Real time application of whole genome sequencing for outbreak investigation – What is an achievable turnaround time?

Diagnostic Microbiology and Infectious Disease

Volumn 85, Issue 3, 2016, Pages 277-282

  McGann, Patrick ^a   Bunin, Jessica L ^b   Snesrud, Erik ^a   Singh, Seema ^b   Maybank, Rosslyn ^a   Ong, Ana C ^a   Kwak, Yoon I ^a   Seronello, Scott ^b   Clifford, Robert J ^a   Hinkle, Mary ^a   Yamada, Stephen ^b   Barnhill, Jason ^b   Lesho, Emil ^a  

^a WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

^b TRIPLER ARMY MEDICAL CENTER   (United States)

Author keywords

Enterococcus faecium; Turnaround time; Whole genome sequencing

Indexed keywords

AMINOGLYCOSIDE ANTIBIOTIC AGENT; BETA LACTAM ANTIBIOTIC; GENTAMICIN; KANAMYCIN; MACROLIDE; QUINOLINE DERIVED ANTIINFECTIVE AGENT; TETRACYCLINE DERIVATIVE; TOBRAMYCIN; VANCOMYCIN;

ADULT; AGED; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL TRANSMISSION; BACTERIUM CULTURE; BACTERIUM DETECTION; BLOOD CULTURE; CASE REPORT; CONTROLLED STUDY; CORYNEBACTERIUM; ENTEROCOCCUS CASSELIFLAVUS; ENTEROCOCCUS FAECALIS; ENTEROCOCCUS FAECIUM; EPIDEMIC; ESCHERICHIA COLI; FEMALE; GENE SEQUENCE; GENOME ANALYSIS; HUMAN; KLEBSIELLA OXYTOCA; MALE; MIDDLE AGED; NONHUMAN; PANTOEA; PEPTOSTREPTOCOCCUS; PERITONEAL FLUID CULTURE; PHYLOGENETIC TREE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STRAIN IDENTIFICATION; TERTIARY CARE CENTER; TURNAROUND TIME; VANCOMYCIN RESISTANT ENTEROCOCCUS FAECIUM; CLASSIFICATION; CROSS INFECTION; DNA SEQUENCE; EVALUATION STUDY; GENETICS; GRAM-POSITIVE BACTERIAL INFECTIONS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR EPIDEMIOLOGY; MOLECULAR TYPING; PROCEDURES; TIME FACTOR; VANCOMYCIN RESISTANT ENTEROCOCCUS;

AGED; CROSS INFECTION; DISEASE OUTBREAKS; ENTEROCOCCUS FAECIUM; FEMALE; GRAM-POSITIVE BACTERIAL INFECTIONS; HUMANS; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; MOLECULAR TYPING; SEQUENCE ANALYSIS, DNA; TERTIARY CARE CENTERS; TIME FACTORS; VANCOMYCIN-RESISTANT ENTEROCOCCI;

EID: 84966680790     PISSN: 07328893     EISSN: 18790070     Source Type: Journal    
DOI: 10.1016/j.diagmicrobio.2016.04.020     Document Type: Article

References (44)

