{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:27:03Z","timestamp":1760059623746,"version":"build-2065373602"},"reference-count":47,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2025,6,24]],"date-time":"2025-06-24T00:00:00Z","timestamp":1750723200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"publisher","award":["K01AI43881"],"award-info":[{"award-number":["K01AI43881"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Bloodstream infections (BSIs) are a major cause of morbidity and mortality in acute myeloid leukemia (AML) patients undergoing induction chemotherapy. Staphylococcus epidermidis, typically a skin commensal, is increasingly recognized as a pathogen in these vulnerable individuals. This study investigated whether genomic differences exist between infectious and gastrointestinal colonizing S. epidermidis isolates from AML patients and how these compare to colonizing and infectious isolates from other patient groups and biogeographic sites. We analyzed 114 isolates\u201444 from AML patients (23 infections, 21 GI colonizers) and 70 from public datasets (34 infections, 36 colonizers). Stool samples underwent 16S rRNA sequencing and culture to identify colonization, while bloodstream isolates were sequenced and compared. Genomic profiling using Roary, Scoary, Phyre2, and InterProScan revealed that infectious and GI-colonizing AML isolates were phylogenetically close but genomically distinct. Infectious isolates from AML patients were significantly enriched for resistance genes (e.g., mecA, mecR1, mecI, ANT(4\u2032)-Ib) and the biofilm-associated gene icaA. AML infectious isolates harbored more resistance genes and mobile elements than non-AML strains but lacked widespread classical virulence factors. These results suggest that S. epidermidis pathogenicity in immunocompromised hosts is driven by genomic adaptability and antibiotic tolerance rather than traditional virulence mechanisms.<\/jats:p>","DOI":"10.3390\/pathogens14070627","type":"journal-article","created":{"date-parts":[[2025,6,24]],"date-time":"2025-06-24T06:49:38Z","timestamp":1750747778000},"page":"627","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Staphylococcus epidermidis in Acute Myeloid Leukemia: A Comparative Genomic Study Against Non-AML Isolates"],"prefix":"10.3390","volume":"14","author":[{"given":"Stephanie","family":"McMahon","sequence":"first","affiliation":[{"name":"Laboratory of Jessica Galloway-Pe\u00f1a, Interdisciplinary Genetics Program, Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2503-6838","authenticated-orcid":false,"given":"Samantha","family":"Franklin","sequence":"additional","affiliation":[{"name":"Laboratory of Jessica Galloway-Pe\u00f1a, Interdisciplinary Genetics Program, Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maliha","family":"Batool","sequence":"additional","affiliation":[{"name":"Laboratory of Jessica Galloway-Pe\u00f1a, Interdisciplinary Genetics Program, Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nitya","family":"Sadasivan","sequence":"additional","affiliation":[{"name":"Laboratory of Jessica Galloway-Pe\u00f1a, Interdisciplinary Genetics Program, Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-2581-8829","authenticated-orcid":false,"given":"Safa","family":"Fatima","sequence":"additional","affiliation":[{"name":"Laboratory of Jessica Galloway-Pe\u00f1a, Interdisciplinary Genetics Program, Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1081-254X","authenticated-orcid":false,"given":"Jessica","family":"Galloway-Pe\u00f1a","sequence":"additional","affiliation":[{"name":"Laboratory of Jessica Galloway-Pe\u00f1a, Interdisciplinary Genetics Program, Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1080\/21505594.2016.1156821","article-title":"Bloodstream infections in neutropenic cancer patients: A practical update","volume":"7","author":"Gustinetti","year":"2016","journal-title":"Virulence"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"195","DOI":"10.14740\/wjon1410","article-title":"Infections in Hospitalized Cancer Patients","volume":"12","author":"Delgado","year":"2021","journal-title":"World J. Oncol."},{"key":"ref_3","first-page":"310","article-title":"Incidence and management of infections in patients with acute leukemia following chemotherapy in general wards","volume":"7","author":"Biswal","year":"2013","journal-title":"Ecancermedicalscience"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e00415-23","DOI":"10.1128\/spectrum.00415-23","article-title":"Contribution of the Oral and Gastrointestinal Microbiomes to Bloodstream Infections in Leukemia Patients","volume":"11","author":"McMahon","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1111\/apt.13302","article-title":"Chemotherapy-driven dysbiosis in the intestinal microbiome","volume":"42","author":"Montassier","year":"2015","journal-title":"Aliment. Pharmacol. Ther."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Francino, M.P. (2016). Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Front. Microbiol., 6.","DOI":"10.3389\/fmicb.2015.01543"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1093\/cid\/ciq147","article-title":"Clinical practice guideline for the use of antimicrobial agents in neutropenic patients with cancer: 2010 Update by the Infectious Diseases Society of America","volume":"52","author":"Freifeld","year":"2011","journal-title":"Clin. