The Occurrence of Antibiotic Resistance Genes in an Urban River in Nepal
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Extraction of Bacterial DNA
2.2. Quantitative Polymerase Chain Reaction (qPCR)
2.3. Statistical Analysis
3. Results
3.1. Detection of Total Bacteria, ARGs, and intI1
3.2. Correlation between Concentrations of Total Bacteria, E. coli, ARGs, and intI1
4. Discussion
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
- Kümmerer, K. Promoting resistance by the emission of antibiotics from hospitals and households into effluent. Clin. Microbiol. Infect. 2003, 9, 1203–1214. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Gullberg, E.; Cao, S.; Berg, O.G.; Ilbäck, C.; Sandegren, L.; Hughes, D.; Andersson, D.I. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathog. 2011, 7. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Partridge, S.R.; Kwong, S.M.; Firth, N.; Jensen, S.O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 2018, 31, 1–61. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Hardwick, S.A.; Stokes, H.W.; Findlay, S.; Taylor, M.; Gillings, M.R. Quantification of class 1 integron abundance in natural environments using real-time quantitative PCR. FEMS Microbiol. Lett. 2008, 278, 207–212. [Google Scholar] [CrossRef] [Green Version]
- Nguyen, T.N.; Kasuga, I.; Liu, M.; Katayama, H. Occurrence of antibiotic resistance genes as emerging contaminants in watersheds of Tama River and Lake Kasumigaura in Japan. IOP Conf. Ser. Earth Environ. Sci. 2019, 266, 4–12. [Google Scholar] [CrossRef]
- Jia, J.; Guan, Y.; Cheng, M.; Chen, H.; He, J.; Wang, S.; Wang, Z. Occurrence and distribution of antibiotics and antibiotic resistance genes in Ba River, China. Sci. Total Environ. 2018, 642, 1136–1144. [Google Scholar] [CrossRef]
- Pallares-Vega, R.; Blaak, H.; van der Plaats, R.; de Roda Husman, A.M.; Hernandez Leal, L.; van Loosdrecht, M.C.M.; Weissbrodt, D.G.; Schmitt, H. Determinants of presence and removal of antibiotic resistance genes during WWTP treatment: A cross-sectional study. Water Res. 2019, 161, 319–328. [Google Scholar] [CrossRef]
- Pruden, A.; Pei, R.; Storteboom, H.; Carlson, K.H. Antibiotic resistance genes as emerging contaminants: Studies in northern Colorado. Environ. Sci. Technol. 2006, 40, 7445–7450. [Google Scholar] [CrossRef]
- Mishra, B.K.; Regmi, R.K.; Masago, Y.; Fukushi, K.; Kumar, P.; Saraswat, C. Assessment of Bagmati river pollution in Kathmandu Valley: Scenario-based modeling and analysis for sustainable urban development. Sustain. Water Qual. Ecol. 2017, 9–10, 67–77. [Google Scholar] [CrossRef]
- Haramoto, E.; Yamada, K.; Nishida, K. Prevalence of protozoa, viruses, coliphages and indicator bacteria in groundwater and river water in the Kathmandu Valley, Nepal. Trans. R. Soc. Trop. Med. Hyg. 2011, 105, 711–716. [Google Scholar] [CrossRef]
- Ghaju Shrestha, R.; Tandukar, S.; Bhandari, D.; Sherchan, S.P.; Tanaka, Y.; Sherchand, J.B.; Haramoto, E. Prevalence of Arcobacter and other pathogenic bacteria in river water in Nepal. Water 2019, 11, 1416. [Google Scholar] [CrossRef] [Green Version]
- Tandukar, S.; Sherchand, J.; Bhandari, D.; Sherchan, S.; Malla, B.; Ghaju Shrestha, R.; Haramoto, E. Presence of human enteric viruses, protozoa, and indicators of pathogens in the Bagmati River, Nepal. Pathogens 2018, 7, 38. [Google Scholar] [CrossRef] [Green Version]
