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Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing. Nucleic Acids Res 2024; 52:e63. [PMID: 38909293 DOI: 10.1093/nar/gkae528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/21/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024] Open
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.
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Affiliation(s)
- Josh L Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Melanie B Prentice
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Gene S Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
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Mullally CA, Fahriani M, Mowlaboccus S, Coombs GW. Non- faecium non- faecalis enterococci: a review of clinical manifestations, virulence factors, and antimicrobial resistance. Clin Microbiol Rev 2024; 37:e0012123. [PMID: 38466110 PMCID: PMC11237509 DOI: 10.1128/cmr.00121-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024] Open
Abstract
SUMMARYEnterococci are a diverse group of Gram-positive bacteria that are typically found as commensals in humans, animals, and the environment. Occasionally, they may cause clinically relevant diseases such as endocarditis, septicemia, urinary tract infections, and wound infections. The majority of clinical infections in humans are caused by two species: Enterococcus faecium and Enterococcus faecalis. However, there is an increasing number of clinical infections caused by non-faecium non-faecalis (NFF) enterococci. Although NFF enterococcal species are often overlooked, studies have shown that they may harbor antimicrobial resistance (AMR) genes and virulence factors that are found in E. faecium and E. faecalis. In this review, we present an overview of the NFF enterococci with a particular focus on human clinical manifestations, epidemiology, virulence genes, and AMR genes.
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Affiliation(s)
- Christopher A Mullally
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marhami Fahriani
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- PathWest Laboratory Medicine-WA, Department of Microbiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- PathWest Laboratory Medicine-WA, Department of Microbiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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3
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El-Banna TES, Sonbol FI, Kamer AMA, Badr SAMM. Genetic diversity of macrolides resistant Staphylococcus aureus clinical isolates and the potential synergistic effect of vitamins, C and K 3. BMC Microbiol 2024; 24:30. [PMID: 38245680 PMCID: PMC10799532 DOI: 10.1186/s12866-023-03169-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 12/22/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Macrolide antibiotics have been extensively used for the treatment of Staphylococcus aureus infections. However, the emergence of macrolide-resistant strains of S. aureus has become a major concern for public health. The molecular mechanisms underlying macrolide resistance in S. aureus are complex and diverse, involving both target site modification and efflux pump systems. In this study, we aim to overcome the molecular diversity of macrolide resistance mechanisms in S. aureus by identifying common molecular targets that could be exploited for the development of novel therapeutics. METHODS About 300 Staphylococcus aureus different isolates were recovered and purified from 921 clinical specimen including urine (88), blood (156), sputum (264), nasal swabs (168), pus (181) and bone (39) collected from different departments in Tanta University Hospital. Macrolide resistant isolates were detected and tested for Multi Drug Resistant (MDR). Gel electrophoresis was performed after the D test and PCR reaction for erm(A), (B), (C), msr(A), and mph(C) genes. Finally, we tried different combinations of Erythromycin or Azithromycin antibiotics with either vitamin K3 or vitamin C. RESULTS Macrolide resistance S. aureus isolates exhibited 7 major resistance patterns according to number of resistance markers and each pattern included sub patterns or subgroups. The PCR amplified products of different erm genes; analysis recorded different phenotypes of the Staphylococcus aureus isolates according to their different genotypes. In addition, our new tested combinations of Erythromycin and vitamin C, Erythromycin, and vitamin K3, Azithromycin and vitamin C and Azithromycin and vitamin K3 showed significant antibacterial effect when using every antibiotic alone. Our findings provide new insights into the molecular mechanisms of macrolide resistance in S. aureus and offer potential strategies for the development of novel protocols to overcome this emerging public health threat.
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Xu R, Wang Q, Wu S, Wang H, Song T, Zhao C, Wang M, Du H, Zhang H. Molecular basis and evolutionary cost of a novel macrolides/lincosamides resistance phenotype in Staphylococcus haemolyticus. Microbiol Spectr 2023; 11:e0044123. [PMID: 37724875 PMCID: PMC10655708 DOI: 10.1128/spectrum.00441-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/23/2023] [Indexed: 09/21/2023] Open
Abstract
Staphylococcus haemolyticus (S. haemolyticus) is a coagulase-negative Staphylococcus that has become one of the primary causes of nosocomial infection. After a long period of antibiotic use, S. haemolyticus has developed multiple resistance phenotypes for macrolides and lincosamides. Herein, we evaluated four S. haemolyticus clinical isolates, of which three had antibiotic resistance patterns reported previously. The fourth isolate was resistant to both erythromycin and clindamycin in the absence of erythromycin induction. This novel phenotype, known as constitutive macrolides-lincosamides-streptogramins resistance, has been reported in other bacteria but has not been previously reported in S. haemolyticus. Investigation of the isolate demonstrated a deletion in the methyltransferase gene ermC, upstream leader peptide. This deletion resulted in constitutive MLS resistance based on whole-genome sequencing and experimental verification. Continuous expression of ermC was shown to inhibit the growth of S. haemolyticus, which turned out to be the fitness cost with no MLS pressure. In summary, this study is the first to report constitutive MLS resistance in S. haemolyticus, which provides a better understanding of MLS resistance in clinical medicine. IMPORTANCE This study identified a novel phenotype of macrolides/lincosamides resistance in Staphylococcus haemolyticus which improved a better guidance for clinical treatment. It also clarified the mechanistic basis for this form of antibiotic resistance that supplemented the drug resistance mechanism of Staphylococcus. In addition, this study elaborated on a possibility that continuous expression of some resistance genes was shown to inhibit the growth of bacteria themselves, which turned out to be the fitness cost in the absence of antibiotic pressure.
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Affiliation(s)
- Ruilin Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life, Nanjing University, Nanjing, Jiangsu, China
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qiang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life, Nanjing University, Nanjing, Jiangsu, China
| | - Shuhua Wu
- Department of Geriatrics, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of General Practice, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Hongqiu Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tianqiang Song
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life, Nanjing University, Nanjing, Jiangsu, China
| | - Chenhao Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Min Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Obana N, Takada H, Crowe-McAuliffe C, Iwamoto M, Egorov AA, Wu KJY, Chiba S, Murina V, Paternoga H, Tresco BIC, Nomura N, Myers AG, Atkinson G, Wilson DN, Hauryliuk V. Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR. Nucleic Acids Res 2023; 51:4536-4554. [PMID: 36951104 PMCID: PMC10201436 DOI: 10.1093/nar/gkad193] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/17/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
Genome-encoded antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F subfamily (ARE-ABCFs) mediate intrinsic resistance in diverse Gram-positive bacteria. The diversity of chromosomally-encoded ARE-ABCFs is far from being fully experimentally explored. Here we characterise phylogenetically diverse genome-encoded ABCFs from Actinomycetia (Ard1 from Streptomyces capreolus, producer of the nucleoside antibiotic A201A), Bacilli (VmlR2 from soil bacterium Neobacillus vireti) and Clostridia (CplR from Clostridium perfringens, Clostridium sporogenes and Clostridioides difficile). We demonstrate that Ard1 is a narrow spectrum ARE-ABCF that specifically mediates self-resistance against nucleoside antibiotics. The single-particle cryo-EM structure of a VmlR2-ribosome complex allows us to rationalise the resistance spectrum of this ARE-ABCF that is equipped with an unusually long antibiotic resistance determinant (ARD) subdomain. We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate that C. difficile CplR (CDIF630_02847) synergises with the transposon-encoded 23S ribosomal RNA methyltransferase Erm to grant high levels of antibiotic resistance to the C. difficile 630 clinical isolate. Finally, assisted by uORF4u, our novel tool for detection of upstream open reading frames, we dissect the translational attenuation mechanism that controls the induction of cplR expression upon an antibiotic challenge.
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Affiliation(s)
- Nozomu Obana
- Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
| | - Hiraku Takada
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Mizuki Iwamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Artyom A Egorov
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Japan
| | | | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ben I C Tresco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu, Institute of Technology, Tartu, Estonia
- Science for Life Laboratory, Lund, Sweden
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6
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Inhibition of Erythromycin and Erythromycin-Induced Resistance among Staphylococcus aureus Clinical Isolates. Antibiotics (Basel) 2023; 12:antibiotics12030503. [PMID: 36978370 PMCID: PMC10044026 DOI: 10.3390/antibiotics12030503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/06/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
The increasing incidence of erythromycin and erythromycin-induced resistance to clindamycin among Staphylococcus aureus (S. aureus) is a serious problem. Patients infected with inducible resistance phenotypes may fail to respond to clindamycin. This study aimed to identify the prevalence of erythromycin and erythromycin-induced resistance and assess for potential inhibitors. A total of 99 isolates were purified from various clinical sources. Phenotypic detection of macrolide-lincosamide-streptogramin B (MLSB)-resistance phenotypes was performed by D-test. MLSB-resistance genes were identified using PCR. Different compounds were tested for their effects on erythromycin and inducible clindamycin resistance by broth microdilution and checkerboard microdilution methods. The obtained data were evaluated using docking analysis. Ninety-one isolates were S. aureus. The prevalence of constitutive MLSB, inducible MLSB, and macrolide-streptogramin (MS) phenotypes was 39.6%, 14.3%, and 2.2%, respectively. Genes including ermC, ermA, ermB, msrA, msrB, lnuA, and mphC were found in 82.6%, 5.8%, 7.7%, 3.8%, 3.8%, 13.5%, and 3.8% of isolates, respectively. Erythromycin resistance was significantly reduced by doxorubicin, neomycin, and omeprazole. Quinine, ketoprofen, and fosfomycin combated and reversed erythromycin/clindamycin-induced resistance. This study highlighted the significance of managing antibiotic resistance and overcoming clindamycin treatment failure. Doxorubicin, neomycin, omeprazole, quinine, ketoprofen, and fosfomycin could be potential inhibitors of erythromycin and inducible clindamycin resistance.
