Metagenomic approach for identification of the pathogens associated with diarrhea in stool specimens

Journal of Clinical Microbiology

Volumn 54, Issue 2, 2016, Pages 368-375

  Zhou, Yanjiao ^a   Wylie, Kristine M ^a   Feghaly, Rana E El ^b   Mihindukulasuriya, Kathie A ^a   Elward, Alexis ^a   Haslam, David B ^c   Storch, Gregory A ^a   Weinstock, George M ^a,d  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF MISSISSIPPI SCHOOL OF MEDICINE   (United States)

^c CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^d JACKSON LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA LACTAMASE; RNA 16S;

ADULT; ANELLOVIRIDAE; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENE; BACTERIUM IDENTIFICATION; BETA LACTAMASE GENE; CANDIDA; CLINICAL LABORATORY; CLINICAL RESEARCH; CLOSTRIDIUM PERFRINGENS; COLONY FORMING UNIT; CONTROLLED STUDY; CORRELATION ANALYSIS; DIARRHEA; FECES; FUNGUS IDENTIFICATION; HUMAN; INTERMETHOD COMPARISON; LABORATORY TEST; MAJOR CLINICAL STUDY; METAGENOMIC SHOTGUN SEQUENCING; METAGENOMICS; NEXT GENERATION SEQUENCING; NONHUMAN; NOROVIRUS; PARECHOVIRUS; PATHOGEN IDENTIFICATION; PEPTOCLOSTRIDIUM DIFFICILE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SAPOVIRUS; TAXONOMIC IDENTIFICATION; TETRACYCLINE RESISTANCE GENE; VIRUS IDENTIFICATION; ADOLESCENT; CHILD; CLUSTER ANALYSIS; GENETICS; HIGH THROUGHPUT SEQUENCING; INFANT; METAGENOME; MICROBIOLOGY; MICROFLORA; NEWBORN; PRESCHOOL CHILD; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; VIROLOGY;

ADOLESCENT; CHILD; CHILD, PRESCHOOL; CLUSTER ANALYSIS; DIARRHEA; DRUG RESISTANCE, MICROBIAL; FECES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFANT; INFANT, NEWBORN; METAGENOME; METAGENOMICS; MICROBIOTA; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 16S;

EID: 84956668654     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.01965-15     Document Type: Article

References (37)

1. Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P. 2013. Metagenomics for pathogen detection in public health. Genome Med 5:81. http://dx.doi.org/10.1186/gm485.
2. Capobianchi MR, Giombini E, Rozera G. 2013. Next-generation sequencing technology in clinical virology. Clin Microbiol Infect 19:15-22. http://dx.doi.org/10.1111/1469-0691.12056.
3. Fournier PE, Drancourt M, Colson P, Rolain JM, La Scola B, Raoult D. 2013. Modern clinical microbiology: new challenges and solutions. Nat Rev Microbiol 11:574-585. http://dx.doi.org/10.1038/nrmicro3068.
4. Koser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, Holden MT, Dougan G, Bentley SD, Parkhill J, Peacock SJ. 2012. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 8:e1002824. http://dx.doi.org/10.1371/journal.ppat.1002824.
5. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ. 2011. Vaginal microbiome of reproductiveage women. Proc Natl Acad Sci U S A 108(Suppl):S4680-S4687.
6. Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS. 2012. Novel bacterial taxa in the human microbiome. PLoS One 7(6):e35294. http://dx.doi.org/10.1371/journal.pone.0035294.
7. Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirkwood CD, Wang D. 2008. Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog 4:e1000011. http://dx.doi.org/10.1371/journal.ppat.1000011.
8. Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA. 2012. Sequence analysis of the human virome in febrile and afebrile children. PLoS One 7(6):e27735. http://dx.doi.org/10.1371/journal.pone.0027735.
9. Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, Sokolic R, Garabedian E, Candotti F, Buckley RH, Reed KD, Meyer TL, Seroogy CM, Galloway R, Henderson SL, Gern JE, DeRisi JL, Chiu CY. 2014. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med 370:2408-2417. http://dx.doi.org/10.1056/NEJMoa1401268.
10. Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214. http://dx.doi.org/10.1038/nature11234.
11. Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI. 2011. Human nutrition, the gut microbiome and the immune system. Nature 474:327-336. http://dx.doi.org/10.1038/nature10213.
12. Wylie KM, Mihindukulasuriya KA, Zhou Y, Sodergren E, Storch GA, Weinstock GM. 2014. Metagenomic Analysis Of Double-Stranded DNA Viruses in Healthy Adults. BMC Biol 12:71. http://dx.doi.org/10.1186/s12915-014-0071-7.
13. Cho I, Blaser MJ. 2012. The human microbiome: At the interface of health and disease. Nat Rev Genet 13:260-270.
14. Madupu R, Szpakowski S, Nelson KE. 2013. Microbiome in human health and disease. Sci Prog 96:153-170. http://dx.doi.org/10.3184/003 685013X13683759820813.
15. Pflughoeft KJ, Versalovic J. 2012. Human microbiome in health and disease. Annu Rev Pathol 7:99-122. http://dx.doi.org/10.1146/annurev-pathol-011811-132421.
16. Antharam VC, Li EC, Ishmael A, Sharma A, Mai V, Rand KH, Wang GP. 2013. Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J Clin Microbiol 51:2884-2892. http://dx.doi.org/10.1128/JCM.00845-13.
17. El Feghaly RE, Stauber JL, Tarr PI, Haslam DB. 2013. Viral co-infections are common and are associated with higher bacterial burden in children with Clostridium difficile infection. J Pediatr Gastroenterol Nutr 57:813-816. http://dx.doi.org/10.1097/MPG.0b013e3182a3202f.
18. El Feghaly RE, Stauber JL, Tarr PI, Haslam DB. 2013. Intestinal inflammatory biomarkers and outcome in pediatric Clostridium difficile infections. J Pediatr 163:1697-1704. http://dx.doi.org/10.1016/j.jpeds.2013.07.029.
19. El Feghaly RE, Stauber JL, Deych E, Gonzalez C, Tarr PI, Haslam DB. 2013. Markers of intestinal inflammation, not bacterial burden, correlate with clinical outcomes in Clostridium difficile infection. Clin Infect Dis 56:1713-1721. http://dx.doi.org/10.1093/cid/cit147.
20. Grant L, Vinje J, Parashar U, Watt J, Reid R, Weatherholtz R, Santosham M, Gentsch J, OBrien K. 2012. Epidemiologic and clinical features of other enteric viruses associated with acute gastroenteritis in American Indian infants. J Pediatr 161:110-115. http://dx.doi.org/10.1016/j.jpeds.2011.12.046.
21. Human Microbiome Project Consortium. 2012. A framework for human microbiome research. Nature 486:215-221. http://dx.doi.org/10.1038/nature11209.
22. Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M, Magrini V, Eldred J, Latreille JP, Wilson RK, Ganem D, DeRisi JL. 2003. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol 1:E2. http://dx.doi.org/10.1371/journal.pbio.0000002.
23. Martin J, Sykes S, Young S, Kota K, Sanka R, Sheth N, Orvis J, Sodergren E, Wang Z, Weinstock GM, Mitreva M. 2012. Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. PLoS One 7:e36427. http://dx.doi.org/10.1371/journal.pone.0036427.
24. Davis CKK, Baldhandapani V, Gong W, Abubucker S, Becker E, Martin J, Wylie K, Khetani R, Hudson M, Weinstock G, Mitreva M. 2013. mBLAST: keeping up with the sequencing explosion for (meta)genome analysis. J Data Mining Genomics Proteomics 4:135.
25. Kircher M, Sawyer S, Meyer M. 2012. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 40:e3. http://dx.doi.org/10.1093/nar/gkr771.
26. Goncalves C, Decre D, Barbut F, Burghoffer B, Petit JC. 2004. Prevalence and characterization of a binary toxin (actin-specific ADPribosyltransferase) from Clostridium difficile. J Clin Microbiol 42:1933-1939. http://dx.doi.org/10.1128/JCM.42.5.1933-1939.2004.
27. Chen J, Zhang L, Paoli GC, Shi C, Tu SI, Shi X. 2010. A real-Time PCR method for the detection of Salmonella enterica from food using a target sequence identified by comparative genomic analysis. Int J Food Microbiol 137:168-174. http://dx.doi.org/10.1016/j.ijfoodmicro.2009.12.004.
28. McElvania TeKippe E, Wylie KM, Deych E, Sodergren E, Weinstock G, Storch GA. 2012. Increased prevalence of anellovirus in pediatric patients with fever. PLoS One 7:e50937. http://dx.doi.org/10.1371/journal.pone.0050937.
29. Nix WA, Maher K, Johansson ES, Niklasson B, Lindberg AM, Pallansch MA, Oberste MS. 2008. Detection of all known parechoviruses by realtime PCR. J Clin Microbiol 46:2519-2524. http://dx.doi.org/10.1128/JCM.00277-08.
30. Zhou Y, Mihindukulasuriya KA, Gao H, La Rosa PS, Wylie KM, Martin JC, Kota K, Shannon WD, Mitreva M, Sodergren E, Weinstock GM. 2014. Exploration of bacterial community classes in major human habitats. Genome Biol 15:R66. http://dx.doi.org/10.1186/gb-2014-15-5-r66.
31. Krause R, Schwab E, Bachhiesl D, Daxbock F, Wenisch C, Krejs GJ, Reisinger EC. 2001. Role of Candida in antibiotic-Associated diarrhea. J Infect Dis 184:1065-1069. http://dx.doi.org/10.1086/323550.
32. Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, Podar M, Warner B, Tarr PI, Nelson DE, Fortenberry JD, Holland MJ, Burr SE, Shannon WD, Sodergren E, Weinstock GM. 2013. Biogeography of the ecosystems of the healthy human body. Genome Biol 14:R1. http://dx.doi.org/10.1186/gb-2013-14-1-r1.
33. Woo PC, Lau SK, Chan KM, Fung AM, Tang BS, Yuen KY. 2005. Clostridium bacteraemia characterised by 16S ribosomal RNA gene sequencing. J Clin Pathol 58:301-307. http://dx.doi.org/10.1136/jcp.2004.022830.
34. Hu Y, Yang X, Qin J, Lu N, Cheng G, Wu N, Pan Y, Li J, Zhu L, Wang X, Meng Z, Zhao F, Liu D, Ma J, Qin N, Xiang C, Xiao Y, Li L, Yang H, Wang J, Yang R, Gao GF, Wang J, Zhu B. 2013. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat Commun 4:2151.
35. Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. 2013. Country-specific antibiotic use practices impact the human gut resistome. Genome Res 23:1163-1169. http://dx.doi.org/10.1101/gr.155465.113.
36. Moore AM, Patel S, Forsberg KJ, Wang B, Bentley G, Razia Y, Qin X, Tarr PI, Dantas G. 2013. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS One 8:e78822. http://dx.doi.org/10.1371/journal.pone.0078822.
37. Ruegger PM, Clark RT, Weger JR, Braun J, Borneman J. 2014. Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer. J Microbiol Methods 105:82-87. http://dx.doi.org/10.1016/j.mimet.2014.07.001.