Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing.
Antimicrobial resistance
Chromosome
ESKAPE pathogens
Mobile genetic element
Mycobacteria
Phage
Plasmid
Virulence
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2023
2023
Historique:
entrez:
13
2
2023
pubmed:
14
2
2023
medline:
16
2
2023
Statut:
ppublish
Résumé
Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and mycobacteria (Mycobacterium tuberculosis and nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages. Nanopore long-read sequencing allows easy and inexpensive analysis of complex bacterial genome structures, although some aspects of sequencing data calculation and genome analysis methods are not systematically understood. Here we describe the latest and most recommended experimental and bioinformatics methods available for the construction of complete bacterial genomes from nanopore sequencing data and the detection and classification of genotypes of bacterial chromosomes, ARGs, VFGs, plasmids, and other MGEs based on their genomic sequences for genomic epidemiological analysis of AMR bacteria.
Identifiants
pubmed: 36781732
doi: 10.1007/978-1-0716-2996-3_16
doi:
Substances chimiques
Anti-Bacterial Agents
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
227-246Informations de copyright
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Antimicrobial Resistance C (2022) Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399(10325):629–655. https://doi.org/10.1016/S0140-6736(21)02724-0
doi: 10.1016/S0140-6736(21)02724-0
Rice LB (2008) Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE. J Infect Dis 197(8):1079–1081. https://doi.org/10.1086/533452
doi: 10.1086/533452
pubmed: 18419525
Cowman S et al (2019) Non-tuberculous mycobacterial pulmonary disease. Eur Respir J 54(1). https://doi.org/10.1183/13993003.00250-2019
Partridge SR et al (2018) Mobile genetic elements associated with Antimicrobial Resistance. Clin Microbiol Rev 31(4). https://doi.org/10.1128/CMR.00088-17
De Oliveira DMP et al (2020) Antimicrobial Resistance in ESKAPE pathogens. Clin Microbiol Rev 33:3. https://doi.org/10.1128/CMR.00181-19
doi: 10.1128/CMR.00181-19
Hashimoto Y et al (2019) Novel multidrug-resistant Enterococcal Mobile linear plasmid pELF1 encoding vanA and vanM gene clusters from a Japanese vancomycin-resistant enterococci isolate. Front Microbiol 10:2568. https://doi.org/10.3389/fmicb.2019.02568
doi: 10.3389/fmicb.2019.02568
pubmed: 31798546
pmcid: 6863802
Hawkey J et al (2022) Linear plasmids in Klebsiella and other Enterobacteriaceae. Microb Genom 8(4). https://doi.org/10.1099/mgen.0.000807
Rabello MC et al (2012) First description of natural and experimental conjugation between Mycobacteria mediated by a linear plasmid. PLoS One 7(1):e29884. https://doi.org/10.1371/journal.pone.0029884
doi: 10.1371/journal.pone.0029884
pubmed: 22235347
pmcid: 3250492
Conlan S et al (2014) Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med 6(254):254ra126. https://doi.org/10.1126/scitranslmed.3009845
doi: 10.1126/scitranslmed.3009845
pubmed: 25232178
pmcid: 4203314
Lemon JK et al (2017) Rapid Nanopore sequencing of plasmids and Resistance gene detection in clinical isolates. J Clin Microbiol 55(12):3530–3543. https://doi.org/10.1128/JCM.01069-17
doi: 10.1128/JCM.01069-17
pubmed: 29021151
pmcid: 5703817
Wang Y et al (2021) Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 39(11):1348–1365. https://doi.org/10.1038/s41587-021-01108-x
doi: 10.1038/s41587-021-01108-x
pubmed: 34750572
pmcid: 8988251
Boolchandani M et al (2019) Sequencing-based methods and resources to study antimicrobial resistance. Nat Rev Genet 20(6):356–370. https://doi.org/10.1038/s41576-019-0108-4
doi: 10.1038/s41576-019-0108-4
pubmed: 30886350
pmcid: 6525649
Bento Lab (2016) Nat Biotechnol 34(5):455. https://doi.org/10.1038/nbt0516-455
doi: 10.1038/nbt0516-455
Hirabayashi A et al (2021) On-site genomic epidemiological analysis of Antimicrobial-resistant bacteria in Cambodia with portable laboratory equipment. Front Microbiol 12:675463. https://doi.org/10.3389/fmicb.2021.675463
