In silico Comparative Genomic Analysis of Different Salmonella enterica Subspecies enterica Strain Isolated from Chicken in Hazaribagh, Jharkhand
DOI:
https://doi.org/10.48165/jfmt.2025.42.2.29Keywords:
Comparative genomics, 16S ribosomal RNA (rRNA), Non-Typhoidal Salmonella (NTS), Salmonella enter ica, Genomic diversityAbstract
Salmonella is a major foodborne pathogen responsible for a range of human and animal infections, including gastro enteritis and invasive non-typhoidal salmonellosis. Accurate identification and classification of Salmonella strains iso lated from chicken samples are essential for epidemiological surveillance, outbreak investigation, and antimicrobial resistance monitoring. In this work, an in silico approach for analyzing the 16S ribosomal RNA (rRNA) gene is pre sented in order to characterize and determine the evolutionary links between Salmonella strains. 16S rRNA sequences were retrieved, aligned, and then made into phylogenetic trees, heatmaps, and nucleotide diversity analysis. Comparative studies between several datasets (AK01–AK04) showed different patterns of sequence variability and conservation; AK03 had the most conserved profile, whereas AK02 had the highest average nucleotide diversity. Phylogenetic heatmaps and dendrograms validated the taxonomic resolution attained by 16S analysis by further demonstrating both divergent lin eages and highly conserved clusters. Furthermore, the rise of serovars resistant to antibiotics was emphasized, highlight ing the significance of genomic methods in assessing resistance patterns. With all aspects considered this in silico process shows how useful 16S rRNA-based methods are for rapid, economical, and educational research of Salmonella diversity and advancement.
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References
Alcaine SD, Warnick LD, Wiedmann M. Antimicrobial resistance in nontyphoidal Salmonella. J Food Prot. 2007 Mar;70(3):780-790. https://doi.org/10.4315/0362-028X-70.3.780
Uelze L, Borowiak M, Deneke C, Jacobs C, Szabó I, Tausch SH, et al. First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep. Gut Pathog. 2019 Jul;11(1):48. https://doi.org/10.1186/s13099-019-0330-9
Rudder SJ, Djeghout B, Elumogo N, Janecko N, Langridge G. Genomic diversity of non-typhoidal Salmonella found in patients suffering from gastroenteritis in Norfolk, UK. bioRxiv. 2025 Mar. https://doi.org/10.1101/2025.03.06.641842
Qiu YF, Nambiar RB, Xu XB, Weng ST, Pan H, Zheng KC, et al. Global genomic characterization of Salmonella enterica serovar Telelkebir. Front Microbiol. 2021 Aug;12:704152. https://doi.org/10.3389/fmicb.2021.704152
Raghuram V, Mafuna T, Ramnath V, Gourlé H, Blom J, Magwedere K, et al. Genomic surveillance of Salmonella enterica serotype Minnesota strains from Brazilian poultry products imported into South Africa. medRxiv. 2025 Apr. https://doi.org/10.1101/2025.04.16.25325939
Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW. Genomic variation in Salmonella enterica core genes for epidemiological typing. BMC Genomics. 2012 Feb;13:88. https://doi.org/10.1186/1471-2164-13-88
Cui L, Wang X, Zhao Y, Peng Z, Gao P, Cao Z, et al. Virulence comparison of Salmonella enterica subsp. enterica isolates from chicken and whole genome analysis of the highly virulent strain S. Enteritidis 211. Microorganisms. 2021 Nov;9(11):2239. https://doi.org/10.3390/microorganisms9112239
Zhao S, Li C, Hsu CH, Tyson GH, Strain E, Tate H, et al. Comparative genomic analysis of 450 strains of Salmonella enterica isolated from diseased animals. Genes (Basel). 2020 Sep;11(9):1025. https://doi.org/10.3390/genes11091025
Dudhane RA, Bankar NJ, Shelke YP, Badge AK, Badge A. The rise of non-typhoidal Salmonella infections in India: Causes, symptoms, and prevention. Cureus. 2023 Jul;15:e46699. https://doi.org/10.7759/cureus.46699
Adzitey F, Awini Tibile B, Addy F, Adu-Bonsu G, Atsu Amagloh AS, Noyoro EJ, et al. Occurrence, antimicrobial susceptibility and genomic characterization of Salmonella enterica isolated from milk and related sources. Cogent Food Agric. 2025 Jan;11(1):2486330. https://doi.org/10.1080/23311932.2025.2486330
Hoffmann M, Zhao S, Pettengill J, Luo Y, Monday SR, Abbott J, et al. Comparative genomic analysis and virulence differences in closely related Salmonella enterica serotype Heidelberg isolates from humans, retail meats, and animals. Genome Biol Evol. 2014 May;6(5):1046-1068. https://doi.org/10.1093/gbe/evu079