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Zaher HA, El Baz S, Alothaim AS, Alsalamah SA, Alghonaim MI, Alawam AS, Eraqi MM. Molecular Basis of Methicillin and Vancomycin Resistance in Staphylococcus aureus from Cattle, Sheep Carcasses and Slaughterhouse Workers. Antibiotics (Basel) 2023; 12:antibiotics12020205. [PMID: 36830115 PMCID: PMC9952529 DOI: 10.3390/antibiotics12020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/21/2023] Open
Abstract
Staphylococcus aureus (S. aureus) is a serious infection-causing pathogen in humans and animal. In particular, methicillin-resistant S. aureus (MRSA) is considered one of the major life-threatening pathogens due to its rapid resistance to several antibiotics in clinical practice. MRSA strains have recently been isolated in a number of animals utilized in food production processes, and these species are thought to be the important sources of the spread of infection and disease in both humans and animals. The main objective of the current study was to assess the prevalence of drug-resistant S. aureus, particularly vancomycin-resistant S. aureus (VRSA) and MRSA, by molecular methods. To address this issue, a total of three hundred samples (200 meat samples from cattle and sheep carcasses (100 of each), 50 hand swabs, and 50 stool samples from abattoir workers) were obtained from slaughterhouses in Egypt provinces. In total, 19% S. aureus was isolated by standard culture techniques, and the antibiotic resistance was confirmed genotypically by amplification nucA gen. Characteristic resistance genes were identified by PCR with incidence of 31.5%, 19.3%, 8.7%, and 7% for the mecA, VanA, ermA, and tet L genes, respectively, while the aac6-aph gene was not found in any of the isolates. In this study, the virulence genes responsible for S. aureus' resistance to antibiotics had the highest potential for infection or disease transmission to animal carcasses, slaughterhouse workers, and meat products.
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Affiliation(s)
- Hanan A. Zaher
- Food Hygiene and Control Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Shimaa El Baz
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Abdulaziz S. Alothaim
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Sulaiman A. Alsalamah
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
| | - Mohammed Ibrahim Alghonaim
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
| | - Abdullah S. Alawam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
| | - Mostafa M. Eraqi
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah 11952, Saudi Arabia
- Microbiology and Immunology Department, Veterinary Research Institute, National Research Centre, Dokki, Giza 12622, Egypt
- Correspondence: ; Tel.: +966-565709849
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Zimenkov D. Variability of Mycobacterium avium Complex Isolates Drug Susceptibility Testing by Broth Microdilution. Antibiotics (Basel) 2022; 11:1756. [PMID: 36551413 PMCID: PMC9774755 DOI: 10.3390/antibiotics11121756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/09/2022] Open
Abstract
Non-tuberculous mycobacteria are widely distributed in environments and are capable of infecting humans, particularly those with a compromised immune system. The most prevalent species that cause nontuberculous mycobacterial lung diseases are slow-growing bacteria from the Mycobacterium avium complex (MAC), mainly M. avium or M. intracellulare. The key treatment of MAC infections includes macrolides, ethambutol, and rifampicin; however, the therapy outcomes are unsatisfactory. Phenotypic drug susceptibility testing is a conditional recommendation prior to treatment, and critical concentrations for clarithromycin, amikacin, moxifloxacin, and linezolid have been established. In this review, data from studies on the determination of MIC of clinical isolates using the broth microdilution method were summarized. A significant variation in the MIC distributions from different studies was found. The main reasons could impact the findings: insufficient reproducibility of the phenotypic testing and variation in species lineages identified in different laboratories, which could have various intrinsic susceptibility to drugs. For most of the drugs analyzed, the MICs are too high, which could undermine the treatment efficiency. Further improvement of treatment outcomes demands the validation of microbiological resistance criteria together with the identification of molecular mechanisms of resistance.
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Affiliation(s)
- Danila Zimenkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Lade H, Joo HS, Kim JS. Molecular Basis of Non-β-Lactam Antibiotics Resistance in Staphylococcus aureus. Antibiotics (Basel) 2022; 11:1378. [PMID: 36290036 PMCID: PMC9598170 DOI: 10.3390/antibiotics11101378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/22/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most successful human pathogens with the potential to cause significant morbidity and mortality. MRSA has acquired resistance to almost all β-lactam antibiotics, including the new-generation cephalosporins, and is often also resistant to multiple other antibiotic classes. The expression of penicillin-binding protein 2a (PBP2a) is the primary basis for β-lactams resistance by MRSA, but it is coupled with other resistance mechanisms, conferring resistance to non-β-lactam antibiotics. The multiplicity of resistance mechanisms includes target modification, enzymatic drug inactivation, and decreased antibiotic uptake or efflux. This review highlights the molecular basis of resistance to non-β-lactam antibiotics recommended to treat MRSA infections such as macrolides, lincosamides, aminoglycosides, glycopeptides, oxazolidinones, lipopeptides, and others. A thorough understanding of the molecular and biochemical basis of antibiotic resistance in clinical isolates could help in developing promising therapies and molecular detection methods of antibiotic resistance.
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Affiliation(s)
- Harshad Lade
- Department of Laboratory Medicine, Hallym University College of Medicine, Kangdong Sacred Heart Hospital, Seoul 05355, Korea
| | - Hwang-Soo Joo
- Department of Biotechnology, College of Engineering, Duksung Women’s University, Seoul 01369, Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Kangdong Sacred Heart Hospital, Seoul 05355, Korea
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Heo S, Kim T, Na HE, Lee G, Lee JH, Jeong DW. Transcriptomic analysis of Staphylococcus equorum KM1031 from the high-salt fermented seafood jeotgal under chloramphenicol, erythromycin and lincomycin stresses. Sci Rep 2022; 12:15541. [PMID: 36109627 PMCID: PMC9477809 DOI: 10.1038/s41598-022-19897-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus equorum strain KM1031 is resistant to chloramphenicol, erythromycin and lincomycin. To shed light on the genetic factors underlying these antibiotic resistances, we determined the global gene expression profile of S. equorum KM1031 using RNA sequencing. During chloramphenicol, erythromycin and lincomycin treatment, 8.3% (183/2,336), 16.0% (354/2,336), and 2.9% (63/2,336) of S. equorum KM1031 genes exhibited significant differences in expression, respectively. These three antibiotics upregulated genes related to efflux and downregulated genes related to transporters. Antibiotic treatment also upregulated osmoprotectant-related genes involved in salt tolerance. To identify specific genes functionally related to antibiotic resistance, we compared the genome of strain KM1031 with those of three S. equorum strains that are sensitive to these three antibiotics. We identified three genes of particular interest: an antibiotic biosynthesis monooxygenase gene (abm, AWC34_RS01805) related to chloramphenicol resistance, an antibiotic ABC transporter ATP-binding protein gene (msr, AWC34_RS11115) related to erythromycin resistance, and a lincosamide nucleotydyltransferase gene (lnuA, AWC34_RS13300) related to lincomycin resistance. These genes were upregulated in response to the corresponding antibiotic; in particular, msr was upregulated more than fourfold by erythromycin treatment. Finally, the results of RNA sequencing were validated by quantitative real-time PCR. This transcriptomic analysis provides genetic evidence regarding antibiotic stress responses of S. equorum strain KM1031.
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Tatsuno I, Isaka M, Hasegawa T. A greater effect on clarithromycin resistance of mef(A)-associated msr(D) than mef(E)-associated msr(D) in Streptococcus pyogenes. Microbiol Immunol 2022; 66:299-306. [PMID: 35238426 DOI: 10.1111/1348-0421.12974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 12/01/2022]
Abstract
The mef(A)- and its subclass mef(E)-systems had long been considered to constitute one of primary macrolide-resistant mechanisms in Streptococcus pyogenes. However, we have previously demonstrated that the msr(D) gene located immediately downstream of the mef(A)/mef(E) genes plays a predominant role in the systems. In the previous studies, furthermore, mef(A)-associated msr(D)10-85 of an S. pyogenes strain 10-85 exhibited a greater increase in clarithromycin MIC than mef(E)-associated msr(D)13-O-10 of another strain 13-O-10. Both the msr(D) genes encode 487 amino acid residues, 13 amino acid residues of which are different from each other. In this study, we performed mutational analysis of the msr(D) genes and showed that a single-nucleotide polymorphism to cause a substitution of Asp238 with Gly is mainly associated with the greater increase in clarithromycin MIC by the msr(D)10-85 than by the msr(D)13-O-10 allele. In addition, another substitution of Ser with Arg at codon 194 is also partially associated with the greater increase by the msr(D)10-85 than by the msr(D)13-O-10 allele. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ichiro Tatsuno
- Department of Bacteriology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Masanori Isaka
- Department of Bacteriology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Tadao Hasegawa
- Department of Bacteriology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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Microbiological Aerosol, Particulate Matter Concentrations and Antibiotic Resistant Staphylococcus spp. in the Premises of Poland’s Oldest Agricultural School. ATMOSPHERE 2021. [DOI: 10.3390/atmos12080934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bioaerosol, particulate matter concentration and antibiotic resistance of airborne Staphylococcus was assessed in animal and public premises (classroom, sports hall, horse stable, cowshed, newborn calf shed and outdoor background control site) of Poland’s oldest agricultural school. The concentration and size distribution of bacteria, fungi, actinomycetes and staphylococci were assessed with a six stage Andersen impactor. Particulate matter (PM10, PM4, PM2.5 and PM1) was determined using the DustTrak aerosol monitor. The Staphylococcus species were determined with MALDI-TOF mass spectrometry and antimicrobial resistance was assessed using disk diffusion. Bioaerosol concentrations differed significantly between sampling points, with the highest levels of all microorganisms occurring in the newborn calf shed. The proportion of respirable fraction exceeded 60% in all sites, indicating potential harmfulness to exposed people. Mean concentrations of particulate matter were the smallest in school rooms and the highest in the newborn calf shed. Neither particulate matter nor microbial aerosol exceeded threshold values for workplaces. Among thirty-four isolated staphylococcal strains, S. equorum (35%), S. succinus (26%) and S. xylosus (15%) were the most prevalent. Resistance to macrolides (erythromycin) and lincosamides (clindamycin) was the most frequent. One strain was methicillin-resistant. Farm animals are significant sources of bioaerosol and therefore attention should be paid with respect to maintaining appropriate sanitary conditions and hygiene of premises and animals.
