Abstract
A comprehensive understanding of genotype-phenotype links in bacteria is the primary theme of bacterial functional genomics. Transposon sequencing (Tn-seq) or its equivalent methods that combine random transposon mutagenesis and next-generation sequencing (NGS) represent a powerful approach to understand gene functions in bacteria on a genome-wide scale. This approach has been utilized in a variety of bacterial species to provide comprehensive information on gene functions related to various phenotypes or biological processes of significance. With further improvements in the molecular protocol for specific amplification of transposon junction sequences and increasing capacity of next generation sequencing technologies, the applications of Tn-seq have been expanding to tackle questions that are important yet difficult to address in the past. In this review, we will discuss the technical aspects of different Tn-seq methods along with their pros and cons to provide a helpful guidance for those who want to implement or improve Tn-seq for their own research projects. In addition, we also provide a comprehensive summary of recent published studies based on Tn-seq methods to give an updated perspective on the current and emerging applications of Tn-seq.
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Ates LS, Ummels R, Commandeur S, van der Weerd R, Sparrius M, Weerdenburg E, Alber M, Kalscheuer R, Piersma SR, Abdallah AM, Abd El Ghany M, Abdel-Haleem AM, Pain A, Jiménez CR, Bitter W, Houben EN (2015) Essential role of the ESX-5 secretion system in outer membrane permeability of pathogenic mycobacteria. PLoS Genet 11(5):e1005190. doi:10.1371/journal.pgen.1005190
Bachman MA, Breen P, Deornellas V, Mu Q, Zhao L, Wu W, Cavalcoli JD, Mobley HL (2015) Genome-wide identification of Klebsiella pneumoniae fitness genes during lung infection. MBio 6(3):e00775. doi:10.1128/mBio.00775-15
Barquist L, Boinett CJ, Cain AK (2013a) Approaches to querying bacterial genomes with transposon-insertion sequencing. RNA Biol 10(7):1161–9. doi:10.4161/rna.24765
Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP (2013b) A comparison of dense transposon insertion libraries in the Salmonella serovars typhi and typhimurium. Nucleic Acids Res 41(8):4549–64. doi:10.1093/nar/gkt148
Brooks JF, Gyllborg MC, Cronin DC, Quillin SJ, Mallama CA, Foxall R, Whistler C, Goodman AL, Mandel MJ (2014) Global discovery of colonization determinants in the squid symbiont Vibrio fischeri. Proc Natl Acad Sci U S A 111(48):17284–9. doi:10.1073/pnas.1415957111
Brutinel ED, Gralnick JA (2012) Anomalies of the anaerobic tricarboxylic acid cycle in Shewanella oneidensis revealed by Tn-seq. Mol Microbiol 86(2):273–83. doi:10.1111/j.1365-2958.2012.08196.x
Burghout P, Zomer A, van der Gaast-de Jongh CE, Janssen-Megens EM, Françoijs KJ, Stunnenberg HG, Hermans PW (2013) Streptococcus pneumoniae folate biosynthesis responds to environmental CO2 levels. J Bacteriol 195(7):1573–82. doi:10.1128/JB.01942-12
Byrne RT, Chen SH, Wood EA, Cabot EL, Cox MM (2014) Escherichia coli genes and pathways involved in surviving extreme exposure to ionizing radiation. J Bacteriol 196(20):3534–45. doi:10.1128/JB.01589-14
Carter R, Wolf J, van Opijnen T, Muller M, Obert C, Burnham C, Mann B, Li Y, Hayden RT, Pestina T, Persons D, Camilli A, Flynn PM, Tuomanen EI, Rosch JW (2014) Genomic analyses of pneumococci from children with sickle cell disease expose host-specific bacterial adaptations and deficits in current interventions. Cell Host Microbe 15(5):587–99. doi:10.1016/j.chom.2014.04.005
