli IM, Suflita JM, Zhou J (2012) GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer. Environ Sci Technol 46:5824–5833
16. Maynard C, Berthiaume F, Lemarchand K, Harel J, Payment P, Bayardelle P, Masson L, Brousseau R (2005) Waterborne pathogen detection by use of oligonucleotide-based microarray. Appl Environ Microbiol 71:8548–8557
17. Miyamoto H, Yamamoto H, Arima K, Fujii J, Maruta K, Izu K, Shiomori T, Yoshida S (1997) Development of a new seminested PCR method for detection of Legionella species and its application to surveillance of legionellae in hospital cooling tower water. Appl Environ Microbiol 63:2489–2494
18. Nagarajan R, Rajmohan N, Mahendran U, Senthamikumar S (2010) Evaluation of groundwater quality and its suitability for drinking and agricultural use in Thanjavur city, Tamil Nadu, India. Environ Monit Assess 171:289–308
19. Pandey VP, Chapagain SK, Kazama F (2010) Evaluation of groundwater environment of Kathmandu Valley. Environ Earth Sci 60:1329–1342
20. Pant BR (2011) Ground water quality in the Kathmandu valley of Nepal. Environ Monit Assess 178:477–485
21. Severijnen AJ, van Kleef R, Hazenberg MP, van de Merwe JP (1990) Chronic arthritis induced in rats by cell wall fragments of Eubacterium species from the human intestinal flora. Infect Immun 58:523–528
22. Shrestha S, Malla SS, Aihara Y, Kondo N, Nishida K (2013) Water quality at supply source and point of use in the Kathmandu Valley. J Water Environ Technol 11:331–340
23. Shrestha S, Nakamura T, Malla R, Nishida K (2014) Seasonal variation in the microbial quality of shallow groundwater in the Kathmandu Valley, Nepal. Water Sci Technol Water Supply 14:390–397
24. Suo B, He Y, Paoli G, Gehring A, Tu SI, Shi X (2010) Development of an oligonucleotide-based microarray to detect multiple foodborne pathogens. Mol Cell Probes 24:77–86
25. Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumura M, Kamagata Y (2005) Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol 71:2162–2169
26. Tanaka Y, Nishida K, Nakamura T, Chapagain SK, Inoue D, Sei K, Mori K, Sakamoto Y, Kazama F (2012) Characterization of microbial communities distributed in the groundwater pumped from deep tube wells in the Kathmandu valley of Nepal. J Water Health 10:170–180
27. Upadhye RR, Inoue D, Ishigaki T, Sei K, Ike M (2008) Microarray analysis of eubacterial community and bacterial pathogens in leachate from three different landfills of Japan. Environ Eng Res 45:195–202
28. Wang M, Cao B, Gao Q, Sun Y, Liu P, Feng L, Wang L (2009) Detection of Enterobacter sakazakii and other pathogens associated with infant formula powder by use of a DNA microarray. J Clin Microbiol 47:3178–3184
29. Warner NR, Levy J, Harpp K, Farruggia F (2008) Drinking water quality in Nepal’s Kathmandu Valley: a survey and assessment of selected controlling site characteristics. Hydrogeol J 16:321–324
30. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
31. Wullings BA, van der Kooij D (2006) Occurrence and genetic diversity of uncultured Legionella spp. in drinking water treated at temperatures below 15 °C. Appl Environ Microbiol 72:157–166
32. Yoo SM, Choi JY, Yun JK, Choi JK, Shin SY, Lee K, Kim JM, Lee SY (2010) DNA microarray-based identification of bacterial and fungal pathogens in bloodstream infections. Mol Cell Probes 24:44–52