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Dharmaratne P, Yu L, Wong RCH, Chan BCL, Lau KM, Wang B, Lau CBS, Fung KP, Ng DKP, Ip M. A Novel Dicationic Boron Dipyrromethene-based Photosensitizer for Antimicrobial Photodynamic Therapy against Methicillin-Resistant Staphylococcus aureus. Curr Med Chem 2021; 28:4283-4294. [PMID: 33292110 PMCID: PMC8287893 DOI: 10.2174/0929867328666201208095105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/23/2022]
Abstract
Background
We report herein the synthesis of a novel dicationic boron dipyrromethene derivative (compound 3) which is symmetrically substituted with two trimethylammonium styryl groups. Methods
The antibacterial photodynamic activity of compound 3 was determined against sixteen methicillin-resistant Staphylococcus aureus (MRSA) strains, including four ATCC type strains (ATCC 43300, ATCC BAA-42, ATCC BAA-43, and ATCC BAA-44), two mutant strains [AAC(6’)-APH(2”) and RN4220/pUL5054], and ten non-duplicate clinical strains of hospital- and community-associated MRSA. Upon light irradiation, the minimum bactericidal concentrations of compound 3 were in the range of 1.56-50 µM against all the sixteen MRSA strains. Interestingly, compound 3 was not only more active than an analogue in which the ammonium groups are not directly connected to the n-conjugated system (compound 4), but also showed significantly higher (p < 0.05) antibacterial potency than the clinically approved photosensitizer methylene blue. The skin irritation of compound 3 during topical application was tested on human 3-D skin constructs and proven to be non-irritant in vivo at concentrations below 1.250 mM. In the murine MRSA infected wound study, the colony forming unit reduction of compound 3 + PDT group showed significantly (p < 0.05) higher value (>2.5 log10) compared to other test groups except for the positive control. Conclusion
In conclusion, the present study provides a scientific basis for future development of compound 3 as a potent photosensitizer for photodynamic therapy for MRSA wound infection.
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Affiliation(s)
- Priyanga Dharmaratne
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Ligang Yu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Roy Chi-Hang Wong
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Ben Chun-Lap Chan
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Kit-Man Lau
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Baiyan Wang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Clara Bik San Lau
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Kwok-Pui Fung
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Dennis Kee-Pui Ng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, N.T., Hong Kong
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14
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Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O'Neill AJ, Hauryliuk V, Wilson DN. Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nat Commun 2021; 12:3577. [PMID: 34117249 PMCID: PMC8196190 DOI: 10.1038/s41467-021-23753-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Target protection proteins confer resistance to the host organism by directly binding to the antibiotic target. One class of such proteins are the antibiotic resistance (ARE) ATP-binding cassette (ABC) proteins of the F-subtype (ARE-ABCFs), which are widely distributed throughout Gram-positive bacteria and bind the ribosome to alleviate translational inhibition from antibiotics that target the large ribosomal subunit. Here, we present single-particle cryo-EM structures of ARE-ABCF-ribosome complexes from three Gram-positive pathogens: Enterococcus faecalis LsaA, Staphylococcus haemolyticus VgaALC and Listeria monocytogenes VgaL. Supported by extensive mutagenesis analysis, these structures enable a general model for antibiotic resistance mediated by these ARE-ABCFs to be proposed. In this model, ABCF binding to the antibiotic-stalled ribosome mediates antibiotic release via mechanistically diverse long-range conformational relays that converge on a few conserved ribosomal RNA nucleotides located at the peptidyltransferase center. These insights are important for the future development of antibiotics that overcome such target protection resistance mechanisms.
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Affiliation(s)
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Kathryn Jane Turnbull
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Marje Kasari
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Merianne Mohamad
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Christine Polte
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Hiraku Takada
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Karolis Vaitkevicius
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Jörgen Johansson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Alex J O'Neill
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
- University of Tartu, Institute of Technology, Tartu, Estonia.
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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15
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Ackers-Johnson G, Kibombo D, Kusiima B, Nsubuga ML, Kigozi E, Kajumbula HM, Kateete DP, Walwema R, Ackers HL, Goodhead IB, Birtles RJ, James CE. Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001000. [PMID: 34032566 PMCID: PMC8290103 DOI: 10.1099/mic.0.001000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/01/2021] [Indexed: 11/23/2022]
Abstract
Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based improvement of antibiotic stewardship measures in the hospital. To address this, we combined existing antimicrobial susceptibility testing (AST) from FPRRH, with whole genome sequencing (WGS) of 41 Staphylococcus aureus isolates (2017-2019). AST revealed 73 % (30 of 41) of isolates were resistant to one or more antibiotics and 29 % (12 of 41) were multi-drug resistant (MDR). Resistance phenotypes were largely explained by the presence of antibiotic resistance genes in WGS data. Five isolates were methicillin-resistant S. aureus (MRSA) and MDR. Although all isolates were susceptible to clindamycin, a 24 % carriage of erm genes suggests potential for rapid development of resistance. We inferred a population structure for the S. aureus isolates by comparing their core genomes. Twenty isolates formed a tight cluster corresponding to multilocus sequence typing clonal complex (CC) 152, a CC found to be particularly prevalent in northern Africa. The frequency of genes associated with methicillin, chloramphenicol and ciprofloxacin resistance were significantly lower among CC152 strains than non-CC152 strains; thus, in keeping with previous work, we find that CC152 is almost exclusively methicillin-sensitive S. aureus (MSSA). Also, in agreement with other studies, we observed that the occurrence of Panton-Valentine leukocidin toxin-encoding genes was significantly higher among CC152 strains than non-CC152 strains. However, we also observed that the coagulase gene was over-represented in this CC, further defining the virulence strategy of this important pathogen. By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, our study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.
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Affiliation(s)
- Gavin Ackers-Johnson
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Daniel Kibombo
- Fort Portal Regional Referral Hospital, Uganda, Uganda
- Infectious Diseases Institute, Kampala, Uganda
| | - Brenda Kusiima
- Fort Portal Regional Referral Hospital, Uganda, Uganda
- Infectious Diseases Institute, Kampala, Uganda
| | - Moses L. Nsubuga
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | | | | | | | - Ian B. Goodhead
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Richard J. Birtles
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Chloë E. James
- School of Science, Engineering and Environment, University of Salford, Salford, UK
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16
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Fostier CR, Monlezun L, Ousalem F, Singh S, Hunt JF, Boël G. ABC-F translation factors: from antibiotic resistance to immune response. FEBS Lett 2020; 595:675-706. [PMID: 33135152 DOI: 10.1002/1873-3468.13984] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Energy-dependent translational throttle A (EttA) from Escherichia coli is a paradigmatic ABC-F protein that controls the first step in polypeptide elongation on the ribosome according to the cellular energy status. Biochemical and structural studies have established that ABC-F proteins generally function as translation factors that modulate the conformation of the peptidyl transferase center upon binding to the ribosomal tRNA exit site. These factors, present in both prokaryotes and eukaryotes but not in archaea, use related molecular mechanisms to modulate protein synthesis for heterogenous purposes, ranging from antibiotic resistance and rescue of stalled ribosomes to modulation of the mammalian immune response. Here, we review the canonical studies characterizing the phylogeny, regulation, ribosome interactions, and mechanisms of action of the bacterial ABC-F proteins, and discuss the implications of these studies for the molecular function of eukaryotic ABC-F proteins, including the three human family members.
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Affiliation(s)
- Corentin R Fostier
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Laura Monlezun
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Shikha Singh
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - John F Hunt
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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17
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Helsens N, Calvez S, Prevost H, Bouju-Albert A, Maillet A, Rossero A, Hurtaud-Pessel D, Zagorec M, Magras C. Antibiotic Resistance Genes and Bacterial Communities of Farmed Rainbow Trout Fillets ( Oncorhynchus mykiss). Front Microbiol 2020; 11:590902. [PMID: 33343530 PMCID: PMC7744637 DOI: 10.3389/fmicb.2020.590902] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/11/2020] [Indexed: 01/28/2023] Open
Abstract
The rise of antibiotic resistance is not only a challenge for human and animal health treatments, but is also posing the risk of spreading among bacterial populations in foodstuffs. Farmed fish-related foodstuffs, the food of animal origin most consumed worldwide, are suspected to be a reservoir of antibiotic resistance genes and resistant bacterial hazards. However, scant research has been devoted to the possible sources of diversity in fresh fillet bacterial ecosystems (farm environment including rivers and practices, and factory environment). In this study bacterial communities and the antibiotic resistance genes of fresh rainbow trout fillet were described using amplicon sequencing of the V3-V4 region of the 16S rRNA gene and high-throughput qPCR assay. The antibiotic residues were quantified using liquid chromatography/mass spectrometry methods. A total of 56 fillets (composed of muscle and skin tissue) from fish raised on two farms on the same river were collected and processed under either factory or laboratory sterile filleting conditions. We observed a core-bacterial community profile on the fresh rainbow trout fillets, but the processing conditions of the fillets has a great influence on their mean bacterial load (3.38 ± 1.01 log CFU/g vs 2.29 ± 0.72 log CFU/g) and on the inter-individual diversity of the bacterial community. The bacterial communities were dominated by Gamma- and Alpha-proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The most prevalent genera were Pseudomonas, Escherichia-Shigella, Chryseobacterium, and Carnobacterium. Of the 73 antibiotic residues searched, only oxytetracycline residues were detected in 13/56 fillets, all below the European Union maximum residue limit (6.40–40.20 μg/kg). Of the 248 antibiotic resistance genes searched, 11 were found to be present in at least 20% of the fish population (tetracycline resistance genes tetM and tetV, β-lactam resistance genes blaDHA and blaACC, macrolide resistance gene mphA, vancomycin resistance genes vanTG and vanWG and multidrug-resistance genes mdtE, mexF, vgaB and msrA) at relatively low abundances calculated proportionally to the 16S rRNA gene.
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Affiliation(s)
- Nicolas Helsens
- INRAE, Oniris, SECALIM, Nantes, France.,INRAE, Oniris, BIOEPAR, Nantes, France
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18
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Dharmaratne P, Wang B, Wong RCH, Chan BCL, Lau KM, Ke MR, Lau CBS, Ng DKP, Fung KP, Ip M. Monosubstituted tricationic Zn(II) phthalocyanine enhances antimicrobial photodynamic inactivation (aPDI) of methicillin-resistant Staphylococcus aureus (MRSA) and cytotoxicity evaluation for topical applications: in vitro and in vivo study. Emerg Microbes Infect 2020; 9:1628-1637. [PMID: 32619386 PMCID: PMC7473158 DOI: 10.1080/22221751.2020.1790305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/28/2020] [Indexed: 12/18/2022]
Abstract
Antimicrobial photodynamic therapy (aPDT) is an innovative approach to combat multi-drug resistant bacteria. It is known that cationic Zn(II) phthalocyanines (ZnPc) are effective in mediating aPDT against methicillin-resistant Staphylococcus aureus (MRSA). Here we used ZnPc-based photosensitizer named ZnPcE previously reported by our research group to evaluate its aPDT efficacy against broad spectrum of clinically relevant MRSAs. Remarkably, in vitro anti-MRSA activity was achieved using near-infrared (NIR, >610 nm) light with minimal bactericidal concentrations ranging <0.019-0.156 µM against the panel of MRSAs. ZnPcE was not only significantly (p < .05) more potent than methylene blue, which is a clinically approved photosensitizer but also demonstrated low cytotoxicity against human fibroblasts cell line (Hs-27) and human immortalized keratinocytes cell line (HaCaT). The toxicity was further evaluated on human 3-D skin constructs and found ZnPcE did not manifest in vivo skin irritation at ≤7.8 µM concentration. In the murine MRSA wound model, ZnPcE with PDT group demonstrated > 4 log10 CFU reduction and the value is significantly higher (p < .05) than all test groups except positive control. To conclude, results of present study provide a scientific basis for future clinical evaluation of ZnPcE-PDT on MRSA wound infection.
