{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T02:08:56Z","timestamp":1785204536620,"version":"3.55.0"},"reference-count":60,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2022,6,9]],"date-time":"2022-06-09T00:00:00Z","timestamp":1654732800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Fondo de Investigaci\u00f3n Sanitaria, Instituto de Salud Carlos III, Ministerio de Econom\u00eda y Competitividad","award":["PI17\/00474"],"award-info":[{"award-number":["PI17\/00474"]}]},{"name":"Fondo de Investigaci\u00f3n Sanitaria, Instituto de Salud Carlos III, Ministerio de Econom\u00eda y Competitividad","award":["BP17-018"],"award-info":[{"award-number":["BP17-018"]}]},{"name":"European Regional Development Fund of the European Union","award":["PI17\/00474"],"award-info":[{"award-number":["PI17\/00474"]}]},{"name":"European Regional Development Fund of the European Union","award":["BP17-018"],"award-info":[{"award-number":["BP17-018"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Salmonella enterica serovar Infantis (S. Infantis) is a broiler-associated pathogen which ranks in the fourth position as a cause of human salmonellosis in the European Union. Here, we report a comparative genomic analysis of two clinical S. Infantis isolates recovered in Spain from children who just returned from Peru. The isolates were selected on the basis of resistance to cefotaxime, one of the antibiotics of choice for treatment of S. enterica infections. Antimicrobial susceptibility testing demonstrated that they were resistant to eight classes of antimicrobial agents: penicillins, cephalosporins, phenicols, aminoglycosides, tetracyclines, inhibitors of folate synthesis, (fluoro)quinolones and nitrofurans, and one of them was also resistant to fosfomycin. As shown by whole-genome sequence analysis, each isolate carried a pESI-like megaplasmid of ca. 300 kb harboring multiple resistance genes [blaCTX-M-65, aph(4)-Ia, aac(3)-IVa, aph(3\u2032)-Ia, floR, dfrA14, sul1, tet(A), aadA1 \u00b1 fosA3], as well as genes for resistance to heavy metals and disinfectants (mer, ars and qacE\u03941). These genes were distributed in two complex regions, separated by DNA belonging to the plasmid backbone, and associated with a wealth of transposable elements. The two isolates had a D87Y amino acid substitution in the GyrA protein, and truncated variants of the nitroreductase genes nfsA and nsfB, accounting for chromosomally encoded resistances to nalidixic acid and nitrofurantoin, respectively. The two S. Infantis isolates were assigned to sequence type ST32 by in silico multilocus sequence typing (MLST). Phylogenetic analysis revealed that they were closely related, differing only by 12 SNPs, although they were recovered from different children two years apart. They were also genetically similar to blaCTX-M-65-positive \u00b1 fosA3 isolates obtained from humans and along the poultry production chain in the USA, South America, as well as from humans in several European countries, usually associated with a travel history to America. However, this is the first time that the S. Infantis blaCTX-M-65 \u00b1 fosA3 MDR clone has been reported in Spain.<\/jats:p>","DOI":"10.3390\/antibiotics11060786","type":"journal-article","created":{"date-parts":[[2022,6,9]],"date-time":"2022-06-09T10:49:14Z","timestamp":1654771754000},"page":"786","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Genomic Analysis of Two MDR Isolates of Salmonella enterica Serovar Infantis from a Spanish Hospital Bearing the blaCTX-M-65 Gene with or without fosA3 in pESI-like Plasmids"],"prefix":"10.3390","volume":"11","author":[{"given":"Xenia","family":"V\u00e1zquez","sequence":"first","affiliation":[{"name":"\u00c1rea de Microbiolog\u00eda, Departamento de Biolog\u00eda Funcional, Universidad de Oviedo (UO), 33006 Oviedo, Spain"},{"name":"Instituto de Investigaci\u00f3n Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7081-0936","authenticated-orcid":false,"given":"Javier","family":"Fern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Instituto de Investigaci\u00f3n Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain"},{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain"},{"name":"Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, 33003 Oviedo, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red-Enfermedades Respiratorias, 20029 