Alikhan NF, Petty NK, Ben Zakour NL et al (2011) BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12:402. https://doi.org/10.1186/1471-2164-12-402
Article CAS PubMed PubMed Central Google Scholar
Alikhan NF, Zhou Z, Sergeant MJ et al (2018) A genomic overview of the population structure of Salmonella. PLoS Genet 5(4):e1007261. https://doi.org/10.1371/journal.pgen.1007261
Allard MW, Bell R, Ferreira CM, Gonzalez et al (2018) Genomics of foodborne pathogens for microbial food safety. Curr Opin Biotechnol 49:224–229. https://doi.org/10.1016/j.copbio.2017.11.002
Article CAS PubMed Google Scholar
Argudín MA, Hoefer A, Butaye P (2019) Heavy metal resistance in bacteria from animals. Res Vet Sci 122:132–147. https://doi.org/10.1016/j.rvsc.2018.11.007
Article CAS PubMed Google Scholar
Autexier C, DuBow MS (1992) The Escherichia coli Mu/D108 phage ner homologue gene (nlp) is transcribed and evolutionarily conserved among the Enterobacteriaceae. Gene 1;114(1):13– 8. https://doi.org/10.1016/0378-1119(92)90701-p
Bortolaia V, Kaas RS, Ruppe E et al (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75(12):3491–3500. https://doi.org/10.1093/jac/dkaa345
Article CAS PubMed PubMed Central Google Scholar
Brown EW, Bell R, Zhang G et al (2021) Salmonella genomics in public health and food safety. EcoSal Plus 9(2):eESP00082020. https://doi.org/10.1128/ecosalplus.ESP-0008-2020
Brüssow H, Canchaya C, Hardt WD (2004) Phagesand the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 68(3):560–602, table of contents. https://doi.org/10.1128/MMBR.68.3.560-602.2004
Campioni F, Cao G, Kastanis G et al (2018) Changing of the genomic pattern of Salmonella Enteritidis strains isolated in Brazil over a 48 year-period revealed by whole genome SNP analyses. Sci Rep 8(1):10478. https://doi.org/10.1038/s41598-018-28844-6
Article CAS PubMed PubMed Central Google Scholar
Carattoli A, Zankari E, García-Fernández A et al (2014) In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58(7):3895–3903. https://doi.org/10.1128/AAC.02412-14
Article CAS PubMed PubMed Central Google Scholar
Carneiro DG, Vidigal PMP, Morgan T et al (2024) Genome sequencing and analysis of Salmonella enterica subsp. enterica serotype enteritidis PT4 578: insights into pathogenicity and virulence. Access Microbiol 6(11):000828v3. https://doi.org/10.1099/acmi.0.000828.v3
U.S. Center for Disease Control and Prevention (CDC) (2023) Salmonella - Information for Healthcare Professionals and Laboratories. Available at https://www.cdc.gov/salmonella/general/technical.html. Accessed in November 13th, 2024
U.S. Center for Disease Control and Prevention (CDC) (2018) National Enteric Disease Surveillance: Salmonella Annual Report, 2016. Available at https://www.cdc.gov/nationalsurveillance/pdfs/2016-Salmonella-report-508.pdf
Center for Disease Control and Prevention (CDC) (2023) Salmonellosis, Nontyphoidal. CDC Yellow Book 2024. Available at https://wwwnc.cdc.gov/travel/yellowbook/2024/infections-diseases/salmonellosis-nontyphoidal
Clinical and Laboratory Standards Institute (CLSI) (2023) Performance Standards for Antimicrobial Susceptibility Testing. 33th edition. CLSI supplement M100. Wayne, PA: Clinical and Laboratory Standards Institute
Eaves DJ, Randall L, Gray DT et al (2004) Prevalence of mutations within the quinolone resistance-determining region of gyrA, gyrB, parC, and ParE and association with antibiotic resistance in quinolone-resistant Salmonella enterica. Antimicrob Agents Chemother 48(10):4012–4015. https://doi.org/10.1128/AAC.48.10.4012-4015.2004
Article CAS PubMed PubMed Central Google Scholar
European Food Safety Authority (EFSA), European Center for Disease Prevention and Control (ECDC) (2021) The European union one health 2019 zoonoses report. EFSA J 19(2):e06406. https://doi.org/10.2903/j.efsa.2021.6406
Article PubMed Central Google Scholar
Faa G, Gerosa C, Fanni D et al (2018) Gold - Old drug with new potentials. Curr Med Chem 25(1):75–84. https://doi.org/10.2174/0929867324666170330091438
Article CAS PubMed Google Scholar