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Affiliation(s)
- Priyanga Dharmaratne
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong (SAR), People’s Republic of China
| | - Baiyan Wang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong (SAR), People’s Republic of China
| | - Roy C. H. Wong
- Department of Chemistry, Faculty of Science, The Chinese University of Hong Kong, Hong Kong (SAR), People’s Republic of China
| | - Ben C. L. Chan
- Institute of Chinese Medicine and State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Hong Kong (SAR), People’s Republic of China
| | - Kit-Man Lau
- Institute of Chinese Medicine and State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Hong Kong (SAR), People’s Republic of China
| | - Mei-Rong Ke
- Department of Chemistry, Faculty of Science, The Chinese University of Hong Kong, Hong Kong (SAR), People’s Republic of China
| | - Clara B. S. Lau
- Institute of Chinese Medicine and State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Hong Kong (SAR), People’s Republic of China
| | - Dennis K. P. Ng
- Department of Chemistry, Faculty of Science, The Chinese University of Hong Kong, Hong Kong (SAR), People’s Republic of China
| | - Kwok-Pui Fung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong (SAR), People’s Republic of China
- Institute of Chinese Medicine and State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Hong Kong (SAR), People’s Republic of China
- CUHK-Zhejiang University Joint Laboratory on Natural Products and Toxicology Research, Hong Kong (SAR), People's Republic of China
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong (SAR), People’s Republic of China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, People’s Republic of China
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19
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Do 1,8-naphthyridine sulfonamides possess an inhibitory action against Tet(K) and MsrA efflux pumps in multiresistant Staphylococcus aureus strains? Microb Pathog 2020; 147:104268. [DOI: 10.1016/j.micpath.2020.104268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/14/2020] [Indexed: 11/17/2022]
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20
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Synergism of sophoraflavanone G with norfloxacin against effluxing antibiotic-resistant Staphylococcus aureus. Int J Antimicrob Agents 2020; 56:106098. [DOI: 10.1016/j.ijantimicag.2020.106098] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/22/2020] [Accepted: 07/13/2020] [Indexed: 11/19/2022]
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21
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Lam AK, Panlilio H, Pusavat J, Wouters CL, Moen EL, Brennan RE, Rice CV. Expanding the Spectrum of Antibiotics Capable of Killing Multidrug-Resistant Staphylococcus aureus and Pseudomonas aeruginosa. ChemMedChem 2020; 15:1421-1428. [PMID: 32497366 PMCID: PMC7485129 DOI: 10.1002/cmdc.202000239] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Indexed: 12/19/2022]
Abstract
Infections from antibiotic-resistant Staphylococcus aureus and Pseudomonas aeruginosa are a serious threat because reduced antibiotic efficacy complicates treatment decisions and prolongs the disease state in many patients. To expand the arsenal of treatments against antimicrobial-resistant (AMR) pathogens, 600-Da branched polyethylenimine (BPEI) can overcome antibiotic resistance mechanisms and potentiate β-lactam antibiotics against Gram-positive bacteria. BPEI binds cell-wall teichoic acids and disables resistance factors from penicillin binding proteins PBP2a and PBP4. This study describes a new mechanism of action for BPEI potentiation of antibiotics generally regarded as agents effective against Gram-positive pathogens but not Gram-negative bacteria. 600-Da BPEI is able to reduce the barriers to drug influx and facilitate the uptake of a non-β-lactam co-drug, erythromycin, which targets the intracellular machinery. Also, BPEI can suppress production of the cytokine interleukin IL-8 by human epithelial keratinocytes. This enables BPEI to function as a broad-spectrum antibiotic potentiator, and expands the opportunities to improve drug design, antibiotic development, and therapeutic approaches against pathogenic bacteria, especially for wound care.
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Affiliation(s)
- Anh K Lam
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Hannah Panlilio
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Jennifer Pusavat
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Cassandra L Wouters
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Erika L Moen
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Robert E Brennan
- Department of Biology, University of Central Oklahoma, 100 North University Drive, Edmond, OK 73034, USA
| | - Charles V Rice
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA
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22
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Naha A, Kumar Miryala S, Debroy R, Ramaiah S, Anbarasu A. Elucidating the multi-drug resistance mechanism of Enterococcus faecalis V583: A gene interaction network analysis. Gene 2020; 748:144704. [DOI: 10.1016/j.gene.2020.144704] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022]
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23
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Dharmaratne P, Wong RCH, Wang J, Lo PC, Wang B, Chan BCL, Lau KM, Lau CBS, Fung KP, Ip M, Ng DKP. Synthesis and In Vitro Photodynamic Activity of Cationic Boron Dipyrromethene-Based Photosensitizers against Methicillin-Resistant Staphylococcus aureus. Biomedicines 2020; 8:E140. [PMID: 32485946 PMCID: PMC7344895 DOI: 10.3390/biomedicines8060140] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 01/07/2023] Open
Abstract
A series of cationic boron dipyrromethene (BODIPY) derivatives were synthesized and characterized with various spectroscopic methods. Having the ability to generate singlet oxygen upon irradiation, these compounds could potentially serve as photosensitizers for antimicrobial photodynamic therapy. Of the five BODIPYs being examined, the dicationic aza-BODIPY analogue (compound 5) demonstrated the highest potency against a broad spectrum of clinically relevant methicillin-resistant Staphylococcus aureus (MRSA), including four ATCC-type strains (ATCC 43300, ATCC BAA-42, ATCC BAA-43, and ATCC BAA-44), two strains carrying specific antibiotic resistance mechanisms [-AAC(6')-APH(2") and RN4220/pUL5054], and ten non-duplicate clinical strains from hospital- and community-associated MRSAs of the important clonal types ST239, ST30, and ST59, which have previously been documented to be prevalent in Hong Kong and its neighboring countries. The in vitro anti-MRSA activity of compound 5 was achieved upon irradiation with near-infrared light (>610 nm) with minimal bactericidal concentrations (MBCs) ranging from 12.5 to 25 µM against the whole panel of MRSAs, except the hospital-associated MRSAs for which the MBCs were in the range of 50-100 µM. Compound 5 was significantly (p < 0.05) more potent than methylene blue, which is a clinically approved photosensitizer, indicating that it is a promising antimicrobial agent that is worthy of further investigation.
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Affiliation(s)
- Priyanga Dharmaratne
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong; (P.D.); (B.W.); (K.-P.F.)
| | - Roy C. H. Wong
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong;
| | - Jun Wang
- Department of Biomedical Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong; (J.W.); (P.-C.L.)
| | - Pui-Chi Lo
- Department of Biomedical Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong; (J.W.); (P.-C.L.)
| | - Baiyan Wang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong; (P.D.); (B.W.); (K.-P.F.)
| | - Ben C. L. Chan
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong; (B.C.L.C.); (K.-M.L.); (C.B.S.L.)
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Kit-Man Lau
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong; (B.C.L.C.); (K.-M.L.); (C.B.S.L.)
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Clara B. S. Lau
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong; (B.C.L.C.); (K.-M.L.); (C.B.S.L.)
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Kwok-Pui Fung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong; (P.D.); (B.W.); (K.-P.F.)
- CUHK-Zhejiang University Joint Laboratory on Natural Products and Toxicology Research, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, N.T., Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
| | - Dennis K. P. Ng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong;
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24
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Feng Z, Liu D, Wang L, Wang Y, Zang Z, Liu Z, Song B, Gu L, Fan Z, Yang S, Chen J, Cui Y. A Putative Efflux Transporter of the ABC Family, YbhFSR, in Escherichia coli Functions in Tetracycline Efflux and Na +(Li +)/H + Transport. Front Microbiol 2020; 11:556. [PMID: 32390957 PMCID: PMC7190983 DOI: 10.3389/fmicb.2020.00556] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/16/2020] [Indexed: 12/20/2022] Open
Abstract
ATP-binding cassette transporters are ubiquitous in almost all organisms. The Escherichia coli genome is predicted to encode 69 ABC transporters. Eleven of the ABC transporters are presumed to be exporters, of which seven are possible drug export transporters. There has been minimal research on the function of YbhFSR, which is one of the putative drug resistance exporters. In this study, the ybhF gene of this transporter was characterized. Overexpression and knockout strains of ybhF were constructed. The ATPase activity of YbhF was studied using the malachite green assay, and the efflux abilities of knockout strains were demonstrated by using ethidium bromide (EB) as a substrate. The substrates of YbhFSR efflux, examined with the minimum inhibitory concentration (MIC), were determined to be tetracycline, oxytetracycline, chlortetracycline, doxycycline, EB, and Hoechst33342. Furthermore, tetracycline and EB efflux and accumulation experiments confirmed that the substrates of YbhFSR were tetracyclines and EB. The MIC assay and the fluorescence test results showed that tetracyclines are likely to be the major antibiotic substrate of YbhFSR. The existence of the signature NatA motif suggested that YbhFSR may also function as a Na+/H+ transporter. Overexpression of YbhF in E. coli KNabc lacking crucial Na+/H+ transporters conferred tolerance to NaCl, LiCl, and an alkaline pH. Together, the results showed that YbhFSR exhibited dual functions as a drug efflux pump and a Na+ (Li+)/H+ antiporter.