doi: 10.3389/fmicb.2021.675463
pubmed: 34054783
pmcid: 8158813
Bolger AM et al (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170
doi: 10.1093/bioinformatics/btu170
pubmed: 24695404
pmcid: 4103590
Wick RR et al (2017) Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom 3(10):e000132. https://doi.org/10.1099/mgen.0.000132
doi: 10.1099/mgen.0.000132
pubmed: 29177090
pmcid: 5695209
Kaser M et al (2009) Optimized method for preparation of DNA from pathogenic and environmental mycobacteria. Appl Environ Microbiol 75(2):414–418. https://doi.org/10.1128/AEM.01358-08
doi: 10.1128/AEM.01358-08
pubmed: 19047396
Koren S et al (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27(5):722–736. https://doi.org/10.1101/gr.215087.116
doi: 10.1101/gr.215087.116
pubmed: 28298431
pmcid: 5411767
Frith MC et al (2010) Parameters for accurate genome alignment. BMC Bioinformatics 11:80. https://doi.org/10.1186/1471-2105-11-80
doi: 10.1186/1471-2105-11-80
pubmed: 20144198
pmcid: 2829014
Vaser R et al (2017) Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27(5):737–746. https://doi.org/10.1101/gr.214270.116
doi: 10.1101/gr.214270.116
pubmed: 28100585
pmcid: 5411768
Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094–3100. https://doi.org/10.1093/bioinformatics/bty191
doi: 10.1093/bioinformatics/bty191
pubmed: 29750242
pmcid: 6137996
Walker BJ et al (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9(11):e112963. https://doi.org/10.1371/journal.pone.0112963
doi: 10.1371/journal.pone.0112963
pubmed: 25409509
pmcid: 4237348
Li H, Durbin R (2010) Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics 26(5):589–595. https://doi.org/10.1093/bioinformatics/btp698
doi: 10.1093/bioinformatics/btp698
pubmed: 20080505
pmcid: 2828108
Vasimuddin Md, Misra S, Li H, Aluru S (2019) Efficient architecture-aware acceleration of BWA-MEM for multicore systems. In: IEEE parallel and distributed processing symposium (IPDPS)
Tanizawa Y et al (2018) DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34(6):1037–1039. https://doi.org/10.1093/bioinformatics/btx713
doi: 10.1093/bioinformatics/btx713
pubmed: 29106469
Tanizawa Y et al (2019) Generating publication-ready prokaryotic genome annotations with DFAST. Methods Mol Biol 1962:215–226. https://doi.org/10.1007/978-1-4939-9173-0_13
doi: 10.1007/978-1-4939-9173-0_13
pubmed: 31020563
Larsen MV et al (2012) Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50(4):1355–1361. https://doi.org/10.1128/JCM.06094-11
doi: 10.1128/JCM.06094-11
pubmed: 22238442
pmcid: 3318499
Zankari E et al (2012) Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67(11):2640–2644. https://doi.org/10.1093/jac/dks261
doi: 10.1093/jac/dks261
pubmed: 22782487
pmcid: 3468078
Florensa AF et al (2022) ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb Genom 8(1). https://doi.org/10.1099/mgen.0.000748
Joensen KG et al (2014) Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 52(5):1501–1510. https://doi.org/10.1128/JCM.03617-13
doi: 10.1128/JCM.03617-13
pubmed: 24574290
pmcid: 3993690
Malberg Tetzschner AM et al (2020) In silico genotyping of Escherichia coli isolates for Extraintestinal virulence genes by use of whole-genome sequencing data. J Clin Microbiol 58(10). https://doi.org/10.1128/JCM.01269-20
Chen L et al (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33(Database issue):D325–D328. https://doi.org/10.1093/nar/gki008
doi: 10.1093/nar/gki008
pubmed: 15608208
Liu B et al (2022) VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res 50(D1):D912–D917. https://doi.org/10.1093/nar/gkab1107
doi: 10.1093/nar/gkab1107
pubmed: 34850947
Abby SS et al (2016) Identification of protein secretion systems in bacterial genomes. Sci Rep 6:23080. https://doi.org/10.1038/srep23080
doi: 10.1038/srep23080
pubmed: 26979785
pmcid: 4793230
Abby SS, Rocha EPC (2017) Identification of protein secretion Systems in Bacterial Genomes Using MacSyFinder. Methods Mol Biol 1615:1–21. https://doi.org/10.1007/978-1-4939-7033-9_1