- Acharya, K.; Wilson, R.T. Antimicrobial Resistance in Nepal. Front. Med. 2019, 6, 105. [Google Scholar] [CrossRef] [PubMed]
- Ishtiaque, A.; Shrestha, M.; Chhetri, N. Rapid Urban Growth in the Kathmandu Valley, Nepal: Monitoring Land Use Land Cover Dynamics of a Himalayan City with Landsat Imageries. Environments 2017, 4, 72. [Google Scholar] [CrossRef]
- Nadkarni, M.A.; Martin, F.E.; Jacques, N.A.; Hunter, N. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 2002, 148, 257–266. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Barraud, O.; Baclet, M.C.; Denis, F.; Ploy, M.C. Quantitative multiplex real-time PCR for detecting class 1, 2 and 3 integrons. J. Antimicrob. Chemother. 2010, 65, 1642–1645. [Google Scholar] [CrossRef] [Green Version]
- Fan, W.; Hamilton, T.; Webster-Sesay, S.; Nikolich, M.P.; Lindler, L.E. Multiplex real-time SYBR Green I PCR assay for detection of tetracycline efflux genes of gram-negative bacteria. Mol. Cell Probes 2007, 21, 245–256. [Google Scholar] [CrossRef]
- Lachmayr, K.L.; Cavanaugh, C.M.; Kerkhof, L.J.; DiRienzo, A.G.; Ford, T.E. Quantifying nonspecific tem β-lactamase (blatem) genes in a wastewater stream. Appl. Environ. Microbiol. 2009, 75, 203–211. [Google Scholar] [CrossRef] [Green Version]
- Chen, J.; Yu, Z.; Michel, F.C.; Wittum, T.; Morrison, M. Development and application of real-time PCR assays for quantification of erm genes conferring resistance to macrolides-lincosamides-streptogramin B in livestock manure and manure management systems. Appl. Environ. Microbiol. 2007, 73, 4407–4416. [Google Scholar] [CrossRef] [Green Version]
- Sabet, N.S.; Subramaniam, G.; Navaratnam, P.; Sekaran, S.D. Detection of methicillin- and aminoglycoside-resistant genes and simultaneous identification of S. aureus using triplex real-time PCR Taqman assay. J. Microbiol. Methods 2007, 68, 157–162. [Google Scholar] [CrossRef]
- Guan, Y.; Jia, J.; Wu, L.; Xue, X.; Zhang, G.; Wang, Z. Analysis of bacterial community characteristics, abundance of antibiotics and antibiotic resistance genes along a pollution gradient of Ba River in Xi’an, China. Front. Microbiol. 2018, 9, 12. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Schwartz, T.; Kohnen, W.; Jansen, B.; Obst, U. Detection of antibiotic resistant bacteria and their resistance genes in wastewater, surface water and drinking water biofilms. FEMS Microbiol. Ecol. 2003, 43, 325–335. [Google Scholar] [CrossRef]
- Volkmann, H.; Schwartz, T.; Bischoff, P.; Kirchen, S.; Obst, U. Detection of clinically relevant antibiotic-resistance genes in municipal wastewater using real-time PCR (TaqMan). J. Microbiol. Methods 2004, 56, 277–286. [Google Scholar] [CrossRef] [PubMed]
- Lanza, V.; Tedim, A.; Martínez, J.; Baquero, F.; Coque, T. The plasmidome of firmicutes: Impact on the emergence and the spread of resistance to antimicrobials. Microbiol. Spectr. 2015, 3. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Karkman, A.; Pärnänen, K.; Larsson, D.G.J. Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments. Nat. Commun. 2019, 10, 80. [Google Scholar] [CrossRef] [PubMed]
