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 9:2072–2092. https://doi.org/10.1021/acsinfecdis.3c00408
Article CAS PubMed Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Article CAS PubMed Google Scholar
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/
Bankevich A, Nurk S et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
Article CAS PubMed PubMed Central Google Scholar
Beceiro A, Tomás M, Bou G (2013) Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world? Clin Microbiol Rev 26:185–230. https://doi.org/10.1128/CMR.00059-12
Article CAS PubMed PubMed Central Google Scholar
Bortolaia V, Kaas RS et al (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75:3491–3500
Article CAS PubMed PubMed Central Google Scholar
Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H (2014) In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–3903. https://doi.org/10.1128/AAC.02412-14
Article CAS PubMed PubMed Central Google Scholar
Chen S, Zhou Y, Chen Y, Gu J (2018) Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. https://doi.org/10.1093/bioinformatics/bty560
Article CAS PubMed PubMed Central Google Scholar
Chow CM, Leung AK, Hon KL (2010) Acute gastroenteritis: from guidelines to real life. Clin Exp Gastroenterol 3:97–112. https://doi.org/10.2147/ceg.s6554
Article PubMed PubMed Central Google Scholar
Dyer NP, Päuker B, Baxter L et al (2025) EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens. Nucleic Acids Res 53(D1):D757–D762. https://doi.org/10.1093/nar/gkae902
Fàbrega A, Vila J (2013) Salmonella enterica serovar Typhimurium skills to succeed in the host: virulence and regulation. Clin Microbiol Rev 26:308–341. https://doi.org/10.1128/CMR.00066-12
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
Article PubMed PubMed Central Google Scholar
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 23:280–284. https://doi.org/10.1089/mdr.2016.0067
Article CAS PubMed Google Scholar
Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. https://doi.org/10.1093/bioinformatics/btt086
Article CAS PubMed PubMed Central Google Scholar
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):1005–1015. https://doi.org/10.1099/mic.0.055459-0
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
Article CAS PubMed PubMed Central Google Scholar
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 19:2279–2287. https://doi.org/10.1101/gr.091017.109
Article CAS PubMed PubMed Central Google Scholar
Langmead B, Salzberg S (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923
Article CAS PubMed PubMed Central Google Scholar
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 183:268–281. https://doi.org/10.1111/j.1469-0691.2011.03570.x
Majowicz SE, Musto J, Scallan E, Angulo FJ, Kirk M, O’Brien SJ, Jones TF, Fazil A, Hoekstra RM & International Collaboration on Enteric Disease ‘Burden of Illness’ Studies (2010) The global burden of nontyphoidal Salmonella gastroenteritis. Clin Infect Dis 50:882–889. https://doi.org/10.1086/650733
McClelland M, Sanderson KE, Spieth J et al (2001) Complete genome sequence of Salmonella enterica serovar typhimurium LT2. Nature 413:852–856. https://doi.org/10.1038/35101614
Article CAS PubMed Google Scholar
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 5:561–567. https://doi.org/10.1016/j.apjtb.2015.03.010
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
Article CAS PubMed PubMed Central Google Scholar
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
Article PubMed PubMed Central Google Scholar
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
Article PubMed PubMed Central Google Scholar
Okoro CK, Kingsley RA et al (2012) Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet 44:1215–1221. https://doi.org/10.1038/ng.2423
Article CAS PubMed PubMed Central Google Scholar
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
Pardo-Roa C, Salazar GA, Noguera LP, Salazar-Echegarai FJ, Vallejos OP, Suazo ID, Schultz BM, Coronado-Arrázola 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
Article CAS PubMed PubMed Central Google Scholar
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
Article CAS PubMed Google Scholar
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 30:1015–1063. https://doi.org/10.1128/CMR.00016-17
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