Proficiency testing for bacterial whole genome sequencing: An end-user survey of current capabilities, requirements and priorities

BMC Infectious Diseases

Volumn 15, Issue 1, 2015, Pages

  Moran Gilad, Jacob ^a,b   Sintchenko, Vitali ^c,d   Pedersen, Susanne Karlsmose ^e   Wolfgang, William J ^f   Pettengill, James ^g   Strain, Errol ^g   Hendriksen, Rene S ^e  

^a MINISTRY OF HEALTH   (Israel)

^b BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^c University of Sydney   (Australia)

^d WESTMEAD HOSPITAL   (Australia)

^e TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^f WADSWORTH CENTER   (United States)

^g CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

Author keywords

Bioinformatics; End users; Microbiology; Next generation sequencing; Proficiency; Public health; Standards; Survey

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL LOAD; BIOINFORMATICS; CAMPYLOBACTER; COMPUTER PROGRAM; ESCHERICHIA COLI; GENE SEQUENCE; GENOME ANALYSIS; HEALTH CARE SURVEY; HUMAN; INTERMETHOD COMPARISON; INTERNET; LISTERIA MONOCYTOGENES; MICROBIAL DIVERSITY; MYCOBACTERIUM TUBERCULOSIS; NEXT GENERATION SEQUENCING; NONHUMAN; ONLINE SYSTEM; PEPTOCLOSTRIDIUM DIFFICILE; PROFICIENCY TESTING; QUALITY CONTROL PROCEDURES; SALMONELLA; STANDARDIZATION; STAPHYLOCOCCUS AUREUS; VALIDATION PROCESS; BIOLOGY; GENOMICS; GOOD LABORATORY PRACTICE; HIGH THROUGHPUT SEQUENCING; QUESTIONNAIRE; STANDARD;

BACTERIAL DNA;

COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LABORATORY PROFICIENCY TESTING; REFERENCE STANDARDS; SURVEYS AND QUESTIONNAIRES;

EID: 84926686219     PISSN: None     EISSN: 14712334     Source Type: Journal    
DOI: 10.1186/s12879-015-0902-3     Document Type: Article

References (21)

1. Bertelli C, Greub G. Rapid bacterial genome sequencing: methods and applications in clinical microbiology. Clin Microbiol Infect. 2013;19:803-13.
2. Long SW, Williams D, Valson C, Cantu CC, Cernoch P, Musser JM, et al. A genomic day in the life of a clinical microbiology laboratory. J Clin Microbiol. 2013;51:1272-7.
3. Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW. Transforming clinical microbiology with bacterial genome sequencing. Nature Rev Genetics. 2012;13:601-12.
4. Kupferschmidt K. Epidemiology. Outbreak detectives embrace the genome era. Science. 2011;333:1818-9.
5. Walker TM, Ip CL, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: A retrospective observational study. Lancet Infect Dis. 2013;13:137-46.
6. Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, et al. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: A longitudinal molecular epidemiological study. PLoS Med. 2013;10:e1001387.
7. Sherry NL, Porter JL, Seemann T, Watkins A, Stinear TP, Howden BP. Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol. 2013;51:1396-401.
8. Maiden M, van Rensburg MJ J, Bray JE, Earle SG, Ford SA, Jolley KA, et al. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol. 2013;11:728-36.
9. Relman DA. Microbial genomics and infectious diseases. New Engl J Med. 2011;365:347-57.
10. Köser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathogens. 2012;8:e1002824.
11. Dunne Jr WM, Westblade LF, Ford B. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis. 2012;31:1719-26.
12. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. New Engl J Med. 2011;364:730-9.
13. Gilmour MW, Graham M, Reimer A, Van Domselaar G. Public health genomics and the new molecular epidemiology of bacterial pathogens. Public Health Genomics. 2013;16:25-30.
14. Aarestrup FM, Brown EW, Detter C, Gerner-Smidt P, Gilmour MW, Harmsen D, et al. Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response. Emerg Infect Dis. 2012;18:e1.
15. Perspectives of a global, real-time microbiological genomic identification system - implications for national and global detection and control of infectious diseases. Consensus report of an expert meeting 1-2 September 2011, Bruxelles, Belgium. Available at: http://www.food.dtu.dk/english/~/media/institutter/foedevareinstituttet/publikationer/pub-2011/consensus%20report%20perspectives%20of%20a%20global,%20real-time.ashx .
16. Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol. 2012;30:1033-6.
17. Underwood AP, Dallman T, Thomson NR, Williams M, Harker K, Perry N, et al. Public health value of next-generation DNA sequencing of enterohaemorrhagic Escherichia coli isolates from an outbreak. J Clin Microbiol. 2013;51:232-7.
18. Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM. Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. PLoS One. 2014;2:e87991.
19. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014;52:1501-10.
20. Gullapalli RR, Desai KV, Santana-Santos L, Kant JA, Becich MJ. Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics. J Pathol Inform. 2012;3:40.
21. Wyres KL, Conway CC, Garg S, Queiroz C, Reumann M, Holt K, et al. WGS Analysis and interpretation in clinical and public health microbiology laboratories: what are the requirements and how do existing tools compare? Pathogens. 2014;3:437-58.