Chaudhuri RR, Morgan E, Peters SE, Pleasance SJ, Hudson DL, Davies HM, Wang J, van Diemen PM, Buckley AM, Bowen AJ, Pullinger GD, Turner DJ, Langridge GC, Turner AK, Parkhill J, Charles IG, Maskell DJ, Stevens MP (2013) Comprehensive assignment of roles for Salmonella typhimurium genes in intestinal colonization of food-producing animals. PLoS Genet 9(4):e1003456. doi:10.1371/journal.pgen.1003456
Christen B, Abeliuk E, Collier JM, Kalogeraki VS, Passarelli B, Coller JA, Fero MJ, McAdams HH, Shapiro L (2011) The essential genome of a bacterium. Mol Syst Biol 7:528. doi:10.1038/msb.2011.58
Christiansen MT, Kaas RS, Chaudhuri RR, Holmes MA, Hasman H, Aarestrup FM (2014) Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus sequence type 398 survival. PLoS One 9(2):e89018. doi:10.1371/journal.pone.0089018
Cullen TW, Schofield WB, Barry NA, Putnam EE, Rundell EA, Trent MS, Degnan PH, Booth CJ, Yu H, Goodman AL (2015) Gut microbiota. Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation. Science 347(6218):170–5. doi:10.1126/science.1260580
Dawoud TM, Jiang T, Mandal RK, Ricke SC, Kwon YM (2014) Improving the efficiency of transposon mutagenesis in Salmonella enteritidis by overcoming host-restriction barriers. Mol Biotechnol 56(11):1004–10. doi:10.1007/s12033-014-9779-4
de Lorenzo V, Timmis KN (1994) Analysis and construction of stable phenotypes in gram-negative bacteria with Tn5- and Tn10-derived minitransposons. Methods Enzymol 235:386–405
de Vries SP, Eleveld MJ, Hermans PW, Bootsma HJ (2013) Characterization of the molecular interplay between Moraxella catarrhalis and human respiratory tract epithelial cells. PLoS One 8(8):e72193. doi:10.1371/journal.pone.0072193
de Vries SP, Rademakers RJ, van der Gaast-de Jongh CE, Eleveld MJ, Hermans PW, Bootsma HJ (2014) Deciphering the genetic basis of Moraxella catarrhalis complement resistance: a critical role for the disulphide bond formation system. Mol Microbiol 91(3):522–37. doi:10.1111/mmi.12475
Dembek M, Barquist L, Boinett CJ, Cain AK, Mayho M, Lawley TD, Fairweather NF, Fagan RP (2015) High-throughput analysis of gene essentiality and sporulation in Clostridium difficile. MBio 6(2):e02383. doi:10.1128/mBio.02383-14
Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C (2009) Systematic map** of genetic interaction networks. Annu Rev Genet 43:601–25. doi:10.1146/annurev.genet.39.073003.114751
Dong TG, Ho BT, Yoder-Himes DR, Mekalanos JJ (2013) Identification of T6SS-dependent effector and immunity proteins by Tn-seq in Vibrio cholerae. Proc Natl Acad Sci U S A 110(7):2623–8. doi:10.1073/pnas.1222783110
Eckert SE, Dziva F, Chaudhuri RR, Langridge GC, Turner DJ, Pickard DJ, Maskell DJ, Thomson NR, Stevens MP (2011) Retrospective application of transposon-directed insertion site sequencing to a library of signature-tagged mini-Tn5Km2 mutants of Escherichia coli O157:H7 screened in cattle. J Bacteriol 193(7):1771–6. doi:10.1128/JB.01292-10
Feaga HA, Viollier PH, Keiler KC (2014) Release of nonstop ribosomes is essential. MBio 5(6):e01916. doi:10.1128/mBio.01916-14
Febrer M, McLay K, Caccamo M, Twomey KB, Ryan RP (2011) Advances in bacterial transcriptome and transposon insertion-site profiling using second-generation sequencing. Trends Biotechnol 29(11):586–94. doi:10.1016/j.tibtech.2011.06.004
Fu Y, Waldor MK, Mekalanos JJ (2013) Tn-Seq analysis of Vibrio cholerae intestinal colonization reveals a role for T6SS-mediated antibacterial activity in the host. Cell Host Microbe 14(6):652–63. doi:10.1016/j.chom.2013.11.001
Gallagher LA, Shendure J, Manoil C (2011) Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq. MBio 2(1):e00315–10. doi:10.1128/mBio.00315-10
Gallagher LA, Ramage E, Weiss EJ, Radey M, Hayden HS, Held KG, Huse HK, Zurawski DV, Brittnacher MJ, Manoil C (2015) Resources for genetic and genomic analysis of emerging pathogen Acinetobacter baumannii. J Bacteriol. doi:10.1128/JB.00131-15
