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Chapter 2 : Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory

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Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory, Page 1 of 2

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Abstract:

The identification of bacteria has traditionally been based upon the phenotypic properties of microorganisms grown in pure culture under optimal conditions. While useful in most circumstances, the physiological characteristics of bacteria are mutable and not always consistent within a given species. Phenotypic identification can, moreover, be tedious, subjective, and inconclusive when conflicting results are obtained. Even with the aid of semiautomated or automated instruments, these methods are still limited in that they cannot fully characterize all bacterial isolates, and the phenotype of an isolate may not be predictable (1, 2). We are beginning to appreciate the growing diversity of bacteria and the complexities in the evolution of a bacterial species. Similarly, we now more fully realize that the physiological properties of bacteria vary from the dynamic interplay between their environmental and ecological niches and their human hosts. With growing numbers of immunocompromised hosts who are susceptible to unusual infections, the distinction between environmental, colonizing, and clinically relevant bacteria is not always clear. Hence, commonly encountered bacteria with unusual physiological properties and the emergence of novel bacterial pathogens with unknown or poorly defined phenotypes pose significant challenges to clinical microbiologists. These challenges underscore the importance of characterizing bacteria by methods that are independent of a microorganism's biochemical characteristics.

Citation: Culbreath K, Simmon K, Petti C. 2016. Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory, p 19-31. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch2
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Figures

Image of FIGURE 1
FIGURE 1

Dye-terminator cycle sequencing of amplified 16S rRNA gene. Purified PCR amplicon, sequencing primer, and limited concentrations of dideoxynucleotide triphosphates (ddNTPs) into which four fluorescent dyes have been incorporated are mixed with unlabeled deoxynucleotides (dNTPs). Synthesis terminates whenever a ddNTP instead of a dNTP is incorporated into a new strand. Strands of various lengths are synthesized and labeled as the terminal ddNTP is incorporated into the strand. Accumulated fragments are separated according to size by electrophoresis. During electrophoresis, labeled products are visualized by fluorescence, with each of the four fluorescent dyes indicating which of the terminal ddNTPs have been incorporated. Combining the terminal ddNTP information with the fragment size allows the determination of sequence information. Reprinted from reference with permission from the publisher.

Citation: Culbreath K, Simmon K, Petti C. 2016. Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory, p 19-31. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch2
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Image of FIGURE 2
FIGURE 2

Schematic for 16S rRNA located on the small ribosomal subunit (30S). Arrows indicate the conserved regions that serve as primer targets for PCR amplification and DNA sequencing of bacteria.

Citation: Culbreath K, Simmon K, Petti C. 2016. Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory, p 19-31. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch2
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Image of FIGURE 3
FIGURE 3

Phylogenetic representation of an unusual clinical isolate, such as this sp., can provide useful information to the clinician if included with the patient results.

Citation: Culbreath K, Simmon K, Petti C. 2016. Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory, p 19-31. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch2
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References

