Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006;34(Database issue):D32–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mahillon J, Chandler M. Insertion sequences. Microbiol Mol Biol Rev. 1998;62:725–74.
PubMed Central
CAS
PubMed
Google Scholar
Siguier P, Gourbeyre E, Chandler M. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol Rev. 2014;38:865–91.
Article
CAS
PubMed
Google Scholar
Olliver A, Vallé M, Chaslus-Dancla E, Cloeckaert A. Overexpression of the multidrug efflux operon acrEF by insertional activation with IS1 or IS10 elements in Salmonella enterica serovar typhimurium DT204 acrB mutants selected with fluoroquinolones. Antimicrob Agents Chemother. 2005;49:289–301.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jellen-Ritter AS, Kern WV. Enhanced expression of the multidrug efflux pumps AcrAB and AcrEF associated with insertion element transposition in Escherichia coli mutants selected with a fluoroquinolone. Antimicrob Agents Chemother. 2001;45:1467–72.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hamidian M, Hall RM. ISAba1 targets a specific position upstream of the intrinsic ampC gene of Acinetobacter baumannii leading to cephalosporin resistance. J Antimicrob Chemother. 2013;68:2682–3.
Article
CAS
PubMed
Google Scholar
Hamidian M, Hancock DP, Hall RM. Horizontal transfer of an ISAba125-activated ampC gene between Acinetobacter baumannii strains leading to cephalosporin resistance. J Antimicrob Chemother. 2013;68:244–5.
Article
CAS
PubMed
Google Scholar
Hamidian M, Hall RM. Tn6168, a transposon carrying an ISAba1-activated ampC gene and conferring cephalosporin resistance in Acinetobacter baumannii. J Antimicrob Chemother. 2014;69:77–80.
Article
CAS
PubMed
Google Scholar
Soto CY, Menéndez MC, Pérez E, Samper S, Gómez AB, García MJ, et al. IS6110 mediates increased transcription of the phoP virulence gene in a multidrug-resistant clinical isolate responsible for tuberculosis outbreaks. J Clin Microbiol. 2004;42:212–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Uria MJ, Zhang Q, Li Y, Chan A, Exley RM, Gollan B, et al. A generic mechanism in Neisseria meningitidis for enhanced resistance against bactericidal antibodies. J Exp Med. 2008;205:1423–34.
Article
PubMed Central
CAS
PubMed
Google Scholar
Van Der Ploeg J, Willemsen M, Van Hall G, Janssen DB. Adaptation of Xanthobacter autotrophicus GJ10 to bromoacetate due to activation and mobilization of the haloacetate dehalogenase gene by insertion element IS1247. J Bacteriol. 1995;177:1348–56.
PubMed Central
PubMed
Google Scholar
Aronson BD, Levinthal M, Somerville RL. Activation of a cryptic pathway for threonine metabolism via specific IS3-mediated alteration of promoter structure in Escherichia coli. J Bacteriol. 1989;171:5503–11.
PubMed Central
CAS
PubMed
Google Scholar
Soria G, Barbé J, Gibert I. Molecular fingerprinting of Salmonella typhimurium by IS200-typing as a tool for epidemiological and evolutionary studies. Microbiologia. 1994;10:57–68.
CAS
PubMed
Google Scholar
Das S, Paramasivan CN, Lowrie DB, Prabhakar R, Narayanan PR. IS6110 restriction fragment length polymorphism typing of clinical isolates of Mycobacterium tuberculosis from patients with pulmonary tuberculosis in Madras, South India. Tuber Lung Dis. 1995;76:550–4.
Article
CAS
PubMed
Google Scholar
Bik EM, Gouw RD, Mooi FR. DNA fingerprinting of Vibrio cholerae strains with a novel insertion sequence element: a tool to identify epidemic strains. J Clin Microbiol. 1996;34:1453–61.
PubMed Central
CAS
PubMed
Google Scholar
Adams MD, Chan ER, Molyneaux ND, Bonomo RA. Genomewide analysis of divergence of antibiotic resistance determinants in closely related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 2010;54:3569–77.
