{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T18:21:12Z","timestamp":1783189272449,"version":"3.54.6"},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,5,31]],"date-time":"2025-05-31T00:00:00Z","timestamp":1748649600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,5,31]],"date-time":"2025-05-31T00:00:00Z","timestamp":1748649600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Department of Science and Technology, Government of Odisha","award":["rant Number ST-BT-GlA-0003-2021"],"award-info":[{"award-number":["rant Number ST-BT-GlA-0003-2021"]}]},{"name":"Department of Science and Technology, Government of Odisha","award":["rant Number ST-BT-GlA-0003-2021"],"award-info":[{"award-number":["rant Number ST-BT-GlA-0003-2021"]}]},{"name":"Department of Science and Technology, Government of Odisha","award":["rant Number ST-BT-GlA-0003-2021"],"award-info":[{"award-number":["rant Number ST-BT-GlA-0003-2021"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Curr Genet"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1007\/s00294-025-01318-9","type":"journal-article","created":{"date-parts":[[2025,5,31]],"date-time":"2025-05-31T04:42:43Z","timestamp":1748666563000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Whole genome sequence analysis of multidrug-resistant Salmonella enterica Typhimurium ms203 provides insights into virulence and antibiotic resistance"],"prefix":"10.1007","volume":"71","author":[{"given":"Saumya Darshana","family":"Patra","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soujanya","family":"Ghosh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rakesh Kumar","family":"Panda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bikash Ranjan","family":"Sahu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Namrata","family":"Misra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1663-2497","authenticated-orcid":false,"given":"Gajraj Singh","family":"Kushwaha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4815-5477","authenticated-orcid":false,"given":"Mrutyunjay","family":"Suar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,5,31]]},"reference":[{"key":"1318_CR1","doi-asserted-by":"publisher","first-page":"2072","DOI":"10.1021\/acsinfecdis.3c00408","volume":"9","author":"SD Akshay","year":"2023","unstructured":"Akshay SD, Deekshit VK, Mohan Raj J, Maiti B (2023) Outer membrane proteins and efflux pumps mediated multi-drug resistance in Salmonella: rising threat to antimicrobial therapy. ACS Infect Dis 9:2072\u20132092. https:\/\/doi.org\/10.1021\/acsinfecdis.3c00408","journal-title":"ACS Infect Dis"},{"key":"1318_CR2","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403\u2013410","journal-title":"J Mol Biol"},{"key":"1318_CR3","unstructured":"Andrews S, FastQC (2024) A quality control tool for high throughput sequence data. Available online: (accessed on May 17, 2024). http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/"},{"key":"1318_CR5","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","volume":"19","author":"A Bankevich","year":"2012","unstructured":"Bankevich A, Nurk S et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455\u2013477. https:\/\/doi.org\/10.1089\/cmb.2012.0021","journal-title":"J Comput Biol"},{"key":"1318_CR6","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1128\/CMR.00059-12","volume":"26","author":"A Beceiro","year":"2013","unstructured":"Beceiro A, Tom\u00e1s M, Bou G (2013) Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world? Clin Microbiol Rev 26:185\u2013230. https:\/\/doi.org\/10.1128\/CMR.00059-12","journal-title":"Clin Microbiol Rev"},{"key":"1318_CR8","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","volume":"75","author":"V Bortolaia","year":"2020","unstructured":"Bortolaia V, Kaas RS et al (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75:3491\u20133500","journal-title":"J Antimicrob Chemother"},{"key":"1318_CR9","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","volume":"58","author":"A Carattoli","year":"2014","unstructured":"Carattoli A, Zankari E, Garc\u00eda-Fern\u00e1ndez A, Voldby Larsen M, Lund O, Villa