{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:00:16Z","timestamp":1791385216314,"version":"4.3.3"},"reference-count":61,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2022,8,27]],"date-time":"2022-08-27T00:00:00Z","timestamp":1661558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Proyecto Concytec\u2013Banco Mundial \u201cMejoramiento y Ampliaci\u00f3n de los Servicios del Sistema Nacional de Ciencia Tecnolog\u00eda e Innovaci\u00f3n Tecnol\u00f3gica\u201d 8682-PE","award":["135-2018-FONDECYT-BM-IADT-AV"],"award-info":[{"award-number":["135-2018-FONDECYT-BM-IADT-AV"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is one of the most important foodborne pathogens that infect humans globally. The gastrointestinal tracts of animals like pigs, poultry or cattle are the main reservoirs of Salmonella serotypes. Guinea pig meat is an important protein source for Andean countries, but this animal is commonly infected by S. Typhimurium, producing high mortality rates and generating economic losses. Despite its impact on human health, food security, and economy, there is no genomic information about the S. Typhimurium responsible for the guinea pig infections in Peru. Here, we sequence and characterize 11 S. Typhimurium genomes isolated from guinea pigs from four farms in Lima-Peru. We were able to identify two genetic clusters (HC100_9460 and HC100_9757) distinguishable at the H100 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing (HierCC-cgMLST) scheme with an average of 608 SNPs of distance. All sequences belonged to sequence type 19 (ST19) and HC100_9460 isolates were typed in silico as monophasic variants (1,4,[5],12:i:-) lacking the fljA and fljB genes. Phylogenomic analysis showed that human isolates from Peru were located within the same genetic clusters as guinea pig isolates, suggesting that these lineages can infect both hosts. We identified a genetic antimicrobial resistance cassette carrying the ant(3)-Ia, dfrA15, qacE, and sul1 genes associated with transposons TnAs3 and IS21 within an IncI1 plasmid in one guinea pig isolate, while antimicrobial resistance genes (ARGs) for \u03b2-lactam (blaCTX-M-65) and colistin (mcr-1) resistance were detected in Peruvian human-derived isolates. The presence of a virulence plasmid highly similar to the pSLT plasmid (LT2 reference strain) containing the spvRABCD operon was found in all guinea pig isolates. Finally, seven phage sequences (STGP_\u03a61 to STGP_\u03a67) were identified in guinea pig isolates, distributed according to the genetic lineage (H50 clusters level) and forming part of the specific gene content of each cluster. This study presents, for the first time, the genomic characteristics of S. Typhimurium isolated from guinea pigs in South America, showing particular diversity and genetic elements (plasmids and prophages) that require special attention and also broader studies in different periods of time and locations to determine their impact on human health.<\/jats:p>","DOI":"10.3390\/microorganisms10091726","type":"journal-article","created":{"date-parts":[[2022,8,29]],"date-time":"2022-08-29T03:34:56Z","timestamp":1661744096000},"page":"1726","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Genomic Characterization of Salmonella Typhimurium Isolated from Guinea Pigs with Salmonellosis in Lima, Peru"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0449-8905","authenticated-orcid":false,"given":"Dennis E.","family":"Carhuaricra Huaman","sequence":"first","affiliation":[{"name":"Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, San Borja, Lima 15021, Peru"},{"name":"Programa de P\u00f3s-Gradua\u00e7\u00e3o Interunidades em Bioinform\u00e1tica, Instituto de Matem\u00e1tica e Estat\u00edstica, Universidade de S\u00e3o Paulo, Rua do Mat\u00e3o 1010, S\u00e3o Paulo CEP 05508-090, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3135-4066","authenticated-orcid":false,"given":"Luis R.","family":"Luna Espinoza","sequence":"additional","affiliation":[{"name":"Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, San Borja, Lima 15021, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0975-6122","authenticated-orcid":false,"given":"Carmen L.","family":"Rodr\u00edguez