{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T18:40:12Z","timestamp":1791312012310,"version":"4.3.1"},"reference-count":90,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,5,10]],"date-time":"2026-05-10T00:00:00Z","timestamp":1778371200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hakkari University Scientific Research Projects Coordination Unit","award":["FM23LTP2"],"award-info":[{"award-number":["FM23LTP2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Veterinary Sciences"],"abstract":"<jats:p>Bacteria associated with unhatched sea turtle eggs remain poorly characterized at the genomic level. This study provides genome-scale characterization of bacterial isolates recovered from unhatched green sea turtle (Chelonia mydas) eggs at Akyatan Beach\u2014a critical nesting site in the Eastern Mediterranean. Sampling 30 nests during the nesting season, we isolated bacteria from infected eggshells and dead embryos. Following Matrix-Assisted Laser Desorption\/Ionization Time-of-Flight Mass Spectrometry(MALDI-TOF MS) identification and 16S rRNA validation, we performed whole-genome sequencing (WGS) on Citrobacter farmeri and Enterobacter cloacae, two opportunistic pathogens of significant clinical and ecological concern. High-quality draft genomes revealed remarkable metabolic versatility, particularly within carbon and nitrogen pathways. Most notably, we identified extensive resistomes including resistance to \u03b2-lactams, fluoroquinolones, and aminoglycosides, alongside virulence factors for adhesion and iron acquisition. ANI analysis confirmed high genomic similarity to clinical reference strains, comparative genomic analysis revealed a substantial accessory gene pool, suggesting potential genomic flexibility between the two isolates. These findings provide the first genome-scale insight into these pathogens in C. mydas nests, and highlighting their genomic potential for opportunistic pathogenicity. Our results advocate for integrating genomic microbial surveillance into nesting beach management through a \u2018One Health\u2019 lens.<\/jats:p>","DOI":"10.3390\/vetsci13050462","type":"journal-article","created":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T07:49:09Z","timestamp":1778572149000},"page":"462","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Whole-Genome Sequencing and Comparative Genomic Analysis of Citrobacter farmeri and Enterobacter cloacae from Unhatched Green Turtle Eggs"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-5534-0535","authenticated-orcid":false,"given":"Nurcan","family":"\u00d6nen","sequence":"first","affiliation":[{"name":"Biology Department, Institute of Graduate Studies, Hakkari University, Hakkari 30000, Turkey"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5142-1882","authenticated-orcid":false,"given":"Bahad\u0131r","family":"T\u00f6r\u00fcn","sequence":"additional","affiliation":[{"name":"Medical Services and Techniques Programme, Vocational School of Health Sciences, Hakkari University, Hakkari 30000, Turkey"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5994-508X","authenticated-orcid":false,"given":"Can","family":"Y\u0131lmaz","sequence":"additional","affiliation":[{"name":"Medical Services and Techniques Programme, Vocational School of Health Sciences, Hakkari University, Hakkari 30000, Turkey"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1038\/33669","article-title":"Oldest known sea turtle","volume":"392","author":"Hirayama","year":"1998","journal-title":"Nature"},{"key":"ref_2","unstructured":"M\u00e1rquez, M.R. (1990). FAO Species Catalogue. Vol. 11. Sea Turtles of the World."},{"key":"ref_3","unstructured":"Lutz, P.L., and Musick, J.A. (2017). Evolution, phylogeny, and current status. The Biology of Sea Turtles, Volume I, CRC Press."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/S0006-3207(03)00179-4","article-title":"A review of sea turtle nesting activity along the Mediterranean coast of Turkey","volume":"116","author":"Canbolat","year":"2004","journal-title":"Biol. Conserv."},{"key":"ref_5","first-page":"197","article-title":"Marine turtles (Chelonia mydas and Caretta caretta) nesting along the eastern Mediterranean coast of Turkey: Results from six years of surveying","volume":"25","year":"2015","journal-title":"Herpetol. J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"209","DOI":"10.3354\/esr01243","article-title":"Marine turtle Regional Management Units 2.0: An updated framework for conservation and research of wide-ranging megafauna species","volume":"52","author":"Wallace","year":"2023","journal-title":"Endanger. Species Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1007\/s00227-022-04068-1","article-title":"Population genetic diversity of green turtles, Chelonia mydas, in the Mediterranean revisited","volume":"169","author":"Karaman","year":"2022","journal-title":"Mar. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e1600730","DOI":"10.1126\/sciadv.1600730","article-title":"Global sea turtle conservation successes","volume":"3","author":"Mazaris","year":"2017","journal-title":"Sci. Adv."