{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T09:33:25Z","timestamp":1774949605442,"version":"3.50.1"},"posted":{"date-parts":[[2026,3,28]]},"group-title":"Microbiology","reference-count":103,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T00:00:00Z","timestamp":1774656000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"name":"Japan Agency for Medical Research and Development (AMED), Japan","award":["JP25fk0108665, JP26fk0108755, and JP25wm0225029 to H. Tomita; JP25fk0108665, JP25fk0108683, JP25fk0108712, JP26fk0108755, JP26fk0108756, JP25gm1610003, JP25wm0225029, JP25wm0225054, JP25wm0325076, and JP25wm0125012 to M. Suzuki; JP25fk0108664, JP25fk0108665, JP25fk0108712, JP26fk0108755, and JP25wm0225029 to I. Kasuga; JP25wm0225029 and JP21wm0125006 to F. Hasebe; JP25wm0225029 to Y. Tsuda; JP25fk0108665, JP25gm1610003, and JP26fk0108755 to K. Shibayama"],"award-info":[{"award-number":["JP25fk0108665, JP26fk0108755, and JP25wm0225029 to H. Tomita; JP25fk0108665, JP25fk0108683, JP25fk0108712, JP26fk0108755, JP26fk0108756, JP25gm1610003, JP25wm0225029, JP25wm0225054, JP25wm0325076, and JP25wm0125012 to M. Suzuki; JP25fk0108664, JP25fk0108665, JP25fk0108712, JP26fk0108755, and JP25wm0225029 to I. Kasuga; JP25wm0225029 and JP21wm0125006 to F. Hasebe; JP25wm0225029 to Y. Tsuda; JP25fk0108665, JP25gm1610003, and JP26fk0108755 to K. Shibayama"]}]},{"DOI":"10.13039\/501100001700","name":"Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan","doi-asserted-by":"crossref","award":["22K16368 to Y. Hashimoto; 22K07067 to H. Tomita; 22KK0058 and 23K06556 to M. Suzuki; 22KK0058 to I. Kasuga; 23KK0151 to K. Shibayama"],"award-info":[{"award-number":["22K16368 to Y. Hashimoto; 22K07067 to H. Tomita; 22KK0058 and 23K06556 to M. Suzuki; 22KK0058 to I. Kasuga; 23KK0151 to K. Shibayama"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Ministry of Health, Labor and Welfare (MHLW), Japan","award":["21KA1004 and 24KA1005 to H. Tomita"],"award-info":[{"award-number":["21KA1004 and 24KA1005 to H. Tomita"]}]},{"name":"Consortium for the Exploration of Microbial Functions of Ohsumi Frontier Science Foundation, Japan","award":["grants to H. Tomita, M. Suzuki, K. Shibayama"],"award-info":[{"award-number":["grants to H. Tomita, M. Suzuki, K. Shibayama"]}]},{"name":"Gunma Foundation for Medicine and Health Science, Japan","award":["Kambe Memorial Research Award to Y. Hashimoto"],"award-info":[{"award-number":["Kambe Memorial Research Award to Y. Hashimoto"]}]},{"name":"National Institutes of Health (NIH), the United States","award":["AI083214 to M.S. Gilmore"],"award-info":[{"award-number":["AI083214 to M.S. Gilmore"]}]},{"name":"National Foundation for Science and Technology Development (NAFOSTED), Vietnam","award":["108.02-2017.320"],"award-info":[{"award-number":["108.02-2017.320"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  As animal hosts adapted to land,\n                  <jats:italic>Enterococcus<\/jats:italic>\n                  species diverged from a common ancestor shared with\n                  <jats:italic>Vagococcus<\/jats:italic>\n                  species by acquiring genes essential for survival and transmission in the exposed arid environment. In addition to their intrinsic ruggedness, human-associated enterococci now frequently exhibit multidrug resistance, largely driven by the accumulation of antimicrobial resistance genes (ARGs) on mobile genetic elements (MGEs). However, the source of these resistance elements, their diversity in natural reservoirs, and the risk that they pose remain unclear. To investigate the movement of novel ARGs from the environmental reservoir and the elements that convey them into clinically important enterococcal lineages, we examined environmental vancomycin-resistant enterococci (VRE) circulating in a polluted urban river in Hanoi, Vietnam. Whole-genome sequencing of VRE isolates revealed multidrug-resistance pELF-type linear plasmids harboring a novel fluoroquinolone resistance gene (\n                  <jats:italic>qrtA<\/jats:italic>\n                  ) encoding a major facilitator superfamily transporter. The\n                  <jats:italic>qrtA<\/jats:italic>\n                  gene appears to have originated on\n                  <jats:italic>Vagococcus<\/jats:italic>\n                  chromosomes and to have been mobilized by IS\n                  <jats:italic>1216E<\/jats:italic>\n                  -associated MGEs.\n                  <jats:italic>Vagococcus<\/jats:italic>\n                  genomes show strong associations between ARGs, IS\n                  <jats:italic>1216E,<\/jats:italic>\n                  and plasmids related to those in enterococci, and conjugation experiments demonstrated that pELF-type linear plasmids can transfer between\n                  <jats:italic>Enterococcus<\/jats:italic>\n                  and\n                  <jats:italic>Vagococcus<\/jats:italic>\n                  without major fitness costs, positioning them as plausible vehicles for importing environmental ARGs into enterococci. Reconstruction of pELF-type linear plasmid evolution in the environment, together with database mining of rare\n                  <jats:italic>qrtA<\/jats:italic>\n                  -positive clinical isolates from Asia and Europe, suggests that\n                  <jats:italic>qrtA<\/jats:italic>\n                  -bearing pELF-type linear plasmids are in an early phase of global dissemination. These findings highlight the need for coordinated international One Health surveillance of ARG and MGE dynamics, including emerging determinants such as\n                  <jats:italic>qrtA<\/jats:italic>\n                  , together with proactive interventions to limit their spread.\n                <\/jats:p>","DOI":"10.64898\/2026.03.26.714403","type":"posted-content","created":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T09:35:12Z","timestamp":1774690512000},"source":"Crossref","is-referenced-by-count":0,"title":["Tracing the emergence of the novel fluoroquinolone resistance gene\n                  <i>qrtA<\/i>\n                  in enterococci through environmental reservoirs and pELF-type linear plasmids"],"prefix":"10.64898","author":[{"given":"Yusuke","family":"Hashimoto","sequence":"first","affiliation":[{"name":"Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masato","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan Institute for Health Security, 4-2-1 Aoba-cho, Higashimurayama, Tokyo, Japan"},{"name":"Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, Japan"},{"name":"Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Trung Duc","family":"Dao","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ikuro","family":"Kasuga","sequence":"additional","affiliation":[{"name":"Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, Japan"},{"name":"Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo Japan"},{"name":"Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thi My","family":"Hanh Vu","sequence":"additional","affiliation":[{"name":"Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, Japan"},{"name":"Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taichiro","family":"Takemura","sequence":"additional","affiliation":[{"name":"Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haruka","family":"Abe","sequence":"additional","affiliation":[{"name":"Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Futoshi","family":"Hasebe","sequence":"additional","affiliation":[{"name":"Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yusuke","family":"Tsuda","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takahiro","family":"Nomura","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Kurushima","sequence":"additional","affiliation":[{"name":"Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hidetada","family":"Hirakawa","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keigo","family":"Shibayama","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hoang H.","family":"Tran","sequence":"additional","affiliation":[{"name":"National Institute of Hygiene and Epidemiology, No.1 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