- Tacão, M.; Correia, A.; Henriques, I. Resistance to broad-spectrum antibiotics in aquatic systems: Anthropogenic activities modulate the dissemination of blaCTX-M-like genes. Appl. Environ. Microbiol. 2012, 78, 4134–4140. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Devarajan, N.; Laffite, A.; Graham, N.D.; Meijer, M.; Prabakar, K.; Mubedi, J.I.; Elongo, V.; Mpiana, P.T.; Ibelings, B.W.; Wildi, W.; et al. Accumulation of clinically relevant antibiotic-resistance genes, bacterial load, and metals in freshwater lake sediments in central Europe. Environ. Sci. Technol. 2015, 49, 6528–6537. [Google Scholar] [CrossRef]
- Poirel, L.; Madec, J.-Y.; Lupo, A.; Schink, A.-K.; Kieffer, N.; Nordmann, P.; Schwarz, S. Antimicrobial resistance in Escherichia coli. Microbiol. Spectr. 2018, 6. [Google Scholar] [CrossRef] [Green Version]
- Lucassen, R.; Rehberg, L.; Heyden, M.; Bockmuhl, D. Strong correlation of total phenotypic resistance of samples from household environments and the prevalence of class 1 integrons suggests for the use of the relative prevalence of intI1 as a screening tool for multi-resistance. PLoS ONE 2019, 14, e0218277. [Google Scholar] [CrossRef]
- Shrestha, S.; Aihara, Y.; Bhattarai, A.P.; Bista, N.; Rajbhandari, S.; Kondo, N.; Kazama, F.; Nishida, K.; Shindo, J. Dynamics of domesticwater consumption in the urban area of the Kathmandu Valley: Situation analysis pre and post 2015 Gorkha Earthquake. Water 2017, 9, 222. [Google Scholar] [CrossRef] [Green Version]
- Rutkowski, T.; Raschid-Sally, L.; Buechler, S. Wastewater irrigation in the developing World-Two case studies from the Kathmandu Valley in Nepal. Agric. Water Manag. 2007, 88, 83–91. [Google Scholar] [CrossRef]
- Bajracharya, R.; Nakamura, T.; Shakya, B.M.; Nishida, K.; Das Shrestha, S.; Tamrakar, N.K. Identification of river water and groundwater interaction at central part of the Kathmandu valley, Nepal using stable isotope tracers. Int. J. Adv. Sci. Technol. Res. 2018, 3, 29–41. [Google Scholar] [CrossRef]
ARGs/MGE | Number of Positive Samples (%) | |||
---|---|---|---|---|
Sundarijal (n = 6) | Thapathali (n = 6) | Chovar (n = 6) | Total (n = 18) | |
blaTEM | 2 (33%) | 6 (100%) | 6 (100%) | 14 (78%) |
ermF | 2 (33%) | 6 (100%) | 6 (100%) | 14 (78%) |
mecA | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
tetA | 1 (17%) | 6 (100%) | 6 (100%) | 13 (72%) |
intI1 | 2 (33%) | 6 (100%) | 6 (100%) | 14 (78%) |
Bacteria/MGE | r Value | |||
---|---|---|---|---|
blaTEM | tetA | ermF | intI1 | |
E. coli# | 0.87 * | 0.94 * | 0.93 * | 0.90 * |
Total Bacteria | 0.91 * | 0.98 * | 0.95 * | 0.97 * |
Total coliforms # | 0.54 * | 0.57 * | 0.58 * | 0.61 * |
intI1 | 0.94 * | 0.97 * | 0.95 * | – |
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Thakali, O.; Tandukar, S.; Brooks, J.P.; Sherchan, S.P.; Sherchand, J.B.; Haramoto, E. The Occurrence of Antibiotic Resistance Genes in an Urban River in Nepal. Water 2020, 12, 450. https://doi.org/10.3390/w12020450
Thakali O, Tandukar S, Brooks JP, Sherchan SP, Sherchand JB, Haramoto E. The Occurrence of Antibiotic Resistance Genes in an Urban River in Nepal. Water. 2020; 12(2):450. https://doi.org/10.3390/w12020450
Chicago/Turabian StyleThakali, Ocean, Sarmila Tandukar, John P. Brooks, Samendra P. Sherchan, Jeevan B. Sherchand, and Eiji Haramoto. 2020. "The Occurrence of Antibiotic Resistance Genes in an Urban River in Nepal" Water 12, no. 2: 450. https://doi.org/10.3390/w12020450
APA StyleThakali, O., Tandukar, S., Brooks, J. P., Sherchan, S. P., Sherchand, J. B., & Haramoto, E. (2020). The Occurrence of Antibiotic Resistance Genes in an Urban River in Nepal. Water, 12(2), 450. https://doi.org/10.3390/w12020450