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Singh G, Rana A, Smriti. Decoding antimicrobial resistance: unraveling molecular mechanisms and targeted strategies. Arch Microbiol 2024; 206:280. [PMID: 38805035 DOI: 10.1007/s00203-024-03998-2] [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: 03/31/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Antimicrobial resistance poses a significant global health threat, necessitating innovative approaches for combatting it. This review explores various mechanisms of antimicrobial resistance observed in various strains of bacteria. We examine various strategies, including antimicrobial peptides (AMPs), novel antimicrobial materials, drug delivery systems, vaccines, antibody therapies, and non-traditional antibiotic treatments. Through a comprehensive literature review, the efficacy and challenges of these strategies are evaluated. Findings reveal the potential of AMPs in combating resistance due to their unique mechanisms and lower propensity for resistance development. Additionally, novel drug delivery systems, such as nanoparticles, show promise in enhancing antibiotic efficacy and overcoming resistance mechanisms. Vaccines and antibody therapies offer preventive measures, although challenges exist in their development. Non-traditional antibiotic treatments, including CRISPR-Cas systems, present alternative approaches to combat resistance. Overall, this review underscores the importance of multifaceted strategies and coordinated global efforts to address antimicrobial resistance effectively.
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Affiliation(s)
- Gagandeep Singh
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India
| | - Anita Rana
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India.
| | - Smriti
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India
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2
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Rahman Z, McLaws M, Thomas T. Genomic characterization of extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli from urban wastewater in Australia. Microbiologyopen 2024; 13:e1403. [PMID: 38488803 PMCID: PMC10941799 DOI: 10.1002/mbo3.1403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
This study investigates extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli isolates from Sydney's wastewater. These isolates exhibit resistance to critical antibiotics and harbor novel resistance mechanisms. The findings highlight the importance of wastewater-based surveillance in monitoring resistance beyond the clinical setting.
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Affiliation(s)
- Zillur Rahman
- School of Biological, Earth and Environmental Sciences, Centre for Marine Science and InnovationUNSW SydneySydneyNew South WalesAustralia
| | - Mary‐Louise McLaws
- School of Population HealthUNSW SydneySydneyNew South WalesAustralia
- UNSW Global Water InstituteUNSW SydneySydneyNew South WalesAustralia
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, Centre for Marine Science and InnovationUNSW SydneySydneyNew South WalesAustralia
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3
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Mei L, Song Y, Liu X, Li K, Guo X, Liu L, Liu Y, Kozlakidis Z, Cheong IH, Wang D, Wei Q. Characterization and Implications of IncP-2A Plasmid pMAS152 Harboring Multidrug Resistance Genes in Extensively Drug-Resistant Pseudomonas aeruginosa. Microorganisms 2024; 12:562. [PMID: 38543613 PMCID: PMC10973999 DOI: 10.3390/microorganisms12030562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/03/2024] [Accepted: 03/08/2024] [Indexed: 04/21/2024] Open
Abstract
Bacterial antimicrobial resistance (AMR) poses a significant global public health challenge. The escalation of AMR is primarily attributed to the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), often facilitated by plasmids. This underscores the critical need for a comprehensive understanding of the resistance mechanisms and transmission dynamics of these plasmids. In this study, we utilized in vitro drug sensitivity testing, conjugation transfer assays, and whole-genome sequencing to investigate the resistance mechanism of an extensively drug-resistant (XDR) Pseudomonas aeruginosa clinical isolate, MAS152. We specifically focused on analyzing the drug-resistant plasmid pMAS152 it harbors and its potential for widespread dissemination. Bioinformatics analysis revealed that MAS152 carries a distinct IncpP-2A plasmid, pMAS152, characterized by a 44.8 kb multidrug resistance (MDR) region. This region houses a 16S rRNA methyltransferase (16S-RMTase) gene, rmtB, conferring high-level resistance to aminoglycoside antibiotics. Notably, this region also contains an extended-spectrum β-Lactamase (ESBL) gene, blaPER-1, and an efflux pump operon, tmexCD-oprJ, which mediate resistance to β-Lactams and quinolone antibiotics, respectively. Such a combination of ARGs, unprecedented in reported plasmids, could significantly undermine the effectiveness of first-line antibiotics in treating P. aeruginosa infections. Investigation into the genetic environment of the MDR region suggests that Tn2 and IS91 elements may be instrumental in the horizontal transfer of rmtB. Additionally, a complex Class I integron with an ISCR1 structure, along with TnAs1, seems to facilitate the horizontal transfer of blaPER-1. The conjugation transfer assay, coupled with the annotation of conjugation-related genes and phylogenetic analysis, indicates that the plasmid pMAS152 functions as a conjugative plasmid, with other genus Pseudomonas species as potential hosts. Our findings provide vital insights into the resistance mechanisms and transmission potential of the XDR P. aeruginosa isolate MAS152, underlining the urgent need for novel strategies to combat the spread of AMR. This study highlights the complex interplay of genetic elements contributing to antibiotic resistance and underscores the importance of continuous surveillance of emerging ARGs in clinical isolates.
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Affiliation(s)
- Li Mei
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.M.); (L.L.); (Y.L.)
| | - Yang Song
- Division of Infectious Disease, National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China;
| | - Xiao Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (X.L.); (K.L.)
| | - Kun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (X.L.); (K.L.)
| | - Xu Guo
- National Immunization Program, Chinese Center for Disease Control and Prevention, Beijing 100050, China;
| | - Li Liu
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.M.); (L.L.); (Y.L.)
| | - Yang Liu
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.M.); (L.L.); (Y.L.)
| | - Zisis Kozlakidis
- International Agency for Research on Cancer, World Health Organization, 69007 Lyon, France;
| | - Io Hong Cheong
- State Key Laboratory of Systems Medicine for Cancer, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China;
| | - Duochun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (X.L.); (K.L.)
| | - Qiang Wei
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (L.M.); (L.L.); (Y.L.)
