Integrative and conjugative elements of Pasteurella multocida: Prevalence and signatures in population evolution

References

• Wilkie IW, Harper M, Boyce JD, et al. Pasteurella multocida: diseases and pathogenesis. Curr Top Microbiol Immunol. 2012;361:1–16.
   PubMed Web of Science ®Google Scholar
• Boyce JD, Seemann T, Adler B, et al. Pathogenomics of Pasteurella multocida. Curr Top Microbiol Immunol. 2012;361:23.
   PubMed Web of Science ®Google Scholar
• Dziva F, Muhairwa AP, Bisgaard M, et al. Diagnostic and typing options for investigating diseases associated with Pasteurella multocida. Vet Microbiol. 2008;128(1–2):1–22. doi: 10.1016/j.vetmic.2007.10.018
   PubMed Web of Science ®Google Scholar
• Kubatzky KF. Pasteurella multocida and immune cells. Curr Top Microbiol Immunol. 2012;361(361):53–72.
   PubMedGoogle Scholar
• Wozniak RA, Waldor MK. Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nature Rev Microbiol. 2010;8(8):552–563. doi: 10.1038/nrmicro2382
   PubMed Web of Science ®Google Scholar
• Bellanger X, Payot S, Leblond-Bourget N, et al. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. FEMS Microbiol Rev. 2014;38(4):720–760. doi: 10.1111/1574-6976.12058
   PubMed Web of Science ®Google Scholar
• Ryan MP, Carraro N, Slattery S, et al. Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria. Critical Reviews In Microbiology. 2023(1):1–22. doi: 10.1080/1040841X.2022.2161870
   Google Scholar
• Johnson CM, Grossman AD. Integrative and conjugative elements (ICEs): what they do and how they work. Ann Rev Genet. 2015;49(1):577–601. doi: 10.1146/annurev-genet-112414-055018
   PubMedGoogle Scholar
• Botelho J, Schulenburg H. The role of integrative and conjugative elements in antibiotic resistance evolution. Trends Microbiol. 2021;29(1):8–18. doi: 10.1016/j.tim.2020.05.011
   PubMed Web of Science ®Google Scholar
• Te Poele EM, Bolhuis H, Dijkhuizen L. Actinomycete integrative and conjugative elements. Antonie Van Leeuwenhoek. 2008;94(1):127–143. doi: 10.1007/s10482-008-9255-x
   PubMed Web of Science ®Google Scholar
• Haenni M, Lupo A, Madec JY, et al. Antimicrobial Resistance in Streptococcus spp. Microbiol Spectr. 2018;6(2). doi: 10.1128/microbiolspec.ARBA-0008-2017
   Web of Science ®Google Scholar
• Russo TA, Marr CM. Hypervirulent Klebsiella pneumoniae. Clin Microbiol Rev. 2019;32(3). doi: 10.1128/CMR.00001-19
   PubMed Web of Science ®Google Scholar
• Botelho J, Grosso F, Peixe L. Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution. Drug Resist Updat. 2019;44:100640. doi: 10.1016/j.drup.2019.07.002
   PubMed Web of Science ®Google Scholar
• Weaver KE, Fischetti VA, Novick RP, et al. Enterococcal Genetics. Microbiol Spectr. 2019;7(2). doi: 10.1128/microbiolspec.GPP3-0055-2018
   PubMed Web of Science ®Google Scholar
• Spagnoletti M, Ceccarelli D, Rieux A, et al. Acquisition and evolution of SXT-R391 integrative conjugative elements in the seventh-pandemic Vibrio cholerae lineage. MBio. 2014;5(4). doi: 10.1128/mBio.01356-14
   PubMed Web of Science ®Google Scholar
• Michael GB, Kadlec K, Sweeney MT, et al. ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer. J Antimicrob Chemother. 2012;67(1):91–100. doi: 10.1093/jac/dkr411
   PubMed Web of Science ®Google Scholar
• Schink AK, Hanke D, Semmler T, et al. Novel multiresistance-mediating integrative and conjugative elements carrying unusual antimicrobial resistance genes in Mannheimia haemolytica and Pasteurella multocida. J Antimicrob Chemother. 2022;77(7):2033–2035. doi: 10.1093/jac/dkac116