/content/book/10.1128/9781555819071.ch02
1. Bosshard PP, Abels S, Altwegg M, Bottger EC, Zbinden R. 2004. Comparison of conventional and molecular methods for identification of aerobic catalase-negative gram-positive cocci in the clinical laboratory. J Clin Microbiol 42:20652073.[CrossRef][PubMed]
2. Tang YW, Ellis NM, Hopkins MK, Smith DH, Dodge DE, Persing DH. 1998. Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. J Clin Microbiol 36:36743679.[PubMed]
3. Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA, Wolfe RS, Balch WE, Tanner RS, Magrum LJ, Zablen LB, Blakemore R, Gupta R, Bonen L, Lewis BJ, Stahl DA, Luehrsen KR, Chen KN, Woese CR. 1980. The phylogeny of prokaryotes. Science 209:457463.[CrossRef][PubMed]
4. Clayton RA, Sutton G, Hinkle PS Jr, Bult C, Fields C. 1995. Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45:595599.[CrossRef][PubMed]
5. Drancourt M, Berger P, Raoult D. 2004. Systematic 16S rRNA gene sequencing of atypical clinical isolates identified 27 new bacterial species associated with humans. J Clin Microbiol 42:21972202.[CrossRef][PubMed]
6. Gautier AL, Dubois D, Escande F, Avril JL, Trieu-Cuot P, Gaillot O. 2005. Rapid and accurate identification of human isolates of Pasteurella and related species by sequencing the sodA gene. J Clin Microbiol 43:23072314.[CrossRef][PubMed]
7. Kumar S, Tamura K, Nei M. 2004. MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5:150163.[CrossRef][PubMed]
8. Petti CA, Polage CR, Schreckenberger P. 2005. The role of 16S rRNA gene sequencing in identification of microorganisms misidentified by conventional methods. J Clin Microbiol 43:61236125.[CrossRef][PubMed]
9. Bottger EC. 1989. Rapid determination of bacterial ribosomal RNA sequences by direct sequencing of enzymatically amplified DNA. FEMS Microbiol Lett 53:171176.[CrossRef][PubMed]
10. Bosshard PP, Abels S, Zbinden R, Bottger EC, Altwegg M. 2003. Ribosomal DNA sequencing for identification of aerobic gram-positive rods in the clinical laboratory (an 18-month evaluation). J Clin Microbiol 41:41344140.[CrossRef][PubMed]
11. Christensen JJ, Andresen K, Justesen T, Kemp M. 2005. Ribosomal DNA sequencing: experiences from use in the Danish National Reference Laboratory for Identification of Bacteria. APMIS 113:621628.[CrossRef][PubMed]
12. Clarridge JE 3rd, Zhang Q. 2002. Genotypic diversity of clinical Actinomyces species: phenotype, source, and disease correlation among genospecies. J Clin Microbiol 40:34423448.[CrossRef][PubMed]
13. Daley P, Church DL, Gregson DB, Elsayed S. 2005. Species-level molecular identification of invasive “Streptococcus milleri” group clinical isolates by nucleic acid sequencing in a centralized regional microbiology laboratory. J Clin Microbiol 43:29872988.[CrossRef][PubMed]
14. Ferroni A, Sermet-Gaudelus I, Abachin E, Quesne G, Lenoir G, Berche P, Gaillard JL. 2002. Use of 16S rRNA gene sequencing for identification of nonfermenting gram-negative bacilli recovered from patients attending a single cystic fibrosis center. J Clin Microbiol 40:37933797.[CrossRef][PubMed]
15. Patel JB, Wallace RJ Jr, Brown-Elliott BA, Taylor T, Imperatrice C, Leonard DG, Wilson RW, Mann L, Jost KC, Nachamkin I. 2004. Sequence-based identification of aerobic actinomycetes. J Clin Microbiol 42:25302540.[CrossRef][PubMed]
16. Relman DA, Loutit JS, Schmidt TM, Falkow S, Tompkins LS. 1990. The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. N Engl J Med 323:15731580.[CrossRef][PubMed]
17. Relman DA, Schmidt TM, MacDermott RP, Falkow S. 1992. Identification of the uncultured bacillus of Whipple's disease. N Engl J Med 327:293301.[CrossRef][PubMed]
18. Woese CR. 1987. Bacterial evolution. Microbiol Rev 51:221271.[PubMed]
19. Fox GE, Wisotzkey JD, Jurtshuk P Jr. 1992. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166170.[CrossRef][PubMed]