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4
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Zhou C, Zhang H, Xu M, Liu Y, Yuan B, Lin Y, Shen F. Within-Host Resistance and Virulence Evolution of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae ST11 Under Antibiotic Pressure. Infect Drug Resist 2023; 16:7255-7270. [PMID: 38023413 PMCID: PMC10658960 DOI: 10.2147/idr.s436128] [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: 08/19/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Background Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) has recently aroused an extremely severe health challenge and public concern. However, the underlying mechanisms of fitness costs that accompany antibiotic resistance acquisition remain largely unexplored. Here, we report a hv-CRKP-associated fatal infection and reveal a reduction in virulence due to the acquisition of aminoglycoside resistance. Methods The bacterial identification, antimicrobial susceptibility, hypermucoviscosity, virulence factors, MLST and serotypes were profiled.The clonal homology and plasmid acquisition among hv-CRKP strains were detected by XbaI and S1-PFGE. The virulence potential of the strains was evaluated using Galleria mellonella larvae infection model, serum resistance assay, capsular polysaccharide quantification, and biofilm formation assay. Genomic variations were identified using whole-genome sequencing (WGS). Results Four K. pneumoniae carbapenemase (KPC)-producing CRKP strains were consecutively isolated from an 86-year-old patient with severe pneumonia. Whole-genome sequencing (WGS) showed that all four hv-CRKP strains belonged to the ST11-KL64 clone. PFGE analysis revealed that the four ST11-KL64 hv-CRKP strains could be grouped into the same PFGE type. Under the pressure of antibiotics, the antimicrobial resistance of the strains increased and the virulence potential decreased. Further sequencing, using the Nanopore platform, was performed on three representative isolates (WYKP586, WYKP589, and WYKP594). Genomic analysis showed that the plasmids of these three strains underwent a large number of breaks and recombination events under antibiotic pressure. We found that as aminoglycoside resistance emerged via acquisition of the rmtB gene, the hypermucoviscosity and virulence of the strains decreased because of internal mutations in the rmpA and rmpA2 genes. Conclusion This study shows that ST11-KL64 hv-CRKP can further evolve to acquire aminoglycoside resistance accompanied by decreased virulence to adapt to antibiotic pressure in the host.
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Affiliation(s)
- Cong Zhou
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Hui Zhang
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Maosuo Xu
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Yajuan Liu
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Baoyu Yuan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yong Lin
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Fang Shen
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
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Sellera FP, Fuentes-Castillo D, Furlan JPR. One Health Spread of 16S Ribosomal RNA Methyltransferase-Harboring Gram-Negative Bacterial Genomes: An Overview of the Americas. Pathogens 2023; 12:1164. [PMID: 37764972 PMCID: PMC10536106 DOI: 10.3390/pathogens12091164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Aminoglycoside antimicrobials remain valuable therapeutic options, but their effectiveness has been threatened by the production of bacterial 16S ribosomal RNA methyltransferases (16S-RMTases). In this study, we evaluated the genomic epidemiology of 16S-RMTase genes among Gram-negative bacteria circulating in the American continent. A total of 4877 16S-RMTase sequences were identified mainly in Enterobacterales and nonfermenting Gram-negative bacilli isolated from humans, animals, foods, and the environment during 1931-2023. Most of the sequences identified were found in the United States, Brazil, Canada, and Mexico, and the prevalence of 16S-RMTase genes have increased in the last five years (2018-2022). The three species most frequently carrying 16S-RMTase genes were Acinetobacter baummannii, Klebsiella pneumoniae, and Escherichia coli. The armA gene was the most prevalent, but other 16S-RMTase genes (e.g., rmtB, rmtE, and rmtF) could be emerging backstage. More than 90% of 16S-RMTase sequences in the Americas were found in North American countries, and although the 16S-RMTase genes were less prevalent in Central and South American countries, these findings may be underestimations due to limited genomic data. Therefore, whole-genome sequence-based studies focusing on aminoglycoside resistance using a One Health approach in low- and middle-income countries should be encouraged.
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Affiliation(s)
- Fábio Parra Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, Brazil;
- School of Veterinary Medicine, Metropolitan University of Santos, Santos 11065-402, Brazil
| | - Danny Fuentes-Castillo
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán 3780000, Chile;
| | - João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, Brazil
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Zhang S, Zhang Y, Liu R, Yuan S, Chen Y, Li W, Lu X, Tong Y, Hou L, Chen L, Sun G. Characterization and Molecular Mechanism of Aminoglycoside-6-Adenyl Transferase Associated with Aminoglycoside Resistance from Elizabethkingia meningoseptica. Infect Drug Resist 2023; 16:5523-5534. [PMID: 37638067 PMCID: PMC10460174 DOI: 10.2147/idr.s423418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Purpose Elizabethkingia meningoseptica (EM) is a multi-drug-resistant bacterium of global concern for its role in nosocomial infection and is generally resistant to aminoglycoside antibiotics. In the whole genome of an EM strain (FMS-007), an aminoglycoside-6-adenyl transferase gene (ant(6)FMS-007) was predicted. This study aimed to characterize the biochemical function of ANT(6)FMS-007 and analyze the relationship between genotype and phenotype of ant(6) in clinical EM isolates, so as to provide evidence for clinical precision drug use. This study could establish a method for the verification of known or unknown functionally resistant genes. Methods A total of 42 EM clinical isolates were collected from clinical departments during 2015-2023. The phenotype of aminoglycoside antibiotics was analyzed by broth microdilution (BMD) and Kirby-Bauer (K-B) methods. The whole-length ant(6) from EM clinical isolates was analyzed by polymerase chain reaction (PCR) and sequencing. The biochemical function of predictive ANT(6)FMS-007 from the FMS-007 whole genome was identified by 3D plate experiment and mass spectrometry analysis. Candidate active sites were predicted by multi-species sequence alignment and molecular docking, and other important sites were identified in the comparison of ant(6) genotypes and phenotypes of EM clinical isolates. Drug susceptibility test was used to verify the function of these sites. Results The predictive ANT(6)FMS-007 protein could inactivate STR by modifying STR with ATP to form STR-AMP. Four active sites (Asp-38, Asp-42, Lys-95, and Lys-213) of ANT(6)FMS-007 were identified. Thirty-one EM clinical isolates (74%) carried the ant(6) gene. Eight EM clinical isolates containing the ant(6) gene had MIC values (<=32μg/mL) lower by at least 16-fold than FMS-007 (512μg/mL) for STR, and N59H and K204Q were the common mutations in the ant(6) gene. Conclusion This assay verified the biochemical function of the predictive gene ant(6)FMS-007 and could provide an alternative method to study resistant gene function in multi-drug-resistant bacteria. The inconsistency between genotype and phenotype of resistant genes indicated that the combination of resistance gene detection and functional analysis could better provide precision medicine for clinical use.