   PubMed Web of Science ®Google Scholar
• Klima CL, Zaheer R, Cook SR, et al. Pathogens of bovine respiratory disease in North American feedlots conferring multidrug resistance via integrative conjugative elements. J Clin Microbiol. 2014;52(2):438. doi: 10.1128/JCM.02485-13
   PubMed Web of Science ®Google Scholar
• Moustafa AM, Seemann T, Gladman S, et al. Comparative genomic analysis of Asian haemorrhagic septicaemia-associated strains of Pasteurella multocida identifies more than 90 haemorrhagic Septicaemia-Specific Genes. PLOS ONE. 2015;10(7):1–16. doi: 10.1371/journal.pone.0130296
   Web of Science ®Google Scholar
• Peng Z, Liang W, Wang Y, et al. Experimental pathogenicity and complete genome characterization of a pig origin Pasteurella multocida serogroup F isolate HN07. Vet Microbiol. 2017;198:23–33. doi: 10.1016/j.vetmic.2016.11.028
   PubMed Web of Science ®Google Scholar
• Delavat F, Miyazaki R, Carraro N, et al. The hidden life of integrative and conjugative elements. FEMS Microbiol Rev. 2017;41(4):512–537. doi: 10.1093/femsre/fux008
   PubMed Web of Science ®Google Scholar
• He J, Sun L, Zhang L, et al. A novel SXT/R391 Integrative and conjugative element carries two copies of the bla NDM-1 gene in Proteus mirabilis. mSphere. 2021;6(4):e0058821. doi: 10.1128/mSphere.00588-21
   PubMed Web of Science ®Google Scholar
• Cury J, Oliveira PH, De La Cruz F, et al. Host range and genetic plasticity explain the coexistence of integrative and extrachromosomal mobile genetic elements. Mol Biol Evol. 2018;35(9):2230–2239. doi: 10.1093/molbev/msy123
   PubMed Web of Science ®Google Scholar
• Korostin D, Kulemin N, Naumov V, et al. Comparative analysis of novel MGISEQ-2000 sequencing platform vs Illumina HiSeq 2500 for whole-genome sequencing. PLoS One. 2020;15(3):e0230301. doi: 10.1371/journal.pone.0230301
   PubMed Web of Science ®Google Scholar
• Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware detection and correction of sequencing errors. Genome Bio. 2010;11(11):R116. doi: 10.1186/gb-2010-11-11-r116
   PubMed Web of Science ®Google Scholar
• Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–477. doi: 10.1089/cmb.2012.0021
   PubMed Web of Science ®Google Scholar
• Parks DH, Imelfort M, Skennerton CT, et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043–1055. doi: 10.1101/gr.186072.114
   PubMed Web of Science ®Google Scholar
• Subaaharan S, Blackall LL, Blackall PJ. Development of a multi-locus sequence typing scheme for avian isolates of Pasteurella multocida. Veterinary Microbiology. 2010;141(3–4):354–361. doi: 10.1016/j.vetmic.2010.01.017
   PubMed Web of Science ®Google Scholar
• Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.Org website and their applications. Wellcome Open Res. 2018;3:124. doi: 10.12688/wellcomeopenres.14826.1
   PubMedGoogle Scholar
• Larsen MV, Cosentino S, Rasmussen S, et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012;50(4):1355–1361. doi: 10.1128/JCM.06094-11
   PubMed Web of Science ®Google Scholar
• Townsend KM, Boyce JD, Jing YC, et al. Genetic organization of Pasteurella multocida cap Loci and development of a multiplex capsular PCR typing system. J Clin Microbiol. 2001;39(3):924–929. doi: 10.1128/JCM.39.3.924-929.2001
   PubMed Web of Science ®Google Scholar
• Harper M, John M, Turni C, et al. Development of a rapid multiplex PCR assay to genotype Pasteurella multocida strains by use of the lipopolysaccharide outer core biosynthesis locus. J Clin Microbiol. 2015;53(2):477–485. doi: 10.1128/JCM.02824-14
