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In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species \u2013 <jats:italic>Acinetobacter baumannii<\/jats:italic>, <jats:italic>Escherichia coli<\/jats:italic>, two <jats:italic>Klebsiella pneumoniae<\/jats:italic>, <jats:italic>Proteus mirabilis<\/jats:italic> and <jats:italic>Pseudomonas aeruginosa<\/jats:italic> \u2013 were characterized using whole genome sequencing. All <jats:italic>Enterobacteriaceae<\/jats:italic> isolates and the <jats:italic>A. baumannii<\/jats:italic> isolate had acquired a large number of antimicrobial resistance genes (7\u201318 different genes per isolate), including the following encoding carbapenemases: <jats:italic>bla<\/jats:italic>\n                  <jats:sub>KPC-2<\/jats:sub>, <jats:italic>bla<\/jats:italic>\n                  <jats:sub>OXA-48<\/jats:sub>, <jats:italic>bla<\/jats:italic>\n                  <jats:sub>OXA-72<\/jats:sub>, <jats:italic>bla<\/jats:italic>\n                  <jats:sub>NDM-1<\/jats:sub>, <jats:italic>bla<\/jats:italic>\n                  <jats:sub>NDM-7<\/jats:sub> and <jats:italic>bla<\/jats:italic>\n                  <jats:sub>VIM-1<\/jats:sub>. In addition, a novel version of <jats:italic>bla<\/jats:italic>\n                  <jats:sub>SHV<\/jats:sub> was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were co-localized on these and other plasmids, suggesting a risk for co-selection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance \u2013 based on acquired resistance determinants \u2013 was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.<\/jats:p>","DOI":"10.1099\/mgen.0.000233","type":"journal-article","created":{"date-parts":[[2018,11,21]],"date-time":"2018-11-21T16:19:15Z","timestamp":1542817155000},"source":"Crossref","is-referenced-by-count":25,"title":["The resistomes of six carbapenem-resistant pathogens \u2013 a critical genotype\u2013phenotype analysis"],"prefix":"10.1099","volume":"4","author":[{"given":"Anna","family":"Johnning","sequence":"first","affiliation":[{"name":"2\u200bCentre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden"},{"name":"1\u200bDepartment of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nahid","family":"Karami","sequence":"additional","affiliation":[{"name":"2\u200bCentre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden"},{"name":"3\u200bDepartment of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erika","family":"T\u00e5ng Hallb\u00e4ck","sequence":"additional","affiliation":[{"name":"3\u200bDepartment of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vilhelm","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"4\u200bDepartment of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lena","family":"Nyberg","sequence":"additional","affiliation":[{"name":"4\u200bDepartment of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariana","family":"Buongermino Pereira","sequence":"additional","affiliation":[{"name":"1\u200bDepartment of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden"},{"name":"2\u200bCentre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Callum","family":"Stewart","sequence":"additional","affiliation":[{"name":"5\u200bDepartment of Astronomy and Theoretical Physics, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias","family":"Ambj\u00f6rnsson","sequence":"additional","affiliation":[{"name":"5\u200bDepartment of Astronomy and Theoretical Physics, Lund University, Lund, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fredrik","family":"Westerlund","sequence":"additional","affiliation":[{"name":"4\u200bDepartment of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingegerd","family":"Adlerberth","sequence":"additional","affiliation":[{"name":"2\u200bCentre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden"},{"name":"3\u200bDepartment of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik","family":"Kristiansson","sequence":"additional","affiliation":[{"name":"1\u200bDepartment of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden"},{"name":"2\u200bCentre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1016\/j.drup.2016.09.002"},{"key":"R2","article-title":"Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics","year":"2017"},{"key":"R3","article-title":"Antibiotic resistance threats in the United States","year":"2013"},{"key":"R4","volume-title":"Antimicrobial resistance surveillance in Europe 2015. 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