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Affiliation(s)
- Shaoxing Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Yuxin Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Ruijie Liu
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Shuying Yuan
- Clinical Laboratory Department, Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang, People’s Republic of China
| | - Yanwen Chen
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Wenjie Li
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
| | - Xinrong Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Yongliang Tong
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Linlin Hou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, People’s Republic of China
| | - Li Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Guiqin Sun
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, People’s Republic of China
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7
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Frost KJ, Hamilton RA, Hughes S, Jamieson C, Rafferty P, Troise O, Jenkins A. Systematic review of high-dose amikacin regimens for the treatment of Gram-negative infections based on EUCAST dosing recommendations. Eur J Hosp Pharm 2023; 30:189-195. [PMID: 36344247 PMCID: PMC10359793 DOI: 10.1136/ejhpharm-2022-003421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Updated European Committee on Antimicrobial Susceptibility Testing (EUCAST) amikacin breakpoints for Enterobacterales and Pseudomonas aeruginosa included revised dosing recommendations of 25-30 mg/kg to achieve key pharmacokinetic/pharmacodynamic parameters, higher than recommended in the British National Formulary. The objectives of this review were to identify clinical evidence for high-dose amikacin regimens and to determine drug exposures that are related to adverse events and toxicity. METHODS The literature search was conducted in October 2021 and updated in May 2022 using electronic databases for any study reporting adult participants treated with amikacin at doses ≥20 mg/kg/day. Reference lists of included papers were also screened for potential papers. Data were extracted for pharmacokinetic parameters and clinical outcomes, presented in a summary table and consolidated narratively. Meta-analysis was not possible. Each study was assessed for bias before, during and after the intervention using the ROBINS-I tool. RESULTS Nine studies (total 501 participants in 10 reports) were identified and included, eight of which were observational studies. Assessment of bias showed substantial flaws. Dosing regimens ranged from 25 to 30 mg/kg/day. Six studies adjusted the dose in obesity when participants had a body mass index of ≥30 kg/m2. Target peak serum concentrations ranged from 60 mg/L to 80 mg/L and 59.6-81.8% of patients achieved these targets, but there was no information on clinical outcomes. Two studies reported the impact of high-dose amikacin on renal function. No studies reporting auditory or vestibular toxicity were identified. CONCLUSION All included papers were limited by a significant risk of bias, while methodological and reporting heterogeneity made drawing conclusions challenging. Lack of information on the impact on renal function or ototoxicity means high-dose regimens should be used cautiously in older people. There is a need for a consensus guideline for high-dose amikacin to be written. TRIAL REGISTRATION NUMBER PROSPERO (CRD42021250022).
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Affiliation(s)
| | - Ryan A Hamilton
- Pharmacy, De Montfort University, Leicester, UK
- Pharmacy, Kettering General Hospital NHS Foundation Trust, Kettering, UK
| | - Stephen Hughes
- Pharmacy, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Conor Jamieson
- NHS England and NHS Improvement Midlands, Birmingham, UK
| | - Paul Rafferty
- Pharmacy, Southern Health and Social Care Trust, Portadown, UK
| | - Oliver Troise
- Pharmacy, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Abi Jenkins
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
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Lu J, Sha Y, Gao M, Shi W, Lin X, Li K, Bao Q, Feng C. Identification and characterization of a novel aminoglycoside O-nucleotidyltransferase ANT(6)-If from Paenibacillus thiaminolyticus PATH554. Front Microbiol 2023; 14:1184349. [PMID: 37455719 PMCID: PMC10343464 DOI: 10.3389/fmicb.2023.1184349] [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: 03/11/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Background Paenibacillus thiaminolyticus, a species of genus Paenibacillus of the family Paenibacillaceae, exists widely in environments and habitats in various plants and worms, and occasionally causes human infections. This work aimed to characterize the function of a novel aminoglycoside O-nucleotidyltransferase resistance gene, designated ant(6)-If, from a P. thiaminolyticus strain PATH554. Methods Molecular cloning, antimicrobial susceptibility testing, enzyme expression and purification, and kinetic analysis were used to validate the function of the novel gene. Whole-genome sequencing and comparative genomic analysis were performed to investigate the phylogenetic relationship of ANT(6)-If and other aminoglycoside O-nucleotidyltransferases, and the synteny of ant(6)-If related sequences. Results The recombinant with the cloned ant(6)-If gene (pMD19-ant(6)-If/DH5α) demonstrated a 128-fold increase of minimum inhibitory concentration level against streptomycin, compared with the control strains (DH5α and pMD19/DH5α). The kinetic parameter kcat/Km of ANT(6)-If for streptomycin was 9.01 × 103 M-1·s-1. Among the function-characterized resistance genes, ANT(6)-If shared the highest amino acid sequence identity of 75.35% with AadK. The ant(6)-If gene was located within a relatively conserved genomic region in the chromosome. Conclusion ant(6)-If conferred resistance to streptomycin. The study of a novel resistance gene in an unusual environmental bacterium in this work contributed to elucidating the resistance mechanisms in the microorganisms.
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Affiliation(s)
- Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Yuning Sha
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, School of Laboratory Medicine and Life Sciences, Institute of Biomedical Informatics, Ministry of Education, Wenzhou Medical University, Wenzhou, China
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9
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Darby EM, Trampari E, Siasat P, Gaya MS, Alav I, Webber MA, Blair JMA. Molecular mechanisms of antibiotic resistance revisited. Nat Rev Microbiol 2023; 21:280-295. [PMID: 36411397 DOI: 10.1038/s41579-022-00820-y] [Citation(s) in RCA: 195] [Impact Index Per Article: 195.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.