   PubMed Web of Science ®Google Scholar
• Bertelli C, Laird MR, Williams KP, et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 2017;45(W1):W30–W35. doi: 10.1093/nar/gkx343
   PubMed Web of Science ®Google Scholar
• Liu M, Li X, Xie Y, et al. ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Res. 2019;47(D1):D660–D665. doi: 10.1093/nar/gky1123
   PubMed Web of Science ®Google Scholar
• Darling AC, Mau B, Blattner FR, et al. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14(7):1394–1403. doi: 10.1101/gr.2289704
   PubMed Web of Science ®Google Scholar
• Ball P. Chemistry: Perkin, the mauve maker. Nature. 2006;440(7083):429. doi: 10.1038/440429a
   PubMed Web of Science ®Google Scholar
• Darling AE, Mau B, Perna NT, et al. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLOS ONE. 2010;5(6):e11147. doi: 10.1371/journal.pone.0011147
   PubMed Web of Science ®Google Scholar
• Dobrindt U, Hochhut B, Hentschel U, et al. Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol. 2004;2(5):414–424. doi: 10.1038/nrmicro884
   PubMed Web of Science ®Google Scholar
• Burrus V, Pavlovic G, Decaris B, et al. Conjugative transposons: the tip of the iceberg. Mol Microbiol. 2002;46(3):601–610. doi: 10.1046/j.1365-2958.2002.03191.x
   PubMed Web of Science ®Google Scholar
• Marchlerbauer A, Derbyshire MK, Gonzales NR, et al. CDD: NCBI’s conserved domain database. Nucleic Acids Research. 2015;43(D1):D222–6. doi: 10.1093/nar/gku1221
   PubMed Web of Science ®Google Scholar
• Siguier P, Perochon J, Lestrade L, et al. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006;34(90001):D32–6. doi: 10.1093/nar/gkj014
   PubMed Web of Science ®Google Scholar
• Florensa AF, Kaas RS, Clausen P, et al. ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb Genom. 2022;8(1):000748. doi: 10.1099/mgen.0.000748
   PubMed Web of Science ®Google Scholar
• Li X, Xie Y, Liu M, et al. oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. Nucleic Acids Res. 2018;46(W1):W229–W34. doi: 10.1093/nar/gky352
   PubMed Web of Science ®Google Scholar
• Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27(7):1009–1010. doi: 10.1093/bioinformatics/btr039
   PubMed Web of Science ®Google Scholar
• Page AJ, Cummins CA, Hunt M, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics (Oxford, England). 2015;31(22):3691. doi: 10.1093/bioinformatics/btv421
   PubMed Web of Science ®Google Scholar
• Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019;20(4):1160–1166. doi: 10.1093/bib/bbx108
   PubMed Web of Science ®Google Scholar
• Nguyen LT, Schmidt HA, Von Haeseler A, et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–274. doi: 10.1093/molbev/msu300
   PubMed Web of Science ®Google Scholar
• Rambaut A, Lam TT, Max Carvalho L, et al. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2(1):vew007. doi: 10.1093/ve/vew007
   PubMed Web of Science ®Google Scholar
• Suchard MA, Lemey P, Baele G, et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018;4(1):vey016. doi: 10.1093/ve/vey016
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Syw H, Phillips MJ, et al. Relaxed phylogenetics and dating with confidence - art. no. e88. PLOS Biol. 2006;4:4. doi: 10.1371/journal.pbio.0040088
   Web of Science ®Google Scholar
• Gernhard T. The conditioned reconstructed process. J Theor Biol. 2008;253(4):769–778. doi: 10.1016/j.jtbi.2008.04.005
   PubMed Web of Science ®Google Scholar
• Carter GR. Studies on Pasteurella multocida. I. A hemagglutination test for the identification of serological types. Am J Vet Res. 1955;16(60):481–484.