Gao B, Lara-Tejero M, Lefebre M, Goodman AL, Galán JE (2014) Novel components of the flagellar system in epsilonproteobacteria. MBio 5(3):e01349–14. doi:10.1128/mBio.01349-14
Gawronski JD, Wong SM, Giannoukos G, Ward DV, Akerley BJ (2009) Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung. Proc Natl Acad Sci U S A 106(38):16422–7. doi:10.1073/pnas.0906627106
Girgis HS, Liu Y, Ryu WS, Tavazoie S (2007) A comprehensive genetic characterization of bacterial motility. PLoS Genet 3(9):1644–60. doi:10.1371/journal.pgen.0030154
Goodarzi H, Hottes AK, Tavazoie S (2009) Global discovery of adaptive mutations. Nat Methods 6(8):581–3. doi:10.1038/nmeth.1352
Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI (2009) Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 6(3):279–89. doi:10.1016/j.chom.2009.08.003
Goryshin IY, Jendrisak J, Hoffman LM, Meis R, Reznikoff WS (2000) Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes. Nat Biotechnol 18(1):97–100. doi:10.1038/72017
Griffin JE, Gawronski JD, Dejesus MA, Ioerger TR, Akerley BJ, Sassetti CM (2011) High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. PLoS Pathog 7(9):e1002251. doi:10.1371/journal.ppat.1002251
Hayes F (2003) Transposon-based strategies for microbial functional genomics and proteomics. Annu Rev Genet 37:3–29. doi:10.1146/annurev.genet.37.110801.142807
Hendrixson DR, Akerley BJ, DiRita VJ (2001) Transposon mutagenesis of Campylobacter jejuni identifies a bipartite energy taxis system required for motility. Mol Microbiol 40(1):214–24
Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St Onge RP, Tyers M, Koller D, Altman RB, Davis RW, Nislow C, Giaever G (2008) The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320(5874):362–5. doi:10.1126/science.1150021
Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, Fraser CM, Smith HO, Venter JC (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286(5447):2165–9
Johnson CM, Grossman AD (2014) Identification of host genes that affect acquisition of an integrative and conjugative element in Bacillus subtilis. Mol Microbiol 93(6):1284–301. doi:10.1111/mmi.12736
Johnson JG, Livny J, Dirita VJ (2014) High-throughput sequencing of Campylobacter jejuni insertion mutant libraries reveals mapA as a fitness factor for chicken colonization. J Bacteriol 196(11):1958–67. doi:10.1128/JB.01395-13
Joshi SM, Pandey AK, Capite N, Fortune SM, Rubin EJ, Sassetti CM (2006) Characterization of mycobacterial virulence genes through genetic interaction map**. Proc Natl Acad Sci U S A 103(31):11760–5. doi:10.1073/pnas.0603179103
Kalamorz F, Reichenbach B, März W, Rak B, Görke B (2007) Feedback control of glucosamine-6-phosphate synthase GlmS expression depends on the small RNA GlmZ and involves the novel protein YhbJ in Escherichia coli. Mol Microbiol 65(6):1518–33. doi:10.1111/j.1365-2958.2007.05888.x
Kamp HD, Patimalla-Dipali B, Lazinski DW, Wallace-Gadsden F, Camilli A (2013) Gene fitness landscapes of Vibrio cholerae at important stages of its life cycle. PLoS Pathog 9(12):e1003800. doi:10.1371/journal.ppat.1003800
Khatiwara A, Jiang T, Sung SS, Dawoud T, Kim JN, Bhattacharya D, Kim HB, Ricke SC, Kwon YM (2012) Genome scanning for conditionally essential genes in Salmonella enterica serotype typhimurium. Appl Environ Microbiol 78(9):3098–107. doi:10.1128/AEM.06865-11
Klein BA, Tenorio EL, Lazinski DW, Camilli A, Duncan MJ, Hu LT (2012) Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis. BMC Genomics 13:578. doi:10.1186/1471-2164-13-578