Cueva","sequence":"additional","affiliation":[{"name":"Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, San Borja, Lima 15021, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7679-0817","authenticated-orcid":false,"given":"Carla G.","family":"Duran Gonzales","sequence":"additional","affiliation":[{"name":"Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, San Borja, Lima 15021, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ra\u00fal H.","family":"Rosadio Alc\u00e1ntara","sequence":"additional","affiliation":[{"name":"Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, San Borja, Lima 15021, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9174-2816","authenticated-orcid":false,"given":"Jo\u00e3o C.","family":"Setubal","sequence":"additional","affiliation":[{"name":"Departamento de Bioqu\u00edmica, Instituto de Qu\u00edmica, Universidade de S\u00e3o Paulo, Av. Prof. Lineu Prestes, 748-Cidade Universit\u00e1ria, S\u00e3o Paulo CEP 05508-000, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8819-7335","authenticated-orcid":false,"given":"Lenin","family":"Maturrano Hern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, San Borja, Lima 15021, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Havelaar, A.H., Kirk, M.D., Torgerson, P.R., Gibb, H.J., Hald, T., Lake, R.J., Praet, N., Bellinger, D.C., de Silva, N.R., and Gargouri, N. (2015). World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010. PLoS Med., 12.","DOI":"10.1371\/journal.pmed.1001923"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"European Centre for Disease Prevention and Control (2017). The European Union Summary Report on Trends and Sources of Zoonoses, Zoonotic Agents and Food-Borne Outbreaks in 2016. EFSA J., 15, e05077.","DOI":"10.2903\/j.efsa.2017.5077"},{"key":"ref_3","unstructured":"(2022, August 03). National Salmonella Surveillance Annual Report, Available online: https:\/\/www.cdc.gov\/nationalsurveillance\/salmonella-surveillance.html."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e00079-18","DOI":"10.1128\/IAI.00079-18","article-title":"Genome Variation and Molecular Epidemiology of Salmonella Enterica Serovar Typhimurium Pathovariants","volume":"86","author":"Branchu","year":"2018","journal-title":"Infect. Immun."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Okoro, C.K., Barquist, L., Connor, T.R., Harris, S.R., Clare, S., Stevens, M.P., Arends, M.J., Hale, C., Kane, L., and Pickard, D.J. (2015). Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa. PLoS Negl. Trop. Dis., 9.","DOI":"10.1371\/journal.pntd.0003848"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Bawn, M., Alikhan, N.-F., Thilliez, G., Kirkwood, M., Wheeler, N.E., Petrovska, L., Dallman, T.J., Adriaenssens, E.M., Hall, N., and Kingsley, R.A. (2020). Evolution of Salmonella Enterica Serotype Typhimurium Driven by Anthropogenic Selection and Niche Adaptation. PLoS Genet., 16.","DOI":"10.1371\/journal.pgen.1008850"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s42003-021-02013-4","article-title":"Ecological Niche Adaptation of Salmonella Typhimurium U288 Is Associated with Altered Pathogenicity and Reduced Zoonotic Potential","volume":"4","author":"Kirkwood","year":"2021","journal-title":"Commun. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Arrieta-Gisasola, A., Atxaerandio-Landa, A., Garrido, V., Grill\u00f3, M.J., Mart\u00ednez-Ballesteros, I., Laorden, L., Garaizar, J., and Bikandi, J. (2020). Genotyping Study of Salmonella 4,[5],12:I:- Monophasic Variant of Serovar Typhimurium and Characterization of the Second-Phase Flagellar Deletion by Whole Genome Sequencing. Microorganisms, 8.","DOI":"10.3390\/microorganisms8122049"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1089\/fpd.2019.2676","article-title":"The Epidemiology of Monophasic Salmonella Typhimurium","volume":"17","author":"Sun","year":"2020","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/nrg.2017.88","article-title":"Towards a Genomics-Informed, Real-Time, Global Pathogen Surveillance System","volume":"19","author":"Gardy","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2879","DOI":"10.1038\/s41467-021-23091-2","article-title":"A Global Resource for Genomic Predictions of Antimicrobial Resistance and Surveillance of Salmonella Typhi at