Article
PubMed Central
CAS
PubMed
Google Scholar
Suzuki M, Matsumoto M, Hata M, Takahashi M, Sakae K. Development of a rapid PCR method using the insertion sequence IS1203 for genotyping Shiga toxin-producing Escherichia coli O157. J Clin Microbiol. 2004;42:5462–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Doig KD, Holt KE, Fyfe JA, Lavender CJ, Eddyani M, Portaels F, et al. On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer. BMC Genomics. 2012;13:258.
Article
PubMed Central
CAS
PubMed
Google Scholar
Doughty EL, Sergeant MJ, Adetifa I, Antonio M, Pallen MJ. Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ. 2014;2:e585.
Article
PubMed Central
PubMed
Google Scholar
Rizk G, Gouin A, Chikhi R, Lemaitre C. MindTheGap: integrated detection and assembly of short and long insertions. Bioinformatics. 2014;30:3451–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009;6:677–81.
Article
PubMed Central
CAS
PubMed
Google Scholar
Thung DT, de Ligt J, Vissers LE, Steehouwer M, Kroon M, de Vries P, et al. Mobster: accurate detection of mobile element insertions in next generation sequencing data. Genome Biol. 2014;15:488.
Article
PubMed Central
PubMed
Google Scholar
Robb SMC, Lu L, Valencia E, Burnette JM, Okumoto Y, Wessler SR, et al. The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice. G3. 2013;3:949–57.
Article
PubMed Central
PubMed
Google Scholar
Keane TM, Wong K, Adams DJ. RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics. 2013;29:389–90.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nakagome M, Solovieva E, Takahashi A, Yasue H, Hirochika H, Miyao A. Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements. BMC Bioinformatics. 2014;15:71.
Article
PubMed Central
PubMed
Google Scholar
Barrick JE, Colburn G, Deatherage DE, Traverse CC, Strand MD, Borges JJ, et al. Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics. 2014;15:1039.
Article
PubMed Central
PubMed
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed Central
PubMed
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2.
Article
PubMed Central
CAS
PubMed
Google Scholar
Faust GG, Hall IM. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics. 2014;30:2503–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.
Article
PubMed Central
PubMed
Google Scholar
Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill F-X, Goodhead I, et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet. 2008;40:987–93.
Article
PubMed Central
CAS
PubMed
Google Scholar
Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ, Tomita T, et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014;6:90.
Article
PubMed Central
PubMed
Google Scholar
Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M, Landraud L, Rolain J-M: ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 2014;58:212–20
McEvoy CRE, Falmer AA, van Pittius NCG, Victor TC, van Helden PD, Warren RM. The role of IS6110 in the evolution of Mycobacterium tuberculosis. Tuberculosis. 2007;87:393–404.
Article
CAS
PubMed
Google Scholar
van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol. 1993;31:406–9.
PubMed Central
PubMed
Google Scholar
Beggs ML, Eisenach KD, Cave MD. Mapping of IS6110 insertion sites in two epidemic strains of Mycobacterium tuberculosis. J Clin Microbiol. 2000;38:2923–8.
PubMed Central
CAS
PubMed
Google Scholar
Alonso H, Aguilo JI, Samper S, Caminero JA, Campos-Herrero MI, Gicquel B, et al. Deciphering the role of IS6110 in a highly transmissible Mycobacterium tuberculosis Beijing strain, GC1237. Tuberculosis. 2011;91:117–26.
Article
CAS
PubMed
Google Scholar
Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet. 2013;45:1176–82.
Article
PubMed Central
CAS
PubMed
Google Scholar
Holt KE, Thieu Nga TV, Thanh DP, Vinh H, Kim DW, Vu Tra MP, et al. Tracking the establishment of local endemic populations of an emergent enteric pathogen. Proc Natl Acad Sci U S A. 2013;110:17522–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Assis PA, Espíndola MS, Paula-Silva FW, Rios WM, Pereira PA, Leão SC, et al. Mycobacterium tuberculosis expressing phospholipase C subverts PGE2 synthesis and induces necrosis and alevolar macrophages. BMC Microbiol. 2014;14:128.
Article
PubMed Central
PubMed
Google Scholar
Vera-Cabrera L, Hernández-Vera MA, Welsh O, Johnson WM, Castro-Garza J. Phospholipase region of Mycobacterium tuberculosis is a preferential locus for IS6110 transposition. J Clin Microbiol. 2001;39:3499–504.
Article
PubMed Central
CAS
PubMed
Google Scholar