   PubMed Web of Science ®Google Scholar
• Rimler RB, Rhoades KR, Serogroup F. A new capsule serogroup of Pasteurella multocida. J Clin Microbiol. 1987;25(4):615–618. doi: 10.1128/jcm.25.4.615-618.1987
   PubMed Web of Science ®Google Scholar
• Flannagan SE, Clewell DB. Conjugative transfer of Tn916 in Enterococcus faecalis: trans activation of homologous transposons. J Bacteriol. 1991;173(22):7136–7141. doi: 10.1128/jb.173.22.7136-7141.1991
   PubMed Web of Science ®Google Scholar
• Watson R. Europe launches 12 point plan to tackle antimicrobial resistance. BMJ. 2011;343(nov21 1):d7528. doi: 10.1136/bmj.d7528
   PubMedGoogle Scholar
• Smith E, Lichten CA, Taylor J, et al. Europe’s plan to tackle antimicrobial resistance: The success stories and challenges. Santa Monica, CA: RAND Corporation; 2016. doi: 10.7249/RB9930
   Google Scholar
• De Briyne N, Atkinson J, Pokludová L, et al. Antibiotics used most commonly to treat animals in Europe. Vet Rec. 2014;175(13):325. doi: 10.1136/vr.102462
   PubMed Web of Science ®Google Scholar
• Rui Y, Qiu G. Analysis of gut microbial communities and resistance genes in pigs and chickens in Central China. Animals (Basel). 2022;12(23):3404. doi: 10.3390/ani12233404
   PubMedGoogle Scholar
• Jiang N, Chen H, Cheng L, et al. Genomic analysis reveals the population structure and antimicrobial resistance of avian Pasteurella multocida in China. J Antimicrob Chemother. 2024;79(1):186–194. doi: 10.1093/jac/dkad365
   PubMed Web of Science ®Google Scholar
• Choufa C, Tidjani AR, Gauthier A, et al. Prevalence and mobility of integrative and conjugative elements within a Streptomyces natural population. Front Microbiol. 2022;13:970179. doi: 10.3389/fmicb.2022.970179
   PubMed Web of Science ®Google Scholar
• Bean EL, Mclellan LK, Grossman AD, et al. Activation of the integrative and conjugative element Tn916 causes growth arrest and death of host bacteria. PLOS Genet. 2022;18(10):e1010467. doi: 10.1371/journal.pgen.1010467
   PubMed Web of Science ®Google Scholar
• The Embassy of the People’s Republic of China in the People’s Republic of Bangladesh. The relations between China and Bangladesh [Z]. 2019. Available from: http://bd.china-embassy.gov.cn/chn/zmgx/gxgk/202003/t20200322_1780848.htm
   Google Scholar
• Partridge SR. Analysis of antibiotic resistance regions in gram-negative bacteria. FEMS Microbiol Rev. 2011;35(5):820–855. doi: 10.1111/j.1574-6976.2011.00277.x
   PubMed Web of Science ®Google Scholar
• Partridge SR, Kwong SM, Firth N, et al. Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev. 2018;31(4). doi: 10.1128/CMR.00088-17
   PubMed Web of Science ®Google Scholar
• Li A, Yu R, Zhao W, et al. Characterization of a genomic Island carrying the tet(X4) gene in porcine Acinetobacter towneri co-harboring plasmid-borne bla (NDM-1) and bla (OXA-58) genes. Front Vet Sci. 2022;9:1002149. doi: 10.3389/fvets.2022.1002149
   PubMed Web of Science ®Google Scholar
• Mbelle N, Osei Sekyere J, Feldman C, et al. Genomic analysis of two drug-resistant clinical Morganella morganii strains isolated from UTI patients in Pretoria, South Africa. Lett Appl Microbiol. 2020;70(1):21–28. doi: 10.1111/lam.13237
   PubMed Web of Science ®Google Scholar
