Abstract
Whole-genome sequencing (WGS) has shown immense value in enabling identification and characterization of bacterial taxa. This is particularly true for mycobacteria, where culture-based characterization becomes delayed by the inherently slow growth rate of these organisms. This chapter reviews the general techniques behind WGS and their optimization, existing techniques for species-level identification and the advantages of WGS for this purpose, and a variety of useful tools for the genomic characterization of mycobacterial strains.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977) Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265(5596):687–695. https://doi.org/10.1038/265687a0
Venter JC, Adams MD, Myers EW et al (2001) The sequence of the human genome. Science 291(5507):1304–1351. https://doi.org/10.1126/science.1058040
International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921. https://doi.org/10.1038/35057062
International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431(7011):931–945. https://doi.org/10.1038/nature03001
Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M, Tanaka EM, Myers EW (2018) The axolotl genome and the evolution of key tissue formation regulators. Nature 554(7690):50–55. https://doi.org/10.1038/nature25458
Wetterstrand K (2019) DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP). http://www.genome.gov/sequencingcostsdata. Accessed Feb 12, 2020
National Center for Biotechnology Information, U.S. National Library of Medicine (2019) GenBank and WGS Statistics. https://www.ncbi.nlm.nih.gov/genbank/statistics/. Accessed Feb 12, 2020
Köser CU, Ellington MJ, Peacock SJ (2014) Whole-genome sequencing to control antimicrobial resistance. Trends Genet 30(9):401–407. https://doi.org/10.1016/j.tig.2014.07.003
Magee JG, Ward AC (2015) Mycobacterium. In: Bergey’s Manual of systematics of archaea and bacteria. Wiley, Hoboken, New Jersey, pp 1–84. https://doi.org/10.1002/9781118960608.gbm00029
CLSI (2018) Laboratory detection and identification of mycobacteria, 2nd Ed. edn. Clinical and Laboratory Standards Institute, Wayne, PA
Tortoli E, Meehan CJ, Grottola A, Fregni Serpini G, Fabio A, Trovato A, Pecorari M, Cirillo DM (2019) Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium. Infect Genet Evol 75:103983. https://doi.org/10.1016/j.meegid.2019.103983
Gupta RS, Lo B, Son J (2018) Phylogenomics and comparative genomic studies robustly support division of the genus Mycobacterium into an emended genus Mycobacterium and four novel genera. Front Microbiol 9:67. https://doi.org/10.3389/fmicb.2018.00067
Tortoli E, Brown-Elliott BA, Chalmers JD, Cirillo DM, Daley CL, Emler S, Floto RA, Garcia MJ, Hoefsloot W, Koh WJ, Lange C, Loebinger M, Maurer FP, Morimoto K, Niemann S, Richter E, Turenne CY, Vasireddy R, Vasireddy S, Wagner D, Wallace RJ Jr, Wengenack N, van Ingen J (2019) Same meat, different gravy: ignore the new names of mycobacteria. Eur Respir J 54(1):1900795. https://doi.org/10.1183/13993003.00795-2019
Fedrizzi T, Meehan CJ, Grottola A, Giacobazzi E, Fregni Serpini G, Tagliazucchi S, Fabio A, Bettua C, Bertorelli R, De Sanctis V, Rumpianesi F, Pecorari M, Jousson O, Tortoli E, Segata N (2017) Genomic characterization of nontuberculous mycobacteria. Sci Rep 7:45258. https://doi.org/10.1038/srep45258
Tortoli E, Fedrizzi T, Meehan CJ, Trovato A, Grottola A, Giacobazzi E, Serpini GF, Tagliazucchi S, Fabio A, Bettua C, Bertorelli R, Frascaro F, De Sanctis V, Pecorari M, Jousson O, Segata N, Cirillo DM (2017) The new phylogeny of the genus Mycobacterium: the old and the news. Infect Genet Evol 56:19–25. https://doi.org/10.1016/j.meegid.2017.10.013
Rosselló-Móra R, Amann R (2015) Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 38(4):209–216. https://doi.org/10.1016/j.syapm.2015.02.001
Riojas MA, McGough KJ, Rider-Riojas CJ, Rastogi N, Hazbon MH (2018) Phylogenomic analysis of the species of the Mycobacterium tuberculosis complex demonstrates that Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii are later heterotypic synonyms of Mycobacterium tuberculosis. Int J Syst Evol Microbiol 68(1):324–332. https://doi.org/10.1099/ijsem.0.002507
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74(12):5463–5467. https://doi.org/10.1073/pnas.74.12.5463
Heather JM, Chain B (2016) The sequence of sequencers: the history of sequencing DNA. Genomics 107(1):1–8. https://doi.org/10.1016/j.ygeno.2015.11.003
Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17(6):333–351. https://doi.org/10.1038/nrg.2016.49
Illumina, Inc. (2010) Technology Spotlight: Illumina® Sequencing
Giani AM, Gallo GR, Gianfranceschi L, Formenti G (2020) Long walk to genomics: history and current approaches to genome sequencing and assembly. Comput Struct Biotechnol J 18:9–19. https://doi.org/10.1016/j.csbj.2019.11.002
Pacific Biosciences of California, Inc. SMRT Sequencing—How it Works. vol PS100–032919
McCombie WR, McPherson JD, Mardis ER (2019) Next-generation sequencing technologies. Cold Spring Harb Perspect Med 9(11). https://doi.org/10.1101/cshperspect.a036798
Marrakchi H, Laneelle MA, Daffe M (2014) Mycolic acids: structures, biosynthesis, and beyond. Chem Biol 21(1):67–85. https://doi.org/10.1016/j.chembiol.2013.11.011
Jackson M (2014) The mycobacterial cell envelope-lipids. Cold Spring Harb Perspect Med 4(10). https://doi.org/10.1101/cshperspect.a021105
Amaro A, Duarte E, Amado A, Ferronha H, Botelho A (2008) Comparison of three DNA extraction methods for Mycobacterium bovis, Mycobacterium tuberculosis and Mycobacterium avium subsp. avium. Lett Appl Microbiol 47(1):8–11. https://doi.org/10.1111/j.1472-765X.2008.02372.x