L, M\u00f8ller Aarestrup F, Hasman H (2014) In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895\u20133903. https:\/\/doi.org\/10.1128\/AAC.02412-14","journal-title":"Antimicrob Agents Chemother"},{"key":"1318_CR10","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen S, Zhou Y, Chen Y, Gu J (2018) Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884\u2013i890. https:\/\/doi.org\/10.1093\/bioinformatics\/bty560","journal-title":"Bioinformatics"},{"key":"1318_CR11","doi-asserted-by":"publisher","first-page":"97","DOI":"10.2147\/ceg.s6554","volume":"3","author":"CM Chow","year":"2010","unstructured":"Chow CM, Leung AK, Hon KL (2010) Acute gastroenteritis: from guidelines to real life. Clin Exp Gastroenterol 3:97\u2013112. https:\/\/doi.org\/10.2147\/ceg.s6554","journal-title":"Clin Exp Gastroenterol"},{"issue":"D1","key":"1318_CR12","doi-asserted-by":"publisher","first-page":"D757","DOI":"10.1093\/nar\/gkae902","volume":"53","author":"NP Dyer","year":"2025","unstructured":"Dyer NP, P\u00e4uker B, Baxter L et al (2025) EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens. Nucleic Acids Res 53(D1):D757\u2013D762. https:\/\/doi.org\/10.1093\/nar\/gkae902","journal-title":"Nucleic Acids Res"},{"key":"1318_CR14","doi-asserted-by":"publisher","unstructured":"F\u00e0brega A, Vila J (2013) Salmonella enterica serovar Typhimurium skills to succeed in the host: virulence and regulation. Clin Microbiol Rev 26:308\u2013341. https:\/\/doi.org\/10.1128\/CMR.00066-12","DOI":"10.1128\/CMR.00066-12"},{"key":"1318_CR13","doi-asserted-by":"publisher","first-page":"1151805","DOI":"10.3389\/fpubh.2023.1151805","volume":"11","author":"S Fatima","year":"2023","unstructured":"Fatima S, Ishaq Z, Irfan M, AlAsmari AF, Achakzai JK, Zaheer T, Ali A, Akbar A (2023) Whole-genome sequencing of multidrug resistance Salmonella Typhi clinical strains isolated from Balochistan, Pakistan. Front Public Health 11:1151805. https:\/\/doi.org\/10.3389\/fpubh.2023.1151805","journal-title":"Front Public Health"},{"key":"1318_CR15","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1089\/mdr.2016.0067","volume":"23","author":"U Fiegen","year":"2017","unstructured":"Fiegen U, Klein G, de Jong A, Kehrenberg C (2017) Detection of a novel qnrB19-Carrying plasmid variant mediating decreased fluoroquinolone susceptibility in Salmonella enterica serovar Hadar. Microb Drug Resist 23:280\u2013284. https:\/\/doi.org\/10.1089\/mdr.2016.0067","journal-title":"Microb Drug Resist"},{"key":"1318_CR16","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","volume":"29","author":"A Gurevich","year":"2013","unstructured":"Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072\u20131075. https:\/\/doi.org\/10.1093\/bioinformatics\/btt086","journal-title":"Bioinformatics"},{"issue":"Pt 4","key":"1318_CR17","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1099\/mic.0.055459-0","volume":"158","author":"KA Jolley","year":"2012","unstructured":"Jolley KA, Bliss CM, Bennett JS et al (2012) Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiol (Reading) 158(Pt 4):1005\u20131015. https:\/\/doi.org\/10.1099\/mic.0.055459-0","journal-title":"Microbiol (Reading)"},{"key":"1318_CR18","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","volume":"3","author":"KA Jolley","year":"2018","unstructured":"Jolley KA, Bray JE, Maiden MCJ (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","journal-title":"Wellcome Open Res"},{"key":"1318_CR19","doi-asserted-by":"publisher","first-page":"2279","DOI":"10.1101\/gr.091017.109","volume":"19","author":"RA Kingsley","year":"2009","unstructured":"Kingsley RA, Msefula CL, Thomson NR et al (2009) Epidemic multiple drug-resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res 19:2279\u20132287. https:\/\/doi.org\/10.1101\/gr.091017.109","journal-title":"Genome Res"},{"key":"1318_CR20","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg S (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9:357\u2013359. https:\/\/doi.org\/10.1038\/nmeth.1923","journal-title":"Nat Methods"},{"key":"1318_CR21","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","volume":"183","author":"AP