20. Petti CA, Bosshard PP, Brandt ME, Clarridge JE, Feldbyum TV, Foxall P, Furtado MR, Pace N, Procop G. 2008. Interpretative Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing; Approved Guideline (MM18-A). Clinical and Laboratory Standards Institute, Wayne, PA.
21. Conville PS, Zelazny AM, Witebsky FG. 2006. Analysis of secA1 gene sequences for identification of Nocardia species. J Clin Microbiol 44:2760–2766.[CrossRef][PubMed]
22. Mahenthiralingam E, Bischof J, Byrne SK, Radomski C, Davies JE, Av-Gay Y, Vandamme P. 2000. DNA-based diagnostic approaches for identification of Burkholderia cepacia complex, Burkholderia vietnamiensis, Burkholderia multivorans, Burkholderia stabilis, and Burkholderia cepacia genomovars I and III. J Clin Microbiol 38:31653173.[PubMed]
23. Marston EL, Sumner JW, Regnery RL. 1999. Evaluation of intraspecies genetic variation within the 60 kDa heat-shock protein gene (groEL) of Bartonella species. Int J Syst Bacteriol 49(Pt 3):10151023.[CrossRef][PubMed]
24. Petti CA, Simmon KE, Miro JM, Hoen B, Marco F, Chu VH, Athan E, Bukovski S, Bouza E, Bradley S, Fowler VG, Giannitsioti E, Gordon D, Reinbott P, Korman T, Lang S, Garcia-de-la-Maria C, Raglio A, Morris AJ, Plesiat P, Ryan S, Doco-Lecompte T, Tripodi F, Utili R, Wray D, Federspiel JJ, Boisson K, Reller LB, Murdoch DR, Woods CW. 2008. Genotypic diversity of coagulase-negative staphylococci causing endocarditis: a global perspective. J Clin Microbiol 46:17801784.[CrossRef][PubMed]
25. Simmon KE, Hall L, Woods CW, Marco F, Miro JM, Cabell C, Hoen B, Marin M, Utili R, Giannitsioti E, Doco-Lecompte T, Bradley S, Mirrett S, Tambic A, Ryan S, Gordon D, Jones P, Korman T, Wray D, Reller LB, Tripodi MF, Plesiat P, Morris AJ, Lang S, Murdoch DR, Petti CA. 2008. Phylogenetic analysis of viridans group streptococci causing endocarditis. J Clin Microbiol 46:30873090.[CrossRef][PubMed]
26. Simmon KE, Pounder JI, Greene JN, Walsh F, Anderson CM, Cohen S, Petti CA. 2007. Identification of an emerging pathogen, Mycobacterium massiliense, by rpoB sequencing of clinical isolates collected in the United States. J Clin Microbiol 45:19781980.[CrossRef][PubMed]
27. Yamamoto S, Bouvet PJ, Harayama S. 1999. Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization. Int J Syst Bacteriol 49(Pt 1):8795.[CrossRef][PubMed]
28. Conville PS, Witebsky FG. 2005. Multiple copies of the 16S rRNA gene in Nocardia nova isolates and implications for sequence-based identification procedures. J Clin Microbiol 43:28812885.[CrossRef][PubMed]
29. Klappenbach JA, Saxman PR, Cole JR, Schmidt TM. 2001. rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res 29:181184.[CrossRef][PubMed]
30. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:52615267.[CrossRef][PubMed]
31. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42:D633642.[CrossRef][PubMed]
32. Conlan S, Kong HH, Segre JA. 2012. Species-level analysis of DNA sequence data from the NIH Human Microbiome Project. PLoS One 7:e47075.[CrossRef][PubMed]
33. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590596.[CrossRef][PubMed]
34. Teng JL, Yeung MY, Yue G, Au-Yeung RK, Yeung EY, Fung AM, Tse H, Yuen KY, Lau SK, Woo PC. 2011. In silico analysis of 16S rRNA gene sequencing based methods for identification of medically important aerobic Gram-negative bacteria. J Med Microbiol 60:12811286.[CrossRef][PubMed]
35. Rampini SK, Bloemberg GV, Keller PM, Buchler AC, Dollenmaier G, Speck RF, Bottger EC. 2011. Broad-range 16S rRNA gene polymerase chain reaction for diagnosis of culture-negative bacterial infections. Clin Infect Dis 53:12451251.[CrossRef][PubMed]
36. Shin JH, Kim SH, Jeong HS, Oh SH, Kim HR, Lee JN, Yoon YC, Kim YW, Kim YH. 2011. Identification of coagulase-negative staphylococci isolated from continuous ambulatory peritoneal dialysis fluid using 16S ribosomal RNA, tuf, and SodA gene sequencing. Perit Dial Int 31:340346.[CrossRef][PubMed]
37. Becker K, Harmsen D, Mellmann A, Meier C, Schumann P, Peters G, von Eiff C. 2004. Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species. J Clin Microbiol 42:49884995.[CrossRef][PubMed]