Epperson LE, Strong M (2020) A scalable, efficient, and safe method to prepare high quality DNA from mycobacteria and other challenging cells. J Clin Tuberc Other Mycobact Dis 19:100150. https://doi.org/10.1016/j.jctube.2020.100150
Hasan NA, Epperson LE, Lawsin A, Rodger RR, Perkins KM, Halpin AL, Perry KA, Moulton-Meissner H, Diekema DJ, Crist MB, Perz JF, Salfinger M, Daley CL, Strong M (2019) Genomic analysis of cardiac surgery-associated Mycobacterium chimaera infections, United States. Emerg Infect Dis 25(3):559–563. https://doi.org/10.3201/eid2503.181282
Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C (2018) NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34(15):2666–2669. https://doi.org/10.1093/bioinformatics/bty149
Chen S, Zhou Y, Chen Y, Gu J (2018) Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17):i884–i890. https://doi.org/10.1093/bioinformatics/bty560
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetJ 17(1). https://doi.org/10.14806/ej.17.1.200
Wick RR Filtlong. https://github.com/rrwick/Filtlong
Illumina, Inc. Effects of Index Misassignment on Multiplexing and Downstream Analysis. vol 770–2017–004-D
Wick RR, Judd LM, Holt KE (2018) Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. PLoS Comput Biol 14(11):e1006583. https://doi.org/10.1371/journal.pcbi.1006583
Wood DE, Lu J, Langmead B (2019) Improved metagenomic analysis with kraken 2. Genome Biol 20(1):257. https://doi.org/10.1186/s13059-019-1891-0
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923
Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997
Zerbino DR (2010) Using the velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics. Chapter 11:Unit 11 15. https://doi.org/10.1002/0471250953.bi1105s31
Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H, Coombe L, Warren RL, Birol I (2017) ABySS 2.0: resource-efficient assembly of large genomes using a bloom filter. Genome Res 27(5):768–777. https://doi.org/10.1101/gr.214346.116
Tadpole Guide. https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/tadpole-guide/
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477. https://doi.org/10.1089/cmb.2012.0021
Chevreux B MIRA—The Genome and Transcriptome Assembler and Mapper. https://github.com/bachev/mira
Li H seqtk. https://github.com/lh3/seqtk
Shen W, Le S, Li Y, Hu F (2016) SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS One 11(10):e0163962. https://doi.org/10.1371/journal.pone.0163962
Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6):e1005595. https://doi.org/10.1371/journal.pcbi.1005595
Li H (2016) Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32(14):2103–2110. https://doi.org/10.1093/bioinformatics/btw152
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27(5):722–736
Kolmogorov M, Yuan J, Lin Y, Pevzner PA (2019) Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 37(5):540–546. https://doi.org/10.1038/s41587-019-0072-8
Wick RR, Holt KE (2019) Benchmarking of long-read assemblers for prokaryote whole genome sequencing. F1000Res 8:2138. https://doi.org/10.12688/f1000research.21782.1
Vaser R, Sović I, Nagarajan N, Šikić M (2017) Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27(5):737–746
Oxford Nanopore Technologies (2018) Medaka. https://github.com/nanoporetech/medaka
Simpson J Nanopolish. https://github.com/jts/nanopolish
De Maio N, Shaw LP, Hubbard A, George S, Sanderson ND, Swann J, Wick R, AbuOun M, Stubberfield E, Hoosdally SJ, Crook DW, Peto TEA, Sheppard AE, Bailey MJ, Read DS, Anjum MF, Walker AS, Stoesser N, On Behalf Of The Rehab C (2019) Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes. Microb Genom 5(9):e000294. https://doi.org/10.1099/mgen.0.000294
Crusoe MR, Alameldin HF, Awad S, Boucher E, Caldwell A, Cartwright R, Charbonneau A, Constantinides B, Edvenson G, Fay S, Fenton J, Fenzl T, Fish J, Garcia-Gutierrez L, Garland P, Gluck J, Gonzalez I, Guermond S, Guo J, Gupta A, Herr JR, Howe A, Hyer A, Harpfer A, Irber L, Kidd R, Lin D, Lippi J, Mansour T, McA'Nulty P, McDonald E, Mizzi J, Murray KD, Nahum JR, Nanlohy K, Nederbragt AJ, Ortiz-Zuazaga H, Ory J, Pell J, Pepe-Ranney C, Russ ZN, Schwarz E, Scott C, Seaman J, Sievert S, Simpson J, Skennerton CT, Spencer J, Srinivasan R, Standage D, Stapleton JA, Steinman SR, Stein J, Taylor B, Trimble W, Wiencko HL, Wright M, Wyss B, Zhang Q, Zyme E, Brown CT (2015) The khmer software package: enabling efficient nucleotide sequence analysis. F1000Res 4:900. https://doi.org/10.12688/f1000research.6924.1
BBNorm Guide. https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbnorm-guide/
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079
Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA (2013) From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 43:11 10 11–11 10 33. https://doi.org/10.1002/0471250953.bi1110s43
Kubica GP, Kim TH, Dunbar FP (1972) Designation of strain H37Rv as the Neotype of Mycobacterium tuberculosis. Int J Syst Bacteriol 22(2):99–106. https://doi.org/10.1099/00207713-22-2-99
Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60(Pt 1):249–266. https://doi.org/10.1099/ijs.0.016949-0
Avery OT, Macleod CM, McCarty M (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a Desoxyribonucleic [sic] acid fraction isolated from pneumococcus type III. J Exp Med 79(2):137–158. https://doi.org/10.1084/jem.79.2.137
Agaisse H, Gominet M, Økstad OA, Kolstø A-B, Lereclus D (1999) PlcR is a pleiotropic regulator of extracellular virulence factor gene expression in Bacillus thuringiensis. Mol Microbiol 32(5):1043–1053. https://doi.org/10.1046/j.1365-2958.1999.01419.x
