{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T17:44:48Z","timestamp":1790790288395,"version":"4.1.0"},"reference-count":17,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2023,8,1]],"date-time":"2023-08-01T00:00:00Z","timestamp":1690848000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,8,1]],"date-time":"2023-08-01T00:00:00Z","timestamp":1690848000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"HHS | National Institutes of Health","award":["R01 HL148184-01"],"award-info":[{"award-number":["R01 HL148184-01"]}]},{"name":"HHS | National Institutes of Health","award":["R01 AI12492093"],"award-info":[{"award-number":["R01 AI12492093"]}]},{"name":"HHS | National Institutes of Health","award":["R01 DC019965"],"award-info":[{"award-number":["R01 DC019965"]}]},{"name":"HHS | National Institutes of Health","award":["R21GM147838"],"award-info":[{"award-number":["R21GM147838"]}]},{"name":"National Science Foundation","award":["GRFP"],"award-info":[{"award-number":["GRFP"]}]},{"name":"HHS | National Institutes of Health","award":["T32 HL129970-06"],"award-info":[{"award-number":["T32 HL129970-06"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Bacteriophages, viruses that parasitize bacteria, are known to be abundant at sites of bacterial colonization, but the relationship between phages and bacteria at sites of infection is unclear. Bacteriophages are highly specific to their bacterial host species, and so we hypothesize that phage populations would mirror those of bacterial pathogens within infected tissues. To test this, here we study publicly available cell-free DNA (cfDNA) generated using next-generation sequencing of infected bodily fluids, including urine, joint fluid, peritoneal fluid, bronchoalveolar lavage fluid, cerebrospinal fluid, and abscess fluid, as well as uninfected control samples. These were analyzed using a computational pipeline for identifying bacteriophage sequences in cfDNA. We find that bacteriophage sequences are present in both infected and uninfected bodily fluids and represent a variety of bacteriophage morphologies and bacterial hosts. Additionally, phages from\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    ,\n                    <jats:italic>Streptococcus<\/jats:italic>\n                    , and\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    are overrepresented both in terms of proportion and diversity in fluids infected with these same pathogens. These data indicate that phages reflect the relative abundance of their bacterial hosts at sites of infection. Bacteriophage sequences may help inform future investigative and diagnostic approaches that utilize cell-free DNA to study the microbiome within infected tissues.\n                  <\/jats:p>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>Bacteriophages are an active area of investigation in microbiome research, but most studies have focused on phage populations at sites of bacterial colonization. Little is known about bacteriophage ecology at sites of active infection. To address this gap in knowledge, we utilized a publicly available data set to study bacteriophage populations in cell-free DNA collected from sites of infection. We find that phages reflect the relative abundance of their bacterial hosts at sites of infection. These studies may lead to future investigative and diagnostic approaches that incorporate phages as well as bacterial cell-free DNA.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.00497-23","type":"journal-article","created":{"date-parts":[[2023,8,1]],"date-time":"2023-08-01T09:00:33Z","timestamp":1690880433000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":7,"title":["Bacteriophage populations mirror those of bacterial pathogens at sites of infection"],"prefix":"10.1128","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2525-1450","authenticated-orcid":true,"given":"N. L.","family":"Haddock","sequence":"first","affiliation":[{"name":"Immunology Program, School of Medicine, Stanford University , Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L. J.","family":"Barkal","sequence":"additional","affiliation":[{"name":"Division of Pulmonary, Allergy, and Critical Care Medicine, School of Medicine, Stanford University , Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2499-9448","authenticated-orcid":true,"given":"P. L.","family":"Bollyky","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, School of Medicine, Stanford University , Stanford, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","published-online":{"date-parts":[[2023,8]]},"reference":[{"key":"e_1_3_1_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(22)02185-7"},{"key":"e_1_3_1_3_2","unstructured":"Report signals increasing resistance to antibiotics in bacterial infections in humans and need for better data. 2022 Available from: https:\/\/www.who.int\/news\/item\/09-12-2022-report-signals-increasing-resistance-to-antibiotics-in-bacterial-infections-in-humans-and-need-for-better-data"},{"key":"e_1_3_1_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2018.08.006"},{"key":"e_1_3_1_5_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00566"},{"key":"e_1_3_1_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2019.01.017"},{"key":"e_1_3_1_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02071-21"},{"key":"e_1_3_1_8_2","doi-asserted-by":"publisher","DOI":"10.4161\/bact.20757"},{"key":"e_1_3_1_9_2","doi-asserted-by":"publisher","DOI":"10.3390\/pharmaceutics14071425"},{"key":"e_1_3_1_10_2","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.00244"},{"key":"e_1_3_1_11_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1601060113"},{"key":"e_1_3_1_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02777-21"},{"key":"e_1_3_1_13_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1707009114"},{"key":"e_1_3_1_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-020-1105-z"},{"key":"e_1_3_1_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-023-01406-x"},{"key":"e_1_3_1_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_1_17_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"e_1_3_1_18_2","doi-asserted-by":"publisher","DOI":"10.1002\/j.1538-7305.1948.tb01338.x"}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00497-23","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/msystems.00497-23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,1]],"date-time":"2023-08-01T09:00:46Z","timestamp":1690880446000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/msystems.00497-23"}},"subtitle":[],"editor":[{"given":"Evelien M.","family":"Adriaenssens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,8]]},"references-count":17,"alternative-id":["10.1128\/msystems.00497-23"],"URL":"https:\/\/doi.org\/10.1128\/msystems.00497-23","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.05.17.541184","asserted-by":"object"}]},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,8]]},"assertion":[{"value":"2023-05-17","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-06-19","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-08-01","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00497-23"}}