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Vancomycin-Resistant\n                      <jats:italic>Enterococcus<\/jats:italic>\n                      (VRE) are candidates for gauging the degree of AMR bacteria in wastewater.\n                      <jats:italic>Enterococcus faecalis<\/jats:italic>\n                      and\n                      <jats:italic>Enterococcus faecium<\/jats:italic>\n                      are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      VRE isolates, including\n                      <jats:italic>E. faecalis<\/jats:italic>\n                      (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200924),\n                      <jats:italic>E. faecium<\/jats:italic>\n                      (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200911),\n                      <jats:italic>E. casseliflavus<\/jats:italic>\n                      (n\u2009=\u20092) and\n                      <jats:italic>E. gallinarum<\/jats:italic>\n                      (n\u2009=\u20092) were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of\n                      <jats:italic>E. faecium<\/jats:italic>\n                      and\n                      <jats:italic>E. faecalis<\/jats:italic>\n                      were both open. The genomic fraction related to the mobilome was positively correlated with genome size in\n                      <jats:italic>E. faecium<\/jats:italic>\n                      (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&lt;\u20090.001) and\n                      <jats:italic>E. faecalis<\/jats:italic>\n                      (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&lt;\u20090.001) and with the number of AMR genes in\n                      <jats:italic>E. faecium<\/jats:italic>\n                      (\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u20090.005). Genes conferring vancomycin resistance, including\n                      <jats:italic>van<\/jats:italic>\n                      A and\n                      <jats:italic>van<\/jats:italic>\n                      M (\n                      <jats:italic>E. faecium<\/jats:italic>\n                      ),\n                      <jats:italic>van<\/jats:italic>\n                      G (\n                      <jats:italic>E. faecalis<\/jats:italic>\n                      ), and\n                      <jats:italic>van<\/jats:italic>\n                      C (\n                      <jats:italic>E. casseliflavus<\/jats:italic>\n                      \/\n                      <jats:italic>E. gallinarum<\/jats:italic>\n                      ), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in\n                      <jats:italic>E. faecium<\/jats:italic>\n                      ,\n                      <jats:italic>E. faecalis<\/jats:italic>\n                      ,\n                      <jats:italic>E. casseliflavus<\/jats:italic>\n                      and\n                      <jats:italic>E. gallinarum,<\/jats:italic>\n                      respectively. Virulence genes were more common in\n                      <jats:italic>E. faecalis<\/jats:italic>\n                      and\n                      <jats:italic>E. faecium<\/jats:italic>\n                      , than\n                      <jats:italic>E. casseliflavus<\/jats:italic>\n                      and\n                      <jats:italic>E. gallinarum<\/jats:italic>\n                      . A number of mobile genetic elements were shared among species. Functional CRISPR\/Cas arrays were detected in 13\n                      <jats:italic>E. faecalis<\/jats:italic>\n                      genomes, with all but one also containing a prophage. The lack of a functional CRISPR\/Cas arrays was associated with multi-drug resistance in\n                      <jats:italic>E. faecium<\/jats:italic>\n                      . Phylogenetic analysis demonstrated differential clustering of isolates based on original source but not WWTP. Genes related to phage and CRISPR\/Cas arrays could potentially serve as environmental biomarkers.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs.\n                      <jats:italic>E. faecalis<\/jats:italic>\n                      and\n                      <jats:italic>E. faecium<\/jats:italic>\n                      have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other\n                      <jats:italic>Enterococcus spp<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12866-019-1683-4","type":"journal-article","created":{"date-parts":[[2020,1,24]],"date-time":"2020-01-24T08:06:07Z","timestamp":1579853167000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":56,"title":["Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants"],"prefix":"10.1186","volume":"20","author":[{"given":"Haley","family":"Sanderson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodrigo","family":"Ortega-Polo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rahat","family":"Zaheer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noriko","family":"Goji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kingsley K.","family":"Amoako","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R. 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