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Affiliation(s)
- Elizabeth M Darby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Ilyas Alav
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
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Srinivas P, Nosrati M, Zelinskaya N, Dey D, Comstock LR, Dunham CM, Conn GL. 30S subunit recognition and G1405 modification by the aminoglycoside-resistance 16S ribosomal RNA methyltransferase RmtC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532395. [PMID: 36993224 PMCID: PMC10054953 DOI: 10.1101/2023.03.13.532395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Acquired ribosomal RNA (rRNA) methylation has emerged as a significant mechanism of aminoglycoside resistance in pathogenic bacterial infections. Modification of a single nucleotide in the ribosome decoding center by the aminoglycoside-resistance 16S rRNA (m 7 G1405) methyltransferases effectively blocks the action of all 4,6-deoxystreptamine ring-containing aminoglycosides, including the latest generation of drugs. To define the molecular basis of 30S subunit recognition and G1405 modification by these enzymes, we used a S-adenosyl-L-methionine (SAM) analog to trap the complex in a post-catalytic state to enable determination of an overall 3.0 Ã… cryo-electron microscopy structure of the m 7 G1405 methyltransferase RmtC bound to the mature Escherichia coli 30S ribosomal subunit. This structure, together with functional analyses of RmtC variants, identifies the RmtC N-terminal domain as critical for recognition and docking of the enzyme on a conserved 16S rRNA tertiary surface adjacent to G1405 in 16S rRNA helix 44 (h44). To access the G1405 N7 position for modification, a collection of residues across one surface of RmtC, including a loop that undergoes a disorder to order transition upon 30S subunit binding, induces significant distortion of h44. This distortion flips G1405 into the enzyme active site where it is positioned for modification by two almost universally conserved RmtC residues. These studies expand our understanding of ribosome recognition by rRNA modification enzymes and present a more complete structural basis for future development of strategies to inhibit m 7 G1405 modification to re-sensitize bacterial pathogens to aminoglycosides.
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11
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Caméléna F, Liberge M, Rezzoug I, Merimèche M, Naas T, Berçot B. In vitro activity of apramycin against 16S-RMTase-producing Gram-negative isolates. J Glob Antimicrob Resist 2023; 33:21-25. [PMID: 36822368 DOI: 10.1016/j.jgar.2023.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/10/2023] [Accepted: 02/02/2023] [Indexed: 02/25/2023] Open
Abstract
OBJECTIVES Apramycin is an aminoglycoside (AG) with a unique structure that is little affected by plasmid-mediated mechanisms of AG resistance, including most AG-modifying enzymes and 16S rRNA methyltransferases (16S-RMTases). We evaluate the activity of apramycin against a collection of 16S-RMTase-producing isolates, including Enterobacterales, non-fermenting bacteria, and carbapenemase producers. METHODS In total, 164 non-duplicate 16S-RMTase-producing isolates, including 84 Enterobacterales, 53 Acinetobacter baumannii and 27 Pseudomonas aeruginosa isolates, were included in the study. Whole-genome sequencing (WGS) was performed on all isolates with Illumina technology. The minimum inhibitory concentration (MIC) of apramycin was determined by broth microdilution with customized Sensititre plates (Thermo Fisher Scientific, Dardilly, France). RESULTS We found that 95% (156/164) of the 16S-RMTase-producing isolates were susceptible to apramycin, with a MIC50 of 4 mg/L and a MIC90 of 16 mg/L, respectively. Resistance rates were higher in P. aeruginosa (11%) than in A. baumannii (4%) or Enterobacterales (4%) (P < 0.0001 for each comparison). Eight isolates were resistant to apramycin, including one isolate with an MIC >64 mg/L due to the acquisition of the aac(3)-IV gene. The genetic environment of the aac(3)-IV gene was similar to that in the pAH01-4 plasmid of an Escherichia coli isolate from chicken in China. CONCLUSION Resistance to apramycin remains rare in 16S-RMTase-producing isolates. Apramycin may, therefore, be an interesting alternative treatment for infections caused by 16S-RMTase and carbapenemase producers.
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Affiliation(s)
- François Caméléna
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; Université de Paris Cité, INSERM 1137, IAME, Paris, France
| | - Mathilde Liberge
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; Université de Paris Cité, INSERM 1137, IAME, Paris, France
| | - Inès Rezzoug
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Manel Merimèche
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; Université de Paris Cité, INSERM 1137, IAME, Paris, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France; Université de Paris-Saclay, INSERM 1184, RESIST Unit, Le Kremlin-Bicêtre, France; French National Reference Centre for Antimicrobial Resistance, Le Kremlin-Bicêtre, France
| | - Béatrice Berçot
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; Université de Paris Cité, INSERM 1137, IAME, Paris, France.
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12
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Current and Emerging Treatment Options for Multidrug Resistant Escherichia coli Urosepsis: A Review. Antibiotics (Basel) 2022; 11:antibiotics11121821. [PMID: 36551478 PMCID: PMC9774639 DOI: 10.3390/antibiotics11121821] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Escherichia coli is a versatile commensal and pathogenic member of the human microflora. As the primary causative pathogen in urosepsis, E. coli places an immense burden on healthcare systems worldwide. To further exacerbate the issue, multi drug resistance (MDR) has spread rapidly through E. coli populations, making infections more troublesome and costlier to treat. This paper aimed to review the literature concerning the development of MDR in uropathogenic E. coli (UPEC) and explore the existing evidence of current and emerging treatment strategies. While some MDR strains maybe treated with β-lactam-β-lactamase inhibitor combinations as well as cephalosporins, cephamycin, temocillin and fosfomycin, current treatment strategies for many MDR UPEC strains are reliant on carbapenems. Carbapenem overreliance may contribute to the alarming dissemination of carbapenem-resistance amongst some UPEC communities, which has ushered in a new age of difficult to treat infections. Alternative treatment options for carbapenem resistant UPEC may include novel β-lactam-β-lactamase or carbapenemase inhibitor combinations, cefiderocol, polymyxins, tigecycline, aminoglycosides or fosfomycin. For metallo-β-lactamase producing strains (e.g., NDM, IMP-4), combinations of cefazidime-avibacam with aztreonam have been used. Additionally, the emergence of new antimicrobials brings new hope to the treatment of such infections. However, continued research is required to successfully bring these into the clinic for the treatment of MDR E. coli urosepsis.