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5509-349X","authenticated-orcid":false,"given":"Jes\u00fas","family":"Rodr\u00edguez-Lozano","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla (IDIVAL), 39008 Santander, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Calvo","sequence":"additional","affiliation":[{"name":"Servicio de Microbiolog\u00eda, Hospital Universitario Marqu\u00e9s de Valdecilla (IDIVAL), 39008 Santander, Spain"},{"name":"CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosaura","family":"Rodicio","sequence":"additional","affiliation":[{"name":"Instituto de Investigaci\u00f3n Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain"},{"name":"Departamento de Bioqu\u00edmica y Biolog\u00eda Molecular, Universidad de Oviedo (UO), 33006 Oviedo, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3402-2908","authenticated-orcid":false,"given":"M. Rosario","family":"Rodicio","sequence":"additional","affiliation":[{"name":"\u00c1rea de Microbiolog\u00eda, Departamento de Biolog\u00eda Funcional, Universidad de Oviedo (UO), 33006 Oviedo, Spain"},{"name":"Instituto de Investigaci\u00f3n Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"EFSA and ECDC (European Food Safety Authority and European Centre for Disease Prevention and Control) (2021). The European Union One Health 2020 Zoonoses Report. EFSA J., 19, e06971.","DOI":"10.2903\/j.efsa.2021.6971"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Burnett, E., Ishida, M., de Janon, S., Naushad, S., Duceppe, M.O., Gao, R., Jardim, A., Chen, J.C., Tagg, K.A., and Ogunremi, D. (2021). Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum \u03b2-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands. Antibiotics, 10.","DOI":"10.3390\/antibiotics10030267"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.3201\/eid1611.100100","article-title":"Multidrug-resistant Salmonella enterica serovar Infantis, Israel","volume":"16","author":"Valinsky","year":"2010","journal-title":"Emerg. Infect. Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"324","DOI":"10.15585\/mmwr.mm6711a3","article-title":"Preliminary Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food\u2014Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2006\u20132017","volume":"67","author":"Griffin","year":"2018","journal-title":"MMWR. Morb. Mortal. Wkly. Rep."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1111\/j.1574-695X.2008.00435.x","article-title":"A comparison of three molecular typing methods for the discrimination of Salmonella enterica serovar Infantis","volume":"53","author":"Ross","year":"2008","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.vetmic.2009.07.007","article-title":"Genetic analysis of multi-drug resistance and the clonal dissemination of \u03b2-lactam resistance in Salmonella Infantis isolated from broilers","volume":"140","author":"Shahada","year":"2010","journal-title":"Vet. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1111\/1462-2920.12351","article-title":"A unique megaplasmid contributes to stress tolerance and pathogenicity of an emergent Salmonella enterica serovar Infantis strain","volume":"16","author":"Aviv","year":"2014","journal-title":"Environ. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1093\/gbe\/evaa048","article-title":"Genome Sequence of an Emerging Salmonella enterica Serovar Infantis and Genomic Comparison with Other S. Infantis Strains","volume":"12","author":"Cohen","year":"2020","journal-title":"Genome Biol. Evol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2284","DOI":"10.3201\/eid2412.180500","article-title":"CTX-M-65 Extended-Spectrum beta-Lactamase-Producing Salmonella enterica Serotype Infantis, United States(1)","volume":"24","author":"Brown","year":"2018","journal-title":"Emerg. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Franco, A., Leekitcharoenphon, P., Feltrin, F., Alba, P., Cordaro, G., Iurescia, M., Tolli, R., D\u2019Incau, M., Staffolani, M., and Di Giannatale, E. (2015). Emergence of a Clonal Lineage of Multidrug-Resistant ESBL-Producing Salmonella Infantis Transmitted from Broilers and Broiler Meat to Humans in Italy between 2011 and 2014. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0144802"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Gymoese, P., Kiil, K., Torpdahl, M., Osterlund, M.T., Sorensen, G., Olsen, J.E., Nielsen, E.M., and Litrup, E. (2019). WGS based study of the population structure of Salmonella enterica serovar Infantis. BMC Genom., 20.","DOI":"10.1186\/s12864-019-6260-6"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.3389\/fmicb.2017.01322","article-title":"Salmonella enterica serovar Infantis from Food and Human Infections, Switzerland, 2010-2015: Poultry-Related Multidrug Resistant Clones and an Emerging ESBL Producing Clonal Lineage","volume":"8","author":"Hindermann","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_13","first-page":"000658","article-title":"Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales","volume":"7","author":"Lee","year":"2021","journal-title":"Microb. Genom."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e00488-17","DOI":"10.1128\/AAC.00488-17","article-title":"Comparative Analysis of Extended-Spectrum-beta-Lactamase CTX-M-65-Producing Salmonella enterica Serovar Infantis Isolates from Humans, Food Animals, and Retail Chickens in the United States","volume":"61","author":"Tate","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e00826-19","DOI":"10.1128\/MRA.00826-19","article-title":"Whole-Genome Sequencing of a Salmonella enterica subsp. enterica Serovar Infantis Strain Isolated from Broiler Chicken in Peru","volume":"8","author":"Bendezu","year":"2019","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_16","first-page":"e000365","article-title":"Molecular epidemiology of Salmonella Infantis in Europe: Insights into the success of the bacterial host and its parasitic pESI-like megaplasmid","volume":"6","author":"Alba","year":"2020","journal-title":"Microb. Genom."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.meegid.2014.06.012","article-title":"Phylogenetic and population genetic analysis of Salmonella enterica subsp. enterica serovar Infantis strains isolated in Japan using whole genome sequence data","volume":"27","author":"Yokoyama","year":"2014","journal-title":"Infect. Genet. Evol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.cmi.2015.12.004","article-title":"Salmonellosis: The role of poultry meat","volume":"22","author":"Antunes","year":"2016","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Clark, C.G., Landgraff, C., Robertson, J., Pollari, F., Parker, S., Nadon, C., Gannon, V.P.J., Johnson, R., and Nash, J. (2020). Distribution of heavy metal resistance elements in Canadian Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0236436"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"715","DOI":"10.3389\/fmicb.2018.00715","article-title":"A comparative genomic analysis provides novel insights into the ecological success of the monophasic Salmonella serovar 4,[5],12:i","volume":"9","author":"Mastrorilli","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"11482","DOI":"10.1038\/s41598-021-90299-z","article-title":"Genomic analysis and phylogenetic position of the complex IncC plasmid found in the Spanish monophasic clone of Salmonella enterica serovar Typhimurium","volume":"11","author":"Vazquez","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1089\/mdr.2016.0227","article-title":"Incidence and Genetic Bases of Nitrofurantoin Resistance in Clinical Isolates of Two Successful Multidrug-Resistant Clones of Salmonella enterica Serovar Typhimurium: Pandemic \u201cDT 104\u201d and pUO-StVR2","volume":"23","author":"Garcia","year":"2017","journal-title":"Microb. Drug Resist."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/35101614","article-title":"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2","volume":"413","author":"McClelland","year":"2001","journal-title":"Nature"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"777817","DOI":"10.3389\/fmicb.2021.777817","article-title":"Long-Read Sequencing Reveals Evolution and Acquisition of Antimicrobial Resistance and Virulence Genes in Salmonella enterica","volume":"12","author":"Li","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"110","DOI":"10.3389\/fmicb.2012.00110","article-title":"CTX-M Enzymes: Origin and Diffusion","volume":"3","author":"Canton","year":"2012","journal-title":"Front. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1128\/AAC.49.2.862-863.2005","article-title":"High-level resistance to fluoroquinolones linked to mutations in gyrA, parC, and parE in Salmonella enterica serovar Schwarzengrund isolates from humans in Taiwan","volume":"49","author":"Baucheron","year":"2005","journal-title":"Agents Chemother."