doi: 10.1007/978-1-4939-7033-9_1
pubmed: 28667599
Cury J et al (2020) Identifying conjugative plasmids and integrative conjugative elements with CONJscan. Methods Mol Biol 2075:265–283. https://doi.org/10.1007/978-1-4939-9877-7_19
doi: 10.1007/978-1-4939-9877-7_19
pubmed: 31584169
Robertson J, Nash JHE (2018) MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom 4(8). https://doi.org/10.1099/mgen.0.000206
Robertson J et al (2020) Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance. Microb Genom 6(10). https://doi.org/10.1099/mgen.0.000435
Page AJ et al (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31(22):3691–3693. https://doi.org/10.1093/bioinformatics/btv421
doi: 10.1093/bioinformatics/btv421
pubmed: 26198102
pmcid: 4817141
Sitto F, Battistuzzi FU (2020) Estimating Pangenomes with Roary. Mol Biol Evol 37(3):933–939. https://doi.org/10.1093/molbev/msz284
doi: 10.1093/molbev/msz284
pubmed: 31848603
Rokas A (2011) Phylogenetic analysis of protein sequence data using the randomized Axelerated maximum likelihood (RAXML) program. Curr Protoc Mol Biol Chapter 19:Unit19 11. https://doi.org/10.1002/0471142727.mb1911s96
doi: 10.1002/0471142727.mb1911s96
pubmed: 21987055
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313. https://doi.org/10.1093/bioinformatics/btu033
doi: 10.1093/bioinformatics/btu033
pubmed: 24451623
pmcid: 3998144
Darling AC et al (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14(7):1394–1403. https://doi.org/10.1101/gr.2289704
doi: 10.1101/gr.2289704
pubmed: 15231754
pmcid: 442156
Darling AE et al (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5(6):e11147. https://doi.org/10.1371/journal.pone.0011147
doi: 10.1371/journal.pone.0011147
pubmed: 20593022
pmcid: 2892488
Sullivan MJ et al (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27(7):1009–1010. https://doi.org/10.1093/bioinformatics/btr039
doi: 10.1093/bioinformatics/btr039
pubmed: 21278367
pmcid: 3065679
De Coster W et al (2018) NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34(15):2666–2669. https://doi.org/10.1093/bioinformatics/bty149
doi: 10.1093/bioinformatics/bty149
pubmed: 29547981
pmcid: 6061794
Bankevich A et al (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
doi: 10.1089/cmb.2012.0021
pubmed: 22506599
pmcid: 3342519
Wick RR et al (2015) Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31(20):3350–3352. https://doi.org/10.1093/bioinformatics/btv383
doi: 10.1093/bioinformatics/btv383
pubmed: 26099265
pmcid: 4595904
Kolmogorov M et al (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
doi: 10.1038/s41587-019-0072-8
pubmed: 30936562
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
doi: 10.1093/bioinformatics/btw152
pubmed: 27153593
pmcid: 4937194
Wick RR, Holt KE (2019) Benchmarking of long-read assemblers for prokaryote whole genome sequencing. F1000Res 8:2138. https://doi.org/10.12688/f1000research.21782.4
doi: 10.12688/f1000research.21782.4
pubmed: 31984131
Kuznetsov A, Bollin CJ (2021) NCBI genome workbench: desktop software for comparative genomics, visualization, and GenBank data submission. Methods Mol Biol 2231:261–295. https://doi.org/10.1007/978-1-0716-1036-7_16
doi: 10.1007/978-1-0716-1036-7_16
pubmed: 33289898
Wick RR et al (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
doi: 10.1371/journal.pcbi.1005595
pubmed: 28594827
pmcid: 5481147
Wick RR et al (2021) Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol 22(1):266. https://doi.org/10.1186/s13059-021-02483-z
doi: 10.1186/s13059-021-02483-z
pubmed: 34521459
pmcid: 8442456
Giardine B et al (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15(10):1451–1455. https://doi.org/10.1101/gr.4086505
doi: 10.1101/gr.4086505
pubmed: 16169926
pmcid: 1240089
Galaxy C (2022) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. https://doi.org/10.1093/nar/gkac247
de Koning W et al (2020) NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy. Gigascience 9(10). https://doi.org/10.1093/gigascience/giaa105