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13
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Aghamohammad S, Rohani M. Antibiotic resistance and the alternatives to conventional antibiotics: The role of probiotics and microbiota in combating antimicrobial resistance. Microbiol Res 2022; 267:127275. [PMID: 36493661 DOI: 10.1016/j.micres.2022.127275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
From the introduction of the first antibiotic to the present day, the emergence of antibiotic resistance has been a difficult problem for medicine. Regardless of the type of antibiotic resistance, the presence of resistant isolates in clinical and even asymptomatic fecal carriers becomes a difficult public health problem. Therefore, the use of new antimicrobial combination therapies or alternative agents with antimicrobial activity that have the least side effects, including plant-, metal-, and nanoparticle-based agents, could be crucial and useful. Recently, the use of probiotics as a hypothetical candidate to combat infectious disease control and antimicrobial resistance has received notable attention. Considering the alteration of the microbiota in fecal carriers and also in patients with resistant bacterial isolates, the use of probiotics could have an appropriate effect on the balance of the microbial population. In this review, we have attempted to discuss the history of antimicrobial resistance and provide an overview of microbiota change and the use of probiotics as new agents with antimicrobial activity associated with the emergence of resistant isolates.
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Affiliation(s)
| | - Mahdi Rohani
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran.
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14
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Wang N, Chen X, Luo J, Deng F, Shi F, Wu Q, Huang Y, Ouyang Q, Qin R, Zhou H. Artemisinin derivative DHA27 enhances the antibacterial effect of aminoglycosides against Pseudomonas aeruginosa by inhibiting mRNA expression of aminoglycoside-modifying enzymes. Front Pharmacol 2022; 13:970400. [DOI: 10.3389/fphar.2022.970400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial resistance is becoming increasingly serious, the present study aimed to investigate the mechanism of antibacterial sensitization effect of DHA27 combined with tobramycin in tobramycin-resistant Pseudomonas aeruginosa (PA). We found that DHA27 combined with aminoglycosides had an antibacterial sensitization effect on PA. Tobramycin, owing to its lower toxic and side effects, was selected to further study the molecular mechanism of drug combination. A sublethal-dose bacterial challenge/sepsis mouse model was established to study the protective effect of DHA27 plus tobramycin. Scanning electron microscopy was used to investigate whether DHA27 exerts the antibacterial sensitization effect by directly affecting bacterial morphology. The effect of DHA27 on daunorubicin accumulation in bacteria was studied, and quantitative reverse transcription PCR was used to study the effect of DHA27 plus tobramycin on 16S rRNA methyltransferase and aminoglycoside-modifying enzyme mRNA expression. Twenty clinical isolates of PA were found to be tobramycin resistant; DHA27 plus tobramycin had a significant antibacterial sensitization effect on many of these resistant strains. DHA27 plus tobramycin reduced the bacterial load in the spleen and lungs of sepsis model mice and levels of proinflammatory cytokines interleukin-1β (IL-1β) and interferon-γ (IFN-γ). DHA27 plus tobramycin significantly inhibited the mRNA expression of aminoglycoside-modifying enzymes in bacteria. DHA27 combined with AGs had an antibacterial sensitization effect on PA; the molecular mechanism underlying this effect is closely related to the inhibition of the mRNA expression of aminoglycoside-modifying enzymes, especially aac(3)-II.
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15
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Yu Z, Ma Y, Guan Y, Zhu Y, Wang K, Wang Y, Liu P, Chen J, Yu Y. Metagenomics of Virus Diversities in Solid-State Brewing Process of Traditional Chinese Vinegar. Foods 2022; 11:3296. [PMCID: PMC9602057 DOI: 10.3390/foods11203296] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Traditional Chinese vinegar offers an exceptional flavor and rich nutrients due to its unique solid-state fermentation process, which is a multiple microbial fermentation system including various bacteria, fungi and viruses. However, few studies on the virus diversities in traditional Chinese vinegar have been reported. In this paper, using Zhenjiang aromatic vinegar as a model system, we systemically explored the viral communities in the solid-state brewing process of traditional Chinese vinegar using bacterial and viral metagenomes. Results showed that the viral diversity in vinegar Pei was extensive and the virus communities varied along with the fermentation process. In addition, there existed some interactions between viral and bacterial communities. Moreover, abundant antibiotic resistance genes were found in viromes, indicating that viruses might protect fermentation bacteria strains from the stress of antibiotics in the fermentation environment. Remarkably, we identified abundant auxiliary carbohydrate metabolic genes (including alcohol oxidases, the key enzymes for acetic acid synthesis) from viromes, implying that viruses might participate in the acetic acid synthesis progress of the host through auxiliary metabolic genes. Taken together, our results indicated the potential roles of viruses in the vinegar brewing process and provided a new perspective for studying the fermentation mechanisms of traditional Chinese vinegar.