Slamti L, Perchat S, Gominet M, Vilas-Boas G, Fouet A, Mock M, Sanchis V, Chaufaux J, Gohar M, Lereclus D (2004) Distinct mutations in PlcR explain why some strains of the Bacillus cereus group are nonhemolytic. J Bacteriol 186(11):3531–3538. https://doi.org/10.1128/JB.186.11.3531-3538.2004
Sastalla I, Maltese LM, Pomerantseva OM, Pomerantsev AP, Keane-Myers A, Leppla SH (2010) Activation of the latent PlcR regulon in Bacillus anthracis. Microbiology 156(Pt 10):2982–2993. https://doi.org/10.1099/mic.0.041418-0
Salamitou S, Ramisse F, Brehelin M, Bourguet D, Gilois N, Gominet M, Hernandez E, Lereclus D (2000) The plcR regulon is involved in the opportunistic properties of Bacillus thuringiensis and Bacillus cereus in mice and insects. Microbiology 146(Pt 11):2825–2832. https://doi.org/10.1099/00221287-146-11-2825
Callegan MC, Kane ST, Cochran DC, Gilmore MS, Gominet M, Lereclus D (2003) Relationship of plcR-regulated factors to Bacillus endophthalmitis virulence. Infect Immun 71(6):3116–3124. https://doi.org/10.1128/iai.71.6.3116-3124.2003
Roth A, Fischer M, Hamid ME, Michalke S, Ludwig W, Mauch H (1998) Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J Clin Microbiol 36(1):139–147
Tortoli E (2003) Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev 16(2):319–354. https://doi.org/10.1128/cmr.16.2.319-354.2003
Clarridge JE 3rd (2004) Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clinical Microbiol Rev 17(4):840–862, table of contents. https://doi.org/10.1128/CMR.17.4.840-862.2004
Dobner P, Feldmann K, Rifai M, Löscher T, Rinder H (1996) Rapid identification of mycobacterial species by PCR amplification of hypervariable 16S rRNA gene promoter region. J Clin Microbiol 34(4):866
Kim SH, Shin JH (2018) Identification of nontuberculous mycobacteria using multilocous sequence analysis of 16S rRNA, hsp65, and rpoB. J Clin Lab Anal 32(1). https://doi.org/10.1002/jcla.22184
Adekambi T, Drancourt M (2004) Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing. Int J Syst Evol Microbiol 54(Pt 6):2095–2105. https://doi.org/10.1099/ijs.0.63094-0
Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J (2005) Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3(9):733–739. https://doi.org/10.1038/nrmicro1236
Glaeser SP, Kampfer P (2015) Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 38(4):237–245. https://doi.org/10.1016/j.syapm.2015.03.007
Saha MS, Pal S, Sarkar I, Roy A, Das Mohapatra PK, Sen A (2019) Comparative genomics of Mycobacterium reveals evolutionary trends of M. avium complex. Genomics 111(3):426–435. https://doi.org/10.1016/j.ygeno.2018.02.019
Lu B, Dong HY, Zhao XQ, Liu ZG, Liu HC, Zhang YY, Jiang Y, Wan KL (2012) A new multilocus sequence analysis scheme for Mycobacterium tuberculosis. Biomed Environ Sci 25(6):620–629. https://doi.org/10.3967/0895-3988.2012.06.003
Tan JL, Khang TF, Ngeow YF, Choo SW (2013) A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus. BMC Genomics 14:879. https://doi.org/10.1186/1471-2164-14-879
Alexander DC, Marras TK, Ma JH, Mirza S, Liu D, Kus JV, Soualhine H, Escuyer V, Warshauer D, Brode SK, Farrell DJ, Jamieson FB (2014) Multilocus sequence typing of Mycobacterium xenopi. J Clin Microbiol 52(11):3973–3977. https://doi.org/10.1128/JCM.01601-14
Kolb J, Hillemann D, Mobius P, Reetz J, Lahiri A, Lewin A, Rusch-Gerdes S, Richter E (2014) Genetic characterization of German Mycobacterium avium strains isolated from different hosts and specimens by multilocus sequence typing. International journal of medical microbiology : IJMM 304(8):941–948. https://doi.org/10.1016/j.ijmm.2014.06.001
Cheng A, Sun HY, Tsai YT, Chang SY, Wu UI, Hsueh PR, Sheng WH, Chen YC, Chang SC (2019) Comparing the Utilities of Different Multilocus Sequence Typing Schemes for identifying outbreak strains of Mycobacterium abscessus subsp. massiliense. J Clin Microbiol 58(1). https://doi.org/10.1128/JCM.01304-19
Macheras E, Konjek J, Roux AL, Thiberge JM, Bastian S, Leao SC, Palaci M, Sivadon-Tardy V, Gutierrez C, Richter E, Rusch-Gerdes S, Pfyffer GE, Bodmer T, Jarlier V, Cambau E, Brisse S, Caro V, Rastogi N, Gaillard JL, Heym B (2014) Multilocus sequence typing scheme for the Mycobacterium abscessus complex. Res Microbiol 165(2):82–90. https://doi.org/10.1016/j.resmic.2013.12.003
Wuzinski M, Bak AK, Petkau A, WH BD, Soualhine H, Sharma MK (2019) A multilocus sequence typing scheme for Mycobacterium abscessus complex (MAB-multilocus sequence typing) using whole-genome sequencing data. Int J Mycobacteriol 8(3):273–280. https://doi.org/10.4103/ijmy.ijmy_106_19
Hayashi Sant'Anna F, Bach E, Porto RZ, Guella F, Hayashi Sant'Anna E, Passaglia LMP (2019) Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy. Crit Rev Microbiol 45(2):182–200. https://doi.org/10.1080/1040841X.2019.1569587
Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI, Trüper HG, Murray RGE, Grimont PAD, Brenner DJ, Starr MP, Moore LH (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37(4):463–464. https://doi.org/10.1099/00207713-37-4-463
Auch AF, von Jan M, Klenk HP, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2(1):117–134. https://doi.org/10.4056/sigs.531120
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68(1):461–466. https://doi.org/10.1099/ijsem.0.002516
Chun J, Rainey FA (2014) Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 64(Pt 2):316–324. https://doi.org/10.1099/ijs.0.054171-0
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57(Pt 1):81–91. https://doi.org/10.1099/ijs.0.64483-0
Hugenholtz P, Skarshewski A, Parks DH (2016) Genome-based microbial taxonomy coming of age. Cold Spring Harb Perspect Biol 8(6):a018085. https://doi.org/10.1101/cshperspect.a018085
Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A (2015) Microbial species delineation using whole genome sequences. Nucleic Acids Res 43(14):6761–6771. https://doi.org/10.1093/nar/gkv657
Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102(7):2567–2572. https://doi.org/10.1073/pnas.0409727102
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106(45):19126–19131. https://doi.org/10.1073/pnas.0906412106
Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9(1):5114. https://doi.org/10.1038/s41467-018-07641-9
Lee I, Kim YO, Park SC, Chun J (2015) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66(2):1100–1103. https://doi.org/10.1099/ijsem.0.000760
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60
Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin LA, Chertkov O, Reddy T, Pati A, Ivanova NN, Markowitz V, Kyrpides NC, Woyke T, Göker M, Klenk HP (2014) Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 9:2. https://doi.org/10.1186/1944-3277-9-2
Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kampfer P, Maiden MC, Nesme X, Rossello-Mora R, Swings J, Truper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52(Pt 3):1043–1047. https://doi.org/10.1099/00207713-52-3-1043
Rossello-Mora R (2012) Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories. Environ Microbiol 14(2):318–334. https://doi.org/10.1111/j.1462-2920.2011.02599.x
Sutcliffe IC, Trujillo ME, Goodfellow M (2012) A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa. Antonie Van Leeuwenhoek 101(1):13–20. https://doi.org/10.1007/s10482-011-9664-0
Thompson CC, Amaral GR, Campeao M, Edwards RA, Polz MF, Dutilh BE, Ussery DW, Sawabe T, Swings J, Thompson FL (2015) Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 197(3):359–370. https://doi.org/10.1007/s00203-014-1071-2
Parker CT, Tindall BJ, Garrity GM (2019) International code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 69(1A):S1–S111. https://doi.org/10.1099/ijsem.0.000778
Tagini F, Aeby S, Bertelli C, Droz S, Casanova C, Prod'hom G, Jaton K, Greub G (2019) Phylogenomics reveal that Mycobacterium kansasii subtypes are species-level lineages. Description of Mycobacterium pseudokansasii sp. nov., Mycobacterium innocens sp. nov. and Mycobacterium attenuatum sp. nov. Int J Syst Evol Microbiol 69(6):1696–1704. https://doi.org/10.1099/ijsem.0.003378
Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R, Butler RM, Chlenski P, Conrad N, Dickerman A, Dietrich EM (2020) The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res 48(D1):D606–D612
Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R (2013) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42(D1):D581–D591
Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL (2016) Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 45(D1):D535–D542
Krueger F (2012) Trim Galore! A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/. Accessed 28 04 2016
Lassmann T, Hayashizaki Y, Daub CO (2010) SAMStat: monitoring biases in next generation sequencing data. Bioinformatics 27(1):130–131
Ondov BD, Bergman NH, Phillippy AM (2011) Interactive metagenomic visualization in a web browser. BMC Bioinformatics 12(1):385
Clausen PT, Aarestrup FM, Lund O (2018) Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 19(1):307
McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57(7):3348–3357
Chen L, Xiong Z, Sun L, Yang J, Jin Q (2011) VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 40(D1):D641–D645
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA (2017) metaSPAdes: a new versatile metagenomic assembler. Genome Res 27(5):824–834
Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner P (2016) plasmidSPAdes: assembling plasmids from whole genome sequencing data. bioRxiv:048942
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9(11):e112963
Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094–3100
Wick RR, Schultz MB, Zobel J, Holt KE (2015) Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31(20):3350–3352
Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365
McNair K, Aziz RK, Pusch GD, Overbeek R, Dutilh BE, Edwards R (2018) Phage genome annotation using the RAST pipeline. In: Bacteriophages. Springer, Berlin, pp 231–238
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7):1043–1055
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33(17):5691–5702
Parrello B, Butler R, Chlenski P, Olson R, Overbeek J, Pusch GD, Vonstein V, Overbeek R (2019) A machine learning-based service for estimating quality of genomes using PATRIC. BMC Bioinformatics 20(1):1–9
Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch GD, Shukla M, Vonstein V, Wattam AR, Yoo H (2016) PATtyFams: protein families for the microbial genomes in the PATRIC database. Front Microbiol 7:118
Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S (2017) PATRIC as a unique resource for studying antimicrobial resistance. Brief Bioinform 20(4):1094–1102
Davis JJ, Boisvert S, Brettin T, Kenyon RW, Mao C, Olson R, Overbeek R, Santerre J, Shukla M, Wattam AR (2016) Antimicrobial resistance prediction in PATRIC and RAST. Sci Rep 6:27930
Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu C-H, McDermott PF (2019) Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother 63(11):e00483–e00419
Sayers S, Li L, Ong E, Deng S, Fu G, Lin Y, Yang B, Zhang S, Fa Z, Zhao B (2019) Victors: a web-based knowledge base of virulence factors in human and animal pathogens. Nucleic Acids Res 47(D1):D693–D700
Mao C, Abraham D, Wattam AR, Wilson MJ, Shukla M, Yoo HS, Sobral BW (2015) Curation, integration and visualization of bacterial virulence factors in PATRIC. Bioinformatics 31(2):252–258
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM (2016) Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17(1):132
Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5(6):e11147
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski BJB (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11):1422–1423
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313
Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57(5):758–771
Li H, Durbin R (2009) Fast and accurate short read alignment with burrows–wheeler transform. Bioinformatics 25(14):1754–1760
Frith MC, Wan R, Horton P (2010) Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res 38(7):e100
Garrison E, Marth G (2012) Haplotype-based variant detection from short-read sequencing. arXiv:1207.3907
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9(1):75
Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36(suppl_2):W5–W9
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45(D1):D353–D361
Federhen S (2012) The NCBI taxonomy database. Nucleic Acids Res 40(D1):D136–D143
Jagielski T, Minias A, van Ingen J, Rastogi N, Brzostek A, Zaczek A, Dziadek J (2016) Methodological and clinical aspects of the molecular epidemiology of Mycobacterium tuberculosis and other mycobacteria. Clin Microbiol Rev 29(2):239–290. https://doi.org/10.1128/CMR.00055-15
Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rusch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D (2006) Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 44(12):4498–4510. https://doi.org/10.1128/JCM.01392-06
Couvin D, Zozio T, Rastogi N (2017) SpolSimilaritySearch - a web tool to compare and search similarities between spoligotypes of Mycobacterium tuberculosis complex. Tuberculosis 105:49–52. https://doi.org/10.1016/j.tube.2017.04.007
Mokrousov I, Rastogi N (2015) Spacer-based macroarrays for CRISPR genotyping. In: Lundgren M, Charpentier E, Fineran PC (eds) CRISPR: methods and protocols. Springer New York, New York, NY, pp 111–131. https://doi.org/10.1007/978-1-4939-2687-9_7
Couvin D, David A, Zozio T, Rastogi N (2019) Macro-geographical specificities of the prevailing tuberculosis epidemic as seen through SITVIT2, an updated version of the Mycobacterium tuberculosis genotyping database. Infect Genet Evol 72:31–43. https://doi.org/10.1016/j.meegid.2018.12.030
Xia E, Teo YY, Ong RT (2016) SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads. Genome Med 8(1):19. https://doi.org/10.1186/s13073-016-0270-7
Sekyere JO, Asante J (2018) Emerging mechanisms of antimicrobial resistance in bacteria and fungi: advances in the era of genomics. Future Microbiol 13:241–262. https://doi.org/10.2217/fmb-2017-0172
Ferri M, Ranucci E, Romagnoli P, Giaccone V (2017) Antimicrobial resistance: a global emerging threat to public health systems. Crit Rev Food Sci Nutr 57(13):2857–2876. https://doi.org/10.1080/10408398.2015.1077192
Nasiri MJ, Haeili M, Ghazi M, Goudarzi H, Pormohammad A, Imani Fooladi AA, Feizabadi MM (2017) New insights in to the intrinsic and acquired drug resistance mechanisms in mycobacteria. Front Microbiol 8:681. https://doi.org/10.3389/fmicb.2017.00681
Smith SE, Showers-Corneli P, Dardenne CN, Harpending HH, Martin DP, Beiko RG (2012) Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution. PLoS One 7(11):e50070. https://doi.org/10.1371/journal.pone.0050070
Adams KN, Takaki K, Connolly LE, Wiedenhoft H, Winglee K, Humbert O, Edelstein PH, Cosma CL, Ramakrishnan L (2011) Drug tolerance in replicating mycobacteria mediated by a macrophage-induced efflux mechanism. Cell 145(1):39–53. https://doi.org/10.1016/j.cell.2011.02.022
Louw GE, Warren RM, Gey van Pittius NC, McEvoy CR, Van Helden PD, Victor TC (2009) A balancing act: efflux/influx in mycobacterial drug resistance. Antimicrob Agents Chemother 53(8):3181–3189. https://doi.org/10.1128/AAC.01577-08
Stephan J, Mailaender C, Etienne G, Daffe M, Niederweis M (2004) Multidrug resistance of a porin deletion mutant of Mycobacterium smegmatis. Antimicrob Agents Chemother 48(11):4163–4170. https://doi.org/10.1128/AAC.48.11.4163-4170.2004
Vianna JS, Machado D, Ramis IB, Silva FP, Bierhals DV, Abril MA, von Groll A, Ramos DF, Lourenco MCS, Viveiros M, da Silva PEA (2019) The contribution of efflux pumps in Mycobacterium abscessus complex resistance to clarithromycin. Antibiotics (Basel) 8(3):153. https://doi.org/10.3390/antibiotics8030153
Kapur V, Li LL, Iordanescu S, Hamrick MR, Wanger A, Kreiswirth BN, Musser JM (1994) Characterization by automated DNA sequencing of mutations in the gene (rpoB) encoding the RNA polymerase beta subunit in rifampin-resistant Mycobacterium tuberculosis strains from new York City and Texas. J Clin Microbiol 32(4):1095
Miotto P, Tessema B, Tagliani E, Chindelevitch L, Starks AM, Emerson C, Hanna D, Kim PS, Liwski R, Zignol M, Gilpin C, Niemann S, Denkinger CM, Fleming J, Warren RM, Crook D, Posey J, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Murray M, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, Ranganathan UDK, McNerney R, Ezewudo M, Cirillo DM, Schito M, Koser CU, Rodwell TC (2017) A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis. Eur Respir J 50(6). https://doi.org/10.1183/13993003.01354-2017
The CRyPTIC Consortium and the 100000 Genomes Project, Allix-Beguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Munoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, DAJ M, Murray M, Niemann S, Omar SV, Ong RT, TEA P, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sanchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, TNT T, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B (2018) Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing. N Engl J Med 379(15):1403–1415. https://doi.org/10.1056/NEJMoa1800474
