Bacterial pathogens and community composition in advanced sewage treatment systems revealed by metagenomics analysis based on high-throughput sequencing

PLoS ONE

Volumn 10, Issue 5, 2015, Pages

  Lu, Xin ^a   Zhang, Xu Xiang ^a   Wang, Zhu ^a   Huang, Kailong ^a   Wang, Yuan ^b   Liang, Weigang ^c   Tan, Yunfei ^c   Liu, Bo ^a   Tang, Junying ^a  

^a NANJING UNIVERSITY   (China)

^b Jiangsu Research Institute of Environmental Science   (China)

^c Zhengzhou Sewage Purification Co Ltd   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MAGNETIC RESIN; RESIN; UNCLASSIFIED DRUG; RNA 16S; SEWAGE; VIRULENCE FACTOR;

AEROMONAS HYDROPHILA; ARCOBACTER BUTZLERI; ARTICLE; BACTERIAL VIRULENCE; BACTERIUM DETECTION; CONTROLLED STUDY; HIGH THROUGHPUT SEQUENCING; INTERMETHOD COMPARISON; KLEBSIELLA PNEUMONIAE; METAGENOMICS; MICROBIAL COMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENICITY ISLAND; POPULATION ABUNDANCE; PYROSEQUENCING; QUANTITATIVE STUDY; REAL TIME POLYMERASE CHAIN REACTION; SAND FILTRATION; SEWAGE EFFLUENT; SEWAGE TREATMENT; SEWAGE TREATMENT PLANT; SPECIES COMPOSITION; BACTERIUM; BIODIVERSITY; CLASSIFICATION; GENETICS; MICROBIOLOGY; MOLECULAR GENETICS; SEWAGE;

AEROMONAS HYDROPHILA; ARCOBACTER; ARCOBACTER BUTZLERI; BACTERIA (MICROORGANISMS); KLEBSIELLA PNEUMONIAE;

BACTERIA; BIODIVERSITY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; MOLECULAR SEQUENCE DATA; RNA, RIBOSOMAL, 16S; SEWAGE; VIRULENCE FACTORS;

EID: 84929090645     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0125549     Document Type: Article

References (54)