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Affiliation(s)
- Zhen Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yan Ma
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yingfen Guan
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yuanyuan Zhu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Ke Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Yuqin Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Peng Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Juan Chen
- College of Food Science and Engineering, Moutai Institute, Renhuai 564501, China
| | - Yongjian Yu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
- Correspondence: ; Tel.: +86-0511-84400686
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16
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Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolates from Two Romanian Hospitals Co-Presenting Resistance and Heteroresistance to Colistin. Antibiotics (Basel) 2022; 11:antibiotics11091171. [PMID: 36139950 PMCID: PMC9495256 DOI: 10.3390/antibiotics11091171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/12/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Klebsiella pneumoniae is a notorious human pathogen involved in healthcare-associated infections. The worldwide expansion of infections induced by colistin-resistant and carbapenemase-producing Enterobacterales (CPE) isolates has been increasingly reported. This study aims to analyze the phenotypic and molecular profiles of 10 colistin-resistant (CR) isolates and 2 pairs of colistin-heteroresistant (ChR) (parental and the corresponding resistant mutants) isolates of K. pneumoniae CPE sourced from two hospitals. The phenotypes of strains in the selected collection had been previously characterized. Antimicrobial susceptibility testing was performed using a Vitek 2 Compact system (BioMérieux SA, Marcy l’Etoile, France), the disc diffusion method, and broth microdilution (BMD) for colistin. Whole-genome sequencing (WGS) did not uncover evidence of any mobile colistin resistance (mcr) genes, although the mgrB gene of seven isolates appeared to be disrupted by insertion sequences (ISKpn25 or ISKpn26). Possible deleterious missense mutations were found in phoP (L4F), phoQ (Q426L, L26Q, L224Q, Q317K), pmrB (R256G, P95L, T157P, V352E), and crrB (P151S) genes. The identified isolates belonged to the following clonal lineages: ST101 (n = 6), ST147 (n = 5), ST258 (n = 2), and ST307 (n = 1). All strains harbored IncF plasmids. OXA-48 producers carried IncL and IncR plasmids, while one blaNDM-1 genome was found to harbor IncC plasmids. Ceftazidime–avibactam remains a therapeutic option for KPC-2 and OXA-48 producers. Resistance to meropenem–vaborbactam has emerged in some blakPC-2-carrying isolates. Our study demonstrates that the results of WGS can provide essential evidence for the surveillance of antimicrobial resistance.
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17
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Zelmer AR, Nelson R, Richter K, Atkins GJ. Can intracellular Staphylococcus aureus in osteomyelitis be treated using current antibiotics? A systematic review and narrative synthesis. Bone Res 2022; 10:53. [PMID: 35961964 PMCID: PMC9374758 DOI: 10.1038/s41413-022-00227-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
Approximately 40% of treatments of chronic and recurrent osteomyelitis fail in part due to bacterial persistence. Staphylococcus aureus, the predominant pathogen in human osteomyelitis, is known to persist by phenotypic adaptation as small-colony variants (SCVs) and by formation of intracellular reservoirs, including those in major bone cell types, reducing susceptibility to antibiotics. Intracellular infections with S. aureus are difficult to treat; however, there are no evidence-based clinical guidelines addressing these infections in osteomyelitis. We conducted a systematic review of the literature to determine the demonstrated efficacy of all antibiotics against intracellular S. aureus relevant to osteomyelitis, including protein biosynthesis inhibitors (lincosamides, streptogramins, macrolides, oxazolidines, tetracyclines, fusidic acid, and aminoglycosides), enzyme inhibitors (fluoroquinolones and ansamycines), and cell wall inhibitors (beta-lactam inhibitors, glycopeptides, fosfomycin, and lipopeptides). The PubMed and Embase databases were screened for articles related to intracellular S. aureus infections that compared the effectiveness of multiple antibiotics or a single antibiotic together with another treatment, which resulted in 34 full-text articles fitting the inclusion criteria. The combined findings of these studies were largely inconclusive, most likely due to the plethora of methodologies utilized. Therefore, the reported findings in the context of the models employed and possible solutions for improved understanding are explored here. While rifampicin, oritavancin, linezolid, moxifloxacin and oxacillin were identified as the most effective potential intracellular treatments, the scientific evidence for these is still relatively weak. We advocate for more standardized research on determining the intracellular effectiveness of antibiotics in S. aureus osteomyelitis to improve treatments and patient outcomes.
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Affiliation(s)
- Anja R Zelmer
- Centre for Orthopaedic and Trauma Research, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Renjy Nelson
- Department of Infectious Diseases, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia.,Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Katharina Richter
- Richter Lab, Department of Surgery, Basil Hetzel Institute for Translational Health Research, University of Adelaide, Adelaide, SA, 5011, Australia
| | - Gerald J Atkins
- Centre for Orthopaedic and Trauma Research, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia.
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18
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Fadare FT, Elsheikh EAE, Okoh AI. In Vitro Assessment of the Combination of Antibiotics against Some Integron-Harbouring Enterobacteriaceae from Environmental Sources. Antibiotics (Basel) 2022; 11:antibiotics11081090. [PMID: 36009959 PMCID: PMC9404769 DOI: 10.3390/antibiotics11081090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 01/21/2023] Open
Abstract
One strategy for combating antimicrobial resistance in many infections is to combine antibacterial compounds to create combinations that outperform each molecule alone. In this study, we examine and study the inhibitory effect of combining two drugs belonging to different antibiotic classes to obtain a possible potentiating effect against some Enterobacteriaceae isolates harbouring integrons recovered from rivers and effluents of hospital and wastewater treatment plants in Eastern Cape Province, South Africa. These integrons could easily enable the isolates to acquire genes that confer additional resistance against conventional antibiotics. The minimum inhibitory concentration of the various antibiotics was determined using the broth microdilution, while the checkerboard method was used to determine the fractional inhibitory concentration indices (FICIs). A total of 26.3% (10/38) of the interactions were categorised as synergistic, while 73.7% (28/38) were indifferent. None of the combinations were antagonistic. The time–kill assays revealed all the synergistic interactions as bactericidal. Therefore, the combinations of gentamicin with tetracycline, ciprofloxacin, and ceftazidime against multidrug-resistant (MDR) Klebsiella pneumoniae, tetracycline–ceftazidime combination against MDR Escherichia coli, colistin combinations with ceftazidime and gentamicin, and tetracycline–gentamicin combinations against MDR Citrobacter freundii may be future therapeutic alternatives. Hence, the synergistic combinations reported in this study must be assessed further in vivo before their clinical applications.