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068–2069. https://doi.org/10.1093/bioinformatics/btu153
doi: 10.1093/bioinformatics/btu153
pubmed: 24642063
Overbeek R et al (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42(Database issue):D206–D214. https://doi.org/10.1093/nar/gkt1226
doi: 10.1093/nar/gkt1226
pubmed: 24293654
Brettin T et al (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. https://doi.org/10.1038/srep08365
doi: 10.1038/srep08365
pubmed: 25666585
pmcid: 4322359
Tatusova T et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44(14):6614–6624. https://doi.org/10.1093/nar/gkw569
doi: 10.1093/nar/gkw569
pubmed: 27342282
pmcid: 5001611
Jain C et al (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
doi: 10.1038/s41467-018-07641-9
pubmed: 30504855
pmcid: 6269478
Parks DH et al (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7):1043–1055. https://doi.org/10.1101/gr.186072.114
doi: 10.1101/gr.186072.114
pubmed: 25977477
pmcid: 4484387
Wattam AR et al (2018) Assembly, annotation, and comparative genomics in PATRIC, the all bacterial bioinformatics resource center. Methods Mol Biol 1704:79–101. https://doi.org/10.1007/978-1-4939-7463-4_4
doi: 10.1007/978-1-4939-7463-4_4
pubmed: 29277864
Davis JJ et al (2020) The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res 48(D1):D606–D612. https://doi.org/10.1093/nar/gkz943
doi: 10.1093/nar/gkz943
pubmed: 31667520
Nayfach S et al (2021) CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat Biotechnol 39(5):578–585. https://doi.org/10.1038/s41587-020-00774-7
doi: 10.1038/s41587-020-00774-7
pubmed: 33349699
Maiden MC et al (2013) MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol 11(10):728–736. https://doi.org/10.1038/nrmicro3093
doi: 10.1038/nrmicro3093
pubmed: 23979428
pmcid: 3980634
Jolley KA et al (2018) Open-access bacterial population genomics: BIGSdb software, the PubMLST.Org website and their applications. Wellcome Open Res 3:124. https://doi.org/10.12688/wellcomeopenres.14826.1
doi: 10.12688/wellcomeopenres.14826.1
pubmed: 30345391
pmcid: 6192448
Zhou Z et al (2020) The EnteroBase user's guide, with case studies on salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res 30(1):138–152. https://doi.org/10.1101/gr.251678.119
doi: 10.1101/gr.251678.119
pubmed: 31809257
pmcid: 6961584
Diancourt L et al (2005) Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol 43(8):4178–4182. https://doi.org/10.1128/JCM.43.8.4178-4182.2005
doi: 10.1128/JCM.43.8.4178-4182.2005
pubmed: 16081970
pmcid: 1233940
Wirth T et al (2006) Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 60(5):1136–1151. https://doi.org/10.1111/j.1365-2958.2006.05172.x
doi: 10.1111/j.1365-2958.2006.05172.x
pubmed: 16689791
pmcid: 1557465
Diancourt L et al (2010) The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. PLoS One 5(4):e10034. https://doi.org/10.1371/journal.pone.0010034
doi: 10.1371/journal.pone.0010034
pubmed: 20383326
pmcid: 2850921
Carter GP et al (2016) Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faecium. J Antimicrob Chemother 71(12):3367–3371. https://doi.org/10.1093/jac/dkw314
doi: 10.1093/jac/dkw314
pubmed: 27530751
Feil EJ et al (2004) eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 186(5):1518–1530. https://doi.org/10.1128/JB.186.5.1518-1530.2004
doi: 10.1128/JB.186.5.1518-1530.2004
pubmed: 14973027
pmcid: 344416
Tang CY, Ong RT (2020) MIRUReader: MIRU-VNTR typing directly from long sequencing reads. Bioinformatics 36(5):1625–1626. https://doi.org/10.1093/bioinformatics/btz771
doi: 10.1093/bioinformatics/btz771
pubmed: 31603462
Feldgarden M et al (2021) AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 11(1):12728. https://doi.org/10.1038/s41598-021-91456-0
doi: 10.1038/s41598-021-91456-0
pubmed: 34135355
pmcid: 8208984
Feldgarden M et al (2022) Curation of the AMRFinderPlus databases: applications, functionality and impact. Microb Genom 8(6). https://doi.org/10.1099/mgen.0.000832