},{"key":"ref_9","unstructured":"Broderick, A.C., T\u00fcrkozan, O., Demetropoulos, S., Mastrogiacomo, A., Demetropoulos, A., Levy, Y., and Leader, N. (2024). Chelonia mydas (Mediterranean Subpopulation), International Union for Conservation of Nature. The IUCN Red List of Threatened Species 2024."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"e4043","DOI":"10.1002\/aqc.4043","article-title":"A 21-year recovery trend in green turtle nesting activity: 2002\u20132022","volume":"34","author":"Mestav","year":"2024","journal-title":"Aquat. Conserv. Mar. Freshw. Ecosyst."},{"key":"ref_11","unstructured":"Seminoff, J.A. (2014). Chelonia mydas, International Union for Conservation of Nature. The IUCN Red List of Threatened Species 2014."},{"key":"ref_12","unstructured":"(2026, April 07). IUCN Species Status List. Chelonia mydas\u2014Global: Least Concern. Available online: https:\/\/www.iucnredlist.org."},{"key":"ref_13","first-page":"9","article-title":"Incubation temperature and sex ratio in hatchling loggerhead turtles: A preliminary report","volume":"11","author":"Yntema","year":"1979","journal-title":"Mar. Turt. Newsl."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Spotila, J.R. (2004). Sea Turtles: A Complete Guide to Their Biology, Behavior, and Conservation, Johns Hopkins University Press.","DOI":"10.56021\/9780801880070"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e02100","DOI":"10.1002\/eap.2100","article-title":"Quantifying the impacts of future sea level rise on nesting sea turtles in the southeastern United States","volume":"30","author":"Lyons","year":"2020","journal-title":"Ecol. Appl."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"151572","DOI":"10.1016\/j.jembe.2021.151572","article-title":"Effect of predicted sea level rise scenarios on green turtle (Chelonia mydas) nesting","volume":"541","author":"Karaman","year":"2021","journal-title":"J. Exp. Mar. Biol. Ecol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"97","DOI":"10.3354\/dao009097","article-title":"A survey of the diseases of marine turtles in northern Australia. 2. Oceanarium-reared and wild turtles","volume":"9","author":"Glazebrook","year":"1990","journal-title":"Dis. Aquat. Org."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1086\/physzool.68.5.30163934","article-title":"Adrenal and hematological responses to stress in juvenile green turtles (Chelonia mydas) with and without fibropapillomas","volume":"68","author":"Aguirre","year":"1995","journal-title":"Physiol. Zool."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Jacobson, E.R. (2007). Infectious Diseases and Pathology of Reptiles: Color Atlas and Text, CRC Press.","DOI":"10.1201\/9781420004038"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1080\/15659801.2015.1047681","article-title":"Loggerhead sea turtle hatchling sex ratio differences between two nesting beaches in Turkey","volume":"61","author":"Kaska","year":"2015","journal-title":"Isr. J. Ecol. Evol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3417","DOI":"10.5433\/1679-0359.2017v38n5p3417","article-title":"The green turtle Chelonia mydas as a marine and coastal environmental sentinels: Anthropogenic activities and diseases","volume":"38","author":"Domiciano","year":"2017","journal-title":"Semin. Ci\u00eanc. Agr\u00e1r."},{"key":"ref_22","unstructured":"S\u00f6nmez, B. (2006). Investigation of the Effectiveness of Conservation Measures Applied to Sea Turtle Nests Under the Threat of Flooding and Erosion at Samanda\u011f Beach. [Master\u2019s Thesis, Hatay Mustafa Kemal University]."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"E290","DOI":"10.33321\/cdi.2017.41.39","article-title":"An outbreak of Salmonella Muenchen after consuming sea turtle, Northern Territory, Australia, 2017","volume":"41","author":"Draper","year":"2017","journal-title":"Commun. Dis. Intell."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"222","DOI":"10.14202\/vetworld.2021.222-229","article-title":"Prevalence and phenotypic characterization of Salmonella enterica isolates from three species of wild marine turtles in Grenada, West Indies","volume":"14","author":"Edwards","year":"2021","journal-title":"Vet. World"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Mashkour, N., Jones, K., Kophamel, S., Hipolito, T., Ahasan, S., Walker, G., Jakob-Hoff, R., Whittaker, M., Hamann, M., and Bell, I. (2020). Disease risk analysis in sea turtles: A baseline study to inform conservation efforts. PLoS ONE, 15.","DOI":"10.1101\/2020.03.10.985432"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"245","DOI":"10.3354\/esr00279","article-title":"Global research priorities for sea turtles: Informing management and conservation in the 21st century","volume":"11","author":"Hamann","year":"2010","journal-title":"Endanger. Species Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"265","DOI":"10.2744\/CCB-1217.1","article-title":"Mycelial fungal diversity associated with the leatherback sea turtle (Dermochelys coriacea) nests from western Puerto Rico","volume":"15","year":"2016","journal-title":"Chelonian Conserv. Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1177\/104063870902100601","article-title":"Postmortem diagnostic investigation of disease in free-ranging marine turtle populations: A review of common pathologic findings and protocols","volume":"21","author":"Flint","year":"2009","journal-title":"J. Vet. Diagn. Investig."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"303","DOI":"10.3354\/esr01278","article-title":"Key issues in assessing threats to sea turtles: Knowledge gaps and future directions","volume":"52","author":"Fuentes","year":"2023","journal-title":"Endanger. Species Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"229","DOI":"10.3354\/esr00901","article-title":"Mediterranean Sea Turtles: Current Knowledge and Priorities for Conservation and Research","volume":"36","author":"Casale","year":"2018","journal-title":"Endanger. Species Res."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Sarmiento-Ram\u00edrez, J.M., van der Voort, M., Raaijmakers, J.M., and Di\u00e9guez-Uribeondo, J. (2014). Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0095206"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"3832","DOI":"10.1128\/AEM.02869-05","article-title":"Microbial diversity in water and sediment of Lake Chaka, an athalassohaline lake in northwestern China","volume":"72","author":"Jiang","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: Improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Wong, T.K.F., Ly-Trong, N., Ren, H., Ba\u00f1os, H., Roger, A.J., Susko, E., Bielow, C., De Maio, N., Goldman, N., and Hahn, M.W. (2025). IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models. EcoEvoRxiv.","DOI":"10.32942\/X2P62N"},{"key":"ref_36","unstructured":"Rambaut, A. (2026, April 07). FigTree, Available online: http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/."},{"key":"ref_37","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_38","unstructured":"Fonseca, N. (2026, May 06). fastq_utils. GitHub Repository. Available online: https:\/\/github.com\/nunofonseca\/fastq_utils."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Wick, R.R., Judd, L.M., Gorrie, C.L., and Holt, K.E. (2017). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol., 13.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1093\/bib\/bbx081","article-title":"Visualizing and comparing circular genomes using the CGView family of tools","volume":"20","author":"Stothard","year":"2019","journal-title":"Brief. Bioinf."},{"key":"ref_41","first-page":"000685","article-title":"Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"Schwengers","year":"2021","journal-title":"Microb. Genom."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"5691","DOI":"10.1093\/nar\/gki866","article-title":"The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes","volume":"33","author":"Overbeek","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"W182","DOI":"10.1093\/nar\/gkm321","article-title":"KAAS: An automatic genome annotation and pathway reconstruction server","volume":"35","author":"Moriya","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkw1017","article-title":"Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center","volume":"45","author":"Wattam","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_46","unstructured":"Seemann, T. (2026, April 07). ABRicate: Mass Screening of Contigs for Antiobiotic Resistance Genes. Available online: https:\/\/github.com\/tseemann\/abricate."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"W246","DOI":"10.1093\/nar\/gky425","article-title":"CRISPRCasFinder, an update of CRISPRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins","volume":"46","author":"Couvin","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41586-020-2649-2","article-title":"Array programming with NumPy","volume":"585","author":"Harris","year":"2020","journal-title":"Nature"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: Freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: A 2D graphics environment","volume":"9","author":"Hunter","year":"2007","journal-title":"Comput. Sci. Eng."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.21105\/joss.03021","article-title":"Seaborn: Statistical data visualization","volume":"6","author":"Waskom","year":"2021","journal-title":"J. Open Source Softw."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"B\u00e9zy, V.S., Valverde, R.A., and Plante, C.J. (2015). Olive Ridley Sea Turtle Hatching Success as a Function of the Microbial Abundance in Nest Sand at Ostional, Costa Rica. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0118579"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"fix139","DOI":"10.1093\/femsec\/fix139","article-title":"Fecal bacterial communities of wild-captured and stranded green turtles (Chelonia mydas) on the Great Barrier Reef","volume":"93","author":"Ahasan","year":"2017","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"137717","DOI":"10.1016\/j.scitotenv.2020.137717","article-title":"Bacterial diversity of the green turtle (Chelonia mydas) nest environment","volume":"720","author":"Candan","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Ebani, V.V. (2023). Bacterial Infections in Sea Turtles. Vet. Sci., 10.","DOI":"10.3390\/vetsci10050333"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"e1363","DOI":"10.1002\/mbo3.1363","article-title":"Potential impacts of environmental bacteria on the microbiota of loggerhead (Caretta caretta) and green (Chelonia mydas) sea turtle eggs and their hatching success","volume":"12","author":"McMaken","year":"2023","journal-title":"MicrobiologyOpen"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1134\/S1062359024613594","article-title":"Bacterial Diversity of Green Turtle Eggs and Nest Sand on Samanda\u011f Beach","volume":"52","author":"Ayhan","year":"2025","journal-title":"Biol. Bull."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"2761","DOI":"10.1128\/JCM.01228-07","article-title":"16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls","volume":"45","author":"Janda","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/nrmicro3330","article-title":"Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences","volume":"12","author":"Yarza","year":"2014","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"3097","DOI":"10.1007\/s10096-025-05282-7","article-title":"Enterobacter cloacae complex taxonomic incongruence may lead to misidentification of outbreaks and hinder infection control in real time","volume":"44","author":"Kaplan","year":"2025","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1093\/sysbio\/syab060","article-title":"Improving phylogenies based on average nucleotide identity, incorporating saturation correction and nonparametric bootstrap support","volume":"71","author":"Gosselin","year":"2022","journal-title":"Syst. Biol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"lxac090","DOI":"10.1093\/jambio\/lxac090","article-title":"De novo genomic analysis of Enterobacter asburiae EBRJ12, a plant growth-promoting rhizobacteria isolated from the rhizosphere of Phaseolus vulgaris L.","volume":"134","author":"Saikia","year":"2023","journal-title":"J. Appl. Microbiol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"21548","DOI":"10.1007\/s11356-022-23564-x","article-title":"Whole genome analysis of Enterobacter cloacae Rs-2 and screening of genes related to plant-growth promotion","volume":"30","author":"Wang","year":"2023","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Aguirre-S\u00e1nchez, J.R., Qui\u00f1ones, B., Ortiz-Mu\u00f1oz, J.A., Prieto-Alvarado, R., Vega-L\u00f3pez, I.F., Mart\u00ednez-Urtaza, J., and Chaidez, C. (2023). Comparative genomic analyses of virulence and antimicrobial resistance in Citrobacter werkmanii, an emerging opportunistic pathogen. Microorganisms, 11.","DOI":"10.3390\/microorganisms11082114"},{"key":"ref_66","unstructured":"Kuzhippanathil Gopi, D. (2024). Genomic Characterization and Bioinformatic Analysis of Citrobacter Species in Sepsis Patients. [Master\u2019s Thesis, University of Sk\u00f6vde]."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s40168-015-0077-6","article-title":"Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria","volume":"3","author":"Baker","year":"2015","journal-title":"Microbiome"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1799","DOI":"10.1038\/s41564-023-01458-z","article-title":"Genome content predicts the carbon catabolic preferences of heterotrophic bacteria","volume":"8","author":"Gralka","year":"2023","journal-title":"Nat. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1186\/s40168-025-02177-9","article-title":"Phylogenetically and metabolically diverse active carbon-fixing microbes reside in mangrove sediments","volume":"13","author":"Wang","year":"2025","journal-title":"Microbiome"},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Kibwana, U.O., Manyahi, J., Sandnes, H.H., Blomberg, B., Mshana, S.E., Langel, N., Roberts, A.P., and Moyo, S.J. (2023). Fluoroquinolone resistance among fecal extended spectrum \u03b2 lactamases positive Enterobacterales isolates from children in Dar es Salaam, Tanzania. BMC Infect. Dis., 23.","DOI":"10.1186\/s12879-023-08086-2"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2333748","DOI":"10.1080\/19490976.2024.2333748","article-title":"The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children","volume":"16","author":"Heston","year":"2024","journal-title":"Gut Microbes"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"31622","DOI":"10.1038\/s41598-025-17379-2","article-title":"Cefiderocol-resistant pathogens in German hospital wastewater: A reservoir for multidrug resistance","volume":"15","author":"Erler","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"146009","DOI":"10.1016\/j.scitotenv.2021.146009","article-title":"A systematic review of antibiotics and antibiotic resistance genes in estuarine and coastal environments","volume":"777","author":"Zheng","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"120440","DOI":"10.1016\/j.envpol.2022.120440","article-title":"Fluoroquinolone antibiotics: Occurrence, mode of action, resistance, environmental detection, and remediation\u2014A comprehensive review","volume":"315","author":"Bhatt","year":"2022","journal-title":"Environ. Pollut."