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Affiliation(s)
- Zhenyue Feng
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Defu Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Lizi Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yanhong Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhongjing Zang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhenhua Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Baifen Song
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Liwei Gu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhaowei Fan
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Siyu Yang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jing Chen
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yudong Cui
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
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25
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The Novel Macrolide Resistance Genes mef(D), msr(F), and msr(H) Are Present on Resistance Islands in Macrococcus canis, Macrococcus caseolyticus, and Staphylococcus aureus. Antimicrob Agents Chemother 2020; 64:AAC.00160-20. [PMID: 32122903 DOI: 10.1128/aac.00160-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 02/27/2020] [Indexed: 12/27/2022] Open
Abstract
Chromosomal resistance islands containing the methicillin resistance gene mecD (McRI mecD ) have been reported in Macrococcus caseolyticus Here, we identified novel macrolide resistance genes in Macrococcus canis on similar elements, called McRI msr These elements were also integrated into the 3' end of the 30S ribosomal protein S9 gene (rpsI), delimited by characteristic attachment (att) sites, and carried a related site-specific integrase gene (int) at the 5' end. They carried novel macrolide resistance genes belonging to the msr family of ABC subfamily F (ABC-F)-type ribosomal protection protein [msr(F) and msr(H)] and the macrolide efflux mef family [mef(D)]. Highly related mef(D)-msr(F) fragments were found on diverse McRI msr elements in M. canis, M. caseolyticus, and Staphylococcus aureus Another McRI msr -like element identified in an M. canis strain lacked the classical att site at the 3' end and carried the msr(H) gene but no neighboring mef gene. The expression of the novel resistance genes in S. aureus resulted in a low-to-moderate increase in the MIC of erythromycin but not streptogramin B. In the mef(D)-msr(F) operon, the msr(F) gene was shown to be the crucial determinant for macrolide resistance. The detection of circular forms of McRI msr and the mef(D)-msr(F) fragment suggested mobility of both the island and the resistance gene subunit. The discovery of McRI msr in different Macrococcus species and S. aureus indicates that these islands have a potential for dissemination of antibiotic resistance within the Staphylococcaceae family.
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26
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Hyun JC, Kavvas ES, Monk JM, Palsson BO. Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. PLoS Comput Biol 2020; 16:e1007608. [PMID: 32119670 PMCID: PMC7067475 DOI: 10.1371/journal.pcbi.1007608] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/12/2020] [Accepted: 12/16/2019] [Indexed: 12/29/2022] Open
Abstract
The evolution of antimicrobial resistance (AMR) poses a persistent threat to global public health. Sequencing efforts have already yielded genome sequences for thousands of resistant microbial isolates and require robust computational tools to systematically elucidate the genetic basis for AMR. Here, we present a generalizable machine learning workflow for identifying genetic features driving AMR based on constructing reference strain-agnostic pan-genomes and training random subspace ensembles (RSEs). This workflow was applied to the resistance profiles of 14 antimicrobials across three urgent threat pathogens encompassing 288 Staphylococcus aureus, 456 Pseudomonas aeruginosa, and 1588 Escherichia coli genomes. We find that feature selection by RSE detects known AMR associations more reliably than common statistical tests and previous ensemble approaches, identifying a total of 45 known AMR-conferring genes and alleles across the three organisms, as well as 25 candidate associations backed by domain-level annotations. Furthermore, we find that results from the RSE approach are consistent with existing understanding of fluoroquinolone (FQ) resistance due to mutations in the main drug targets, gyrA and parC, in all three organisms, and suggest the mutational landscape of those genes with respect to FQ resistance is simple. As larger datasets become available, we expect this approach to more reliably predict AMR determinants for a wider range of microbial pathogens.
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Affiliation(s)
- Jason C. Hyun
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California, United States of America
| | - Erol S. Kavvas
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
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27
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Ndagi U, Falaki AA, Abdullahi M, Lawal MM, Soliman ME. Antibiotic resistance: bioinformatics-based understanding as a functional strategy for drug design. RSC Adv 2020; 10:18451-18468. [PMID: 35685616 PMCID: PMC9122625 DOI: 10.1039/d0ra01484b] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022] Open
Abstract
The use of antibiotics to manage infectious diseases dates back to ancient civilization, but the lack of a clear distinction between the therapeutic and toxic dose has been a major challenge. This precipitates the notion that antibiotic resistance was from time immemorial, principally because of a lack of adequate knowledge of therapeutic doses and continuous exposure of these bacteria to suboptimal plasma concentration of antibiotics. With the discovery of penicillin by Alexander Fleming in 1924, a milestone in bacterial infections' treatment was achieved. This forms the foundation for the modern era of antibiotic drugs. Antibiotics such as penicillins, cephalosporins, quinolones, tetracycline, macrolides, sulphonamides, aminoglycosides and glycopeptides are the mainstay in managing severe bacterial infections, but resistant strains of bacteria have emerged and hampered the progress of research in this field. Recently, new approaches to research involving bacteria resistance to antibiotics have appeared; these involve combining the molecular understanding of bacteria systems with the knowledge of bioinformatics. Consequently, many molecules have been developed to curb resistance associated with different bacterial infections. However, because of increased emphasis on the clinical relevance of antibiotics, the synergy between in silico study and in vivo study is well cemented and this facilitates the discovery of potent antibiotics. In this review, we seek to give an overview of earlier reviews and molecular and structural understanding of bacteria resistance to antibiotics, while focusing on the recent bioinformatics approach to antibacterial drug discovery. Understanding the evolution of antibiotic resistance at the molecular level as a functional tool for bioinformatic-based drug design.![]()
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Affiliation(s)
- Umar Ndagi
- Centre for Trans-Sahara Disease, Vaccine and Drug Research
- Ibrahim Badamasi Babangida University
- Lapai
- Nigeria
| | - Abubakar A. Falaki
- Department of Microbiology
- School of Agriculture and Applied Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Maryam Abdullahi
- Faculty of Pharmaceutical Sciences
- Ahmadu Bello University Zaria
- Nigeria
| | - Monsurat M. Lawal
- School of Laboratory Medicine and Medical Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Mahmoud E. Soliman
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences
- University of KwaZulu Natal
- Durban 4001
- South Africa
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28
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Mycobacterial HflX is a ribosome splitting factor that mediates antibiotic resistance. Proc Natl Acad Sci U S A 2019; 117:629-634. [PMID: 31871194 DOI: 10.1073/pnas.1906748117] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antibiotic resistance in bacteria is typically conferred by proteins that function as efflux pumps or enzymes that modify either the drug or the antibiotic target. Here we report an unusual mechanism of resistance to macrolide-lincosamide antibiotics mediated by mycobacterial HflX, a conserved ribosome-associated GTPase. We show that deletion of the hflX gene in the pathogenic Mycobacterium abscessus, as well as the nonpathogenic Mycobacterium smegmatis, results in hypersensitivity to the macrolide-lincosamide class of antibiotics. Importantly, the level of resistance provided by Mab_hflX is equivalent to that conferred by erm41, implying that hflX constitutes a significant resistance determinant in M. abscessus We demonstrate that mycobacterial HflX associates with the 50S ribosomal subunits in vivo and can dissociate purified 70S ribosomes in vitro, independent of GTP hydrolysis. The absence of HflX in a ΔMs_hflX strain also results in a significant accumulation of 70S ribosomes upon erythromycin exposure. Finally, a deletion of either the N-terminal or the C-terminal domain of HflX abrogates ribosome splitting and concomitantly abolishes the ability of mutant proteins to mediate antibiotic tolerance. Together, our results suggest a mechanism of macrolide-lincosamide resistance in which the mycobacterial HflX dissociates antibiotic-stalled ribosomes and rescues the bound mRNA. Given the widespread presence of hflX genes, we anticipate this as a generalized mechanism of macrolide resistance used by several bacteria.
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29
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Phage Transduction is Involved in the Intergeneric Spread of Antibiotic Resistance-Associated bla CTX-M, mel, and tetM Loci in Natural Populations of Some Human and Animal Bacterial Pathogens. Curr Microbiol 2019; 77:185-193. [PMID: 31754824 DOI: 10.1007/s00284-019-01817-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022]
Abstract
The horizontal genetic transfer (HGT) of antibiotic resistance genes (ARGs) mediated by species-specific bacteriophages contributes to the emergence of antibiotic-resistant strains in natural populations of human and animal bacterial pathogens posing a significant threat to global public health. However, it is unclear and needs to be determined whether polyvalent bacteriophages play any role in the intergeneric transmission of ARGs. In this study, we examined the genome sequences of 2239 bacteriophages from different sources for the presence of ARGs. The identified ARG-carrying bacteriophages were then analyzed by PHACTS, PHAST, and HostPhinder programs to determine their lifestyles, genes coding for bacterial cell lysis, recombinases, and a spectrum of their potential host species, respectively. We employed the SplitsTree, RDP4 and SimPlot software packages in recombination tests to identify HGT events of ARGs between these bacteriophages and bacteria. In our analyses, some ARG-carrying bacteriophages exhibited temperate and/or polyvalent patterns. The bootstrap values (97-100) for the SplitsTree-generated parallelograms, fit values (97-100) for splits networks, Phi P values (< 10-17 to 3.9 × 10-16), RDP4 P values (≤ 7.8 × 10-03), and the SimPlot results, provided strong statistical evidence for the phage transduction events of blaCTX-M, mel, and tetM loci on inter-species level. These events involved several host species such as Escherichia coli, Salmonella enterica, Shigella sonnei, Streptococcus pneumoniae and Bacillus coagulans. HGT of mel loci between Erysipelothrix and Streptococcus phages were also detected. These results firmly suggest that certain bacteriophages possibly with temperate properties induce the intergeneric dissemination of blaCTX-M, mel and tetM in the above species.