38. Heikens E, Fleer A, Paauw A, Florijn A, Fluit AC. 2005. Comparison of genotypic and phenotypic methods for species-level identification of clinical isolates of coagulase-negative staphylococci. J Clin Microbiol 43:22862290.[CrossRef][PubMed]
39. Hwang SM, Kim MS, Park KU, Song J, Kim EC. 2011. Tuf gene sequence analysis has greater discriminatory power than 16S rRNA sequence analysis in identification of clinical isolates of coagulase-negative staphylococci. J Clin Microbiol 49:41424149.[CrossRef][PubMed]
40. Cercenado E, Garcia-Leoni ME, Diaz MD, Sanchez-Carrillo C, Catalan P, De Quiros JC, Bouza E. 1996. Emergence of teicoplanin-resistant coagulase-negative staphylococci. J Clin Microbiol 34:17651768.[PubMed]
41. Aubry-Damon H, Soussy CJ, Courvalin P. 1998. Characterization of mutations in the rpoB gene that confer rifampin resistance in Staphylococcus aureus. Antimicrob Agents Chemother 42:25902594.[PubMed]
42. Jensen A, Kilian M. 2012. Delineation of Streptococcus dysgalactiae, its subspecies, and its clinical and phylogenetic relationship to Streptococcus pyogenes. J Clin Microbiol 50:113126.[CrossRef][PubMed]
43. Arbique JC, Poyart C, Trieu-Cuot P, Quesne G, Carvalho Mda G, Steigerwalt AG, Morey RE, Jackson D, Davidson RJ, Facklam RR. 2004. Accuracy of phenotypic and genotypic testing for identification of Streptococcus pneumoniae and description of Streptococcus pseudopneumoniae sp. nov. J Clin Microbiol 42:46864696.[CrossRef][PubMed]
44. Park HK, Yoon JW, Shin JW, Kim JY, Kim W. 2010. rpoA is a useful gene for identification and classification of Streptococcus pneumoniae from the closely related viridans group streptococci. FEMS Microbiol Lett 305:5864.[CrossRef][PubMed]
45. Summanen PH, Rowlinson MC, Wooton J, Finegold SM. 2009. Evaluation of genotypic and phenotypic methods for differentiation of the members of the Anginosus group streptococci. Eur J Clin Microbiol Infect Dis 28:11231128.[CrossRef][PubMed]
46. Jensen A, Hoshino T, Kilian M. 2013. Taxonomy of the Anginosus group of the genus Streptococcus and description of Streptococcus anginosus subsp. whileyi subsp. nov. and Streptococcus constellatus subsp. viborgensis subsp. nov. Int J Syst Evol Microbiol 63:25062519.[CrossRef][PubMed]
47. Patel R, Piper KE, Rouse MS, Steckelberg JM, Uhl JR, Kohner P, Hopkins MK, Cockerill FR 3rd, Kline BC. 1998. Determination of 16S rRNA sequences of enterococci and application to species identification of nonmotile Enterococcus gallinarum isolates. J Clin Microbiol 36:33993407.[PubMed]
48. Naser SM, Vancanneyt M, Hoste B, Snauwaert C, Vandemeulebroecke K, Swings J. 2006. Reclassification of Enterococcus flavescens Pompei et al. 1992 as a later synonym of Enterococcus casseliflavus (ex Vaughan et al. 1979) Collins et al. 1984 and Enterococcus saccharominimus Vancanneyt et al. 2004 as a later synonym of Enterococcus italicus Fortina et al. 2004. Int J Syst Evol Microbiol 56:413416.[CrossRef][PubMed]
49. Finegold SM, Vaisanen ML, Rautio M, Eerola E, Summanen P, Molitoris D, Song Y, Liu C, Jousimies-Somer H. 2004. Porphyromonas uenonis sp. nov., a pathogen for humans distinct from P. asaccharolytica and P. endodontalis. J Clin Microbiol 42:52985301.[CrossRef][PubMed]
50. Marchandin H, Teyssier C, Simeon De Buochberg M, Jean-Pierre H, Carriere C, Jumas-Bilak E. 2003. Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: implications for phylogeny and taxonomy. Microbiology 149:14931501.[CrossRef][PubMed]
51. Simmon KE, Mirrett S, Reller LB, Petti CA. 2008. Genotypic diversity of anaerobic isolates from bloodstream infections. J Clin Microbiol 46:15961601.[CrossRef][PubMed]
52. Kim HS, Lee DS, Chang YH, Kim MJ, Koh S, Kim J, Seong JH, Song SK, Shin HS, Son JB, Jung MY, Park SN, Yoo SY, Cho KW, Kim DK, Moon S, Kim D, Choi Y, Kim BO, Jang HS, Kim CS, Kim C, Choe SJ, Kook JK. 2010. Application of rpoB and zinc protease gene for use in molecular discrimination of Fusobacterium nucleatum subspecies. J Clin Microbiol 48:545553.[CrossRef][PubMed]