1. Zhou CE, Smith J, Lam M, Zemla A, Dyer MD, Slezak T. MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. Nucleic Acids Res. 2007; 35(Database issue): D391-394. PMID: 17090593
2. Okoh AI, Odjadjare EE, Igbinosa EO, Osode AN. Wastewater treatment plants as a source of microbial pathogens in receiving watersheds. Afr J Biotechnol. 2007; 6(25): 2932-2944.
3. Varela AR, Manaia CM. Human health implications of clinically relevant bacteria in wastewater habitats. Environ Sci Pollut Res Int. 2013; 20(6): 3550-3569. doi: 10.1007/s11356-013-1594-0 PMID: 23508533
4. Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 2005; 33(Database issue): D325-328. PMID: 15608208
5. George T, Franklin L, Stensel H. Wastewater engineering: treatment and reuse. Edition 4th. Metcalf and Eddi Inc. 2003.
6. Sonune A, Ghate R. Developments in wastewater treatment methods. Desalination. 2004; 167: 55-63.
7. Godfree A, Farrell J. Processes for managing pathogens. J Environ Qual. 2005; 34(1): 105-113. PMID: 15647539
8. Fu C, Xie X, Huang J, Zhang T, Wu Q, Chen J, et al. Monitoring and evaluation of removal of pathogens at municipal wastewater treatment plants. Water Sci Technol. 2010; 61(6): 1589-1599. doi: 10.2166/wst.2010.757 PMID: 20351439
9. Lucena F, Duran A, Moron A, Calderon E, Campos C, Gantzer C, et al. Reduction of bacterial indicators and bacteriophages infecting faecal bacteria in primary and secondary wastewater treatments. J Appl Microbiol. 2004; 97(5): 1069-1076. PMID: 15479424
10. Wen Q, Tutuka C, Keegan A, Jin B. Fate of pathogenic microorganisms and indicators in secondary activated sludge wastewater treatment plants. J Environ Manage. 2009; 90(3): 1442-1447. doi: 10.1016/j.jenvman.2008.09.002 PMID: 18977580
11. Cheng HWA, Lucy FE, Broaders MA, Mastitsky SE, Chen CH, Murray A. Municipal wastewater treatment plants as pathogen removal systems and as a contamination source of noroviruses and Enterococcus faecalis. J Water Health. 2012; 10(3): 380-389. doi: 10.2166/wh.2012.138 PMID: 22960482
12. Olsen JS, Aarskaug T, Thrane I, Pourcel C, Ask E, Johansen G, et al. Alternative routes for dissemination of Legionella pneumophila causing three outbreaks in Norway. Environ Sci Technol. 2010; 44(22): 8712-8717. doi: 10.1021/es1007774 PMID: 20949911
13. Huang J-J, Hu H-Y, Tang F, Li Y, Lu S-Q, Lu Y. Inactivation and reactivation of antibiotic-resistant bacteria by chlorination in secondary effluents of a municipal wastewater treatment plant. Water Res. 2011; 45(9): 2775-2781. doi: 10.1016/j.watres.2011.02.026 PMID: 21440281
14. Richardson SD, Postigo C. Drinking water disinfection by-products, in emerging organic contaminants and human health. 2012, Springer. P. 93-137.
15. Shi P, Jia S, Zhang XX, Zhang T, Cheng S, Li A. Metagenomic insights into chlorination effects on microbial antibiotic resistance in drinking water. Water Res. 2013; 47(1): 111-120. doi: 10.1016/j.watres.2012.09.046 PMID: 23084468
16. Savichtcheva O, Okabe S. Alternative indicators of fecal pollution: Relations with pathogens and conventional indicators, current methodologies for direct pathogen monitoring and future application perspectives. Water Res. 2006; 40(13): 2463-2476. PMID: 16808958
17. Vartoukian SR, Palmer RM, Wade WG. Strategies for culture of 'unculturable' bacteria. FEMS Microbiol Lett. 2010; 309(1): 1-7. doi: 10.1111/j.1574-6968.2010.02000.x PMID: 20487025
18. Toze S. PCR and the detection of microbial pathogens in water and wastewater. Water Res. 1999; 33(17): 3545-3556.
19. Srinivasan S, Aslan A, Xagoraraki I, Alocilja E, Rose JB. Escherichia coli, enterococci, and Bacteroides thetaiotaomicron qPCR signals through wastewater and septage treatment. Water Res. 2011; 45(8): 2561-2572. doi: 10.1016/j.watres.2011.02.010 PMID: 21420709
20. Lee DY, Shannon K, Beaudette LA. Detection of bacterial pathogens in municipal wastewater using an oligonucleotide microarray and real-time quantitative PCR. J Microbiol Methods. 2006; 65(3): 453-467. PMID: 16239042
21. Zhang T, Shao MF, Ye L. 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J. 2012; 6(6): 1137-1147. doi: 10.1038/ismej.2011.188 PMID: 22170428
22. Ye L, Zhang T. Pathogenic bacteria in sewage treatment plants as revealed by 454 pyrosequencing. Environ Sci Technol. 2011; 45(17): 7173-7179. doi: 10.1021/es201045e PMID: 21780772
23. Cai L, Zhang T. Detecting human bacterial pathogens in wastewater treatment plants by a highthroughput shotgun sequencing technique. Environ Sci Technol. 2013; 47(10): 5433-5441. doi: 10. 1021/es400275r PMID: 23594284
24. Bibby K, Peccia J. Identification of viral pathogen diversity in sewage sludge by metagenome analysis. Environ Sci Technol 2013; 47(4): 1945-1951. doi: 10.1021/es305181x PMID: 23346855
25. Wang Z, Zhang XX, Huang K, Miao Y, Shi P, Liu B, et al. Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant. PLOS ONE. 2013; 8(10): e76079. doi: 10.1371/journal.pone.0076079 PMID: 24098424
26. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007; 35(21): 7188-7196. PMID: 17947321
27. Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011; 21(9): 1552-1560. doi: 10.1101/gr.120618.111 PMID: 21690186