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30
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Bojang A, Baines SL, Donovan L, Guerillot R, Stevens K, Higgs C, Bottomley C, Secka O, Schultz MB, Gonçalves da Silva A, Seemann T, Stinear TP, Roca A, Howden BP. Genomic investigation of Staphylococcus aureus recovered from Gambian women and newborns following an oral dose of intra-partum azithromycin. J Antimicrob Chemother 2019; 74:3170-3178. [PMID: 31424550 PMCID: PMC6798832 DOI: 10.1093/jac/dkz341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Oral azithromycin given during labour reduces carriage of bacteria responsible for neonatal sepsis, including Staphylococcus aureus. However, there is concern that this may promote drug resistance. OBJECTIVES Here, we combine genomic and epidemiological data on S. aureus isolated from mothers and babies in a randomized intra-partum azithromycin trial (PregnAnZI) to describe bacterial population dynamics and resistance mechanisms. METHODS Participants from both arms of the trial, who carried S. aureus in day 3 and day 28 samples post-intervention, were included. Sixty-six S. aureus isolates (from 7 mothers and 10 babies) underwent comparative genome analyses and the data were then combined with epidemiological data. Trial registration (main trial): ClinicalTrials.gov Identifier NCT01800942. RESULTS Seven S. aureus STs were identified, with ST5 dominant (n = 40, 61.0%), followed by ST15 (n = 11, 17.0%). ST5 predominated in the placebo arm (73.0% versus 49.0%, P = 0.039) and ST15 in the azithromycin arm (27.0% versus 6.0%, P = 0.022). In azithromycin-resistant isolates, msr(A) was the main macrolide resistance gene (n = 36, 80%). Ten study participants, from both trial arms, acquired azithromycin-resistant S. aureus after initially harbouring a susceptible isolate. In nine (90%) of these cases, the acquired clone was an msr(A)-containing ST5 S. aureus. Long-read sequencing demonstrated that in ST5, msr(A) was found on an MDR plasmid. CONCLUSIONS Our data reveal in this Gambian population the presence of a dominant clone of S. aureus harbouring plasmid-encoded azithromycin resistance, which was acquired by participants in both arms of the study. Understanding these resistance dynamics is crucial to defining the public health drug resistance impacts of azithromycin prophylaxis given during labour in Africa.
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Affiliation(s)
- Abdoulie Bojang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Sarah L Baines
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Liam Donovan
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Romain Guerillot
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Charlie Higgs
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Christian Bottomley
- Medical Research Council Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
| | - Ousman Secka
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Mark B Schultz
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Benjamin P Howden
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
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31
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Ayaz M, Ullah F, Sadiq A, Ullah F, Ovais M, Ahmed J, Devkota HP. Synergistic interactions of phytochemicals with antimicrobial agents: Potential strategy to counteract drug resistance. Chem Biol Interact 2019; 308:294-303. [PMID: 31158333 DOI: 10.1016/j.cbi.2019.05.050] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/18/2019] [Accepted: 05/29/2019] [Indexed: 01/22/2023]
Abstract
The emergence of multidrug resistant (MDR) pathogens is a global threat and has created problems in providing adequate treatment of many infectious diseases. Although the conventional antimicrobial agents are quite effective against several pathogens, yet there is a need for more effective antimicrobial agents against MDR pathogens. Herbal drugs and phytochemicals have been used for their effective antimicrobial activity from ancient times and there is an increasing trend for development of plant based natural products for the prevention and treatment of pathogenic diseases. One of the strategies for effective resistance modification is the use of antimicrobial agent-phytochemical combinations that will neutralize the resistance mechanism, enabling the drug to still be effective against resistant microbes. These phytochemicals can work by several strategies, such as inhibition of target modifying and drug degrading enzymes or as efflux pumps inhibitors. A plethora of herbal extracts, essential oils and isolated pure compounds have been reported to act synergistically with existing antibiotics, antifungals and chemotherapeutics and augment the activity of these drugs. Considerable increases in the susceptibility pattern of several microbes towards the natural antimicrobials and their combinations were observed as indicated by significant decline in minimum inhibitory concentrations. This review paper summarizes the current developments regarding synergistic interactions of plant extracts and isolated pure compounds in combination with existing antibacterial, antifungal agents and chemotherapeutics. The effect of these agents on the susceptibility patterns of these pathogens and possible mechanisms of action are described in detail. In conclusion, many phytochemicals in combination with existing drugs were found to act as resistance modifying agents and proper combinations may rescue the efficacy of important lifesaving antimicrobial agents.
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Affiliation(s)
- Muhammad Ayaz
- Department of Pharmacy, University of Malakand, Khyber Pakhtunkhwa (KP), 18000, Pakistan.
| | - Farhat Ullah
- Department of Pharmacy, University of Malakand, Khyber Pakhtunkhwa (KP), 18000, Pakistan.
| | - Abdul Sadiq
- Department of Pharmacy, University of Malakand, Khyber Pakhtunkhwa (KP), 18000, Pakistan.
| | - Farman Ullah
- Department of Pharmacy, Kohat University of Science and Technology (KUST), Khyber Pakhtunkhwa (KP), Pakistan.
| | - Muhammad Ovais
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.
| | - Jawad Ahmed
- Institute of Basic Medical Sciences (IBMS), Khyber Medical University, Peshawar, Pakistan.
| | - Hari Prasad Devkota
- (e)Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto City, Kumamoto, 862-0973, Japan.
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32
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Zeevi D, Korem T, Godneva A, Bar N, Kurilshikov A, Lotan-Pompan M, Weinberger A, Fu J, Wijmenga C, Zhernakova A, Segal E. Structural variation in the gut microbiome associates with host health. Nature 2019; 568:43-48. [PMID: 30918406 DOI: 10.1038/s41586-019-1065-y] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022]
Abstract
Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences. Here we systematically identify microbial genomic structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. SVs are enriched for CRISPR-associated and antibiotic-producing functions and depleted from housekeeping genes, suggesting that they have a role in microbial adaptation. We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort. Exploring genes that are clustered in the same SV, we uncover several possible mechanistic links between the microbiome and its host, including a region in Anaerostipes hadrus that encodes a composite inositol catabolism-butyrate biosynthesis pathway, the presence of which is associated with lower host metabolic disease risk. Overall, our results uncover a nascent layer of variability in the microbiome that is associated with microbial adaptation and host health.
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Affiliation(s)
- David Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. .,Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA.
| | - Tal Korem
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.,Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Bar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Kurilshikov
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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33
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Murina V, Kasari M, Takada H, Hinnu M, Saha CK, Grimshaw JW, Seki T, Reith M, Putrinš M, Tenson T, Strahl H, Hauryliuk V, Atkinson GC. ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic Resistance: Structural and Functional Diversification across the Tree of Life. J Mol Biol 2018; 431:3568-3590. [PMID: 30597160 PMCID: PMC6723617 DOI: 10.1016/j.jmb.2018.12.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/11/2018] [Accepted: 12/15/2018] [Indexed: 10/27/2022]
Abstract
Within the larger ABC superfamily of ATPases, ABCF family members eEF3 in Saccharomyces cerevisiae and EttA in Escherichia coli have been found to function as ribosomal translation factors. Several other ABCFs including biochemically characterized VgaA, LsaA and MsrE confer resistance to antibiotics that target the peptidyl transferase center and exit tunnel of the ribosome. However, the diversity of ABCF subfamilies, the relationships among subfamilies and the evolution of antibiotic resistance (ARE) factors from other ABCFs have not been explored. To address this, we analyzed the presence of ABCFs and their domain architectures in 4505 genomes across the tree of life. We find 45 distinct subfamilies of ABCFs that are widespread across bacterial and eukaryotic phyla, suggesting that they were present in the last common ancestor of both. Surprisingly, currently known ARE ABCFs are not confined to a distinct lineage of the ABCF family tree, suggesting that ARE can readily evolve from other ABCF functions. Our data suggest that there are a number of previously unidentified ARE ABCFs in antibiotic producers and important human pathogens. We also find that ATPase-deficient mutants of all four E. coli ABCFs (EttA, YbiT, YheS and Uup) inhibit protein synthesis, indicative of their ribosomal function, and demonstrate a genetic interaction of ABCFs Uup and YheS with translational GTPase BipA involved in assembly of the 50S ribosome subunit. Finally, we show that the ribosome-binding resistance factor VmlR from Bacillus subtilis is localized to the cytoplasm, ruling out a role in antibiotic efflux.
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Affiliation(s)
- Victoriia Murina
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Marje Kasari
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Hiraku Takada
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - Mariliis Hinnu
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Chayan Kumar Saha
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - James W Grimshaw
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Takahiro Seki
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 263-8522 Chiba, Japan
| | - Michael Reith
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Marta Putrinš
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden; University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
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34
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Abstract
During the past decades resistance to virtually all antimicrobial agents has been observed in bacteria of animal origin. This chapter describes in detail the mechanisms so far encountered for the various classes of antimicrobial agents. The main mechanisms include enzymatic inactivation by either disintegration or chemical modification of antimicrobial agents, reduced intracellular accumulation by either decreased influx or increased efflux of antimicrobial agents, and modifications at the cellular target sites (i.e., mutational changes, chemical modification, protection, or even replacement of the target sites). Often several mechanisms interact to enhance bacterial resistance to antimicrobial agents. This is a completely revised version of the corresponding chapter in the book Antimicrobial Resistance in Bacteria of Animal Origin published in 2006. New sections have been added for oxazolidinones, polypeptides, mupirocin, ansamycins, fosfomycin, fusidic acid, and streptomycins, and the chapters for the remaining classes of antimicrobial agents have been completely updated to cover the advances in knowledge gained since 2006.
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Sarrou S, Malli E, Tsilipounidaki K, Florou Z, Medvecky M, Skoulakis A, Hrabak J, Papagiannitsis CC, Petinaki E. MLS B-Resistant Staphylococcus aureus in Central Greece: Rate of Resistance and Molecular Characterization. Microb Drug Resist 2018; 25:543-550. [PMID: 30403546 DOI: 10.1089/mdr.2018.0259] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aim of the present study was to determine the rate and mechanisms of resistance to macrolides, lincosamides, and streptogramin B (MLSB) antibiotics of Staphylococcus aureus collected in Central Greece. Of the 2,893 S. aureus collected during 2012-2017, 1,161 isolates (40.2%) exhibited resistance to at least one of the MLSB agents. The rate of erythromycin resistance was statistically significantly higher in methicillin-resistant S. aureus (MRSA) (58.6%) than in methicillin-sensitive S. aureus (MSSA) isolates (20.7%) (p = 0.002). Two hundred seventy-five representative MLSB-resistant S. aureus, including 81 MSSA and 194 MRSA isolates, were further studied. Thirty-eight MSSA isolates carried ermC, 26 MSSA were positive for ermA, whereas 17 isolates carried msrA gene. Among MRSA, the ermA gene was identified in the majority of the isolates (n = 153). Thirty-seven MRSA isolates carried ermC; three isolates carried msrA, whereas the remaining MRSA was positive for two genes (ermA and ermC). Phylogenetic analysis showed that ST225, which belongs to CC5, was the most prevalent, accounting for 137 MRSA isolates. Higher genetic diversity was found in the group of MSSA isolates, which comprised of 13 sequence types. Whole-genome sequencing data showed that all ermA-positive S. aureus, with the exception of one ST398 isolate, harbored the ermA-carrying Tn554 transposon integrated into their chromosomes. Furthermore, Illumina sequencing followed by polymerase chain reaction screening identified that ermC, which was identified in a polyclonal population of MSSA and MRSA isolates, was carried by small plasmids, like pNE131. These findings highlighted the important role of high-risk clones and of mobile elements carrying resistance genes in the successful dissemination of MLSB-resistant staphylococci.
