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Halfon Y, Matzov D, Eyal Z, Bashan A, Zimmerman E, Kjeldgaard J, Ingmer H, Yonath A. Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant. Sci Rep 2019; 9:11460. [PMID: 31391518 PMCID: PMC6685948 DOI: 10.1038/s41598-019-48019-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/25/2019] [Indexed: 12/16/2022] Open
Abstract
The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms include deletion or insertion mutations in ribosomal protein uL22, which lead to alterations of the exit tunnel shape, located 16 Å away from the drug's binding site. We determined the cryo-EM structures of the Staphylococcus aureus 70S ribosome, and its ery bound complex with a two amino acid deletion mutation in its ß hairpin loop, which grants the bacteria resistance to ery. The structures reveal that, although the binding of ery is stable, the movement of the flexible shorter uL22 loop towards the tunnel wall creates a wider path for nascent proteins, thus enabling bypass of the barrier formed by the drug. Moreover, upon drug binding, the tunnel widens further.
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Affiliation(s)
- Yehuda Halfon
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel
| | - Donna Matzov
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel
| | - Zohar Eyal
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel
| | - Anat Bashan
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel
| | - Ella Zimmerman
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel
| | - Jette Kjeldgaard
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800, Kgs, Lyngby, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870, Frederiksberg, Denmark
| | - Ada Yonath
- The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel.
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Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Röder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, Vogt JK, Leekitcharoenphon P, van de Schans MGM, Zuidema T, de Roda Husman AM, Rasmussen S, Petersen B, Amid C, Cochrane G, Sicheritz-Ponten T, Schmitt H, Alvarez JRM, Aidara-Kane A, Pamp SJ, Lund O, Hald T, Woolhouse M, Koopmans MP, Vigre H, Petersen TN, Aarestrup FM. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat Commun 2019; 10:1124. [PMID: 30850636 PMCID: PMC6408512 DOI: 10.1038/s41467-019-08853-3] [Citation(s) in RCA: 455] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/31/2019] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
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Affiliation(s)
- Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Patrick Njage
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Bram van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Luke McNally
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JD, UK
| | - Oksana Lukjancenko
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Timo Röder
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | | | - Jette Kjeldgaard
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Rolf S Kaas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Josef Korbinian Vogt
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | | | - Tina Zuidema
- RIKILT Wageningen University and Research, Wageningen, 6708, The Netherlands
| | - Ana Maria de Roda Husman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721, The Netherlands
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Bent Petersen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Thomas Sicheritz-Ponten
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, 08100, Malaysia
| | - Heike Schmitt
- National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721, The Netherlands
| | | | | | - Sünje J Pamp
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Tine Hald
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Marion P Koopmans
- Viroscience, Erasmus Medical Center, Rotterdam, 3015, The Netherlands
| | - Håkan Vigre
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.
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Wekselman I, Zimmerman E, Davidovich C, Belousoff M, Matzov D, Krupkin M, Rozenberg H, Bashan A, Friedlander G, Kjeldgaard J, Ingmer H, Lindahl L, Zengel JM, Yonath A. The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel. Structure 2017; 25:1233-1241.e3. [PMID: 28689968 DOI: 10.1016/j.str.2017.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 05/08/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
Erythromycin is a clinically useful antibiotic that binds to an rRNA pocket in the ribosomal exit tunnel. Commonly, resistance to erythromycin is acquired by alterations of rRNA nucleotides that interact with the drug. Mutations in the β hairpin of ribosomal protein uL22, which is rather distal to the erythromycin binding site, also generate resistance to the antibiotic. We have determined the crystal structure of the large ribosomal subunit from Deinococcus radiodurans with a three amino acid insertion within the β hairpin of uL22 that renders resistance to erythromycin. The structure reveals a shift of the β hairpin of the mutated uL22 toward the interior of the exit tunnel, triggering a cascade of structural alterations of rRNA nucleotides that propagate to the erythromycin binding pocket. Our findings support recent studies showing that the interactions between uL22 and specific sequences within nascent chains trigger conformational rearrangements in the exit tunnel.