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"3263","DOI":"10.1158\/1078-0432.CCR-16-3173","article-title":"Can Consideration of the Microbiome Improve Antimicrobial Utilization and Treatment Outcomes in the Oncology Patient?","volume":"23","author":"Jenq","year":"2017","journal-title":"Clin. Cancer Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5135","DOI":"10.7150\/jca.47470","article-title":"Antibiotics for cancer treatment: A double-edged sword","volume":"11","author":"Gao","year":"2020","journal-title":"J. Cancer"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1093\/cid\/cis580","article-title":"Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation","volume":"55","author":"Taur","year":"2012","journal-title":"Clin. Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1128\/IAI.05496-11","article-title":"Profound Alterations of Intestinal Microbiota following a Single Dose of Clindamycin Results in Sustained Susceptibility to Clostridium difficile-Induced Colitis","volume":"80","author":"Buffie","year":"2012","journal-title":"Infect. Immun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1016\/j.tim.2017.06.006","article-title":"Impact of the Microbiota on Bacterial Infections during Cancer Treatment","volume":"25","author":"Brumlow","year":"2017","journal-title":"Trends Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1038\/s41591-018-0202-8","article-title":"Precision identification of diverse bloodstream pathogens in the gut microbiome","volume":"24","author":"Tamburini","year":"2018","journal-title":"Nat. Med."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Gu, C.H., Khatib, L.A., Fitzgerald, A.S., Graham-Wooten, J., Ittner, C.A., Sherrill-Mix, S., Chuang, Y., Glaser, L.J., Meyer, N.J., and Bushman, F.D. (2023). Tracking gut microbiome and bloodstream infection in critically ill adults. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0289923"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Franklin, S., Aitken, S.L., Shi, Y., Sahasrabhojane, P.V., Robinson, S., Peterson, C.B., Daver, N., Ajami, N.A., Kontoyiannis, D.P., and Shelburne, S.A. (2022). Oral and Stool Microbiome Coalescence and Its Association with Antibiotic Exposure in Acute Leukemia Patients. Front. Cell Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.848580"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2814","DOI":"10.1002\/cam4.1231","article-title":"Patterns of infectious complications in acute myeloid leukemia and myelodysplastic syndromes patients treated with 10-day decitabine regimen","volume":"6","author":"Ali","year":"2017","journal-title":"Cancer Med."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3089","DOI":"10.1128\/JCM.00881-17","article-title":"Comparative Genomics Study of Staphylococcus epidermidis Isolates from Orthopedic-Device-Related Infections Correlated with Patient Outcome","volume":"55","author":"Post","year":"2017","journal-title":"J. Clin. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Brown, M.M., and Horswill, A.R. (2020). Staphylococcus epidermidis\u2014Skin friend or foe?. PLoS Pathog., 16.","DOI":"10.1371\/journal.ppat.1009026"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/nrmicro2182","article-title":"Staphylococcus epidermidis\u2014The \u201caccidental\u201d pathogen","volume":"7","author":"Otto","year":"2009","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e01907-24","DOI":"10.1128\/mbio.01907-24","article-title":"Staphylococcus epidermidis ST2 strains associated with bloodstream infections contain a unique mobile genetic element encoding a plasmin inhibitor","volume":"15","author":"Gomez","year":"2024","journal-title":"mBio"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Ehlers, M.M., Strasheim, W., Lowe, M., Ueckermann, V., and Kock, M.M. (2018). Molecular Epidemiology of Staphylococcus epidermidis Implicated in Catheter-Related Bloodstream Infections at an Academic Hospital in Pretoria, South Africa. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.00417"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e61704","DOI":"10.5812\/archcid.61704","article-title":"Molecular Characteristics of Biofilm-Producing Methicillin-Resistant Staphylococcus epidermidis Isolates Causing Urinary Tract Infections","volume":"13","author":"Rahimi","year":"2018","journal-title":"Arch. Clin. Infect. Dis."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"He, W.-P., Gu, F.-F., Zhang, J., Li, X.-X., Xiao, S.-Z., Zeng, Q., Ni, Y.-X., and Han, L.-Z. (2021). Molecular characteristics and risk factor analysis of Staphylococcus aureus colonization put insight into CC1 colonization in three nursing homes in Shanghai. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0253858"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Altayb, H.N., Elbadawi, H.S., Baothman, O., Kazmi, I., Alzahrani, F.A., Nadeem, M.S., Hosawi, S., and Chaieb, K. (2022). Whole-Genome Sequence of Multidrug-Resistant Methicillin-Resistant Staphylococcus epidermidis Carrying Biofilm-Associated Genes and a Unique Composite of SCCmec. Antibiotics, 11.","DOI":"10.3390\/antibiotics11070861"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1128\/IAI.00089-14","article-title":"The psm\u03b1 locus regulates production of Staphylococcus aureus alpha-toxin during infection","volume":"82","author":"Berube","year":"2014","journal-title":"Infect. Immun."