Feldgarden M, Brover V, Haft DH et al (2019) Validating the amrfinder tool and resistance gene database by using antimicrobial resistance Genotype-Phenotype correlations in a collection of isolates. Antimicrob Agents Chemother 63(11):e00483–e00419. https://doi.org/10.1128/AAC.00483-19
Article CAS PubMed PubMed Central Google Scholar
Gao R, Naushad S, Moineau S et al (2020) Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica. BMC Genomics 26(211):374. https://doi.org/10.1186/s12864-020-6765-z
Gilmour MW, Graham M, Reimer A et al (2013) Public health genomics and the new molecular epidemiology of bacterial pathogens. Public Health Genomics 16(1–2):25–30. https://doi.org/10.1159/000342709
Article CAS PubMed Google Scholar
Haghjoo E, Galán JE (2004) Salmonella typhi encodes a functional cytolethal distending toxin that is delivered into host cells by a bacterial-internalization pathway. Proc Natl Acad Sci USA 101(13):4614–4619. https://doi.org/10.1073/pnas.0400932101
Article CAS PubMed PubMed Central Google Scholar
Hasegawa LA, Vilela FP, Falcão JP (2024) Antimicrobial resistance, virulence potential and genomic epidemiology of global genomes of the rare Salmonella enterica serovar Orion. Zoonoses Public Health 71(5):591–599. https://doi.org/10.1111/zph.13140
Article CAS PubMed Google Scholar
Hurley D, McCusker MP, Fanning S et al (2014) Salmonella-host interactions - modulation of the host innate immune system. Front Immunol 5:481. https://doi.org/10.3389/fimmu.2014.00481
Article CAS PubMed PubMed Central Google Scholar
Ikuta KS, Swetschinski LR, Aguilar GR et al (2022) Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the global burden of disease study 2019. Lancet 400(10369):2221–2248. https://doi.org/10.1016/S0140-6736(22)02185-7
Ju X, Wang S, Yang X et al (2022) Epidemiology and Molecular Characteristics of mcr-9 in Citrobacter spp. from Healthy Individuals and Patients in China. Microbiol Spectr 10(6):e0134622. https://doi.org/10.1128/spectrum.01346-22
Kingsley RA, Humphries AD, Weening EH et al (2003) Molecular and phenotypic analysis of the CS54 Island of Salmonella enterica serotype typhimurium: identification of intestinal colonization and persistence determinants. Infect Immun 71(2):629–640. https://doi.org/10.1128/IAI.71.2.629–640.2003
Kraychete GB, Botelho LAB, Monteiro-Dias PV et al (2022) qnrVC occurs in different genetic contexts in Klebsiella and Enterobacter strains isolated from Brazilian coastal waters. J Glob Antimicrob Resist 31:38–44. https://doi.org/10.1016/j.jgar.2022.08.004
Larsen MV, Cosentino S, Rasmussen S et al (2012) Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50(4):1355–1361. https://doi.org/10.1128/JCM.06094-11
Article CAS PubMed PubMed Central Google Scholar
Lee W, Kim E, Zin H et al (2022) Genomic characteristics and comparative genomics analysis of Salmonella enterica subsp. enterica serovar Thompson isolated from an outbreak in South Korea. Sci Rep 29(121):20553. https://doi.org/10.1038/s41598-022-22168-2
Liu B, Zheng D, Jin Q et al (2019) VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 47D1:D687–D692. https://doi.org/110.1093/nar/gky1080
Meneguzzi M, Pissetti C, Rebelatto R et al (2021) Re-Emergence of salmonellosis in hog farms: outbreak and bacteriological characterization. Microorganisms 9(5):947. https://doi.org/10.3390/microorganisms9050947
Article CAS PubMed PubMed Central Google Scholar
Monte DFM, Nethery MA, Barrangou R (2021) Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources. Food Microbiol 93:103601. https://doi.org/10.1016/j.fm.2020.103601
Article CAS PubMed Google Scholar
Nossair MA, Habib HM, Mansour AM et al (2023) Antimicrobial resistance of Salmonella species isolated from some food products and human in Alexandria, Egypt. J Adv Vet Anim Res 13(9):1803–1808
Osman KM, Marouf SH, Zolnikov TR et al (2014) Isolation and characterization of Salmonella enterica in day-old ducklings in Egypt. Pathog Glob Health 108(1):37–48. https://doi.org/10.1179/2047773213Y.0000000118
Article CAS PubMed PubMed Central Google Scholar
Pradhan D, Devi Negi V (2019) Stress-induced adaptations in Salmonella: A ground for shaping its pathogenesis. Microbiol Res 229:126311. https://doi.org/10.1016/j.micres.2019.126311
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