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Affiliation(s)
- Stela Sarrou
- 1 Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Ergina Malli
- 1 Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | | | - Zoi Florou
- 1 Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Matej Medvecky
- 2 Veterinary Research Institute, Brno, Czech Republic.,3 Faculty of Science, National Center for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Anargyros Skoulakis
- 1 Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Jaroslav Hrabak
- 4 Faculty of Medicine, Biomedical Center, Charles University, Pilsen, Czech Republic
| | | | - Efi Petinaki
- 1 Department of Microbiology, University Hospital of Larissa, Larissa, Greece
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36
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Abstract
ABSTRACT
Antimicrobial resistance among staphylococci of animal origin is based on a wide variety of resistance genes. These genes mediate resistance to many classes of antimicrobial agents approved for use in animals, such as penicillins, cephalosporins, tetracyclines, macrolides, lincosamides, phenicols, aminoglycosides, aminocyclitols, pleuromutilins, and diaminopyrimidines. In addition, numerous mutations have been identified that confer resistance to specific antimicrobial agents, such as ansamycins and fluoroquinolones. The gene products of some of these resistance genes confer resistance to only specific members of a class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents, including agents approved solely for human use. The resistance genes code for all three major resistance mechanisms: enzymatic inactivation, active efflux, and protection/modification/replacement of the cellular target sites of the antimicrobial agents. Mobile genetic elements, in particular plasmids and transposons, play a major role as carriers of antimicrobial resistance genes in animal staphylococci. They facilitate not only the exchange of resistance genes among members of the same and/or different staphylococcal species, but also between staphylococci and other Gram-positive bacteria. The observation that plasmids of staphylococci often harbor more than one resistance gene points toward coselection and persistence of resistance genes even without direct selective pressure by a specific antimicrobial agent. This chapter provides an overview of the resistance genes and resistance-mediating mutations known to occur in staphylococci of animal origin.
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Feßler AT, Wang Y, Wu C, Schwarz S. Mobile macrolide resistance genes in staphylococci. Plasmid 2018; 99:2-10. [PMID: 29807043 DOI: 10.1016/j.plasmid.2018.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/30/2018] [Accepted: 05/24/2018] [Indexed: 01/12/2023]
Abstract
Macrolide resistance in staphylococci is based on the expression of a number of genes which specify four major resistance mechanisms: (i) target site modification by methylation of the ribosomal target site in the 23S rRNA, (ii) ribosome protection via ABC-F proteins, (iii) active efflux via Major Facilitator Superfamily (MFS) transporters, and (iv) enzymatic inactivation by phosphotransferases or esterases. So far, 14 different classes of erm genes, which code for 23S rRNA methylases, have been reported to occur in staphylococci from humans, animals and environmental sources. Inducible or constitutive expression of the erm genes depends on the presence and intactness of a regulatory region known as translational attenuator. The erm genes commonly confer resistance not only to macrolides, but also to lincosamides and streptogramin B compounds. In contrast, the msr(A) gene codes for an ABC-F protein which confers macrolide and streptogramin B resistance whereas the mef(A) gene codes for a Major Facilitator Superfamily protein that can export only macrolides. Enzymatic inactivation of macrolides may be due to the macrolide phosphotransferase gene mph(C) or the macrolide esterase genes ere(A) or ere(B). Many of these macrolide resistance genes are part of either plasmids, transposons, genomic islands or prophages and as such, can easily be transferred across strain, species and genus boundaries. The co-location of other antimicrobial or metal resistance genes on the same mobile genetic element facilitates co-selection and persistence of macrolide resistance genes under the selective pressure of metals or other antimicrobial agents.
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Affiliation(s)
- Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Congming Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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38
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Sharkey LKR, O’Neill AJ. Antibiotic Resistance ABC-F Proteins: Bringing Target Protection into the Limelight. ACS Infect Dis 2018; 4:239-246. [PMID: 29376318 DOI: 10.1021/acsinfecdis.7b00251] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Members of the ATP-binding cassette (ABC)-F protein subfamily collectively mediate resistance to a broader range of clinically important antibiotic classes than any other group of resistance proteins and are widespread in pathogenic bacteria. Following over 25 years' of controversy regarding the mechanism by which these proteins work, it has recently been established that they provide antibiotic resistance through the previously recognized but underappreciated phenomenon of target protection; they bind to the ribosome to effect the release of ribosome-targeted antibiotics, thereby rescuing the translation apparatus from antibiotic-mediated inhibition. Here we review the ABC-F resistance proteins with an emphasis on their mechanism of action, first exploring the history of the debate about how these proteins work and outlining our current state of knowledge and then considering key questions to be addressed in understanding the molecular detail of their function.
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Affiliation(s)
- Liam K. R. Sharkey
- Antimicrobial Research Centre and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Alex J. O’Neill
- Antimicrobial Research Centre and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
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39
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Dinos GP. The macrolide antibiotic renaissance. Br J Pharmacol 2017; 174:2967-2983. [PMID: 28664582 DOI: 10.1111/bph.13936] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/29/2017] [Accepted: 06/20/2017] [Indexed: 12/19/2022] Open
Abstract
Macrolides represent a large family of protein synthesis inhibitors of great clinical interest due to their applicability to human medicine. Macrolides are composed of a macrocyclic lactone of different ring sizes, to which one or more deoxy-sugar or amino sugar residues are attached. Macrolides act as antibiotics by binding to bacterial 50S ribosomal subunit and interfering with protein synthesis. The high affinity of macrolides for bacterial ribosomes, together with the highly conserved structure of ribosomes across virtually all of the bacterial species, is consistent with their broad-spectrum activity. Since the discovery of the progenitor macrolide, erythromycin, in 1950, many derivatives have been synthesised, leading to compounds with better bioavailability and acid stability and improved pharmacokinetics. These efforts led to the second generation of macrolides, including well-known members such as azithromycin and clarithromycin. Subsequently, in order to address increasing antibiotic resistance, a third generation of macrolides displaying improved activity against many macrolide resistant strains was developed. However, these improvements were accompanied with serious side effects, leading to disappointment and causing many researchers to stop working on macrolide derivatives, assuming that this procedure had reached the end. In contrast, a recent published breakthrough introduced a new chemical platform for synthesis and discovery of a wide range of diverse macrolide antibiotics. This chemical synthesis revolution, in combination with reduction in the side effects, namely, 'Ketek effects', has led to a macrolide renaissance, increasing the hope for novel and safe therapeutic agents to combat serious human infectious diseases.
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Affiliation(s)
- George P Dinos
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
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40
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Abstract
Emergence of resistance among the most important bacterial pathogens is recognized as a major public health threat affecting humans worldwide. Multidrug-resistant organisms have not only emerged in the hospital environment but are now often identified in community settings, suggesting that reservoirs of antibiotic-resistant bacteria are present outside the hospital. The bacterial response to the antibiotic "attack" is the prime example of bacterial adaptation and the pinnacle of evolution. "Survival of the fittest" is a consequence of an immense genetic plasticity of bacterial pathogens that trigger specific responses that result in mutational adaptations, acquisition of genetic material, or alteration of gene expression producing resistance to virtually all antibiotics currently available in clinical practice. Therefore, understanding the biochemical and genetic basis of resistance is of paramount importance to design strategies to curtail the emergence and spread of resistance and to devise innovative therapeutic approaches against multidrug-resistant organisms. In this chapter, we will describe in detail the major mechanisms of antibiotic resistance encountered in clinical practice, providing specific examples in relevant bacterial pathogens.
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Buege MJ, Brown JE, Aitken SL. Solithromycin: A novel ketolide antibiotic. Am J Health Syst Pharm 2017; 74:875-887. [DOI: 10.2146/ajhp160934] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Michael J. Buege
- Division of Pharmacy, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jack E. Brown
- Department of Pharmacy, University of Rochester Medical Center, Rochester, NY
- Wegmans School of Pharmacy at St. John Fisher College, Rochester, NY
| | - Samuel L. Aitken
- Division of Pharmacy, University of Texas MD Anderson Cancer Center, Houston, TX
- Center for Antimicrobial Resistance and Microbial Genomics, UTHealth McGovern Medical School, Houston, TX
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Zaza G, Dalla Gassa A, Felis G, Granata S, Torriani S, Lupo A. Impact of maintenance immunosuppressive therapy on the fecal microbiome of renal transplant recipients: Comparison between an everolimus- and a standard tacrolimus-based regimen. PLoS One 2017; 12:e0178228. [PMID: 28542523 PMCID: PMC5443527 DOI: 10.1371/journal.pone.0178228] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/10/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The gut microbiome is the full set of microbes living in the gastrointestinal tract and is emerging as an important dynamic/fluid system that, if altered by environmental, dietetic or pharmacological factors, could considerably influence drug response. However, the immunosuppressive drug-induced modifications of this system are still poorly defined. METHODS We employed an innovative bioinformatics approach to assess differences in the whole-gut microbial metagenomic profile of 20 renal transplant recipients undergoing maintenance treatment with two different immunosuppressive protocols. Nine patients were treated with everolimus plus mycophenolate mofetil (EVE+MMF group), and 11 patients were treated with a standard therapy with tacrolimus plus mycophenolate mofetil (TAC+MMF group). RESULTS A statistical analysis of comparative high-throughput data demonstrated that although similar according to the degree of Shannon diversity (alpha diversity) at the taxonomic level, three functional genes clearly discriminated EVE+MMF versus TAC+MMF (cutoff: log2 fold change≥1, FDR≤0.05). Flagellar motor switch protein (fliNY) and type IV pilus assembly protein pilM (pilM) were significantly enriched in TAC+MMF-treated patients, while macrolide transport system mrsA (msrA) was more abundant in patients treated with EVE+MMF. Finally, PERMANOVA revealed that among the variables analyzed and included in our model, only the consumption of sugar significantly influenced beta diversity. CONCLUSIONS Our study, although performed on a relatively small number of patients, showed, for the first time, specific immunosuppressive-related effects on fecal microbiome of renal transplant recipients and it suggested that the analysis of the gut microbes community could represent a new tool to better understand the effects of drugs currently employed in organ transplantations. However, multicenter studies including healthy controls should be undertaken to better address this objective.