McArthur AG et al (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57(7):3348–3357. https://doi.org/10.1128/AAC.00419-13
doi: 10.1128/AAC.00419-13
pubmed: 23650175
pmcid: 3697360
Alcock BP et al (2020) CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48(D1):D517–D525. https://doi.org/10.1093/nar/gkz935
doi: 10.1093/nar/gkz935
pubmed: 31665441
Altschul SF et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
doi: 10.1016/S0022-2836(05)80360-2
pubmed: 2231712
Andini N, Nash KA (2006) Intrinsic macrolide resistance of the mycobacterium tuberculosis complex is inducible. Antimicrob Agents Chemother 50(7):2560–2562. https://doi.org/10.1128/AAC.00264-06
doi: 10.1128/AAC.00264-06
pubmed: 16801446
pmcid: 1489773
Brown-Elliott BA et al (2012) Antimicrobial susceptibility testing, drug resistance mechanisms, and therapy of infections with nontuberculous mycobacteria. Clin Microbiol Rev 25(3):545–582. https://doi.org/10.1128/CMR.05030-11
doi: 10.1128/CMR.05030-11
pubmed: 22763637
pmcid: 3416486
Bradford PA et al (2022) Consensus on beta-lactamase nomenclature. Antimicrob Agents Chemother 66(4):e0033322. https://doi.org/10.1128/aac.00333-22
doi: 10.1128/aac.00333-22
pubmed: 35380458
Carattoli A et al (2014) In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58(7):3895–3903. https://doi.org/10.1128/AAC.02412-14
doi: 10.1128/AAC.02412-14
pubmed: 24777092
pmcid: 4068535
Carattoli A, Hasman H (2020) PlasmidFinder and in silico pMLST: identification and typing of plasmid replicons in whole-genome sequencing (WGS). Methods Mol Biol 2075:285–294. https://doi.org/10.1007/978-1-4939-9877-7_20
doi: 10.1007/978-1-4939-9877-7_20
pubmed: 31584170
Arndt D et al (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44(W1):W16–W21. https://doi.org/10.1093/nar/gkw387
doi: 10.1093/nar/gkw387
pubmed: 27141966
pmcid: 4987931
Arndt D et al (2019) PHAST, PHASTER and PHASTEST: tools for finding prophage in bacterial genomes. Brief Bioinform 20(4):1560–1567. https://doi.org/10.1093/bib/bbx121
doi: 10.1093/bib/bbx121
pubmed: 29028989
Roux S et al (2015) VirSorter: mining viral signal from microbial genomic data. PeerJ 3:e985. https://doi.org/10.7717/peerj.985
doi: 10.7717/peerj.985
pubmed: 26038737
pmcid: 4451026
Johansson MHK et al (2021) Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother 76(1):101–109. https://doi.org/10.1093/jac/dkaa390
doi: 10.1093/jac/dkaa390
pubmed: 33009809
Siguier P et al (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34(Database issue):D32–D36. https://doi.org/10.1093/nar/gkj014
doi: 10.1093/nar/gkj014
pubmed: 16381877
Siguier P et al (2012) Exploring bacterial insertion sequences with ISfinder: objectives, uses, and future developments. Methods Mol Biol 859:91–103. https://doi.org/10.1007/978-1-61779-603-6_5
doi: 10.1007/978-1-61779-603-6_5
pubmed: 22367867
Liu M et al (2019) ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Res 47(D1):D660–D665. https://doi.org/10.1093/nar/gky1123
doi: 10.1093/nar/gky1123
pubmed: 30407568
Shintani M et al (2022) Precise classification of antimicrobial resistance-associated IncP-2 megaplasmids for molecular epidemiological studies on Pseudomonas species. J Antimicrob Chemother 77(4):1203–1205. https://doi.org/10.1093/jac/dkac006
doi: 10.1093/jac/dkac006
pubmed: 35084026
Hirabayashi A et al (2021) Plasmid analysis of NDM metallo-beta-lactamase-producing Enterobacterales isolated in Vietnam. PLoS One 16(7):e0231119. https://doi.org/10.1371/journal.pone.0231119
doi: 10.1371/journal.pone.0231119
pubmed: 34319973
pmcid: 8318238
Payne LJ et al (2021) Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Res 49(19):10868–10878. https://doi.org/10.1093/nar/gkab883
doi: 10.1093/nar/gkab883
pubmed: 34606606
pmcid: 8565338
Payne LJ et al (2022) PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. Nucleic Acids Res. https://doi.org/10.1093/nar/gkac400
Tesson F et al (2022) Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat Commun 13(1):2561. https://doi.org/10.1038/s41467-022-30269-9