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.ijfoodmicro.2011.01.037","article-title":"Characterization of the quinolone resistance mechanism in foodborne Salmonella isolates with high nalidixic acid resistance","volume":"146","author":"Kim","year":"2011","journal-title":"Food Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Vazquez, X., Fernandez, J., Hernaez, S., Rodicio, R., and Rodicio, M.R. (2022). Plasmid-Mediated Quinolone Resistance (PMQR) in Two Clinical Strains of Salmonella enterica Serovar Corvallis. Microorganisms, 10.","DOI":"10.3390\/microorganisms10030579"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.3201\/eid1210.060589","article-title":"Ciprofloxacin-resistant Salmonella Kentucky in travelers","volume":"12","author":"Weill","year":"2006","journal-title":"Emerg. Infect. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"353","DOI":"10.2165\/00003495-200161030-00004","article-title":"An update on the role of nitrofurans in the management of urinary tract infections","volume":"61","author":"Guay","year":"2001","journal-title":"Drugs"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1139\/m75-220","article-title":"Nitrofurazone-reducing enzymes in E. coli and their role in drug activation in vivo","volume":"21","author":"McCalla","year":"1975","journal-title":"Can. J. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1093\/jac\/dkn222","article-title":"Nitrofurantoin resistance mechanism and fitness cost in Escherichia coli","volume":"62","author":"Sandegren","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"5529","DOI":"10.1128\/JB.180.21.5529-5539.1998","article-title":"Oxygen-insensitive nitroreductases: Analysis of the roles of nfsA and nfsB in development of resistance to 5-nitrofuran derivatives in Escherichia coli","volume":"180","author":"Whiteway","year":"1998","journal-title":"J. Bacteriol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2473","DOI":"10.3389\/fmicb.2018.02473","article-title":"Distribution of Arsenic Resistance Genes in Prokaryotes","volume":"9","author":"Zhang","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"187373","DOI":"10.1155\/2010\/187373","article-title":"Functional Promiscuity of Homologues of the Bacterial ArsA ATPases","volume":"2010","author":"Castillo","year":"2010","journal-title":"Int. J. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/B978-0-12-394390-3.00012-4","article-title":"Pathways of arsenic uptake and efflux","volume":"69","author":"Yang","year":"2012","journal-title":"Curr. Top. Membr."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.bj.2015.08.003","article-title":"New mechanisms of bacterial arsenic resistance","volume":"39","author":"Yang","year":"2016","journal-title":"Biomed. J."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"McMillan, E.A., Wasilenko, J.L., Tagg, K.A., Chen, J.C., Simmons, M., Gupta, S.K., Tillman, G.E., Folster, J., Jackson, C.R., and Frye, J.G. (2020). Carriage and Gene Content Variability of the pESI-Like Plasmid Associated with Salmonella Infantis Recently Established in United States Poultry Production. Genes, 11.","DOI":"10.3390\/genes11121516"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e1135","DOI":"10.1002\/mbo3.1135","article-title":"Mobile fosfomycin resistance genes in Enterobacteriaceae-An increasing threat","volume":"9","author":"Zurfluh","year":"2020","journal-title":"Microbiologyopen"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.jmii.2017.10.006","article-title":"Update on fosfomycin-modified genes in Enterobacteriaceae","volume":"52","author":"Yang","year":"2019","journal-title":"J. Microbiol. Immunol. Infect."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e01395-16","DOI":"10.1128\/mBio.01395-16","article-title":"Horizontal Transfer of the Salmonella enterica Serovar Infantis Resistance and Virulence Plasmid pESI to the Gut Microbiota of Warm-Blooded Hosts","volume":"7","author":"Aviv","year":"2016","journal-title":"mBio"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1055\/s-0039-1685502","article-title":"Presence of Extended-Spectrum \u03b2-lactamase, CTX-M-65 in Salmonella enterica serovar Infantis Isolated from Children with Diarrhea in Lima, Peru","volume":"14","author":"Granda","year":"2019","journal-title":"J. Pediatr. Infect. Dis."