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Affiliation(s)
- Folake Temitope Fadare
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
- Correspondence:
| | - Elsiddig A. E. Elsheikh
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Anthony Ifeanyin Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
- Department of Environmental Health Sciences, College of Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
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Turton JF, Pike R, Perry C, Jenkins C, Turton JA, Meunier D, Hopkins KL. Wide distribution of Escherichia coli carrying IncF plasmids containing bla NDM-5 and rmtB resistance genes from hospitalized patients in England. J Med Microbiol 2022; 71. [PMID: 35925786 DOI: 10.1099/jmm.0.001569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. The New Delhi metallo-β-lactamase (NDM) variant NDM-5 was first described in 2011 in an isolate of Escherichia coli. We noted that a high proportion of isolates of E. coli positive for bla NDM carbapenemase genes submitted to the UK Health Security Agency (formerly Public Health England) between 2019 and mid-2021 carried the bla NDM-5 allele, with many co-harbouring rmtB, rendering them highly resistant to aminoglycosides as well as to most β-lactams.Hypothesis/Gap Statement. This observation suggested that a common plasmid may be circulating.Aim. To compare these isolates and describe the plasmids carrying these resistance elements.Methodology. All isolates were sequenced on an Illumina platform, with five also subjected to long-read nanopore sequencing to provide complete assemblies. The locations of bla NDM-5, rmtB and other associated genetic elements were identified. Susceptibility testing to a wide range of antibiotics was carried out on representative isolates.Results. The 34 isolates co-harbouring bla NDM-5 and rmtB were from 14 hospital groups and six different regions across England and consisted of 11 distinct sequence types. All carried IncF plasmids. Assembly of the NDM plasmids in five isolates revealed that they carried rmtB and bla NDM-5 in an IncF conjugative plasmid ranging in size from 85.5 to 161 kb. All carried a highly conserved region, previously described in E. coli plasmid pHC105-NDM, that included bla TEM-1B and rmtB followed by sequence bounded by two IS26 elements containing ΔISAba125, bla NDM-5, ble, trpF and tat followed by ISCR1 and an integron with sul1, aadA2 and dfrA12 cassettes. This arrangement has been described in isolates from other countries and continents, suggesting that such plasmids are widely distributed, at least in E. coli, with similar plasmids also found in Klebsiella pneumoniae. Tested isolates were resistant to most antibiotics except colistin, fosfomycin and tigecycline.Conclusion. These observations suggest that conjugative plasmids carrying a highly conserved resistance gene segment have become widespread in England and elsewhere. This study highlights the value of routine whole-genome sequencing in identifying genetic elements responsible for resistance dissemination.
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Affiliation(s)
- Jane F Turton
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
| | - Rachel Pike
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | - Claire Perry
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | - Claire Jenkins
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | | | - Danièle Meunier
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
| | - Katie L Hopkins
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
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20
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Research Updates of Plasmid-Mediated Aminoglycoside Resistance 16S rRNA Methyltransferase. Antibiotics (Basel) 2022; 11:antibiotics11070906. [PMID: 35884160 PMCID: PMC9311965 DOI: 10.3390/antibiotics11070906] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/27/2023] Open
Abstract
With the wide spread of multidrug-resistant bacteria, a variety of aminoglycosides have been used in clinical practice as one of the effective options for antimicrobial combinations. However, in recent years, the emergence of high-level resistance against pan-aminoglycosides has worsened the status of antimicrobial resistance, so the production of 16S rRNA methyltransferase (16S-RMTase) should not be ignored as one of the most important resistance mechanisms. What is more, on account of transferable plasmids, the horizontal transfer of resistance genes between pathogens becomes easier and more widespread, which brings challenges to the treatment of infectious diseases and infection control of drug-resistant bacteria. In this review, we will make a presentation on the prevalence and genetic environment of 16S-RMTase encoding genes that lead to high-level resistance to aminoglycosides.
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21
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Sacco F, Raponi G, Oliva A, Bibbolino G, Mauro V, Lella FMD, Volpicelli L, Antonelli G, Venditti M, Carattoli A, Arcari G. An outbreak sustained by ST15 Klebsiella pneumoniae carrying 16S rRNA methyltransferases and bla NDM: evaluation of the global dissemination of these resistance determinants. Int J Antimicrob Agents 2022; 60:106615. [PMID: 35691602 DOI: 10.1016/j.ijantimicag.2022.106615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/05/2022]
Abstract
The spread of extremely-drug resistant Klebsiella pneumoniae has become a major health threat worldwide. This is largely mediated by certain lineages, recognized as high-risk clones dispersed in all the world. The analysis of an outbreak of nine ST15, NDM-1 metallo-β-lactamase producing K. pneumoniae was performed. An IncC plasmid carrying the blaNDM-1 gene also carried the rare rmtC gene, encoding for a 16S rRNA methyltransferases (16RMTases), conferring resistance to all aminoglycosides. We studied the global spread of NDM variants and their association with the 16RMTases among K. pneumoniae complete genomes available in GenBank, producing a complete overview of the association of 16RMTases and NDM in K. pneumoniae genomics. NDM is more and more often associated with16RMTases and both are spreading in K. pneumoniae, conferring resistance to every beta-lactam and aminoglycoside. Our analysis suggest that aminoglycosides have limited future as second line treatment against NDM-producing K. pneumoniae.