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Affiliation(s)
- Gianluigi Zaza
- Renal Unit, Department of Medicine, University Hospital of Verona, Verona, Italy
- * E-mail:
| | | | - Giovanna Felis
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Simona Granata
- Renal Unit, Department of Medicine, University Hospital of Verona, Verona, Italy
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Antonio Lupo
- Renal Unit, Department of Medicine, University Hospital of Verona, Verona, Italy
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43
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Zulkeflle SNM, Yusaimi YA, Sugiura N, Iwamoto K, Goto M, Utsumi M, Othman NB, Zakaria Z, Hara H. Phenotypic and genetic characterization of multidrug-resistant Staphylococcus aureus in the tropics of Southeast Asia. MICROBIOLOGY-SGM 2016; 162:2064-2074. [PMID: 27902427 DOI: 10.1099/mic.0.000392] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Antibiotic resistance has become a major public health problem throughout the world. The presence of antibiotic-resistant bacteria such as Staphylococcus aureus and antibiotic resistance genes (ARGs) in hospital wastewater is a cause for great concern today. In this study, 276 Staph. aureus isolates were recovered from hospital wastewater samples in Malaysia. All of the isolates were screened for susceptibility to nine different classes of antibiotics: ampicillin, ciprofloxacin, gentamicin, kanamycin, erythromycin, vancomycin, trimethoprim and sulfamethoxazole, chloramphenicol, tetracycline and nalidixic acid. Screening tests showed that 100 % of Staph.aureus isolates exhibited resistance against kanamycin, vancomycin, trimethoprim and sulfamethoxazole and nalidixic acid. Additionally, 91, 87, 50, 43, 11 and 8.7 % of isolates showed resistance against erythromycin, gentamicin, ciprofloxacin, ampicillin, chloramphenicol and tetracycline, respectively. Based on these results, 100 % of isolates demonstrated multidrug-resistant (MDR) characteristics, displaying resistance against more than three classes of antibiotics. Of 276 isolates, nine exhibited resistance to more than nine classes of tested antibiotics; these were selected for antibiotic susceptibility testing and examined for the presence of conserved ARGs. Interestingly, a high percentage of the selected MDR Staph.aureus isolates did not contain conserved ARGs. These results indicate that non-conserved MDR gene elements may have already spread into the environment in the tropics of Southeast Asia, and unique resistance mechanisms against several antibiotics may have evolved due to stable, moderate temperatures that support growth of bacteria throughout the year.
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Affiliation(s)
- Siti Norayuni Mohd Zulkeflle
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Yus Amira Yusaimi
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Norio Sugiura
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia.,Graduate School of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Koji Iwamoto
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia.,Graduate School of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Masafumi Goto
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Motoo Utsumi
- Graduate School of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Nor'azizi Bin Othman
- Department of Mechanical Precision Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Zuriati Zakaria
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Hirofumi Hara
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
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44
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Schwarz S, Shen J, Kadlec K, Wang Y, Brenner Michael G, Feßler AT, Vester B. Lincosamides, Streptogramins, Phenicols, and Pleuromutilins: Mode of Action and Mechanisms of Resistance. Cold Spring Harb Perspect Med 2016; 6:a027037. [PMID: 27549310 PMCID: PMC5088508 DOI: 10.1101/cshperspect.a027037] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lincosamides, streptogramins, phenicols, and pleuromutilins (LSPPs) represent four structurally different classes of antimicrobial agents that inhibit bacterial protein synthesis by binding to particular sites on the 50S ribosomal subunit of the ribosomes. Members of all four classes are used for different purposes in human and veterinary medicine in various countries worldwide. Bacteria have developed ways and means to escape the inhibitory effects of LSPP antimicrobial agents by enzymatic inactivation, active export, or modification of the target sites of the agents. This review provides a comprehensive overview of the mode of action of LSPP antimicrobial agents as well as of the mutations and resistance genes known to confer resistance to these agents in various bacteria of human and animal origin.
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Affiliation(s)
- Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Geovana Brenner Michael
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Andrea T Feßler
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Birte Vester
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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45
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Fyfe C, Grossman TH, Kerstein K, Sutcliffe J. Resistance to Macrolide Antibiotics in Public Health Pathogens. Cold Spring Harb Perspect Med 2016; 6:a025395. [PMID: 27527699 PMCID: PMC5046686 DOI: 10.1101/cshperspect.a025395] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Macrolide resistance mechanisms can be target-based with a change in a 23S ribosomal RNA (rRNA) residue or a mutation in ribosomal protein L4 or L22 affecting the ribosome's interaction with the antibiotic. Alternatively, mono- or dimethylation of A2058 in domain V of the 23S rRNA by an acquired rRNA methyltransferase, the product of an erm (erythromycin ribosome methylation) gene, can interfere with antibiotic binding. Acquired genes encoding efflux pumps, most predominantly mef(A) + msr(D) in pneumococci/streptococci and msr(A/B) in staphylococci, also mediate resistance. Drug-inactivating mechanisms include phosphorylation of the 2'-hydroxyl of the amino sugar found at position C5 by phosphotransferases and hydrolysis of the macrocyclic lactone by esterases. These acquired genes are regulated by either translation or transcription attenuation, largely because cells are less fit when these genes, especially the rRNA methyltransferases, are highly induced or constitutively expressed. The induction of gene expression is cleverly tied to the mechanism of action of macrolides, relying on antibiotic-bound ribosomes stalled at specific sequences of nascent polypeptides to promote transcription or translation of downstream sequences.
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Affiliation(s)
- Corey Fyfe
- Tetraphase Pharmaceuticals, Watertown, Massachusetts 02472
| | | | - Kathy Kerstein
- Tetraphase Pharmaceuticals, Watertown, Massachusetts 02472
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46
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Amino acid amides of piperic acid (PA) and 4-ethylpiperic acid (EPA) as NorA efflux pump inhibitors of Staphylococcus aureus. Bioorg Med Chem Lett 2016; 26:4174-8. [DOI: 10.1016/j.bmcl.2016.07.062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/21/2016] [Accepted: 07/27/2016] [Indexed: 11/20/2022]
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47
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Mu XQ, Liu BB, Hui E, Huang W, Yao LC, Duo LB, Sun WY, Li GQ, Wang FX, Liu SL. A rapid loop-mediated isothermal amplification (LAMP) method for detection of the macrolide-streptogramin type B resistance gene msrA in Staphylococcus aureus. J Glob Antimicrob Resist 2016; 7:53-58. [PMID: 27607914 DOI: 10.1016/j.jgar.2016.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/10/2016] [Accepted: 07/18/2016] [Indexed: 12/25/2022] Open
Abstract
Macrolide-streptogramin type B resistance (the MSB phenotype) is a multidrug resistance phenotype in Staphylococcus aureus conferred by the resistance gene msrA. However, bacteria having the MSB phenotype are susceptible to lincosamides and 16-membered ring macrolides, which makes profiling resistance genes necessary and urgent for timely and appropriate use of antimicrobials. In this study, the loop-mediated isothermal amplification (LAMP) assay was optimized for prompt detection of the msrA gene. msrA gene sequences were obtained from the National Center for Biotechnology Information (NCBI) database and primers were designed using the LAMP primer designing software PrimerExplorer v.4, which together recognize seven distinct regions of the msrA gene. The specific LAMP primer set designed in this study could amplify the msrA gene within 25min at an isothermal temperature of 62°C. More importantly, the msrA gene could be detected at a sensitivity as low as 100pg. Furthermore, this optimized LAMP assay provided swift detection of the msrA gene even directly from human specimens. In conclusion, this assay may have great clinical application potential for detection of the msrA gene.
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Affiliation(s)
- Xiao-Qin Mu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Bin-Bin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Ephraim Hui
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - William Huang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Li-Chen Yao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Li-Bo Duo
- Department of Medicine Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wen-Ying Sun
- Department of Medicine Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Gui-Qiu Li
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fu-Xiang Wang
- Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China; HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
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Schindler BD, Kaatz GW. Multidrug efflux pumps of Gram-positive bacteria. Drug Resist Updat 2016; 27:1-13. [DOI: 10.1016/j.drup.2016.04.003] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/28/2016] [Accepted: 04/22/2016] [Indexed: 11/16/2022]
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Abstract
Members of the ABC-F subfamily of ATP-binding cassette proteins mediate resistance to a broad array of clinically important antibiotic classes that target the ribosome of Gram-positive pathogens. The mechanism by which these proteins act has been a subject of long-standing controversy, with two competing hypotheses each having gained considerable support: antibiotic efflux versus ribosomal protection. Here, we report on studies employing a combination of bacteriological and biochemical techniques to unravel the mechanism of resistance of these proteins, and provide several lines of evidence that together offer clear support to the ribosomal protection hypothesis. Of particular note, we show that addition of purified ABC-F proteins to an in vitro translation assay prompts dose-dependent rescue of translation, and demonstrate that such proteins are capable of displacing antibiotic from the ribosome in vitro. To our knowledge, these experiments constitute the first direct evidence that ABC-F proteins mediate antibiotic resistance through ribosomal protection. Antimicrobial resistance ranks among the greatest threats currently facing human health. Elucidation of the mechanisms by which microorganisms resist the effect of antibiotics is central to understanding the biology of this phenomenon and has the potential to inform the development of new drugs capable of blocking or circumventing resistance. Members of the ABC-F family, which include lsa(A), msr(A), optr(A), and vga(A), collectively yield resistance to a broader range of clinically significant antibiotic classes than any other family of resistance determinants, although their mechanism of action has been controversial since their discovery 25 years ago. Here we present the first direct evidence that proteins of the ABC-F family act to protect the bacterial ribosome from antibiotic-mediated inhibition.
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Discovery of Novel MLSB Resistance Methylase Genes and Their Associated Genetic Elements in Staphylococci. CURRENT CLINICAL MICROBIOLOGY REPORTS 2016. [DOI: 10.1007/s40588-016-0030-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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