Chakravorty S, Kothari H, Aladegbami B, Cho EJ, Lee JS, Roh SS, Kim H, Kwak H, Lee EG, Hwang SH, Banada PP, Safi H, Via LE, Cho SN, Barry CE 3rd, Alland D (2012) Rapid, high-throughput detection of rifampin resistance and heteroresistance in Mycobacterium tuberculosis by use of sloppy molecular beacon melting temperature coding. J Clin Microbiol 50(7):2194–2202. https://doi.org/10.1128/JCM.00143-12
Ng KC, Meehan CJ, Torrea G, Goeminne L, Diels M, Rigouts L, de Jong BC, Andre E (2018) Potential application of digitally linked tuberculosis diagnostics for real-time surveillance of drug-resistant tuberculosis transmission: validation and analysis of test results. JMIR Med Inform 6(1):e12. https://doi.org/10.2196/medinform.9309
Ng KCS, van Deun A, Meehan CJ, Torrea G, Driesen M, Gabriels S, Rigouts L, Andre E, de Jong BC (2018) Xpert ultra can unambiguously identify specific rifampin resistance-conferring mutations. J Clin Microbiol 56(9):e00686–e00618. https://doi.org/10.1128/JCM.00686-18
Piddock LJ, Williams KJ, Ricci V (2000) Accumulation of rifampicin by Mycobacterium aurum, Mycobacterium smegmatis and Mycobacterium tuberculosis. J Antimicrob Chemother 45(2):159–165. https://doi.org/10.1093/jac/45.2.159
Li XZ, Zhang L, Nikaido H (2004) Efflux pump-mediated intrinsic drug resistance in Mycobacterium smegmatis. Antimicrob Agents Chemother 48(7):2415–2423. https://doi.org/10.1128/AAC.48.7.2415-2423.2004
Andre E, Goeminne L, Cabibbe A, Beckert P, Kabamba Mukadi B, Mathys V, Gagneux S, Niemann S, Van Ingen J, Cambau E (2017) Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria. Clin Microbiol Infect 23(3):167–172. https://doi.org/10.1016/j.cmi.2016.09.006
Meehan CJ, Goig GA, Kohl TA, Verboven L, Dippenaar A, Ezewudo M, Farhat MR, Guthrie JL, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton PM, Brites D, Cabibbe AM, de Jong BC, de Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM, Zhao Y, Zignol M, Schito M, Gardy J, Cirillo DM, Niemann S, Comas I, Van Rie A (2019) Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol 17(9):533–545. https://doi.org/10.1038/s41579-019-0214-5
Satta G, Lipman M, Smith GP, Arnold C, Kon OM, McHugh TD (2018) Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential? Clin Microbiol Infect 24(6):604–609. https://doi.org/10.1016/j.cmi.2017.10.030
Ezewudo M, Borens A, Chiner-Oms A, Miotto P, Chindelevitch L, Starks AM, Hanna D, Liwski R, Zignol M, Gilpin C, Niemann S, Kohl TA, Warren RM, Crook D, Gagneux S, Hoffner S, Rodrigues C, Comas I, Engelthaler DM, Alland D, Rigouts L, Lange C, Dheda K, Hasan R, McNerney R, Cirillo DM, Schito M, Rodwell TC, Posey J (2018) Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase. Sci Rep 8(1):15382. https://doi.org/10.1038/s41598-018-33731-1
Kohl TA, Utpatel C, Schleusener V, De Filippo MR, Beckert P, Cirillo DM, Niemann S (2018) MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates. PeerJ 6:e5895. https://doi.org/10.7717/peerj.5895
Ngo TM, Teo YY (2019) Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms. BMC Bioinformatics 20(1):68. https://doi.org/10.1186/s12859-019-2658-z
Schleusener V, Koser CU, Beckert P, Niemann S, Feuerriegel S (2017) Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools. Sci Rep 7:46327. https://doi.org/10.1038/srep46327
Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, van Soolingen D, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook DW, Iqbal Z (2019) Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe. Wellcome Open Res 4:191. https://doi.org/10.12688/wellcomeopenres.15603.1
Phelan JE, O'Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino S, O'Grady J, McNerney R, Hibberd ML, Viveiros M, Huggett JF, Clark TG (2019) Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med 11(1):41. https://doi.org/10.1186/s13073-019-0650-x
Feuerriegel S, Schleusener V, Beckert P, Kohl TA, Miotto P, Cirillo DM, Cabibbe AM, Niemann S, Fellenberg K (2015) PhyResSE: a web tool delineating Mycobacterium tuberculosis antibiotic resistance and lineage from whole-genome sequencing data. J Clin Microbiol 53(6):1908–1914. https://doi.org/10.1128/JCM.00025-15
Macedo R, Nunes A, Portugal I, Duarte S, Vieira L, Gomes JP (2018) Dissecting whole-genome sequencing-based online tools for predicting resistance in Mycobacterium tuberculosis: can we use them for clinical decision guidance? Tuberculosis 110:44–51. https://doi.org/10.1016/j.tube.2018.03.009
Lipworth S, Hough N, Leach L, Morgan M, Jeffery K, Andersson M, Robinson E, Smith EG, Crook D, Peto T, Walker T (2019) Whole-genome sequencing for predicting clarithromycin resistance in Mycobacterium abscessus. Antimicrob Agents Chemother 63(1):e01204–e01218. https://doi.org/10.1128/AAC.01204-18
Gupta SK, Drancourt M, Rolain JM (2017) In Silico prediction of antibiotic resistance in Mycobacterium ulcerans Agy99 through whole genome sequence analysis. Am J Trop Med Hyg 97(3):810–814. https://doi.org/10.4269/ajtmh.16-0478
Lavania M, Singh I, Turankar RP, Gupta AK, Ahuja M, Pathak V, Sengupta U (2018) Enriched whole genome sequencing identified compensatory mutations in the RNA polymerase gene of rifampicin-resistant Mycobacterium leprae strains. Infect Drug Resist 11:169–175. https://doi.org/10.2147/IDR.S152082
Benjak A, Avanzi C, Singh P, Loiseau C, Girma S, Busso P, Fontes ANB, Miyamoto Y, Namisato M, Bobosha K, Salgado CG, da Silva MB, Bouth RC, Frade MAC, Filho FB, Barreto JG, Nery JAC, Buhrer-Sekula S, Lupien A, Al-Samie AR, Al-Qubati Y, Alkubati AS, Bretzel G, Vera-Cabrera L, Sakho F, Johnson CR, Kodio M, Fomba A, Sow SO, Gado M, Konate O, Stefani MMA, Penna GO, Suffys PN, Sarno EN, Moraes MO, Rosa PS, Baptista I, Spencer JS, Aseffa A, Matsuoka M, Kai M, Cole ST (2018) Phylogenomics and antimicrobial resistance of the leprosy bacillus Mycobacterium leprae. Nat Commun 9(1):352. https://doi.org/10.1038/s41467-017-02576-z