53. Song Y, Liu C, McTeague M, Finegold SM. 2003. 16S ribosomal DNA sequence-based analysis of clinically significant gram-positive anaerobic cocci. J Clin Microbiol 41:13631369.[CrossRef][PubMed]
54. Warren YA, Tyrrell KL, Citron DM, Goldstein EJ. 2006. Clostridium aldenense sp. nov. and Clostridium citroniae sp. nov. isolated from human clinical infections. J Clin Microbiol 44:24162422.[CrossRef][PubMed]
55. Kakinuma K, Fukushima M, Kawaguchi R. 2003. Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene. Biotechnol Bioeng 83:721728.[CrossRef][PubMed]
56. Paradis S, Boissinot M, Paquette N, Belanger SD, Martel EA, Boudreau DK, Picard FJ, Ouellette M, Roy PH, Bergeron MG. 2005. Phylogeny of the Enterobacteriaceae based on genes encoding elongation factor Tu and F-ATPase beta-subunit. Int J Syst Evol Microbiol 55:20132025.[CrossRef][PubMed]
57. Alperi A, Figueras MJ, Inza I, Martinez-Murcia AJ. 2008. Analysis of 16S rRNA gene mutations in a subset of Aeromonas strains and their impact in species delineation. Int Microbiol 11:185194.[PubMed]
58. Beaz-Hidalgo R, Martinez-Murcia A, Figueras MJ. 2013. Reclassification of Aeromonas hydrophila subsp. dhakensis Huys et al. 2002 and Aeromonas aquariorum Martinez-Murcia et al. 2008 as Aeromonas dhakensis sp. nov. comb nov. and emendation of the species Aeromonas hydrophila. Syst Appl Microbiol 36:171176.[CrossRef][PubMed]
59. Drancourt M, Bollet C, Carta A, Rousselier P. 2001. Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov. Int J Syst Evol Microbiol 51:925932.[CrossRef][PubMed]
60. Brady C, Cleenwerck I, Venter S, Coutinho T, De Vos P. 2013. Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter. Syst Appl Microbiol 36:309319.[CrossRef][PubMed]
61. Cesarini S, Bevivino A, Tabacchioni S, Chiarini L, Dalmastri C. 2009. RecA gene sequence and multilocus sequence typing for species-level resolution of Burkholderia cepacia complex isolates. Lett Appl Microbiol 49:580588.[CrossRef][PubMed]
62. Norskov-Lauritsen N. 2014. Classification, identification, and clinical significance of haemophilus and aggregatibacter species with host specificity for humans. Clin Microbiol Rev 27:214240.[CrossRef][PubMed]
63. Wang J, Ruan Z, Feng Y, Fu Y, Jiang Y, Wang H, Yu Y. 2014. Species distribution of clinical Acinetobacter isolates revealed by different identification techniques. PLoS One 9(8):e104882. doi:10.1371/journal.pone.0104882.[CrossRef][PubMed]
64. Diavatopoulos DA, Cummings CA, van der Heide HG, van Gent M, Liew S, Relman DA, Mooi FR. 2006. Characterization of a highly conserved island in the otherwise divergent Bordetella holmesii and Bordetella pertussis genomes. J Bacteriol 188:83858394.[CrossRef][PubMed]
65. Vielemeyer O, Crouch JY, Edberg SC, Howe JG. 2004. Identification of Bordetella pertussis in a critically ill human immunodeficiency virus-infected patient by direct genotypical analysis of Gram-stained material and discrimination from B. holmesii by using a unique recA gene restriction enzyme site. J Clin Microbiol 42:847849[CrossRef].[PubMed]
66. Guan W, Xu Y, Chen DL, Xu JN, Tian Y, Chen JP. 2012. Application of multilocus sequence analysis (MLSA) for accurate identification of Legionella spp. isolated from municipal fountains in Chengdu, China, based on 16S rRNA, mip, and rpoB genes. J Microbiol 50:127136.[CrossRef][PubMed]
67. Cunningham SA, Mainella JM, Patel R. 2014. Misidentification of Neisseria polysaccharea as Neisseria meningitidis with the use of matrix-assisted laser desorption ionizationtime of flight mass spectrometry. J Clin Microbiol 52:22702271.[CrossRef][PubMed]
68. Bennett JS, Watkins ER, Jolley KA, Harrison OB, Maiden MC. 2014. Identifying Neisseria species by use of the 50S ribosomal protein L6 (rplF) gene. J Clin Microbiol 52:13751381.[CrossRef][PubMed]
69. Scholz HC, Al Dahouk S, Tomaso H, Neubauer H, Witte A, Schloter M, Kampfer P, Falsen E, Pfeffer M, Engel M. 2008. Genetic diversity and phylogenetic relationships of bacteria belonging to the Ochrobactrum-Brucella group by recA and 16S rRNA gene-based comparative sequence analysis. Syst Appl Microbiol 31:116.[CrossRef][PubMed]
70. Hill JE, Paccagnella A, Law K, Melito PL, Woodward DL, Price L, Leung AH, Ng LK, Hemmingsen SM, Goh SH. 2006. Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database. J Med Microbiol 55:393399.[CrossRef][PubMed]
71. Funke G, von Graevenitz A, Clarridge JE 3rd, Bernard KA. 1997. Clinical microbiology of coryneform bacteria. Clin Microbiol Rev 10:125159.[PubMed]
72. Tang YW, Von Graevenitz A, Waddington MG, Hopkins MK, Smith DH, Li H, Kolbert CP, Montgomery SO, Persing DH. 2000. Identification of coryneform bacterial isolates by ribosomal DNA sequence analysis. J Clin Microbiol 38:16761678.[PubMed]
73. Khamis A, Raoult D, Scola BL. 2005. Comparison between rpoB and 16S rRNA gene sequencing for molecular identification of 168 clinical isolates of corynebacterium. J Clin Microbiol 43:19341936.[CrossRef][PubMed]
74. Henssge U, Do T, Radford DR, Gilbert SC, Clark D, Beighton D. 2009. Emended description of Actinomyces naeslundii and descriptions of Actinomyces oris sp. nov. and Actinomyces johnsonii sp. nov., previously identified as Actinomyces naeslundii genospecies 1, 2 and WVA 963. Int J Syst Evol Microbiol 59:509516.[CrossRef][PubMed]
75. Kong F, Wang H, Zhang E, Sintchenko V, Xiao M, Sorrell TC, Chen X, Chen SC. 2010. secA1 gene sequence polymorphisms for species identification of Nocardia species and recognition of intraspecies genetic diversity. J Clin Microbiol 48:39283934.[CrossRef][PubMed]
76. Carrasco G, Valdezate S, Garrido N, Villalon P, Medina-Pascual MJ, Saez-Nieto JA. 2013. Identification, typing, and phylogenetic relationships of the main clinical Nocardia species in Spain according to their gyrB and rpoB genes. J Clin Microbiol 51:36023608.[CrossRef][PubMed]
77. McTaggart LR, Richardson SE, Witkowska M, Zhang SX. 2010. Phylogeny and identification of Nocardia species on the basis of multilocus sequence analysis. J Clin Microbiol 48:45254533.[CrossRef][PubMed]
78. Lee SH, Vigliotti JS, Vigliotti VS, Jones W, Moorcroft TA, Lantsman K. 2014. DNA sequencing diagnosis of off-season spirochetemia with low bacterial density in Borrelia burgdorferi and Borrelia miyamotoi infections. Int J Mol Sci 15:1136411386.[CrossRef][PubMed]
79. Geissdorfer W, Moos V, Moter A, Loddenkemper C, Jansen A, Tandler R, Morguet AJ, Fenollar F, Raoult D, Bogdan C, Schneider T. 2012. High frequency of Tropheryma whipplei in culture-negative endocarditis. J Clin Microbiol 50:216222.[CrossRef][PubMed]
80. Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Ponten T, Aarestrup FM, Ussery DW, Lund O. 2014. Benchmarking of methods for genomic taxonomy. J Clin Microbiol 52:15291539.[CrossRef][PubMed]

Tables

Generic image for table
TABLE 1

Select microorganisms with indistinguishable 16S rRNA gene sequences and suggested supplemental phenotypic tests

Citation: Culbreath K, Simmon K, Petti C. 2016. Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory, p 19-31. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch2
Generic image for table
TABLE 2

Frequently used primer sequences for gene sequence-based identification of bacteria

Citation: Culbreath K, Simmon K, Petti C. 2016. Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory, p 19-31. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch2
Generic image for table
TABLE 3

Comparison of features of various nucleotide sequence databases

Citation: Culbreath K, Simmon K, Petti C. 2016. Application of Identification of Bacteria by DNA Target Sequencing in a Clinical Microbiology Laboratory, p 19-31. In Persing D, Tenover F, Hayden R, Ieven M, Miller M, Nolte F, Tang Y, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555819071.ch2

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