{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T05:07:59Z","timestamp":1779167279270,"version":"3.51.4"},"reference-count":50,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T00:00:00Z","timestamp":1778630400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Antimicrobial resistance is a growing threat to human and animal health and is recognized as a global One Health issue. Strategies to reduce its impact include judicious usage of antibiotics guided by accurate bacterial identification and antimicrobial susceptibility. Next-generation sequencing (NGS) offers a DNA-based diagnostic approach that profiles the bacteria microbiota and can help support more informed antibiotic selection. We utilized NGS to identify Fusobacterium gonidiaformans in the neck abscess of a wild California sea lion (Zalophus californianus) undergoing rehabilitation. Initially, NGS revealed that the microbial population was dominated by F. gonidiaformans. Following treatment, the microbial profile shifted over the following eight weeks, during which 13 other bacterial species were detected, demonstrating the need for repeated testing to monitor changes in persistent lesions. Despite effective treatment to eliminate F. gonidiaformans from the abscess, the patient died during treatment due to suspected unrelated causes. Necropsy and histopathology identified bacterial pneumonia and sepsis associated with a large squamous cell carcinoma of the oropharynx and neck, all contributing to a deadly outcome. To our knowledge, this is the first case report of the use of longitudinal NGS sampling with the identification of Fusobacterium gonidiaformans associated with an abscess in the neck in a California sea lion. These findings support the utility of NGS in monitoring microbial dynamics to allow informed decision-making in antimicrobial selection in complex infections.<\/jats:p>","DOI":"10.3390\/ani16101498","type":"journal-article","created":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T16:26:37Z","timestamp":1778689597000},"page":"1498","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Longitudinal Monitoring of Abscess Microbiota in a Wild California Sea Lion (Zalophus californianus) Using Next-Generation Sequencing"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9025-8029","authenticated-orcid":false,"given":"Jenna","family":"Archambeau","sequence":"first","affiliation":[{"name":"MiDOG Animal Diagnostics, Tustin, CA 92780, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lauren","family":"Palmer","sequence":"additional","affiliation":[{"name":"Marine Mammal Care Center Los Angeles, San Pedro, CA 90731, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Megan","family":"Wier","sequence":"additional","affiliation":[{"name":"Marine Mammal Care Center Los Angeles, San Pedro, CA 90731, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathan","family":"Sharp","sequence":"additional","affiliation":[{"name":"Perris Animal Hospital, Perris, CA 92570, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janina","family":"Krumbeck","sequence":"additional","affiliation":[{"name":"MiDOG Animal Diagnostics, Tustin, CA 92780, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"7515","DOI":"10.2147\/IDR.S428837","article-title":"Potential Causes of Spread of Antimicrobial Resistance and Preventive Measures in One Health Perspective\u2014A Review","volume":"16","author":"Endale","year":"2023","journal-title":"Infect. Drug Resist."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Salam, M.A., Al-Amin, Y., Salam, M.T., Pawar, J.S., Akhter, N., Rabaan, A.A., and Alqumber, M.A.A. (2023). Antimicrobial Resistance: A Growing Serious Threat for Global Public Health. Healthcare, 11.","DOI":"10.20944\/preprints202305.0555.v1"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","article-title":"Global burden of bacterial antimicrobial resistance in 2019: A systematic analysis","volume":"399","author":"Murray","year":"2022","journal-title":"Lancet"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Hay, S.I., Rao, P.C., Dolecek, C., Day, N.P.J., Stergachis, A., Lopez, A.D., and Murray, C.J.L. (2018). Measuring and mapping the global burden of antimicrobial resistance. BMC Med., 16.","DOI":"10.1186\/s12916-018-1073-z"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Zalewska, M., B\u0142a\u017cejewska, A., Czapko, A., and Popowska, M. (2021). Antibiotics and Antibiotic Resistance Genes in Animal Manure\u2014Consequences of Its Application in Agriculture. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.610656"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"171532","DOI":"10.1016\/j.scitotenv.2024.171532","article-title":"From remote to urbanized: Dispersal of antibiotic-resistant bacteria under the aspect of anthropogenic influence","volume":"924","author":"Gattinger","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1016\/S0140-6736(24)01867-1","article-title":"Global burden of bacterial antimicrobial resistance 1990\u20132021: A systematic analysis with forecasts to 2050","volume":"404","author":"Naghavi","year":"2024","journal-title":"Lancet"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1111\/jvim.12562","article-title":"ACVIM Consensus Statement on Therapeutic Antimicrobial Use in Animals and Antimicrobial Resistance","volume":"29","author":"Weese","year":"2015","journal-title":"J. Vet. Intern. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1128\/microbiolspec.ARBA-0023-2017","article-title":"Antimicrobial Stewardship in Veterinary Medicine","volume":"6","author":"Lloyd","year":"2018","journal-title":"Microbiol. Spectr."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1177\/003335490812300316","article-title":"Conrad, Risk Factors for Infection with Pathogenic and Antimicrobial-Resistant Fecal Bacteria in Northern Elephant Seals in California","volume":"123","author":"Stoddard","year":"2008","journal-title":"Public Health Rep."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"lxaf017","DOI":"10.1093\/jambio\/lxaf017","article-title":"Making sense of sentinels: Wildlife as the One Health bridge for environmental antimicrobial resistance surveillance","volume":"136","author":"Doyle","year":"2025","journal-title":"J. Appl. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"741","DOI":"10.2460\/javma.24.02.0123","article-title":"Spread and mitigation of antimicrobial resistance at the wildlife-urban and wildlife-livestock interfaces","volume":"262","author":"Vezeau","year":"2024","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1111\/j.1574-6941.2009.00648.x","article-title":"Occurrence and patterns of antibiotic resistance in vertebrates off the Northeastern United States coast","volume":"67","author":"Rose","year":"2009","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"100298","DOI":"10.1016\/j.onehlt.2021.100298","article-title":"Antimicrobial resistance in wildlife and in the built environment in a wildlife rehabilitation center","volume":"13","author":"Jorquera","year":"2021","journal-title":"One Health"},{"key":"ref_15","first-page":"288","article-title":"Antimicrobial Susceptibility of Bacteria Isolated from Pinnipeds Stranded in Central and Northern California","volume":"29","author":"Johnson","year":"1998","journal-title":"J. Zoo Wildl. Med."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Dubey, A., Malla, M.A., and Kumar, A. (2022). Role of Next-Generation Sequencing (NGS) in Understanding the Microbial Diversity. Molecular Genetics and Genomics Tools in Biodiversity Conservation, Springer Nature.","DOI":"10.1007\/978-981-16-6005-4_16"},{"key":"ref_17","first-page":"e47106","article-title":"Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques","volume":"15","author":"Goyal","year":"2023","journal-title":"Cureus"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1038\/s41396-020-00832-7","article-title":"Ecology and evolution of antimicrobial resistance in bacterial communities","volume":"15","author":"Bottery","year":"2021","journal-title":"ISME J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1111\/wrr.12309","article-title":"Use of 16S rRNA sequencing and quantitative PCR to correlate venous leg ulcer bacterial bioburden dynamics with wound expansion, antibiotic therapy, and healing","volume":"23","author":"Sprockett","year":"2015","journal-title":"Wound Repair Regen."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"40","DOI":"10.7589\/0090-3558-42.1.40","article-title":"Lesions associated with a novel Mycoplasma sp. in California sea lions (Zalophus californianus) undergoing rehabilitation","volume":"42","author":"Haulena","year":"2006","journal-title":"J. Wildl. Dis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1638\/2020-0225","article-title":"Clinical and microbiological characterization of lymph node abscessation in pup and yearling California sea lions (Zalophus californianus) undergoing rehabilitation in a marine mammal center","volume":"52","author":"Ready","year":"2021","journal-title":"J. Zoo Wildl. Med."