Starks AM, Aviles E, Cirillo DM, Denkinger CM, Dolinger DL, Emerson C, Gallarda J, Hanna D, Kim PS, Liwski R, Miotto P, Schito M, Zignol M (2015) Collaborative effort for a centralized worldwide tuberculosis relational sequencing data platform. Clin Infect Dis 61(Suppl 3):S141–S146. https://doi.org/10.1093/cid/civ610
Schito M, Dolinger DL (2015) A collaborative approach for "ReSeq-ing" Mycobacterium tuberculosis drug resistance: convergence for drug and diagnostic developers. EBioMedicine 2(10):1262–1265. https://doi.org/10.1016/j.ebiom.2015.10.008
Zignol M, Cabibbe AM, Dean AS, Glaziou P, Alikhanova N, Ama C, Andres S, Barbova A, Borbe-Reyes A, Chin DP, Cirillo DM, Colvin C, Dadu A, Dreyer A, Driesen M, Gilpin C, Hasan R, Hasan Z, Hoffner S, Hussain A, Ismail N, Kamal SMM, Khanzada FM, Kimerling M, Kohl TA, Mansjö M, Miotto P, Mukadi YD, Mvusi L, Niemann S, Omar SV, Rigouts L, Schito M, Sela I, Seyfaddinova M, Skenders G, Skrahina A, Tahseen S, Wells WA, Zhurilo A, Weyer K, Floyd K, Raviglione MC (2018) Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study. Lancet Infect Dis 18(6):675–683. https://doi.org/10.1016/s1473-3099(18)30073-2
Comas I (2017) Genomic epidemiology of tuberculosis. In: Gagneux S (ed) Strain variation in the Mycobacterium tuberculosis complex: its role in biology, Epidemiology and Control. Springer International Publishing, Cham, pp 79–93. https://doi.org/10.1007/978-3-319-64371-7_4
Gori A, Bandera A, Marchetti G, Degli Esposti A, Catozzi L, Nardi GP, Gazzola L, Ferrario G, van Embden JD, van Soolingen D, Moroni M, Franzetti F (2005) Spoligotyping and Mycobacterium tuberculosis. Emerg Infect Dis 11(8):1242–1248. https://doi.org/10.3201/eid1108.040982
Jonsson J, Hoffner S, Berggren I, Bruchfeld J, Ghebremichael S, Pennhag A, Groenheit R (2014) Comparison between RFLP and MIRU-VNTR genotyping of Mycobacterium tuberculosis strains isolated in Stockholm 2009 to 2011. PLoS One 9(4):e95159. https://doi.org/10.1371/journal.pone.0095159
Meehan CJ, Moris P, Kohl TA, Pecerska J, Akter S, Merker M, Utpatel C, Beckert P, Gehre F, Lempens P, Stadler T, Kaswa MK, Kuhnert D, Niemann S, de Jong BC (2018) The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology. EBioMedicine 37:410–416. https://doi.org/10.1016/j.ebiom.2018.10.013
Wyllie DH, Davidson JA, Grace Smith E, Rathod P, Crook DW, Peto TEA, Robinson E, Walker T, Campbell C (2018) A quantitative evaluation of MIRU-VNTR typing against whole-genome sequencing for identifying Mycobacterium tuberculosis transmission: a prospective observational cohort study. EBioMedicine 34:122–130. https://doi.org/10.1016/j.ebiom.2018.07.019
Jajou R, de Neeling A, van Hunen R, de Vries G, Schimmel H, Mulder A, Anthony R, van der Hoek W, van Soolingen D (2018) Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: a population-based study. PLoS One 13(4):e0195413. https://doi.org/10.1371/journal.pone.0195413
Alaridah N, Hallback ET, Tangrot J, Winqvist N, Sturegard E, Floren-Johansson K, Jonsson B, Tenland E, Welinder-Olsson C, Medstrand P, Kaijser B, Godaly G (2019) Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden. Sci Rep 9(1):4931. https://doi.org/10.1038/s41598-019-39971-z
Guthrie JL, Strudwick L, Roberts B, Allen M, McFadzen J, Roth D, Jorgensen D, Rodrigues M, Tang P, Hanley B, Johnston J, Cook VJ, Gardy JL (2019) Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region. Epidemiol Infect 147:e188. https://doi.org/10.1017/S0950268819000670
Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, Tang P (2011) Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 364(8):730–739. https://doi.org/10.1056/NEJMoa1003176
Walker TM, Ip CLC, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ, Hawkey PM, Crook DW, Parkhill J, Harris D, Walker AS, Bowden R, Monk P, Smith EG, Peto TEA (2013) Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 13(2):137–146. https://doi.org/10.1016/s1473-3099(12)70277-3
Lee RS, Radomski N, Proulx JF, Levade I, Shapiro BJ, McIntosh F, Soualhine H, Menzies D, Behr MA (2015) Population genomics of Mycobacterium tuberculosis in the Inuit. Proc Natl Acad Sci U S A 112(44):13609–13614. https://doi.org/10.1073/pnas.1507071112
Glynn JR, Guerra-Assuncao JA, Houben RM, Sichali L, Mzembe T, Mwaungulu LK, Mwaungulu JN, McNerney R, Khan P, Parkhill J, Crampin AC, Clark TG (2015) Whole genome sequencing shows a low proportion of tuberculosis disease is attributable to known close contacts in rural Malawi. PLoS One 10(7):e0132840. https://doi.org/10.1371/journal.pone.0132840
Hatherell HA, Colijn C, Stagg HR, Jackson C, Winter JR, Abubakar I (2016) Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review. BMC Med 14:21. https://doi.org/10.1186/s12916-016-0566-x
Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, Harris SR, Niemann S, Diel R, Aseffa A, Gao Q, Young D, Gagneux S (2013) Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet 45(10):1176–1182. https://doi.org/10.1038/ng.2744
O'Neill MB, Shockey A, Zarley A, Aylward W, Eldholm V, Kitchen A, Pepperell CS (2019) Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia. Mol Ecol 28(13):3241–3256. https://doi.org/10.1111/mec.15120
Zink AR, Sola C, Reischl U, Grabner W, Rastogi N, Wolf H, Nerlich AG (2003) Characterization of Mycobacterium tuberculosis complex DNAs from Egyptian mummies by spoligotyping. J Clin Microbiol 41(1):359–367. https://doi.org/10.1128/jcm.41.1.359-367.2003
Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, Comas I, Forrest SA, Bryant JM, Harris SR, Schuenemann VJ, Campbell TJ, Majander K, Wilbur AK, Guichon RA, Wolfe Steadman DL, Cook DC, Niemann S, Behr MA, Zumarraga M, Bastida R, Huson D, Nieselt K, Young D, Parkhill J, Buikstra JE, Gagneux S, Stone AC, Krause J (2014) Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 514(7523):494–497. https://doi.org/10.1038/nature13591
Crispell J, Zadoks RN, Harris SR, Paterson B, Collins DM, de-Lisle GW, Livingstone P, Neill MA, Biek R, Lycett SJ, Kao RR, Price-Carter M (2017) Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand. BMC Genomics 18(1):180. https://doi.org/10.1186/s12864-017-3569-x
Crispell J, Benton CH, Balaz D, De Maio N, Ahkmetova A, Allen A, Biek R, Presho EL, Dale J, Hewinson G, Lycett SJ, Nunez-Garcia J, Skuce RA, Trewby H, Wilson DJ, Zadoks RN, Delahay RJ, Kao RR (2019) Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system. elife 8. https://doi.org/10.7554/eLife.45833
Merker M, Barbier M, Cox H, Rasigade JP, Feuerriegel S, Kohl TA, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Nubel U, Supply P, Wirth T, Niemann S (2018) Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia. elife 7. https://doi.org/10.7554/eLife.38200
Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, Blum MG, Rusch-Gerdes S, Mokrousov I, Aleksic E, Allix-Beguec C, Antierens A, Augustynowicz-Kopec E, Ballif M, Barletta F, Beck HP, Barry CE 3rd, Bonnet M, Borroni E, Campos-Herrero I, Cirillo D, Cox H, Crowe S, Crudu V, Diel R, Drobniewski F, Fauville-Dufaux M, Gagneux S, Ghebremichael S, Hanekom M, Hoffner S, Jiao WW, Kalon S, Kohl TA, Kontsevaya I, Lillebaek T, Maeda S, Nikolayevskyy V, Rasmussen M, Rastogi N, Samper S, Sanchez-Padilla E, Savic B, Shamputa IC, Shen A, Sng LH, Stakenas P, Toit K, Varaine F, Vukovic D, Wahl C, Warren R, Supply P, Niemann S, Wirth T (2015) Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet 47(3):242–249. https://doi.org/10.1038/ng.3195
Menardo F, Duchene S, Brites D, Gagneux S (2019) The molecular clock of Mycobacterium tuberculosis. PLoS Pathog 15(9):e1008067. https://doi.org/10.1371/journal.ppat.1008067
Folkvardsen DB, Norman A, Andersen AB, Michael Rasmussen E, Jelsbak L, Lillebaek T (2017) Genomic epidemiology of a major Mycobacterium tuberculosis outbreak: retrospective cohort study in a low-incidence setting using sparse time-series sampling. J Infect Dis 216(3):366–374. https://doi.org/10.1093/infdis/jix298
Stimson J, Gardy J, Mathema B, Crudu V, Cohen T, Colijn C (2019) Beyond the SNP threshold: identifying outbreak clusters using inferred transmissions. Mol Biol Evol 36(3):587–603. https://doi.org/10.1093/molbev/msy242
Fawzy A, Zschock M, Ewers C, Eisenberg T (2018) Genotyping methods and molecular epidemiology of Mycobacterium avium subsp. paratuberculosis (MAP). Int J Vet Sci Med 6(2):258–264. https://doi.org/10.1016/j.ijvsm.2018.08.001
Harris KA, Underwood A, Kenna DT, Brooks A, Kavaliunaite E, Kapatai G, Tewolde R, Aurora P, Dixon G (2015) Whole-genome sequencing and epidemiological analysis do not provide evidence for cross-transmission of Mycobacterium abscessus in a cohort of pediatric cystic fibrosis patients. Clin Infect Dis 60(7):1007–1016. https://doi.org/10.1093/cid/ciu967
Doyle RM, Rubio M, Dixon G, Hartley J, Klein N, Coll P, Harris KA (2019) Cross-transmission is not the source of new Mycobacterium abscessus infections in a multi-Centre cohort of cystic fibrosis patients. Clin Infect Dis 70(9):1855–1864. https://doi.org/10.1093/cid/ciz526
Nishiuchi Y, Iwamoto T, Maruyama F (2017) Infection sources of a common non-tuberculous mycobacterial pathogen, Mycobacterium avium Complex. Front Med (Lausanne) 4:27. https://doi.org/10.3389/fmed.2017.00027
Kreutzfeldt KM, McAdam PR, Claxton P, Holmes A, Seagar AL, Laurenson IF, Fitzgerald JR (2013) Molecular longitudinal tracking of Mycobacterium abscessus spp. during chronic infection of the human lung. PLoS One 8(5):e63237. https://doi.org/10.1371/journal.pone.0063237
Schuenemann VJ, Avanzi C, Krause-Kyora B, Seitz A, Herbig A, Inskip S, Bonazzi M, Reiter E, Urban C, Dangvard Pedersen D, Taylor GM, Singh P, Stewart GR, Veleminsky P, Likovsky J, Marcsik A, Molnar E, Palfi G, Mariotti V, Riga A, Belcastro MG, Boldsen JL, Nebel A, Mays S, Donoghue HD, Zakrzewski S, Benjak A, Nieselt K, Cole ST, Krause J (2018) Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe. PLoS Pathog 14(5):e1006997. https://doi.org/10.1371/journal.ppat.1006997
Mendum TA, Schuenemann VJ, Roffey S, Taylor GM, Wu H, Singh P, Tucker K, Hinds J, Cole ST, Kierzek AM, Nieselt K, Krause J, Stewart GR (2014) Mycobacterium leprae genomes from a British medieval leprosy hospital: towards understanding an ancient epidemic. BMC Genomics 15:270. https://doi.org/10.1186/1471-2164-15-270
Vandelannoote K, Meehan CJ, Eddyani M, Affolabi D, Phanzu DM, Eyangoh S, Jordaens K, Portaels F, Mangas K, Seemann T, Marsollier L, Marion E, Chauty A, Landier J, Fontanet A, Leirs H, Stinear TP, de Jong BC (2017) Multiple introductions and recent spread of the emerging human pathogen Mycobacterium ulcerans across Africa. Genome Biol Evol 9(3):414–426. https://doi.org/10.1093/gbe/evx003
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Riojas, M.A. et al. (2021). Identification and Characterization of Mycobacterial Species Using Whole-Genome Sequences. In: Parish, T., Kumar, A. (eds) Mycobacteria Protocols. Methods in Molecular Biology, vol 2314. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1460-0_19
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1460-0_19
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1459-4
Online ISBN: 978-1-0716-1460-0
eBook Packages: Springer Protocols