Huang J, Alzahrani KO, Zhou G, Alsalman SA, Alsufyani AT, Alotaibi NM, et al. Genomic survey of multidrug resistant Salmonella enterica serovar Minnesota clones in chicken products. npj Antimicrob Resist. 2025 Feb;3(1):10. https://doi.org/10.1038/s44259-025-00077-4
Wang Y, Jia B, Xu X, Zhang L, Wei C, Ou H, et al. Comparative genomic analysis and characterization of two Salmonella enterica serovar Enteritidis isolates from poultry with notably different survival abilities in egg whites. Front Microbiol. 2018 Sep;9:2111. https://doi.org/10.3389/fmicb.2018.02111
Gao R, Naushad S, Moineau S, Levesque R, Goodridge L, Ogunremi D. Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica. BMC Genomics. 2020 Jan;21(1):13. https://doi.org/10.1186/s12864-020-6765-z
Lee W, Kim E, Zin H, Sung S, Woo J, Lee MJ, et al. Genomic characteristics and comparative genomics analysis of Salmonella enterica subsp. enterica serovar Thompson isolated from an outbreak in South Korea. Sci Rep. 2022 Nov;12(1):20553. https://doi.org/10.1038/s41598-022-22168-2
Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Dore J. A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res. 2008 Sep;36(16):5180-5188. https://doi.org/10.1093/nar/gkn496
Watts GS, Youens-Clark K, Slepian MJ, Wolk DM, Oshiro MM, Metzger GS, et al. 16S rRNA gene sequencing on a benchtop sequencer: Accuracy for identification of clinically important bacteria. J Appl Microbiol. 2017 Dec;123(6):1584-1596. https://doi.org/10.1111/jam.13590
Clarridge JE III. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev. 2004 Oct;17(4):840-862. https://doi.org/10.1128/cmr.17.4.840-862.2004
Falcäo LL, Silva-Werneck JO, Vilarinho BR, Da Silva JP, Pomella AWV, Marcellino LH. Antimicrobial and plant growth-promoting properties of the cacao endophyte Bacillus subtilis ALB629. J Appl Microbiol. 2014 Jun;116(6):1584-1592. https://doi.org/10.1111/jam.12485
Cilia V, Lafay B, Christen R. Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol Biol Evol. 1996 Mar;13(3):451-461. https://doi.org/10.1093/oxfordjournals.molbev.a025606
Wan Makhtar WR, Bharudin I, Samsulrizal NH, Yusof NY. Whole genome sequencing analysis of Salmonella enterica serovar Typhi: History and current approaches. Microorganisms. 2021 Oct;9(10):2155. https://doi.org/10.3390/microorganisms9102155
Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C. The Salmonella enterica pan-genome. Microb Ecol. 2011 Nov;62(3):487-487. https://doi.org/10.1007/s00248-011-9880-1
Stanley J, Baquar N, Threlfall EJ. Genotypes and phylogenetic relationships of Salmonella typhimurium defined by molecular fingerprinting of IS200 and 16S rrn loci. Microbiology (Reading). 1993 Jun;139(6):1133-1140. https://doi.org/10.1099/00221287-139-6-1133
Tajbakhsh M, Nayer BN, Motavaze K, Kharaziha P, Chiani M, Zali MR, et al. Phylogenetic relationship of Salmonella enterica strains in Tehran, Iran, using 16S rRNA and gyrB gene sequences. J Infect Dev Ctries. 2011 Jun;5(6):465-472. https://doi.org/10.3855/jidc.1504
Ponce AG, Roura SI, del Valle CE, Moreira MR. Antimicrobial and antioxidant activities of edible coatings enriched with natural plant extracts: In vitro and in vivo studies. Postharvest Biol Technol. 2008 May;49(2):294-300. https://doi.org/10.1016/j.postharvbio.2008.02.013
Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: Pluses, perils, and pitfalls. J Clin Microbiol. 2007 Sep;45(9):2761-2764. https://doi.org/10.1128/jcm.01228-07
Kim M, Chun J. 16S rRNA gene-based identification of bacteria and archaea using the EzTaxon server. Methods Microbiol. 2014 Aug;41:61-74. https://doi.org/10.1016/bs.mim.2014.08.001
Stackebrandt E, Goebel BM. Taxonomic note: A place for DNA–DNA reassociation and 16S rRNA sequence analysis in species definition in bacteriology. Int J Syst Evol Microbiol. 1994 Aug;44(4):846-849. https://doi.org/10.1099/00207713-44-4-846
Ashrafudoulla M, Na KW, Byun KH, Kim DH, Yoon JW, Mizan MFR, et al. Isolation and characterization of Salmonella spp. from food and food contact surfaces in a chicken processing factory. Poult Sci. 2021 Aug;100(8):101234. https://doi.org/10.1016/j.psj.2021.101234
Ibrahim A, Goebel BM, Liesack W, Griffiths M, Stackebrandt E. The phylogeny of the genus Yersinia based on 16S rDNA sequences. FEMS Microbiol Lett. 1993 Dec;114(2):173-177. https://doi.org/10.1111/j.1574-6968.1993.tb06576.x