28. Ye L, Zhang T, Wang T, Fang Z. Microbial structures, functions, and metabolic pathways in wastewater treatment bioreactors revealed using high-throughput sequencing. Environ Sci Technol. 2012; 46(24): 13244-13252. doi: 10.1021/es303454k PMID: 23151157
29. Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods. 2012; 9(8): 811-814. doi: 10.1038/nmeth.2066 PMID: 22688413
30. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. IntroducingMothur: opensource, platform-independent, community-supported software for describing and comparingmicrobial communities. Appl EnvironMicrobiol. 2009; 75(23): 7537-7541. doi: 10.1128/AEM.01541-09 PMID: 19801464
31. Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLOS ONE. 2011; 6(12): e27310. doi: 10.1371/journal.pone. 0027310 PMID: 22194782
32. Feazel LM, Baumgartner LK, Peterson KL, Frank DN, Harris JK, Pace NR. Opportunistic pathogens enriched in showerhead biofilms. Proc Natl Acad Sci USA. 2009; 106(38): 16393-16399. doi: 10.1073/pnas.0908446106 PMID: 19805310
33. Ahmed W, Huygens F, Goonetilleke A, Gardner T. Real-time PCR detection of pathogenic microorganisms in roof-harvested rainwater in Southeast Queensland, Australia. Appl Environ Microbiol. 2008; 74(17): 5490-5496. doi: 10.1128/AEM.00331-08 PMID: 18621865
34. Abdelbaqi K, Buissonniere A, Prouzet-Mauleon V, Gresser J, Wesley I, Megraud F, et al. Development of a real-time fluorescence resonance energy transfer PCR to detect arcobacter species. J Clin Microbiol. 2007; 45(9): 3015-3021. PMID: 17652482
35. Sun F, Wu D, Qiu Z, Jin M, Wang X, Li J. Development of real-time PCR systems based on SYBR Green for the specific detection and quantification of Klebsiella pneumoniae in infant formula. Food Control. 2010; 21(4): 487-491.
36. Zhang XX, Zhang T. Occurrence, abundance, and diversity of tetracycline resistance genes in 15 sewage treatment plants across China and other global locations. Environ Sci Technol. 2011; 45(7): 2598-2604. doi: 10.1021/es103672x PMID: 21388174
37. Zhang T, Zhang M, Zhang XX, Fang HH. Tetracycline resistance genes and tetracycline resistant lactose-fermenting Enterobacteriaceae in activated sludge of sewage treatment plants. Environ Sci Technol. 2009; 43(10): 3455-3460. PMID: 19544839
38. Luo CW, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLOS ONE. 2012; 7(2): e30087. doi: 10.1371/journal.pone.0030087 PMID: 22347999
39. Collado L, Figueras MJ. Taxonomy, epidemiology, and clinical relevance of the genus Arcobacter. Clin Microbiol Rev. 2011; 24(1): 174-192. doi: 10.1128/CMR.00034-10 PMID: 21233511
40. Collado L, Inza I, Guarro J, Figueras MJ. Presence of Arcobacter spp. in environmental waters correlates with high levels of fecal pollution. Environ Microbiol. 2008; 10(6): 1635-1640. doi: 10.1111/j.1462-2920.2007.01555.x PMID: 18215159
41. Monfort P, Baleux B. Dynamics of Aeromonas hydrophila, Aeromonas sobria, and Aeromonas caviae in a sewage treatment pond. Appl Environ Microbiol. 1990; 56(7): 1999-2006. PMID: 2389929
42. Elmund GK, Allen MJ, Rice EW. Comparison of Escherichia coli, total coliform, and fecal coliform populations as indicators of wastewater treatment efficiency. Water Environ Res. 1999; 71(3): 332-339.
43. Pillar CM, Gilmore MS. Enterococcal virulence-Pathogenicity island of E-faecalis. Front Biosci. 2004; 9: 2335-2346. PMID: 15353291
44. Hacker J, Kaper JB. Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol. 2000; 54: 641-679. PMID: 11018140
45. Finlay BB, McFadden G. Anti-immunology: Evasion of the host immune system by bacterial and viral pathogens. Cell. 2006; 124(4): 767-782. PMID: 16497587
46. Hueck CJ. Type III protein secretion systems in bacterial pathogens of animals and plants. Microbiol Mol Biol Rev. 1998; 62(2): 379-433. PMID: 9618447
47. Figueroa-Bossi N, Bossi L. Inducible prophages contribute to Salmonella virulence in mice. Mol Microbiol. 1999; 33(1): 167-176. PMID: 10411733
48. Neckers L, Tatu U. Molecular chaperones in pathogen virulence: emerging new targets for therapy. Cell Host Microbe. 2008; 4(6): 519-527. doi: 10.1016/j.chom.2008.10.011 PMID: 19064253
49. Poffe R, Beeck EO. Enumeration of Aeromonas hydrophila from domestic wastewater treatment plants and surface waters. J Appl Microbiol. 1991; 71(4): 366-370.
50. Ma LP, Zhang XX, Zhao FZ, Wu B, Cheng SP, Yang LY. Sewage treatment plant serves as a hot-spot reservoir of integrons and gene cassettes. J Environ Biol. 2013; 34(2): 391-399. PMID: 24620610
51. Ma L, Zhang X-X, Cheng S, Zhang Z, Shi P, Liu B, et al. Occurrence, abundance and elimination of class 1 integrons in one municipal sewage treatment plant. Ecotoxicology. 2011; 20(5): 968-973. doi: 10.1007/s10646-011-0652-y PMID: 21431316
52. Zhang R, Vigneswaran S, Ngo HH, Nguyen H. Magnetic ion exchange (MIEX) resin as a pre-treatment to a submerged membrane system in the treatment of biologically treated wastewater. Desalination. 2006; 192(1-3): 296-302.
53. Atia AA, Donia AM, Yousif AM. Removal of some hazardous heavy metals from aqueous solution using magnetic chelating resin with iminodiacetate functionality. Sep Purif Technol. 2008; 61(3): 348-357.
54. Wert EC, Edwards-Brandt JC, Singer PC, Budd GC. Evaluating magnetic ion exchange resin (MIEX) pretreatment to increase ozone disinfection and reduce bromate formation. Ozone: Sci Eng. 2005; 27(5): 371-379.