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"108764","DOI":"10.1016\/j.vetmic.2020.108764","article-title":"The canine skin and ear microbiome: A comprehensive survey of pathogens implicated in canine skin and ear infections using a novel next-generation-sequencing-based assay","volume":"247","author":"Tang","year":"2020","journal-title":"Vet. Microbiol."},{"key":"ref_23","unstructured":"Oksanen, J., Simpson, G., Solymos, P., Lahti, L., and Weedon, J. (Vegandevs\/Vegan: CRAN Release, 2025). Vegandevs\/Vegan: CRAN Release, version 2.6-10."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"McMurdie, P.J., and Holmes, S. (2013). phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0061217"},{"key":"ref_25","unstructured":"Dahl, E., Neer, E., and Karstens, L. (2026, March 07). Microshades: A Custom Color Palette for Improving Data Visualization. R Package, Available online: https:\/\/karstenslab.github.io\/microshades."},{"key":"ref_26","unstructured":"Wickham, H. (2026, March 07). Forcats: Tools for Working with Categorical Variables (Factors). R Package, Available online: https:\/\/forcats.tidyverse.org."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Wickham, H. (2016). Ggplot2: Elegant Graphics for Data Analysis, Springer.","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/0002-9343(77)90867-1","article-title":"Group Y meningococcal disease in United States Air Force recruits","volume":"62","author":"Koppes","year":"1977","journal-title":"Am. J. Med."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"284","DOI":"10.4103\/IJPM.IJPM_209_17","article-title":"Fatal meningococcal septicemia without meningeal signs, contribution of the peripheral smear in diagnosis: Report of a case","volume":"61","author":"Mutreja","year":"2018","journal-title":"Indian J. Pathol. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1001\/archpedi.1974.02110210023003","article-title":"Skin manifestations of meningococcal infection; an immediate indicator of prognosis","volume":"127","author":"Toews","year":"1974","journal-title":"Am. J. Dis. Child."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.idcr.2018.03.008","article-title":"Cellulitis and Bacteremia due to Neisseria weaveri following a dog bite","volume":"12","author":"Shinha","year":"2018","journal-title":"IDCases"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Pinpimai, K., Banlunara, W., Roe, W.D., Dittmer, K., Biggs, P.J., Tantilertcharoen, R., Chankow, K., Bunpapong, N., Boonkam, P., and Pirarat, N. (2022). Genetic characterization of hypervirulent Klebsiella pneumoniae responsible for acute death in captive marmosets. Front. Vet. Sci., 9.","DOI":"10.3389\/fvets.2022.940912"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1177\/0300985817705172","article-title":"Hypervirulent Klebsiella pneumoniae in California Sea Lions (Zalophus californianus): Pathologic Findings in Natural Infections","volume":"54","author":"Seguel","year":"2017","journal-title":"Vet. Pathol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"659","DOI":"10.7589\/2017-07-178","article-title":"Hypermucoviscous klebsiella pneumoniae isolates from stranded and wild-caught marine mammals of the us pacific coast: Prevalence, phenotype, and genotype","volume":"54","author":"Whitaker","year":"2018","journal-title":"J. Wildl. Dis."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Michael, S.A., Hayman, D.T.S., Gray, R., and Roe, W.D. (2022). Clinical parameters of hypervirulent Klebsiella pneumoniae disease and ivermectin treatment in New Zealand sea lion (Phocarctos hookeri) pups. PLoS ONE, 17.","DOI":"10.1371\/journal.pone.0264582"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/j.vetmic.2015.01.019","article-title":"Septicaemia and meningitis caused by infection of New Zealand sea lion pups with a hypermucoviscous strain of Klebsiella pneumoniae","volume":"176","author":"Roe","year":"2015","journal-title":"Vet. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.vetmic.2007.07.030","article-title":"Characterization of Klebsiella pneumoniae isolates from New Zealand sea lion pups","volume":"125","author":"Prescott","year":"2007","journal-title":"Vet. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"461","DOI":"10.7589\/0090-3558-43.3.461","article-title":"Neonatal mortality in New Zealand sea lions (Phocarctos hookeri) at Sandy Bay, Enderby Island, Auckland Islands from 1998 to 2005","volume":"43","author":"Castinel","year":"2007","journal-title":"J. Wildl. Dis."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"109307","DOI":"10.1016\/j.vetmic.2021.109307","article-title":"Genetics and pathology associated with Klebsiella pneumoniae and Klebsiella spp. isolates from North American Pacific coastal marine mammals","volume":"265","author":"Chang","year":"2022","journal-title":"Vet. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"8","DOI":"10.7589\/0090-3558-44.1.8","article-title":"Humoral immune response to Klebsiella spp. In New Zealand sea lions (Phocarctos hookeri) and the passive transfer of immunity to pups","volume":"44","author":"Castinel","year":"2008","journal-title":"J. Wildl. Dis."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e02078","DOI":"10.1016\/j.idcr.2024.e02078","article-title":"Mediastinal abscess and bacteremia due to Streptococcus dysgalactiae complicated by aorto-esophageal fistula leading to death with massive bleeding in a 70-year-old Japanese man with gastric cancer","volume":"38","author":"Oshima","year":"2024","journal-title":"IDCases"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"12827","DOI":"10.1038\/s41598-024-63774-6","article-title":"Bacteroidetes promotes esophageal squamous carcinoma invasion and metastasis through LPS-mediated TLR4\/Myd88\/NF-\u03baB pathway and inflammatory changes","volume":"14","author":"Wu","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1741","DOI":"10.1099\/ijs.0.63096-0","article-title":"Psychrobacter maritimus sp. nov. and Psychrobacter arenosus sp. nov., isolated from coastal sea ice and sediments of the Sea of Japan","volume":"54","author":"Romanenko","year":"2004","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1099\/ijsem.0.003739","article-title":"Psychrobacter pygoscelis sp. nov. isolated from the penguin Pygoscelis papua","volume":"70","author":"Glaeser","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.3201\/eid1907.121599","article-title":"Psychrobacter arenosus bacteremia after blood transfusion, France","volume":"19","author":"Caspar","year":"2013","journal-title":"Emerg. Infect. Dis."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1093\/clinids\/2.6.914","article-title":"Gram-negative anaerobic bacilli: Their role in infection and patterns of susceptibility to antimicrobial agents. I. Little-known Bacteroides species","volume":"2","author":"Kirby","year":"1980","journal-title":"Rev. Infect. Dis."},{"key":"ref_47","unstructured":"(2026, April 29). Marine Mammal Health and Stranding Response Program; National Marine Fisheries Service Office of Protected Resources. Standards for Release of Marine Mammals Following Rehabilitation, Available online: https:\/\/repository.library.noaa.gov\/view\/noaa\/48559."},{"key":"ref_48","unstructured":"(2026, April 29). Marine Mammal Health and Stranding Response Program; National Marine Fisheries Service Office of Protected Resources. NMFS Standards for Rehabilitation Facilities, Available online: https:\/\/repository.library.noaa.gov\/view\/noaa\/48555."},{"key":"ref_49","unstructured":"(2026, April 29). Marine Mammal Commission, The Marine Mammal Protection Act of 1972 As Amended, Bethesda, Available online: https:\/\/www.mmc.gov\/wp-content\/uploads\/MMPA_2023.pdf."},{"key":"ref_50","unstructured":"(2026, April 29). National Marine Fisheries Service Office of Protected Resources, Marine Mammal Health and Stranding Response Program, Available online: https:\/\/www.fisheries.noaa.gov\/national\/marine-life-distress\/marine-mammal-health-and-stranding-response-program."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/10\/1498\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T04:18:52Z","timestamp":1779164332000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/10\/1498"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,13]]},"references-count":50,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["ani16101498"],"URL":"https:\/\/doi.org\/10.3390\/ani16101498","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,13]]}}}