Pathogenwatch","volume":"12","author":"Yeats","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"8901","DOI":"10.1038\/s41598-020-65784-6","article-title":"Ancient DNA of Guinea Pigs (Cavia Spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution","volume":"10","author":"Lord","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.meatsci.2018.05.004","article-title":"Guinea Pig for Meat Production: A Systematic Review of Factors Affecting the Production, Carcass and Meat Quality","volume":"143","year":"2018","journal-title":"Meat Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1038\/s41576-018-0032-z","article-title":"Population Genomics of Bacterial Host Adaptation","volume":"19","author":"Sheppard","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"11018","DOI":"10.1073\/pnas.1917168117","article-title":"Agricultural Intensification and the Evolution of Host Specialism in the Enteric Pathogen Campylobacter Jejuni","volume":"117","author":"Mourkas","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_16","first-page":"93","article-title":"Susceptibilidad a Antibacterianos in Vitro de Salmonella Enterica Aislada de Cuyes de Crianza Familiar-Comercial En La Provincia de Carhuaz, \u00c1ncash","volume":"21","author":"Matsuura","year":"2010","journal-title":"Rev. Investig. Vet. Per\u00fa"},{"key":"ref_17","unstructured":"Moya, A.L. (2019). Prevalencia de Salmonelosis en Cuyes (Cavia porcellus) Procedentes de Granjas del Centro Poblado Huancaquito Alto\u2013Vir\u00fa\u2013La Libertad, Universidad Privada Antenor Orrego\u2013UPAO."},{"key":"ref_18","first-page":"e864640","article-title":"Family Outbreaks of Nontyphoidal Salmonellosis Following a Meal of Guinea Pigs","volume":"2015","author":"Fournier","year":"2015","journal-title":"Case Rep. Infect. Dis."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"411","DOI":"10.15381\/rivep.v28i2.13074","article-title":"Identificaci\u00f3n de Salmonella Enteritidis y Salmonella Typhimurium En Cuyes Mediante La T\u00e9cnica de PCR M\u00faltiple","volume":"28","author":"Marcelo","year":"2017","journal-title":"Rev. Investig. Vet. Per\u00fa"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1038\/s41564-022-01124-w","article-title":"A Bottom-up View of Antimicrobial Resistance Transmission in Developing Countries","volume":"7","author":"Ikhimiukor","year":"2022","journal-title":"Nat. Microbiol."},{"key":"ref_21","unstructured":"Jamshidi, A., Kalidari, G.A., and Hedayati, M. (2022, August 06). Isolation and Identification of Salmonella Enteritidis and Salmonella Typhimurium from the Eggs of Retail Stores in Mashhad, Iran Using Conventional Culture Method and Multiplex Pcr Assay. Available online: https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1111\/j.1745-4565.2010.00225.x."},{"key":"ref_22","unstructured":"Andrews, S. (2022, May 16). FastQC A Quality Control Tool for High Throughput Sequence Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid Phylogenetic Analysis of Large Samples of Recombinant Bacterial Whole Genome Sequences Using Gubbins","volume":"43","author":"Croucher","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"Ggtree: An r Package for Visualization and Annotation of Phylogenetic Trees with Their Covariates and other Associated Data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol. Evol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e01746-19","DOI":"10.1128\/AEM.01746-19","article-title":"SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data","volume":"85","author":"Zhang","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"4333","DOI":"10.1038\/s41598-020-61254-1","article-title":"Genome-Based Salmonella Serotyping as the New Gold Standard","volume":"10","author":"Banerji","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: A Better, Faster Version of the PHAST Phage Search Tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Alikhan, N.-F., Petty, N.K., Ben Zakour, N.L., and Beatson, S.A. (2011). BLAST Ring Image Generator (BRIG): Simple Prokaryote Genome Comparisons. BMC Genomics, 12.","DOI":"10.1186\/1471-2164-12-402"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Wickham, H. (2016). Ggplot2: Elegant Graphics for Data Analysis, Springer. [1st ed.].","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"ref_34","unstructured":"Chauca, L. (1997). Producci\u00f3n de Cuyes (Cavia Porcellus), FAO."