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Doijad SP, Gisch N, Frantz R, Kumbhar BV, Falgenhauer J, Imirzalioglu C, Falgenhauer L, Mischnik A, Rupp J, Behnke M, Buhl M, Eisenbeis S, Gastmeier P, Gölz H, Häcker GA, Käding N, Kern WV, Kola A, Kramme E, Peter S, Rohde AM, Seifert H, Tacconelli E, Vehreschild MJGT, Walker SV, Zweigner J, Schwudke D, Chakraborty T, Thoma N, Weber A, Vavra M, Schuster S, Peyerl-Hoffmann G, Hamprecht A, Proske S, Stelzer Y, Wille J, Lenke D, Bader B, Dinkelacker A, Hölzl F, Kunstle L, Chakraborty T. Resolving colistin resistance and heteroresistance in Enterobacter species. Nat Commun 2023; 14:140. [PMID: 36627272 PMCID: PMC9832134 DOI: 10.1038/s41467-022-35717-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Species within the Enterobacter cloacae complex (ECC) include globally important nosocomial pathogens. A three-year study of ECC in Germany identified Enterobacter xiangfangensis as the most common species (65.5%) detected, a result replicated by examining a global pool of 3246 isolates. Antibiotic resistance profiling revealed widespread resistance and heteroresistance to the antibiotic colistin and detected the mobile colistin resistance (mcr)-9 gene in 19.2% of all isolates. We show that resistance and heteroresistance properties depend on the chromosomal arnBCADTEF gene cassette whose products catalyze transfer of L-Ara4N to lipid A. Using comparative genomics, mutational analysis, and quantitative lipid A profiling we demonstrate that intrinsic lipid A modification levels are genospecies-dependent and governed by allelic variations in phoPQ and mgrB, that encode a two-component sensor-activator system and specific inhibitor peptide. By generating phoPQ chimeras and combining them with mgrB alleles, we show that interactions at the pH-sensing interface of the sensory histidine kinase phoQ dictate arnBCADTEF expression levels. To minimize therapeutic failures, we developed an assay that accurately detects colistin resistance levels for any ECC isolate.
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Affiliation(s)
- Swapnil Prakash Doijad
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Renate Frantz
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed-to-be) University, Vile Parle, Mumbai, India
| | - Jane Falgenhauer
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany
| | - Can Imirzalioglu
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany
| | - Linda Falgenhauer
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany.,Institute of Hygiene and Environmental Medicine, Justus Liebig University, Gießen, Germany
| | - Alexander Mischnik
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Michael Behnke
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität of Berlin and Berlin Institute of Health, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - Michael Buhl
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology and Hygiene, Tübingen University, Tübingen, Germany.,Division of Infectious Diseases, Department of Internal Medicine I, Tübingen University, Tübingen, Germany.,Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Klinikum Nürnberg, Nürnberg, Germany
| | - Simone Eisenbeis
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Diseases, Department of Internal Medicine I, Tübingen University, Tübingen, Germany
| | - Petra Gastmeier
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität of Berlin and Berlin Institute of Health, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - Hanna Gölz
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology and Hygiene, Albert-Ludwigs-University, Freiburg, Germany
| | - Georg Alexander Häcker
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology and Hygiene, Albert-Ludwigs-University, Freiburg, Germany
| | - Nadja Käding
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Winfried V Kern
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Diseases, Department of Medicine II, Faculty of Medicine and University Hospital and Medical Center, Albert-Ludwigs-University, Freiburg, Germany
| | - Axel Kola
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität of Berlin and Berlin Institute of Health, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - Evelyn Kramme
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität of Berlin and Berlin Institute of Health, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - Silke Peter
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute of Medical Microbiology and Hygiene, Tübingen University, Tübingen, Germany
| | - Anna M Rohde
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität of Berlin and Berlin Institute of Health, Institute of Hygiene and Environmental Medicine, Berlin, Germany
| | - Harald Seifert
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology, and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Evelina Tacconelli
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Division of Infectious Diseases, Department of Internal Medicine I, Tübingen University, Tübingen, Germany
| | - Maria J G T Vehreschild
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Sarah V Walker
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology, and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Janine Zweigner
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Institute for Medical Microbiology, Immunology, and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Dominik Schwudke
- German Center for Infection Research (DZIF), Braunschweig, Germany.,Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.,Airway Research Center North, Member of the German Center for Lung Research (DZL), Site: Research Center Borstel, Borstel, Germany
| | | | - Trinad Chakraborty
- German Center for Infection Research (DZIF), Braunschweig, Germany. .,Institute of Medical Microbiology, Justus Liebig University, Gießen, Germany.
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