Magiorakos","year":"2012","unstructured":"Magiorakos AP, Srinivasan A, Carey RB et al (2012) Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 183:268\u2013281. https:\/\/doi.org\/10.1111\/j.1469-0691.2011.03570.x","journal-title":"Clin Microbiol Infect"},{"key":"1318_CR22","doi-asserted-by":"publisher","unstructured":"Majowicz SE, Musto J, Scallan E, Angulo FJ, Kirk M, O\u2019Brien SJ, Jones TF, Fazil A, Hoekstra RM & International Collaboration on Enteric Disease \u2018Burden of Illness\u2019 Studies (2010) The global burden of nontyphoidal Salmonella gastroenteritis. Clin Infect Dis 50:882\u2013889. https:\/\/doi.org\/10.1086\/650733","DOI":"10.1086\/650733"},{"key":"1318_CR23","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/35101614","volume":"413","author":"M McClelland","year":"2001","unstructured":"McClelland M, Sanderson KE, Spieth J et al (2001) Complete genome sequence of Salmonella enterica serovar typhimurium LT2. Nature 413:852\u2013856. https:\/\/doi.org\/10.1038\/35101614","journal-title":"Nature"},{"key":"1318_CR24","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1016\/j.apjtb.2015.03.010","volume":"5","author":"IA Mir","year":"2015","unstructured":"Mir IA, Kashyap SK, Maherchandani S (2015) Isolation, serotype diversity and antibiogram of Salmonella enterica isolated from different species of poultry in India. Asian Pac J Trop Biomed 5:561\u2013567. https:\/\/doi.org\/10.1016\/j.apjtb.2015.03.010","journal-title":"Asian Pac J Trop Biomed"},{"key":"1318_CR25","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/s13099-022-00498-w","volume":"14","author":"NK Mohakud","year":"2022","unstructured":"Mohakud NK, Panda RK, Patra SD, Sahu BR, Ghosh M, Kushwaha GS, Misra N, Suar M (2022) Genome analysis and virulence gene expression profile of a multi drug resistant Salmonella enterica serovar typhimurium ms202. Gut Pathog 14:28. https:\/\/doi.org\/10.1186\/s13099-022-00498-w","journal-title":"Gut Pathog"},{"key":"1318_CR26","doi-asserted-by":"publisher","first-page":"1496685","DOI":"10.3389\/fmicb.2025.1496685","volume":"16","author":"MJ Nagpala","year":"2025","unstructured":"Nagpala MJ, Mora JF, Pavon RD, Rivera WL (2025) Genomic characterization of antimicrobial-resistant Salmonella enterica in chicken meat from wet markets in metro Manila, Philippines. Front Microbiol 16:1496685","journal-title":"Front Microbiol"},{"key":"1318_CR27","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1186\/s12879-025-10478-5","volume":"25","author":"J Nazir","year":"2025","unstructured":"Nazir J, Manzoor T, Saleem A, Gani U, Bhat SS, Khan S, Haq Z, Jha P, Ahmad SM (2025) Combatting Salmonella: a focus on antimicrobial resistance and the need for effective vaccination. BMC Infect Dis 25:84. https:\/\/doi.org\/10.1186\/s12879-025-10478-5","journal-title":"BMC Infect Dis"},{"key":"1318_CR28","doi-asserted-by":"publisher","first-page":"1215","DOI":"10.1038\/ng.2423","volume":"44","author":"CK Okoro","year":"2012","unstructured":"Okoro CK, Kingsley RA et al (2012) Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet 44:1215\u20131221. https:\/\/doi.org\/10.1038\/ng.2423","journal-title":"Nat Genet"},{"key":"1318_CR30","doi-asserted-by":"publisher","first-page":"147248","DOI":"10.1016\/j.gene.2023.147248","volume":"863","author":"RK Panda","year":"2023","unstructured":"Panda RK, Patra SD, Mohakud NK, Sahu BR, Ghosh M, Misra N, Suar M (2023) Draft genome of clinical isolate Salmonella enterica typhimurium ms204 from Odisha, India, reveals multi drug resistance and decreased virulent gene expression. Gene 863:147248","journal-title":"Gene"},{"key":"1318_CR29","doi-asserted-by":"publisher","first-page":"e1008152","DOI":"10.1371\/journal.ppat.1008152","volume":"15","author":"C Pardo-Roa","year":"2019","unstructured":"Pardo-Roa C, Salazar GA, Noguera LP, Salazar-Echegarai FJ, Vallejos OP, Suazo ID, Schultz BM, Coronado-Arr\u00e1zola I, Kalergis AM, Bueno SM (2019) Pathogenicity Island excision during an infection by Salmonella enterica serovar enteritidis is required for crossing the intestinal epithelial barrier in mice to cause systemic infection. PLoS