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"319","DOI":"10.15381\/rivep.v29i1.14089","article-title":"Resistencia Antimicrobiana y Genotipificaci\u00f3n de Cepas de Salmonella Typhimurium Aisladas de Cuyes (Cavia Porcellus) Provenientes de Granjas de Producci\u00f3n Intensiva de La Ciudad de Lima, Per\u00fa","volume":"29","author":"Salvatierra","year":"2018","journal-title":"Rev. Investig. Vet. Per\u00fa"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e21331","DOI":"10.15381\/rivep.v32i5.21331","article-title":"Evaluaci\u00f3n de Factores de Virulencia En Cepas de Salmonella Typhimurium Aisladas de Cuyes (Cavia Porcellus) Enfermos y Sanos","volume":"32","year":"2021","journal-title":"Rev. Investig. Vet. Per\u00fa"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Ido, N., Lee, K., Iwabuchi, K., Izumiya, H., Uchida, I., Kusumoto, M., Iwata, T., Ohnishi, M., and Akiba, M. (2014). Characteristics of Salmonella Enterica Serovar 4,[5],12:I:- As a Monophasic Variant of Serovar Typhimurium. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0104380"},{"key":"ref_38","first-page":"722","article-title":"Molecular and Phenotypic Characterization of Salmonella Typhimurium Monophasic Variant (1,4,[5],12:I:-) From Colombian Clinical Isolates","volume":"40","author":"Villarreal","year":"2020","journal-title":"Biomed. Rev. Inst. Nac. Salud"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e17542","DOI":"10.15381\/rivep.v31i1.17542","article-title":"Caracterizaci\u00f3n Gen\u00e9tica y Patrones de Resistencia Antimicrobiana En Cepas de Salmonella Enterica Subsp. Enterica Serovar Typhimurium En Cuyes de Crianza Intensiva","volume":"31","author":"Killerby","year":"2020","journal-title":"Rev. Investig. Vet. Per\u00fa"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.15585\/mmwr.mm6742a6","article-title":"Notes from the Field: Recurrence of a Multistate Outbreak of Salmonella Enteritidis Infections Linked to Contact with Guinea Pigs\u2013Eight States, 2015\u20132017","volume":"67","author":"Robertson","year":"2018","journal-title":"Morb. Mortal. Wkly. Rep."},{"key":"ref_41","first-page":"1975530","article-title":"Zoonotic Potential and Prevalence of Salmonella Serovars Isolated from Pets","volume":"11","author":"Paluch","year":"2021","journal-title":"Infect. Ecol. Epidemiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2225","DOI":"10.3201\/eid1012.040286","article-title":"Animal-to-Human Transmission of Salmonella Typhimurium DT104A Variant","volume":"10","author":"Hendriksen","year":"2004","journal-title":"Emerg. Infect. Dis."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2709","DOI":"10.1098\/rstb.2009.0094","article-title":"Molecular Insights into Farm Animal and Zoonotic Salmonella Infections","volume":"364","author":"Stevens","year":"2009","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1089\/fpd.2009.0411","article-title":"Transmission Dynamics of a Multidrug-Resistant Salmonella Typhimurium Outbreak in a Dairy Farm","volume":"7","author":"Lanzas","year":"2010","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1093\/molbev\/msg074","article-title":"Determining the Limits of the Evolutionary Potential of an Antibiotic Resistance Gene","volume":"20","author":"Salipante","year":"2003","journal-title":"Mol. Biol. Evol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"e02829.17","DOI":"10.1128\/AEM.02829-17","article-title":"Serotype Diversity and Antimicrobial Resistance among Salmonella Enterica Isolates from Patients at an Equine Referral Hospital","volume":"84","author":"Leon","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Almeida, F., Seribelli, A.A., Medeiros, M.I.C., Rodrigues, D.D.P., de MelloVarani, A., Luo, Y., Allard, M.W., and Falc\u00e3o, J.P. (2018). Phylogenetic and Antimicrobial Resistance Gene Analysis of Salmonella Typhimurium Strains Isolated in Brazil by Whole Genome Sequencing. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0201882"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1864","DOI":"10.3389\/fmicb.2020.01864","article-title":"Frequency of Antimicrobial Resistance Genes in Salmonella from Brazil by in Silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades","volume":"11","author":"Rodrigues","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/0010-406X(69)90812-3","article-title":"Effect of Antibiotics on Intestinal Absorption in Guinea-Pigs","volume":"30","author":"Madge","year":"1969","journal-title":"Comp. Biochem. Physiol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"e00140-17","DOI":"10.1128\/AEM.00140-17","article-title":"Whole-Genome Sequencing of Drug-Resistant Salmonella Enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations","volume":"83","author":"Carroll","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"e01435-19","DOI":"10.1128\/MRA.01435-19","article-title":"Whole-Genome Sequences of 66 Incompatibility Group FIB Plasmid-Carrying Salmonella Enterica Serovar Typhimurium Isolates from Food Animal Sources","volume":"9","author":"Aljahdali","year":"2020","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"4926","DOI":"10.1128\/AAC.00133-11","article-title":"F33:A\u2212:B\u2212 and F2:A\u2212:B\u2212 Plasmids Mediate Dissemination of RmtB-BlaCTX-M-9 Group Genes and RmtB-QepA in Enterobacteriaceae Isolates from Pets in China","volume":"55","author":"Deng","year":"2011","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Han, J., Lynne, A.M., David, D.E., Tang, H., Xu, J., Nayak, R., Kaldhone, P., Logue, C.M., and Foley, S.L. (2012). DNA Sequence Analysis of Plasmids from Multidrug Resistant Salmonella Enterica Serotype Heidelberg Isolates. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0051160"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"102392","DOI":"10.1016\/j.plasmid.2018.12.001","article-title":"Contemporary IncI1 Plasmids Involved in the Transmission and Spread of Antimicrobial Resistance in Enterobacteriaceae","volume":"118","author":"Carattoli","year":"2021","journal-title":"Plasmid"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"e00056-20","DOI":"10.1128\/mSphere.00056-20","article-title":"Emergence of a Novel Salmonella Enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America","volume":"5","author":"Miller","year":"2020","journal-title":"mSphere"},{"key":"ref_56","first-page":"873","article-title":"Dutch Patients, Retail Chicken Meat and Poultry Share the Same ESBL Genes, Plasmids and Strains","volume":"17","author":"Dierikx","year":"2011","journal-title":"Clin. Microbiol. Infect. Off. Publ. Eur. Soc. Clin. Microbiol. Infect. Dis."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.plasmid.2011.07.003","article-title":"Comparative Genomics and Phylogeny of the IncI1 Plasmids: A Common Plasmid Type among Porcine Enterotoxigenic Escherichia Coli","volume":"66","author":"Johnson","year":"2011","journal-title":"Plasmid"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"e00418-20","DOI":"10.1128\/mSphere.00418-20","article-title":"The Association between Insertion Sequences and Antibiotic Resistance Genes","volume":"5","author":"Razavi","year":"2020","journal-title":"mSphere"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"836","DOI":"10.3389\/fmicb.2018.00836","article-title":"Salmonella Enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping","volume":"9","author":"Mottawea","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Parker, C.T., Huynh, S., Alexander, A., Oliver, A.S., and Cooper, K.K. (2021). Genomic Characterization of Salmonella Typhimurium DT104 Strains Associated with Cattle and Beef Products. Pathogens, 10.","DOI":"10.3390\/pathogens10050529"},{"key":"ref_61","first-page":"391","article-title":"Same Species, Different Diseases: How and Why Typhoidal and Non-Typhoidal Salmonella Enterica Serovars Differ","volume":"5","author":"Boyle","year":"2014","journal-title":"Front. Microbiol."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/9\/1726\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:16:19Z","timestamp":1760141779000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/9\/1726"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8,27]]},"references-count":61,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2022,9]]}},"alternative-id":["microorganisms10091726"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms10091726","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,8,27]]}}}