• Mbelle NM, Osei Sekyere J, Amoako DG, et al. Genomic analysis of a multidrug-resistant clinical Providencia rettgeri (PR002) strain with the novel integron ln1483 and an A/C plasmid replicon. Ann N Y Acad Sci. 2020;1462(1):92–103. doi: 10.1111/nyas.14237
   PubMed Web of Science ®Google Scholar
• Nusrin S, Asad A, Hayat S, et al. Multiple mechanisms confer resistance to azithromycin in Shigella in Bangladesh: a comprehensive whole genome-based approach. Microbiol Spectr. 2022;10(4):e0074122. doi: 10.1128/spectrum.00741-22
   PubMed Web of Science ®Google Scholar
• Nhung NT, Chansiripornchai N, Carrique-Mas JJ. Antimicrobial Resistance in Bacterial Poultry Pathogens: A Review. Front Vet Sci. 2017;4:126. doi: 10.3389/fvets.2017.00126
   PubMed Web of Science ®Google Scholar
• Kehrenberg C, Schwarz S. Plasmid-borne florfenicol resistance in Pasteurella multocida. J Antimicrob Chemother. 2005;55(5):773–775. doi: 10.1093/jac/dki102
   PubMed Web of Science ®Google Scholar
• Jamali H, Rezagholipour M, Fallah S, et al. Prevalence, characterization and antibiotic resistance of Pasteurella multocida isolated from bovine respiratory infection. Vet J (London, England: 1997). 2014;202(2):381–383. doi: 10.1016/j.tvjl.2014.07.024
   PubMed Web of Science ®Google Scholar
• Asgin N, Otlu B, Cakmakliogullari EK, et al. High prevalence of TEM, VIM, and OXA-2 beta-lactamases and clonal diversity among Acinetobacter baumannii isolates in Turkey. J Infect Dev Ctries. 2019;13(9):794–801. doi: 10.3855/jidc.11684
   PubMed Web of Science ®Google Scholar
• Lasarte-Monterrubio C, Fraile-Ribot PA, Vázquez-Ucha JC, et al. Activity of cefiderocol, imipenem/relebactam, cefepime/taniborbactam and cefepime/zidebactam against ceftolozane/tazobactam- and ceftazidime/avibactam-resistant Pseudomonas aeruginosa. J Antimicrob Chemother. 2022;77(10):2809–2815. doi: 10.1093/jac/dkac241
   PubMed Web of Science ®Google Scholar
• Iovleva A, Mettus RT, Mcelheny CL, et al. Reduced ceftazidime and ertapenem susceptibility due to production of OXA-2 in Klebsiella pneumoniae ST258. J Antimicrob Chemother. 2019;74(8):2203–2208. doi: 10.1093/jac/dkz183
   PubMed Web of Science ®Google Scholar
• Huang J, Deng S, Ren J, et al. Characterization of a blaNDM‑1‑harboring plasmid from a Salmonella enterica clinical isolate in China. Mol Med Rep. 2017;16(2):1087–1092. doi: 10.3892/mmr.2017.6733
   PubMed Web of Science ®Google Scholar
• Bonnin RA, Poirel L, Carattoli A, et al. Characterization of an IncFII plasmid encoding NDM-1 from Escherichia coli ST131. PLOS ONE. 2012;7(4):e34752. doi: 10.1371/journal.pone.0034752
   PubMed Web of Science ®Google Scholar
• Ahmad N, Ali SM, Khan AU. Molecular characterization of novel sequence type of carbapenem-resistant new delhi metallo-β-lactamase-1-producing Klebsiella pneumoniae in the neonatal intensive care unit of an Indian hospital. Int J Antimicrob Agents. 2019;53(4):525–529. doi: 10.1016/j.ijantimicag.2018.12.005
   PubMed Web of Science ®Google Scholar
• Semon D, Movva NR, Smith TF, et al. Plasmid-determined bleomycin resistance in Staphylococcus aureus. Plasmid. 1987;17(1):46–53. doi: 10.1016/0147-619X(87)90007-2
   PubMed Web of Science ®Google Scholar