Pathog 15:e1008152. https:\/\/doi.org\/10.1371\/journal.ppat.1008152","journal-title":"PLoS Pathog"},{"key":"1318_CR31","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1007\/s11274-021-03146-8","volume":"37","author":"SD Patra","year":"2021","unstructured":"Patra SD, Mohakud NK, Panda RK et al (2021) Prevalence and multidrug resistance in Salmonella enterica typhimurium: an overview in South East Asia. World J Microbiol Biotechnol 37:185. https:\/\/doi.org\/10.1007\/s11274-021-03146-8","journal-title":"World J Microbiol Biotechnol"},{"key":"1318_CR32","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1128\/CMR.00016-17","volume":"30","author":"S Quainoo","year":"2017","unstructured":"Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL (2017) Whole-genome sequencing of bacterial pathogens: the future of nosocomial outbreak analysis. Clin Microbiol Rev 30:1015\u20131063. https:\/\/doi.org\/10.1128\/CMR.00016-17","journal-title":"Clin Microbiol Rev"},{"key":"1318_CR35","doi-asserted-by":"publisher","first-page":"S30","DOI":"10.1111\/jcpe.12079","volume":"14","author":"L Reyes","year":"2013","unstructured":"Reyes L, Herrera D, Kozarov E, Rold\u00e1n S, Progulske-Fox A (2013) Periodontal bacterial invasion and infection: contribution to atherosclerotic pathology. J Clin Periodontol 14:S30\u2013S50. https:\/\/doi.org\/10.1111\/jcpe.12079","journal-title":"J Clin Periodontol"},{"issue":"3","key":"1318_CR33","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/mSystems.00009-16","volume":"1","author":"L Roer","year":"2016","unstructured":"Roer L, Hendriksen RS, Leekitcharoenphon P, Lukjancenko O, Kaas RS, Hasman H, Aarestrup FM (2016) Is the evolution of Salmonella enterica subsp. enterica linked to restriction-modification systems? Msystems 1(3):10\u20131128","journal-title":"Msystems"},{"key":"1318_CR34","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1093\/jac\/dkx488","volume":"73","author":"M Rozwandowicz","year":"2018","unstructured":"Rozwandowicz M, Brouwer MSM, Fischer J, Wagenaar JA, Gonzalez-Zorn B, Guerra B, Mevius DJ, Hordijk J (2018) Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother 73:1121\u20131137. https:\/\/doi.org\/10.1093\/jac\/dkx488","journal-title":"J Antimicrob Chemother"},{"key":"1318_CR36","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068\u20132069","journal-title":"Bioinformatics"},{"key":"1318_CR38","doi-asserted-by":"publisher","first-page":"2177","DOI":"10.1093\/nar\/28.10.2177","volume":"28","author":"CK Sherburne","year":"2000","unstructured":"Sherburne CK, Lawley TD, Gilmour MW, Blattner FR, Burland V, Grotbeck E, Rose DJ, Taylor DE (2000) The complete DNA sequence and analysis of R27, a large IncHI plasmid from Salmonella typhi that is temperature sensitive for transfer. Nucleic Acids Res 28:2177\u20132186. https:\/\/doi.org\/10.1093\/nar\/28.10.2177","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"1318_CR37","doi-asserted-by":"publisher","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","volume":"51","author":"D Szklarczyk","year":"2023","unstructured":"Szklarczyk D, Kirsch R et al (2023) The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res 51(D1):D638\u2013D646","journal-title":"Nucleic Acids Res"},{"key":"1318_CR39","doi-asserted-by":"publisher","first-page":"e00875","DOI":"10.1128\/spectrum.00875-24","volume":"13","author":"TP Thirumoorthy","year":"2025","unstructured":"Thirumoorthy TP, Jacob JJ, Velmurugan A et al (2025) Recent emergence of cephalosporin-resistant Salmonella Typhi in India due to the endemic clone acquiring IncFIB(K) plasmid encoding blaCTX-M-15 gene. Microbiol Spectr 13:e00875\u2013e00824. https:\/\/doi.org\/10.1128\/spectrum.00875-24","journal-title":"Microbiol Spectr"},{"key":"1318_CR40","doi-asserted-by":"publisher","first-page":"e01859","DOI":"10.1128\/AEM.01859-18","volume":"84","author":"CP Thompson","year":"2018","unstructured":"Thompson CP, Doak AN, Amirani N, Schroeder EA, Wright J, Kariyawasam S, Lamendella R, Shariat NW (2018) High-Resolution identification of multiple Salmonella serovars in a single sample by using CRISPR-SeroSeq. Appl Environ Microbiol 84:e01859\u2013e01818. https:\/\/doi.org\/10.1128\/AEM.01859-18","journal-title":"Appl Environ Microbiol"},{"key":"1318_CR41","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1111\/mmi.14167","volume":"111","author":"A Wahl","year":"2019","unstructured":"Wahl A, Battesti A, Ansaldi M (2019) Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host? Mol Microbiol 111:303\u2013316. https:\/\/doi.org\/10.1111\/mmi.14167","journal-title":"Mol Microbiol"},{"key":"1318_CR42","doi-asserted-by":"crossref","unstructured":"Wang D, Su Y, Gao F, Guo S, Yang J, Wu D, Jiang Q, Chen J, Sun J, Fang L, Liao X (2025) Comparison of ST19 Salmonella Typhimurium and ST34 Salmonella I, 4,[5], 12: i:-: a trade-off between plasmid-mediated antibiotic resistance and virulence. LWT (2025): 117868","DOI":"10.1016\/j.lwt.2025.117868"},{"key":"1318_CR43","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1093\/molbev\/msx319","volume":"35","author":"RM Waterhouse","year":"2018","unstructured":"Waterhouse RM, Seppey M et al (2018) BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol 35:543\u2013548","journal-title":"Mol Biol Evol"},{"issue":"W1","key":"1318_CR44","doi-asserted-by":"publisher","first-page":"W443","DOI":"10.1093\/nar\/gkad382","volume":"51","author":"DS Wishart","year":"2023","unstructured":"Wishart DS, Han S, Saha S, Oler E, Peters H, Grant JR, Stothard P, Gautam V (2023) PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Res 51(W1):W443\u2013W450. https:\/\/doi.org\/10.1093\/nar\/gkad382","journal-title":"Nucleic Acids Res"},{"key":"1318_CR45","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1007\/s10482-017-0844-4","volume":"110","author":"SH Yoon","year":"2017","unstructured":"Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281\u20131286","journal-title":"Antonie Van Leeuwenhoek"},{"key":"1318_CR46","doi-asserted-by":"publisher","first-page":"e01746","DOI":"10.1128\/AEM.01746-19","volume":"85","author":"S Zhang","year":"2019","unstructured":"Zhang S, den Bakker HC, Li S, Chen J, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X (2019) SeqSero2: rapid and improved Salmonella serotype determination using whole-genome sequencing data. Appl Environ Microbiol 85:e01746\u2013e01719. https:\/\/doi.org\/10.1128\/AEM.01746-19","journal-title":"Appl Environ Microbiol"}],"container-title":["Current Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00294-025-01318-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00294-025-01318-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00294-025-01318-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T14:33:47Z","timestamp":1767623627000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00294-025-01318-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,31]]},"references-count":44,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["1318"],"URL":"https:\/\/doi.org\/10.1007\/s00294-025-01318-9","relation":{},"ISSN":["0172-8083","1432-0983"],"issn-type":[{"value":"0172-8083","type":"print"},{"value":"1432-0983","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,31]]},"assertion":[{"value":"15 March 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 May 2025","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 May 2025","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 May 2025","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Ethical approval for using fecal samples of patients with gastroenteritis was approved by the Institutional Ethics Committee with file no KIMS\/KIIT\/IEC\/627\/2019 of the hospitals taken under the study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Informed consent was obtained from all individual participants included in the study.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Informed consent"}},{"value":"All authors in this manuscript have thoroughly read and agreed to the content and have given their consent for publication.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":5,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"This content has been made available to all.","name":"free","label":"Free to read"}],"article-number":"12"}}