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Affiliation(s)
- Itai Wekselman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimmerman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Chen Davidovich
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Matthew Belousoff
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Donna Matzov
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilgi Friedlander
- The Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jette Kjeldgaard
- Department of Veterinary Disease Biology, University of Copenhagen, 1870 Frederiksbergc, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, University of Copenhagen, 1870 Frederiksbergc, Denmark
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Janice M Zengel
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Ada Yonath
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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Rasmussen LH, Kjeldgaard J, Christensen JP, Ingmer H. Multilocus sequence typing and biocide tolerance of Arcobacter butzleri from Danish broiler carcasses. BMC Res Notes 2013; 6:322. [PMID: 23941403 PMCID: PMC3751686 DOI: 10.1186/1756-0500-6-322] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 08/08/2013] [Indexed: 11/10/2022] Open
Abstract
Background Arcobacter spp. have in recent years received increasing interest as potential emerging enteropathogens and zoonotic agents. They are associated with various animals including poultry and can be isolated from meat products. The possibilities of persistence and cross-contamination in slaughterhouses during meat processing are not well established. We have evaluated the occurrence and persistence of Arcobacter spp. in a Danish slaughterhouse and determined the sensitivity of isolates to sodium hypochlorite, a commonly used biocide. Results Arcobacter contamination was examined in a broiler slaughterhouse by selective enrichment of 235 swabs from the processing line during two production days and after sanitizing in between. In total 13.6% of samples were positive for A. butzleri with the majority (29 of 32 isolates) originating from the evisceration machine. No Arcobacter spp. was isolated after cleaning. A. butzleri isolates confirmed by PCR were typed by multilocus sequence typing (MLST) resulting in 10 new sequence types (STs). Two sequence types were isolated on both processing days. Minimum inhibitory concentration (MIC) to sodium hypochlorite was determined to 0.5% hypochlorite biocide (500 ppm chlorine) for most isolates, which allows growth of A. butzleri within the working concentration of the biocide (0.2 - 0.5%). Conclusions A. butzleri was readily isolated from a Danish broiler slaughterhouse, primarily in the evisceration machine. Typing by MLST showed high strain variability but the recurrence of two STs indicate that some persistence or cross-contamination takes place. Importantly, the isolates tolerated sodium hypochlorite, a biocide commonly employed in slaughterhouse sanitizing, at levels close to the disinfection concentration, and thus, A. butzleri may survive the disinfection process although this was not observed in our study.
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Affiliation(s)
- Louise Hesselbjerg Rasmussen
- Department of Veterinary Disease Biology, University of Copenhagen, Faculty of Health and Medical Sciences, Stigboejlen 4, DK-1870 Frederiksberg, Denmark
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Kjeldgaard J, Jørgensen K, Ingmer H. Growth and survival at chiller temperatures of Arcobacter butzleri. Int J Food Microbiol 2009; 131:256-9. [PMID: 19297052 DOI: 10.1016/j.ijfoodmicro.2009.02.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Revised: 02/14/2009] [Accepted: 02/17/2009] [Indexed: 11/16/2022]
Abstract
Arcobacter butzleri is prevalent on chicken products. Arcobacter spp. are generally isolated in only low numbers from the chicken gut, so chicken carcasses may be contaminated by A. butzleri that proliferate in the slaughterhouse environment. To address this issue, we examined the behaviour of A. butzleri ATCC 49616 and newly isolated A. butzleri strains under conditions likely to prevail in the slaughterhouse environment using a chicken meat juice medium (CMJ). CMJ supported growth of A. butzleri at 15 degrees C, the recognised minimal growth temperature of this organism, and at 10 degrees C. At 5 degrees C, CMJ enhanced survival of A. butzleri as compared with survival in Brain Heart Infusion with less than a one log reduction after 77 days incubation. Lastly, we examined the ability of A. butzleri to form biofilms and found that the organism produces biofilm at temperatures ranging from 5 to 37 degrees C. Given the ability to survive, multiply and form biofilm under chilled conditions A. butzleri appears well suited for establishment in food processing and slaughterhouse environments.
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Affiliation(s)
- Jette Kjeldgaard
- Department of Veterinary Disease Biology, Faculty of Life Sciences, Stigbøjlen 4, University of Copenhagen, DK-1870 Frederiksberg, Denmark
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