Knierim E, Lucke B, Schwarz JM, Schuelke M, Seelow D (2011) Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing. PLoS One 6(11):e28240. doi:10.1371/journal.pone.0028240
Langereis JD, Weiser JN (2014) Shielding of a lipooligosaccharide IgM epitope allows evasion of neutrophil-mediated killing of an invasive strain of nontypeable Haemophilus influenzae. MBio 5(4):e01478–14. doi:10.1128/mBio.01478-14
Langereis JD, Zomer A, Stunnenberg HG, Burghout P, Hermans PW (2013) Nontypeable Haemophilus influenzae carbonic anhydrase is important for environmental and intracellular survival. J Bacteriol 195(12):2737–46. doi:10.1128/JB.01870-12
Langridge GC, Phan MD, Turner DJ, Perkins TT, Parts L, Haase J, Charles I, Maskell DJ, Peters SE, Dougan G, Wain J, Parkhill J, Turner AK (2009) Simultaneous assay of every Salmonella typhi gene using one million transposon mutants. Genome Res 19(12):2308–16. doi:10.1101/gr.097097.109
Lazinski DW, Camilli A (2013) Homopolymer tail-mediated ligation PCR: a streamlined and highly efficient method for DNA cloning and library construction. Biotechniques 54(1):25–34. doi:10.2144/000113981
Le Breton Y, Belew AT, Valdes KM, Islam E, Curry P, Tettelin H, Shirtliff ME, El-Sayed NM, McIver KS (2015) Essential genes in the core genome of the human pathogen Streptococcus pyogenes. Sci Rep 5:9838. doi:10.1038/srep09838
Lee SA, Gallagher LA, Thongdee M, Staudinger BJ, Lippman S, Singh PK, Manoil C (2015) General and condition-specific essential functions of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 112(16):5189–94. doi:10.1073/pnas.1422186112
Maloy SR (2007) Use of antibiotic-resistant transposons for mutagenesis. Methods Enzymol 421:11–7. doi:10.1016/S0076-6879(06)21002-4
Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ, Ridout G, Camilli A, Tuomanen EI, Rosch JW (2012) Control of virulence by small RNAs in Streptococcus pneumoniae. PLoS Pathog 8(7):e1002788. doi:10.1371/journal.ppat.1002788
Martínez-García E, Calles B, Arévalo-Rodríguez M, de Lorenzo V (2011) pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes. BMC Microbiol 11:38. doi:10.1186/1471-2180-11-38
Mazurkiewicz P, Tang CM, Boone C, Holden DW (2006) Signature-tagged mutagenesis: barcoding mutants for genome-wide screens. Nat Rev Genet 7(12):929–39. doi:10.1038/nrg1984
McDonough E, Lazinski DW, Camilli A (2014) Identification of in vivo regulators of the Vibrio cholerae xds gene using a high-throughput genetic selection. Mol Microbiol 92(2):302–15. doi:10.1111/mmi.12557
Merrell DS, Camilli A (2002) Information overload: assigning genetic functionality in the age of genomics and large-scale screening. Trends Microbiol 10(12):571–4
Moule MG, Hemsley CM, Seet Q, Guerra-Assunção JA, Lim J, Sarkar-Tyson M, Clark TG, Tan PB, Titball RW, Cuccui J, Wren BW (2014) Genome-wide saturation mutagenesis of Burkholderia pseudomallei K96243 predicts essential genes and novel targets for antimicrobial development. MBio 5(1):e00926–13. doi:10.1128/mBio.00926-13
Palace SG, Proulx MK, Lu S, Baker RE, Goguen JD (2014) Genome-wide mutant fitness profiling identifies nutritional requirements for optimal growth of Yersinia pestis in deep tissue. MBio 5(4):e01385–14. doi:10.1128/mBio.01385-14
Phan MD, Peters KM, Sarkar S, Lukowski SW, Allsopp LP, Gomes Moriel D, Achard ME, Totsika M, Marshall VM, Upton M, Beatson SA, Schembri MA (2013) The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli clone. PLoS Genet 9(10):e1003834. doi:10.1371/journal.pgen.1003834
Phan MD, Forde BM, Peters KM, Sarkar S, Hancock S, Stanton-Cook M, Ben Zakour NL, Upton M, Beatson SA, Schembri MA (2015) Molecular characterization of a multidrug resistance IncF plasmid from the globally disseminated Escherichia coli ST131 clone. PLoS One 10(4):e0122369. doi:10.1371/journal.pone.0122369
