Towards diagnostic metagenomics of Campylobacter in fecal samples

BMC Microbiology

Volumn 17, Issue 1, 2017, Pages

  Andersen, Sandra Christine ^a   Kiil, Kristoffer ^b   Harder, Christoffer Bugge ^b   Josefsen, Mathilde Hasseldam ^a   Persson, Søren ^b   Nielsen, Eva Møller ^b   Hoorfar, Jeffrey ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b STATENS SERUM INSTITUT   (Denmark)

Author keywords

Culture independent; Molecular typing; Next generation sequencing

Indexed keywords

ARTICLE; CAMPYLOBACTER ENTERITIS; CAMPYLOBACTER JEJUNI; CHICKEN; COLONY FORMING UNIT; CONTROLLED STUDY; DATA ANALYSIS; FECES ANALYSIS; HUMAN; LIMIT OF DETECTION; METAGENOMICS; NEXT GENERATION SEQUENCING; NONHUMAN; SEQUENCE ANALYSIS; ANIMAL; CAMPYLOBACTERIOSIS; DNA SEQUENCE; FECES; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; PROCEDURES; SENSITIVITY AND SPECIFICITY;

BACTERIAL DNA;

ANIMALS; BACTERIOLOGICAL TECHNIQUES; CAMPYLOBACTER INFECTIONS; CAMPYLOBACTER JEJUNI; CHICKENS; DNA, BACTERIAL; FECES; HUMANS; METAGENOMICS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 85020416195     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/s12866-017-1041-3     Document Type: Article

References (18)

1. Hoorfar J. Rapid Detection, Characterization and Enumeration of Foodborne Pathogens. 2011.
2. Pallen MJ. Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections. Parasitology. 2014;141(14):1856-62. doi: 10.1017/S0031182014000134.
3. Nakamura S, Maeda N, Miron IM, Yoh M, Izutsu K, Kataoka C, et al. Metagenomic diagnosis of bacterial infections. Emerg Infect Dis. 2008;14:1784-6. doi: 10.3201/eid1411.080589.
4. Loman NJ. A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4. JAMA. 2013;309:1502. doi: 10.1001/jama.2013.3231.
5. Palacios G, Druce J, Du L, Tran T, Birch C, Briese T, et al. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med. 2008;358:991-8.
6. Willner D, Haynes MR, Furlan M, Hanson N, Kirby B, Lim YW, et al. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. Am J Respir Cell Mol Biol. 2012;46:127-31.
7. Bzhalava D, Johansson H, Ekström J, Faust H, Möller B, Eklund C, et al. Unbiased Approach for Virus Detection in Skin Lesions. PLoS One. 2013;8(6):e65953.
8. Hasman H, Saputra D, Sicheritz-Ponten T, Lund O, Svendsen CA, Frimodt-Møller N, et al. Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol. 2014;52:139-46. doi: 10.1128/JCM.02452-13.
9. Josefsen MH, Andersen SC, Christensen J, Hoorfar J. Microbial food safety: Potential of DNA extraction methods for use in diagnostic metagenomics. J Microbiol Methods. 2015;114:30-4. doi: 10.1016/j.mimet.2015.04.016.
10. Ariefdjohan MW, Savaiano DA, Nakatsu CH. Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens. Nutr J. 2010;9:23.
11. Krause M, Josefsen MH, Lund M, Jacobsen NR, Brorsen L, Moos M, et al. Comparative, collaborative, and on-site validation of a TaqMan PCR method as a tool for certified production of fresh, Campylobacter-free chickens. Appl Environ Microbiol. 2006;72:5463-8.
12. Josefsen MH, Krause M, Hansen F, Hoorfar J. Optimization of a 12-hour TaqMan PCR-based method for detection of Salmonella bacteria in meat. Appl Environ Microbiol. 2007;73:3040-8.
13. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537-41.
14. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15:R46. doi: 10.1186/gb-2014-15-3-r46.
15. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-10.
16. Ounit R, Wanamaker S, Close TJ, Lonardi S. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics. 2015;16:236. doi: 10.1186/s12864-015-1419-2.
17. The National Center for Biotechnology Information. Genbank. http://www.ncbi.nlm.nih.gov/genbank/. Accessed 1 Jul 2015.
18. McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 2014;10(4):e1003531.