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Lapierre, L., Cornejo, J., Zavala, S., Galarce, N., Sanchez, F., Benavides, M.B., Guzman, M., and Saenz, L. (2020). Phenotypic and Genotypic Characterization of Virulence Factors and Susceptibility to Antibiotics in Salmonella Infantis Strains Isolated from Chicken Meat: First Findings in Chile. Animals, 10.","DOI":"10.3390\/ani10061049"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"863104","DOI":"10.3389\/fmicb.2022.863104","article-title":"Genomic comparison of eight closed genomes of multidrug resistant Salmonella enterica strains isolated from broiler farms and processing plants in Trinidad and Tobago","volume":"13","author":"Maguire","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"109109","DOI":"10.1016\/j.ijfoodmicro.2021.109109","article-title":"Dissemination of a multidrug resistant CTX-M-65 producer Salmonella enterica serovar Infantis clone between marketed chicken meat and children","volume":"344","author":"Riveros","year":"2021","journal-title":"Int. J. Food Microbiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1089\/mdr.2020.0389","article-title":"A Multidrug-Resistant Salmonella Infantis Clone is Spreading and Recombining in the United States","volume":"27","author":"Tyson","year":"2021","journal-title":"Drug Resist."},{"key":"ref_47","unstructured":"CLSI (2019). Performance Standards for Antimicrobial Susceptibility Testing, Clinical and Laboratory Standards Institute. CLSI supplement M100."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"3796","DOI":"10.1093\/bioinformatics\/btx462","article-title":"PLACNETw: A web-based tool for plasmid reconstruction from bacterial genomes","volume":"33","author":"Vielva","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1007\/978-1-4939-9877-7_21","article-title":"MOBscan: Automated Annotation of MOB Relaxases","volume":"2075","author":"Vielva","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1128\/JCM.00323-15","article-title":"Salmonella serotype determination utilizing high-throughput genome sequencing data","volume":"53","author":"Zhang","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2764","DOI":"10.1093\/jac\/dkx217","article-title":"PointFinder: A novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens","volume":"72","author":"Zankari","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Agents Chemother."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Kaas, R.S., Leekitcharoenphon, P., Aarestrup, F.M., and Lund, O. (2014). Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0104984"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"783","DOI":"10.2307\/2408678","article-title":"Confidence limits on phylogenies: An approach using the bootstrap","volume":"39","author":"Felsenstein","year":"1985","journal-title":"Evolution"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1080\/22221751.2021.1951124","article-title":"Infection dynamics of Salmonella Infantis strains displaying different genetic backgrounds\u2014with or without pESI-like plasmid\u2014Vary considerably","volume":"10","author":"Drauch","year":"2021","journal-title":"Emerg. Microbes. Infect."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Pietsch, M., Simon, S., Meinen, A., Trost, E., Banerji, S., Pfeifer, Y., and Flieger, A. (2021). Third generation cephalosporin resistance in clinical non-typhoidal Salmonella enterica in Germany and emergence of blaCTX-M-harbouring pESI plasmids. Microb. Genom., 7.","DOI":"10.1099\/mgen.0.000698"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.3389\/fmicb.2018.01880","article-title":"Colistin Resistance Mediated by mcr-1 in ESBL-Producing, Multidrug Resistant Salmonella Infantis in Broiler Chicken Industry, Italy (2016\u20132017)","volume":"9","author":"Carfora","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1007\/s00203-019-01694-0","article-title":"Construction and in vitro characterisation of aroA defective (aroA\u0394) mutant Salmonella Infantis","volume":"201","author":"Yardimci","year":"2019","journal-title":"Arch. Microbiol."}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/11\/6\/786\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:26:47Z","timestamp":1760138807000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/11\/6\/786"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,9]]},"references-count":60,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2022,6]]}},"alternative-id":["antibiotics11060786"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics11060786","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,9]]}}}