Pickard D, Kingsley RA, Hale C, Turner K, Sivaraman K, Wetter M, Langridge G, Dougan G (2013) A genomewide mutagenesis screen identifies multiple genes contributing to Vi capsular expression in Salmonella enterica serovar typhi. J Bacteriol 195(6):1320–6. doi:10.1128/JB.01632-12
Reid AN, Pandey R, Palyada K, Whitworth L, Doukhanine E, Stintzi A (2008) Identification of Campylobacter jejuni genes contributing to acid adaptation by transcriptional profiling and genome-wide mutagenesis. Appl Environ Microbiol 74(5):1598–612. doi:10.1128/AEM.01508-07
Roggo C, Coronado E, Moreno-Forero SK, Harshman K, Weber J, van der Meer JR (2013) Genome-wide transposon insertion scanning of environmental survival functions in the polycyclic aromatic hydrocarbon degrading bacterium Sphingomonas wittichii RW1. Environ Microbiol 15(10):2681–95. doi:10.1111/1462-2920.12125
Rohmer L, Hocquet D, Miller SI (2011) Are pathogenic bacteria just looking for food? Metabolism and microbial pathogenesis. Trends Microbiol 19(7):341–8. doi:10.1016/j.tim.2011.04.003
Roux D, Danilchanka O, Guillard T, Cattoir V, Aschard H, Fu Y, Angoulvant F, Messika J, Ricard JD, Mekalanos JJ, Lory S, Pier GB, Skurnik D (2015) Fitness cost of antibiotic susceptibility during bacterial infection. Sci Transl Med 7(297):297ra114. doi:10.1126/scitranslmed.aab1621
Santa Maria JP, Sadaka A, Moussa SH, Brown S, Zhang YJ, Rubin EJ, Gilmore MS, Walker S (2014) Compound-gene interaction map** reveals distinct roles for Staphylococcus aureus teichoic acids. Proc Natl Acad Sci U S A 111(34):12510–5. doi:10.1073/pnas.1404099111
Santiago M, Matano LM, Moussa SH, Gilmore MS, Walker S, Meredith TC (2015) A new platform for ultra-high density Staphylococcus aureus transposon libraries. BMC Genomics 16:252. doi:10.1186/s12864-015-1361-3
Sarmiento F, Mrázek J, Whitman WB (2013) Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis. Proc Natl Acad Sci U S A 110(12):4726–31. doi:10.1073/pnas.1220225110
Sassetti C, Rubin EJ (2002) Genomic analyses of microbial virulence. Curr Opin Microbiol 5(1):27–32
Sassetti CM, Rubin EJ (2003) Genetic requirements for mycobacterial survival during infection. Proc Natl Acad Sci U S A 100(22):12989–94. doi:10.1073/pnas.2134250100
Sassetti CM, Boyd DH, Rubin EJ (2001) Comprehensive identification of conditionally essential genes in mycobacteria. Proc Natl Acad Sci U S A 98(22):12712–7. doi:10.1073/pnas.231275498
Shan Y, Lazinski D, Rowe S, Camilli A, Lewis K (2015) Genetic basis of persister tolerance to aminoglycosides in Escherichia coli. MBio 6(2):e00078–15. doi:10.1128/mBio.00078-15
Sharma CM, Vogel J (2009) Experimental approaches for the discovery and characterization of regulatory small RNA. Curr Opin Microbiol 12(5):536–46. doi:10.1016/j.mib.2009.07.006
Skurnik D, Roux D, Aschard H, Cattoir V, Yoder-Himes D, Lory S, Pier GB (2013) A comprehensive analysis of in vitro and in vivo genetic fitness of Pseudomonas aeruginosa using high-throughput sequencing of transposon libraries. PLoS Pathog 9(9):e1003582. doi:10.1371/journal.ppat.1003582
Subashchandrabose S, Smith SN, Spurbeck RR, Kole MM, Mobley HL (2013) Genome-wide detection of fitness genes in uropathogenic Escherichia coli during systemic infection. PLoS Pathog 9(12):e1003788. doi:10.1371/journal.ppat.1003788
Turner KH, Wessel AK, Palmer GC, Murray JL, Whiteley M (2015) Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum. Proc Natl Acad Sci U S A 112(13):4110–5. doi:10.1073/pnas.1419677112
Valentino MD, Foulston L, Sadaka A, Kos VN, Villet RA, Santa Maria J, Lazinski DW, Camilli A, Walker S, Hooper DC, Gilmore MS (2014) Genes contributing to Staphylococcus aureus fitness in abscess- and infection-related ecologies. MBio 5(5):e01729–14. doi:10.1128/mBio.01729-14