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1093\/cid\/ciz777","article-title":"Gut Microbiome Signatures Are Predictive of Infectious Risk Following Induction Therapy for Acute Myeloid Leukemia","volume":"71","author":"Shi","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"ref_27","unstructured":"(2021, October 10). (EN)\u2014QIAamp DNA Stool Handbook\u2014June 2012\u2014QIAGEN. Available online: https:\/\/www.qiagen.com\/us\/resources\/resourcedetail?id=e5f66d36-1f1c-4e89-828e-257088bdad53&lang=en."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13073-017-0409-1","article-title":"Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients","volume":"9","author":"Smith","year":"2017","journal-title":"Genome Med."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2186","DOI":"10.1002\/cncr.30039","article-title":"The Role of the Gastrointestinal Microbiome in Infectious Complications During Induction Chemotherapy for Acute Myeloid Leukemia","volume":"122","author":"Smith","year":"2016","journal-title":"Cancer"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Edgar, R.C. (2016). UNOISE2: Improved error-correction for Illumina 16S and ITS amplicon sequencing. BioRxiv.","DOI":"10.1101\/081257"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Brynildsrud, O., Bohlin, J., Scheffer, L., and Eldholm, V. (2016). Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol., 17.","DOI":"10.1186\/s13059-016-1108-8"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: Rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: Genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1007\/s00239-024-10173-0","article-title":"Phylogenetic Analysis and Comparative Genomics of Brucella abortus and Brucella melitensis Strains in Egypt","volume":"92","author":"Elrashedy","year":"2024","journal-title":"J. Mol. Evol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/s41182-019-0180-7","article-title":"Virulence factors and antibiotic resistance properties of the Staphylococcus epidermidis strains isolated from hospital infections in Ahvaz, Iran","volume":"47","author":"Chabi","year":"2019","journal-title":"Trop. Med. Health"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1093\/jac\/dkx524","article-title":"Dissemination of linezolid-dependent, linezolid-resistant Staphylococcus epidermidis clinical isolates belonging to CC5 in German hospitals","volume":"73","author":"Layer","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.ijid.2023.07.014","article-title":"Staphylococcus epidermidis bloodstream infections are a cause of septic shock in intensive care unit patients","volume":"135","author":"Demiselle","year":"2023","journal-title":"Int. J. Infect. Dis."},{"key":"ref_41","unstructured":"Duygu Mert, A.M. (2025, April 30). Evaluation of Risk Factors and Causative Pathogens in Bloodstream Infections in Cancer Patients. Available online: https:\/\/gulhanemedj.org\/articles\/evaluation-of-risk-factors-and-causative-pathogens-in-bloodstream-infections-in-cancer-patients\/doi\/gulhane.galenos.2020.1320?utm_source=chatgpt.com."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"VanAken, S.M., Newton, D., and VanEpps, J.S. (2021). Improved diagnostic prediction of the pathogenicity of bloodstream isolates of Staphylococcus epidermidis. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0241457"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"e0023622","DOI":"10.1128\/iai.00236-22","article-title":"The Small RNA Teg41 Is a Pleiotropic Regulator of Virulence in Staphylococcus aureus","volume":"90","author":"Briaud","year":"2022","journal-title":"Infect. Immun."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Sabat\u00e9 Bresc\u00f3, M., Harris, L.G., Thompson, K., Stanic, B., Morgenstern, M., O\u2019Mahony, L., Richards, R.G., and Moriarty, T.F. (2017). Pathogenic Mechanisms and Host Interactions in Staphylococcus epidermidis Device-Related Infection. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.01401"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Ahmad, S., Rahman, H., Qasim, M., Nawab, J., Alzahrani, K.J., Alsharif, K.F., and Alzahrani, F.M. (2022). Staphylococcus epidermidis Pathogenesis: Interplay of icaADBC Operon and MSCRAMMs in Biofilm Formation of Isolates from Pediatric Bacteremia in Peshawar, Pakistan. Medicina, 58.","DOI":"10.3390\/medicina58111510"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"eadg5562","DOI":"10.1126\/scitranslmed.adg5562","article-title":"Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit","volume":"15","author":"Schwartz","year":"2023","journal-title":"Sci. Transl. Med."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Garcia-Gutierrez, E., Walsh, C.J., Sayavedra, L., Diaz-Calvo, T., Thapa, D., Ruas-Madiedo, P., Mayer, M.J., Cotter, P.D., and Narbad, A. (2020). Genotypic and Phenotypic Characterization of Fecal Staphylococcus epidermidis Isolates Suggests Plasticity to Adapt to Different Human Body Sites. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00688"}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/7\/627\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:57:37Z","timestamp":1760032657000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/7\/627"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,24]]},"references-count":47,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2025,7]]}},"alternative-id":["pathogens14070627"],"URL":"https:\/\/doi.org\/10.3390\/pathogens14070627","relation":{},"ISSN":["2076-0817"],"issn-type":[{"type":"electronic","value":"2076-0817"}],"subject":[],"published":{"date-parts":[[2025,6,24]]}}}