doi: 10.1038/s41467-022-30269-9
pubmed: 35538097
pmcid: 9090908
Kaya H et al (2018) SCCmecFinder, a web-based tool for typing of staphylococcal cassette chromosome mec in Staphylococcus aureus using whole-genome sequence data. mSphere 3(1):e00612-17. https://doi.org/10.1128/mSphere.00612-17
doi: 10.1128/mSphere.00612-17
pubmed: 29468193
pmcid: 5812897
Lam MMC et al (2021) A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun 12(1):4188. https://doi.org/10.1038/s41467-021-24448-3
doi: 10.1038/s41467-021-24448-3
pubmed: 34234121
pmcid: 8263825
Beghain J et al (2018) ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microb Genom 4(7). https://doi.org/10.1099/mgen.0.000192
Bayliss SC et al (2019) PIRATE: a fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria. Gigascience 8(10). https://doi.org/10.1093/gigascience/giz119
Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402. https://doi.org/10.1093/nar/25.17.3389
doi: 10.1093/nar/25.17.3389
pubmed: 9254694
pmcid: 146917
Price MN et al (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26(7):1641–1650. https://doi.org/10.1093/molbev/msp077
doi: 10.1093/molbev/msp077
pubmed: 19377059
pmcid: 2693737
Price MN et al (2010) FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One 5(3):e9490. https://doi.org/10.1371/journal.pone.0009490
doi: 10.1371/journal.pone.0009490
pubmed: 20224823
pmcid: 2835736
Guindon S et al (2009) Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 537:113–137. https://doi.org/10.1007/978-1-59745-251-9_6
doi: 10.1007/978-1-59745-251-9_6
pubmed: 19378142
Guindon S et al (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59(3):307–321. https://doi.org/10.1093/sysbio/syq010
doi: 10.1093/sysbio/syq010
pubmed: 20525638
Tamura K et al (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38(7):3022–3027. https://doi.org/10.1093/molbev/msab120
doi: 10.1093/molbev/msab120
pubmed: 33892491
pmcid: 8233496
Letunic I, Bork P (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23(1):127–128. https://doi.org/10.1093/bioinformatics/btl529
doi: 10.1093/bioinformatics/btl529
pubmed: 17050570
Letunic I, Bork P (2021) Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49(W1):W293–W296. https://doi.org/10.1093/nar/gkab301
doi: 10.1093/nar/gkab301
pubmed: 33885785
pmcid: 8265157
Hadfield J et al (2018) Phandango: an interactive viewer for bacterial population genomics. Bioinformatics 34(2):292–293. https://doi.org/10.1093/bioinformatics/btx610
doi: 10.1093/bioinformatics/btx610
pubmed: 29028899
Argimon S et al (2016) Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom 2(11):e000093. https://doi.org/10.1099/mgen.0.000093
doi: 10.1099/mgen.0.000093
pubmed: 28348833
pmcid: 5320705
Petit RA 3rd, Read TD (2020) Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems 5(4). https://doi.org/10.1128/mSystems.00190-20
Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21(4):537–539. https://doi.org/10.1093/bioinformatics/bti054
doi: 10.1093/bioinformatics/bti054
pubmed: 15479716
Grant JR, Stothard P (2008) The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36(Web Server issue):W181–W184. https://doi.org/10.1093/nar/gkn179
doi: 10.1093/nar/gkn179
pubmed: 18411202
pmcid: 2447734
Grant JR et al (2012) Comparing thousands of circular genomes using the CGView comparison tool. BMC Genomics 13:202. https://doi.org/10.1186/1471-2164-13-202
doi: 10.1186/1471-2164-13-202
pubmed: 22621371
pmcid: 3469350
Galata V et al (2019) PLSDB: a resource of complete bacterial plasmids. Nucleic Acids Res 47(D1):D195–D202. https://doi.org/10.1093/nar/gky1050
doi: 10.1093/nar/gky1050
pubmed: 30380090
Schmartz GP et al (2022) PLSDB: advancing a comprehensive database of bacterial plasmids. Nucleic Acids Res 50(D1):D273–D278. https://doi.org/10.1093/nar/gkab1111
doi: 10.1093/nar/gkab1111
pubmed: 34850116
Robinson JT et al (2011) Integrative genomics viewer. Nat Biotechnol 29(1):24–26. https://doi.org/10.1038/nbt.1754
doi: 10.1038/nbt.1754
pubmed: 21221095
pmcid: 3346182