van Opijnen T, Camilli A (2012) A fine scale phenotype-genotype virulence map of a bacterial pathogen. Genome Res. doi:10.1101/gr.137430.112
van Opijnen T, Camilli A (2013) Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nat Rev Microbiol 11(7):435–42. doi:10.1038/nrmicro3033
van Opijnen T, Bodi KL, Camilli A (2009) Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat Methods 6(10):767–72. doi:10.1038/nmeth.1377
Wang N, Ozer EA, Mandel MJ, Hauser AR (2014) Genome-wide identification of Acinetobacter baumannii genes necessary for persistence in the lung. MBio 5(3):e01163–14. doi:10.1128/mBio.01163-14
Wang Q, Millet YA, Chao MC, Sasabe J, Davis BM, Waldor MK (2015) A genome-wide screen reveals that the Vibrio cholerae phosphoenolpyruvate phosphotransferase system modulates virulence gene expression. Infect Immun 83(9):3381–95. doi:10.1128/IAI.00411-15
Watson M (2014) Illuminating the future of DNA sequencing. Genome Biol 15(2):108. doi:10.1186/gb4165
Weerdenburg EM, Abdallah AM, Rangkuti F, Abd El Ghany M, Otto TD, Adroub SA, Molenaar D, Ummels R, Ter Veen K, van Stempvoort G, van der Sar AM, Ali S, Langridge GC, Thomson NR, Pain A, Bitter W (2015) Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts. Infect Immun 83(5):1778–88. doi:10.1128/IAI.03050-14
Wetmore KM, Price MN, Waters RJ, Lamson JS, He J, Hoover CA, Blow MJ, Bristow J, Butland G, Arkin AP, Deutschbauer A (2015) Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. MBio 6(3):e00306–15. doi:10.1128/mBio.00306-15
Wong SM, Gawronski JD, Lapointe D, Akerley BJ (2011) High-throughput insertion tracking by deep sequencing for the analysis of bacterial pathogens. Methods Mol Biol 733:209–22. doi:10.1007/978-1-61779-089-8_15
Wong SM, Bernui M, Shen H, Akerley BJ (2013) Genome-wide fitness profiling reveals adaptations required by Haemophilus in coinfection with influenza a virus in the murine lung. Proc Natl Acad Sci U S A 110(38):15413–8. doi:10.1073/pnas.1311217110
Wu M, McNulty NP, Rodionov DA, Khoroshkin MS, Griffin NW, Cheng J, Latreille P, Kerstetter RA, Terrapon N, Henrissat B, Osterman AL, Gordon JI (2015) Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Science 350 (6256). doi:10.1126/science.aac5992
Yamaichi Y, Chao MC, Sasabe J, Clark L, Davis BM, Yamamoto N, Mori H, Kurokawa K, Waldor MK (2015) High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4. Nucleic Acids Res 43(1):348–60. doi:10.1093/nar/gku1262
Yung MC, Park DM, Overton KW, Blow MJ, Hoover CA, Smit J, Murray SR, Ricci DP, Christen B, Bowman GR, Jiao Y (2015) Transposon mutagenesis paired with deep sequencing of Caulobacter crescentus under uranium stress reveals genes essential for detoxification and stress tolerance. J Bacteriol 197(19):3160–72. doi:10.1128/JB.00382-15
Zhang YJ, Ioerger TR, Huttenhower C, Long JE, Sassetti CM, Sacchettini JC, Rubin EJ (2012) Global assessment of genomic regions required for growth in Mycobacterium tuberculosis. PLoS Pathog 8(9):e1002946. doi:10.1371/journal.ppat.1002946
Zhang YJ, Reddy MC, Ioerger TR, Rothchild AC, Dartois V, Schuster BM, Trauner A, Wallis D, Galaviz S, Huttenhower C, Sacchettini JC, Behar SM, Rubin EJ (2013) Tryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing. Cell 155(6):1296–308. doi:10.1016/j.cell.2013.10.045
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Kwon, Y.M., Ricke, S.C. & Mandal, R.K. Transposon sequencing: methods and expanding applications. Appl Microbiol Biotechnol 100, 31–43 (2016). https://doi.org/10.1007/s00253-015-7037-8
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DOI: https://doi.org/10.1007/s00253-015-7037-8