1. Agren, J., Sundstrom, A., Hafstrom, T., Segerman, B., Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLoS One, 7, 2012, e39107.
2. Ankala, A., Hegde, M., Genomic technologies and the new era of genomic medicine. J Mol Diagn 16 (2014), 7–10.
3. Aziz, N., Zhao, Q., Bry, L., Driscoll, D.K., Funke, B., Gibson, J.S., et al. College of American Pathologists' laboratory standards for next-generation sequencing clinical tests. Arch Pathol Lab Med 139 (2015), 481–493.
4. Chin, E.L., da Silva, C., Hegde, M., Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations. BMC Genet, 14, 2013.
5. Didelot, X., Bowden, R., Wilson, D.J., Peto, T.E., Crook, D.W., Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13 (2012), 601–612.
6. Diene, S.M., Rolain, J.M., Investigation of antibiotic resistance in the genomic era of multidrug-resistant Gram-negative bacilli, especially Enterobacteriaceae, Pseudomonas and Acinetobacter. Expert Rev Anti-Infect Ther 11 (2013), 277–296.
7. Dunne, W.M. Jr., Westblade, L.F., Ford, B., Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis 31 (2012), 1719–1726.
8. Eyre, D.W., Golubchik, T., Gordon, N.C., Bowden, R., Piazza, P., Batty, E.M., et al. A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open, 2, 2012, e001124.
9. Fournier, P.E., Drancourt, M., Raoult, D., Bacterial genome sequencing and its use in infectious diseases. Lancet Infect Dis 7 (2007), 711–723.
10. Fricke, W.F., Rasko, D.A., Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat Rev Genet 15 (2014), 49–55.
11. Gargis, A.S., Kalman, L., Berry, M.W., Bick, D.P., Dimmock, D.P., Hambuch, T., et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 30 (2012), 1033–1036.
12. Goldberg, B., Sichtig, H., Geyer, C., Ledeboer, N., Weinstock, G.M., Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics. Mbio 6 (2015), e01888–115.
13. Gordon, N.C., Price, J.R., Cole, K., Everitt, R., Morgan, M., Finney, J., et al. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J Clin Microbiol 52 (2014), 1182–1191.
14. Grad, Y.H., Lipsitch, M., Feldgarden, M., Arachchi, H.M., Cerqueira, G.C., Fitzgerald, M., et al. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci U S A 109 (2012), 3065–3070.
15. Harris, S.R., Feil, E.J., Holden, M.T., Quail, M.A., Nickerson, E.K., Chantratita, N., et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327 (2010), 469–474.
16. Harris, S.R., Clarke, I.N., Seth-Smith, H.M., Solomon, A.W., Cutcliffe, L.T., Marsh, P., et al. Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet, 44(413–419), 2012, S1.
17. Harris, S.R., Cartwright, E.J., Torok, M.E., Holden, M.T., Brown, N.M., Ogilvy-Stuart, A.L., et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis 13 (2013), 130–136.
18. Harrison, E.M., Paterson, G.K., Holden, M.T., Larsen, J., Stegger, M., Larsen, A.R., et al. Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC. EMBO Mol Med 5 (2013), 509–515.
19. He, M., Miyajima, F., Roberts, P., Ellison, L., Pickard, D.J., Martin, M.J., et al. Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet 45 (2013), 109–113.
20. Junemann, S., Sedlazeck, F.J., Prior, K., Albersmeier, A., John, U., Kalinowski, J., et al. Updating benchtop sequencing performance comparison. Nat Biotechnol 31 (2013), 294–296.
21. Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28 (2012), 1647–1649.
22. Komp Lindgren, P., Higgins, P.G., Seifert, H., Cars, O., Prevalence of hypermutators among clinical Acinetobacter baumannii isolates. J Antimicrob Chemother 71 (2016), 661–665.
23. Koser, C.U., Ellington, M.J., Cartwright, E.J., Gillespie, S.H., Brown, N.M., Farrington, M., et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog, 8, 2012, e1002824.
24. Koser, C.U., Holden, M.T., Ellington, M.J., Cartwright, E.J., Brown, N.M., Ogilvy-Stuart, A.L., et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med 366 (2012), 2267–2275.
25. Koser, C.U., Ellington, M.J., Peacock, S.J., Whole-genome sequencing to control antimicrobial resistance. Trends Genet 30 (2014), 401–407.
26. La Scola, B., Elkarkouri, K., Li, W., Wahab, T., Fournous, G., Rolain, J.M., et al. Rapid comparative genomic analysis for clinical microbiology: the Francisella tularensis paradigm. Genome Res 18 (2008), 742–750.
27. Laing, C., Buchanan, C., Taboada, E.N., Zhang, Y., Kropinski, A., Villegas, A., et al. Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics, 11, 2010, 461.
28. Lopez-Camacho, E., Gomez-Gil, R., Tobes, R., Manrique, M., Lorenzo, M., Galvan, B., et al. Genomic analysis of the emergence and evolution of multidrug resistance during a Klebsiella pneumoniae outbreak including carbapenem and colistin resistance. J Antimicrob Chemother 69 (2014), 632–636.
29. Mardis, E.R., A decade's perspective on DNA sequencing technology. Nature 470 (2011), 198–203.
30. Pak, T.R., Kasarskis, A., How Next-Generation Sequencing and Multiscale Data Analysis Will Transform Infectious Disease Management. Clin Infect Dis 61 (2015), 1695–1702.
31. Pallen, M.J., Loman, N.J., Penn, C.W., High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Curr Opin Microbiol 13 (2010), 625–631.
32. Ramirez, M.S., Tolmasky, M.E., Aminoglycoside modifying enzymes. Drug Resist Updat 13 (2010), 151–171.
33. Rasko, D.A., Webster, D.R., Sahl, J.W., Bashir, A., Boisen, N., Scheutz, F., et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 365 (2011), 709–717.
34. Rice, L.B., Bellais, S., Carias, L.L., Hutton-Thomas, R., Bonomo, R.A., Caspers, P., et al. Impact of specific pbp5 mutations on expression of beta-lactam resistance in Enterococcus faecium. Antimicrob Agents Chemother 48 (2004), 3028–3032.
35. Rouch, D.A., Byrne, M.E., Kong, Y.C., Skurray, R.A., The aacA-aphD gentamicin and kanamycin resistance determinant of Tn4001 from Staphylococcus aureus: expression and nucleotide sequence analysis. J Gen Microbiol 133 (1987), 3039–3052.
36. Serizawa, M., Sekizuka, T., Okutani, A., Banno, S., Sata, T., Inoue, S., et al. Genomewide screening for novel genetic variations associated with ciprofloxacin resistance in Bacillus anthracis. Antimicrob Agents Chemother 54 (2010), 2787–2792.
37. Snitkin, E.S., Zelazny, A.M., Thomas, P.J., Stock, F., Group, NCSP, Henderson, D.K., et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med, 4, 2012, 148ra116.
38. Stoesser, N., Batty, E.M., Eyre, D.W., Morgan, M., Wyllie, D.H., Del Ojo Elias, C., et al. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother 68 (2013), 2234–2244.
39. Underwood, A.P., Dallman, T., Thomson, N.R., Williams, M., Harker, K., Perry, N., et al. Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak. J Clin Microbiol 51 (2013), 232–237.
40. van Dijk, E.L., Auger, H., Jaszczyszyn, Y., Thermes, C., Ten years of next-generation sequencing technology. Trends Genet 30 (2014), 418–426.
41. Werner, G., Fleige, C., Ewert, B., Laverde-Gomez, J.A., Klare, I., Witte, W., High-level ciprofloxacin resistance among hospital-adapted Enterococcus faecium (CC17). Int J Antimicrob Agents 35 (2010), 119–125.
42. Willems, R.J., Top, J., van Santen, M., Robinson, D.A., Coque, T.M., Baquero, F., et al. Global spread of vancomycin-resistant Enterococcus faecium from distinct nosocomial genetic complex. Emerg Infect Dis 11 (2005), 821–828.
43. Woodford, N., Turton, J.F., Livermore, D.M., Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance. FEMS Microbiol Rev 35 (2011), 736–755.
44. Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, S., Lund, O., et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67 (2012), 2640–2644.