},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Barrantes-Jim\u00e9nez, K., Mendoza-Guido, B., Morales-Mora, E., Rivera-Montero, L., Montiel-Mora, J., Chac\u00f3n-Jim\u00e9nez, L., Rojas-Jim\u00e9nez, K., and Arias-Andr\u00e9s, M. (2025). Influence of Seasonality and Pollution on the Presence of Antibiotic Resistance Genes and Potentially Pathogenic Bacteria in a Tropical Urban River. Antibiotics, 14.","DOI":"10.20944\/preprints202506.1549.v1"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.vetmic.2015.03.024","article-title":"Interplay between iron homeostasis and virulence: Fur and RyhB as major regulators of bacterial pathogenicity","volume":"179","author":"Porcheron","year":"2015","journal-title":"Vet. Microbiol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.chom.2016.07.009","article-title":"Bacterial Stress Responses during Host Infection","volume":"20","author":"Fang","year":"2016","journal-title":"Cell Host Microbe"},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Li, Y., Dai, J., Zhuge, X., Wang, H., Hu, L., Ren, J., Chen, L., Li, D., and Tang, F. (2016). Iron-regulated gene ireA in avian pathogenic Escherichia coli participates in adhesion and stress-resistance. BMC Vet. Res., 12.","DOI":"10.1186\/s12917-016-0800-y"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"173","DOI":"10.3892\/ijmm.2025.5614","article-title":"Pathogen virulence genes: Advances, challenges and future directions in infectious disease research (Review)","volume":"56","author":"Chen","year":"2025","journal-title":"Int. J. Mol. Med."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"151180","DOI":"10.1016\/j.jembe.2019.151180","article-title":"Embryonic mortality in green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtle nests increases with cumulative exposure to elevated temperatures","volume":"518","author":"Bladow","year":"2019","journal-title":"J. Exp. Mar. Biol. Ecol."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Zhang, Q., and Ye, Y. (2017). Not all predicted CRISPR\u2013Cas systems are equal: Isolated cas genes and classes of CRISPR like elements. BMC Bioinf., 18.","DOI":"10.1186\/s12859-017-1512-4"},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Slukin, P.V., Fursov, M.V., Volkov, D.V., Sizova, A.A., Detushev, K.V., Dyatlov, I.A., and Fursova, N.K. (2025). Diversity of CRISPR-Cas Systems Identified in Urological Escherichia coli Strains. Microorganisms, 13.","DOI":"10.20944\/preprints202510.2396.v1"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1038\/s41396-020-0623-5","article-title":"The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments","volume":"14","author":"Zheng","year":"2020","journal-title":"ISME J."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"17040","DOI":"10.1038\/nmicrobiol.2017.40","article-title":"Why prokaryotes have pangenomes","volume":"2","author":"McInerney","year":"2017","journal-title":"Nat. Microbiol."},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Tettelin, H., and Medini, D. (2020). The Pangenome: Diversity, Dynamics and Evolution of Genomes, Springer Nature.","DOI":"10.1007\/978-3-030-38281-0"},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"De Maayer, P., Green, T., Jordan, S., Smits, T.H., and Coutinho, T.A. (2025). Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen. BMC Genom., 26.","DOI":"10.1186\/s12864-025-11590-1"},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"M\u00e9ric, G., Yahara, K., Mageiros, L., Pascoe, B., Maiden, M.C., Jolley, K.A., and Sheppard, S.K. (2014). A reference pan-genome approach to comparative bacterial genomics: Identification of novel epidemiological markers in pathogenic Campylobacter. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0092798"},{"key":"ref_88","first-page":"912","article-title":"Core genome expansion in Brevibacterium across marine provinces reveals genomic footprint for long-term marine adaptation","volume":"17","author":"Sarkar","year":"2025","journal-title":"Iran. J. Microbiol."},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Croll, D., and McDonald, B.A. (2012). The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1002608"},{"key":"ref_90","unstructured":"Urhan, A. (2024). The Microbial World Magnified Through the Bright Lens of Comparative Genomics. [Ph.D Thesis, Delft University of Technology]."}],"container-title":["Veterinary Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-7381\/13\/5\/462\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T09:24:57Z","timestamp":1778577897000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-7381\/13\/5\/462"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,10]]},"references-count":90,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["vetsci13050462"],"URL":"https:\/\/doi.org\/10.3390\/vetsci13050462","relation":{},"ISSN":["2306-7381"],"issn-type":[{"value":"2306-7381","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,10]]}}}