{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T19:41:04Z","timestamp":1768506064099,"version":"3.49.0"},"posted":{"date-parts":[[2023,7,14]]},"group-title":"Microbiology","reference-count":30,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,7,14]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  <jats:italic>Stenotrophomonas maltophilia<\/jats:italic>\n                  is a Gram-negative emerging opportunistic pathogen often found in respiratory diseases such as cystic fibrosis (CF). Patients with CF experience lifelong polymicrobial infections of the respiratory mucosa. Our prior work showed that\n                  <jats:italic>P. aeruginosa<\/jats:italic>\n                  promotes persistence of\n                  <jats:italic>S. maltophilia<\/jats:italic>\n                  mouse respiratory infections. As is typical for environmental opportunistic pathogens,\n                  <jats:italic>S. maltophilia<\/jats:italic>\n                  has a large genome and a high degree of genetic diversity. In this study, we evaluated the genomic content of\n                  <jats:italic>S. maltophilia,<\/jats:italic>\n                  combining short and long read sequencing to construct complete genomes of 10 clinical isolates which were then compared with the larger phylogeny of\n                  <jats:italic>S. maltophilia<\/jats:italic>\n                  genomic sequence data, and compared colonization\/persistence in vivo, alone and in coinfection with\n                  <jats:italic>P. aeruginosa<\/jats:italic>\n                  . We found that while the overall genome size and GC content were fairly consistent, there was considerable variability in arrangement and gene content. Similarly, there was significant variability in\n                  <jats:italic>S. maltophilia<\/jats:italic>\n                  colonization and persistence in vivo in experimental mouse respiratory infection. Ultimately, this study gives us a greater understanding of the genomic diversity of\n                  <jats:italic>S. maltophilia<\/jats:italic>\n                  isolated from patients, and how this genomic diversity relates to interactions with other pulmonary pathogens, and to host disease progression. Identifying the molecular determinants of infection with\n                  <jats:italic>S. maltophilia<\/jats:italic>\n                  can facilitate development of novel antimicrobial strategies for a highly drug-resistant pathogen.\n                <\/jats:p>","DOI":"10.1101\/2023.07.14.549068","type":"posted-content","created":{"date-parts":[[2023,7,15]],"date-time":"2023-07-15T00:40:10Z","timestamp":1689381610000},"source":"Crossref","is-referenced-by-count":1,"title":["Comparative genomics of clinical\n                  <i>Stenotrophomonas maltophilia<\/i>\n                  isolates reveals regions of diversity which correlate with colonization and persistence in vivo"],"prefix":"10.64898","author":[{"given":"Melissa S.","family":"McDaniel","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas A.","family":"Sumpter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalie R.","family":"Lindgren","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caitlin E.","family":"Billiot","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"W. Edward","family":"Swords","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023071812550729000_2023.07.14.549068v1.1","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00019-11"},{"key":"2023071812550729000_2023.07.14.549068v1.2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.36.7.1953-1958.1998"},{"key":"2023071812550729000_2023.07.14.549068v1.3","doi-asserted-by":"publisher","DOI":"10.1097\/MCP.0b013e328358d49a"},{"key":"2023071812550729000_2023.07.14.549068v1.4","first-page":"787","article-title":"The relevance of the polymicrobial nature of airway infection in the acute and chronic management of patients with cystic fibrosis","volume":"10","year":"2009","journal-title":"Curr Opin Investig Drugs"},{"key":"2023071812550729000_2023.07.14.549068v1.5","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201306-159MG"},{"key":"2023071812550729000_2023.07.14.549068v1.6","doi-asserted-by":"crossref","first-page":"S13","DOI":"10.1093\/jpids\/piac036","article-title":"Exploring the Cystic Fibrosis Lung Microbiome: Making the Most of a Sticky Situation","volume":"11","year":"2022","journal-title":"J Pediatric Infect Dis Soc"},{"key":"2023071812550729000_2023.07.14.549068v1.7","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201609-668OC"},{"key":"2023071812550729000_2023.07.14.549068v1.8","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00810-3"},{"key":"2023071812550729000_2023.07.14.549068v1.9","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-2-14"},{"key":"2023071812550729000_2023.07.14.549068v1.10","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2907"},{"key":"2023071812550729000_2023.07.14.549068v1.11","doi-asserted-by":"publisher","DOI":"10.1016\/S1286-4579(00)01259-4"},{"key":"2023071812550729000_2023.07.14.549068v1.12","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1721270115"},{"key":"2023071812550729000_2023.07.14.549068v1.13","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0602138103"},{"key":"2023071812550729000_2023.07.14.549068v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2015.07.006"},{"key":"2023071812550729000_2023.07.14.549068v1.15","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens4010066"},{"key":"2023071812550729000_2023.07.14.549068v1.16","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2016.01.008"},{"key":"2023071812550729000_2023.07.14.549068v1.17","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15123-0"},{"key":"2023071812550729000_2023.07.14.549068v1.18","doi-asserted-by":"crossref","unstructured":"Mercier-Darty M , Royer G , Lamy B , Charron C , Lemenand O , Gomart C , Fourreau F , Madec JY , Jumas-Bilak E , Decousser JW . 2020. Comparative Whole-Genome Phylogeny of Animal, Environmental, and Human Strains Confirms the Genogroup Organization and Diversity of the Stenotrophomonas maltophilia Complex. Appl Environ Microbiol 86.","DOI":"10.1128\/AEM.02919-19"},{"key":"2023071812550729000_2023.07.14.549068v1.19","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.01551"},{"key":"2023071812550729000_2023.07.14.549068v1.20","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00806"},{"key":"2023071812550729000_2023.07.14.549068v1.21","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02817-09"},{"key":"2023071812550729000_2023.07.14.549068v1.22","doi-asserted-by":"crossref","unstructured":"McDaniel MS , Schoeb T , Swords WE . 2020. Cooperativity between Stenotrophomonas maltophilia and Pseudomonas aeruginosa during Polymicrobial Airway Infections. 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