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Affiliation(s)
- Federica Sacco
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giammarco Raponi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome; Microbiology and Virology Unit, University Hospital Policlinico Umberto I, Rome, Italy
| | - Alessandra Oliva
- Department of Public Health and Infectious Diseases, Sapienza University of Rome
| | - Giulia Bibbolino
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples
| | - Vera Mauro
- Department of Public Health and Infectious Diseases, Sapienza University of Rome
| | | | - Lorenzo Volpicelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Mario Venditti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome
| | | | - Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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22
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Wang S, Wei L, Gao Y, Rong Y, Zha Z, Lv Y, Feng Z. Novel amikacin resistance genes identified from human gut microbiota by functional metagenomics. J Appl Microbiol 2022; 133:898-907. [PMID: 35543338 DOI: 10.1111/jam.15615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
AIMS The aim of this study was to evaluate the diversity and potential for horizontal transfer of amikacin resistance genes from the human gut. METHODS AND RESULTS A library of human fecal microbiota was constructed and subjected to functional screening for amikacin resistance. In total, five amikacin resistance genes that conferred relatively high amikacin resistance, with minimum inhibitory concentrations (MICs) ranging from 64 to >512, were identified from the library, including a novel aminoglycoside acetyltransferase gene and a 16S rRNA methyltransferase (MTase) gene, labeled aac(6')-Iao and rmtI respectively. AAC(6')-Iao showed the highest identity of 48% to AAC(6')-Ian from a clinical isolate Serratia marcescens, whereas RmtI shared the closest amino acid identity of 32% with ArmA from Klebsiella pneumonia. The MICs of these five subclones to six commonly used aminoglycosides were determined. Susceptibility analysis indicated that RmtI was associated with high resistance phenotype to 4,6-disubstituted 2-DOS aminoglycosides, whereas AAC(6')-Iao conferred resistance to amikacin and kanamycin. In addition, kinetic parameters of AAC(6')-Iao were determined, suggesting a strong catalytic effect on amikacin and kanamycin. CONCLUSIONS Antibiotic resistance genes with low identity to known sequences can be uncovered by functional metagenomics. In addition, the diversity and prevalence of amikacin resistance genes merit further investigation in extended habitats, especially the 16S rRNA MTase gene that might have been underestimated in previous cognition. SIGNIFICANCE AND IMPACT OF STUDY Two novel amikacin resistance genes were identified in this study, including a 16S rRNA methyltransferase gene rmtI and an aminoglycoside acetyltransferase gene aac(6')-Iao. This work would contribute to the in-depth study of the diversity and horizontal transfer potential of amikacin resistance genes in the microbiome of the human gut.
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Affiliation(s)
- Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Lin Wei
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuejiao Gao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Rong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhengqi Zha
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yunbin Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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23
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Laughlin ZT, Nandi S, Dey D, Zelinskaya N, Witek MA, Srinivas P, Nguyen HA, Kuiper EG, Comstock LR, Dunham CM, Conn GL. 50S subunit recognition and modification by the Mycobacterium tuberculosis ribosomal RNA methyltransferase TlyA. Proc Natl Acad Sci U S A 2022; 119:e2120352119. [PMID: 35357969 PMCID: PMC9168844 DOI: 10.1073/pnas.2120352119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/22/2022] [Indexed: 11/18/2022] Open
Abstract
Changes in bacterial ribosomal RNA (rRNA) methylation status can alter the activity of diverse groups of ribosome-targeting antibiotics. These modifications are typically incorporated by a single methyltransferase that acts on one nucleotide target and rRNA methylation directly prevents drug binding, thereby conferring drug resistance. Loss of intrinsic methylation can also result in antibiotic resistance. For example, Mycobacterium tuberculosis becomes sensitized to tuberactinomycin antibiotics, such as capreomycin and viomycin, due to the action of the intrinsic methyltransferase TlyA. TlyA is unique among antibiotic resistance-associated methyltransferases as it has dual 16S and 23S rRNA substrate specificity and can incorporate cytidine-2′-O-methylations within two structurally distinct contexts. Here, we report the structure of a mycobacterial 50S subunit-TlyA complex trapped in a postcatalytic state with a S-adenosyl-L-methionine analog using single-particle cryogenic electron microscopy. Together with complementary functional analyses, this structure reveals critical roles in 23S rRNA substrate recognition for conserved residues across an interaction surface that spans both TlyA domains. These interactions position the TlyA active site over the target nucleotide C2144, which is flipped from 23S Helix 69 in a process stabilized by stacking of TlyA residue Phe157 on the adjacent A2143. Base flipping may thus be a common strategy among rRNA methyltransferase enzymes, even in cases where the target site is accessible without such structural reorganization. Finally, functional studies with 30S subunit suggest that the same TlyA interaction surface is employed to recognize this second substrate, but with distinct dependencies on essential conserved residues.
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Affiliation(s)
- Zane T. Laughlin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Suparno Nandi
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Natalia Zelinskaya
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Marta A. Witek
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Pooja Srinivas
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Graduate Program in Molecular and Systems Pharmacology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322
| | - Ha An Nguyen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Department of Chemistry Graduate Program, Emory University, Atlanta, GA 30322
| | - Emily G. Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | | | - Christine M. Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Emory Antibiotic Resistance Center, Emory University, Atlanta, GA 30322
| | - Graeme L. Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
- Emory Antibiotic Resistance Center, Emory University, Atlanta, GA 30322
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24
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Wang N, Luo J, Deng F, Huang Y, Zhou H. Antibiotic Combination Therapy: A Strategy to Overcome Bacterial Resistance to Aminoglycoside Antibiotics. Front Pharmacol 2022; 13:839808. [PMID: 35281905 PMCID: PMC8905495 DOI: 10.3389/fphar.2022.839808] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
After the first aminoglycoside antibiotic streptomycin being applied in clinical practice in the mid-1940s, aminoglycoside antibiotics (AGAs) are widely used to treat clinical bacterial infections and bacterial resistance to AGAs is increasing. The bacterial resistance to AGAs is owed to aminoglycoside modifying enzyme modification, active efflux pump gene overexpression and 16S rRNA ribosomal subunit methylation, leading to modification of AGAs' structures and decreased concentration of drugs within bacteria. As AGAs's side effects and bacterial resistance, the development of AGAs is time-consuming and difficult. Because bacterial resistance may occur in a short time after application in clinical practice, it was found that the antibacterial effect of the combination was not only better than that of AGAs alone but also reduce the dosage of antibiotics, thereby reducing the occurrence of side effects. This article reviews the clinical use of AGAs, the antibacterial mechanisms, the molecular mechanisms of bacterial resistance, and especially focuses a recent development of the combination of AGAs with other drugs to exert a synergistic antibacterial effect to provide a new strategy to overcome bacterial resistance to AGAs.
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Affiliation(s)
- Nuoyan Wang
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Jing Luo
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Fei Deng
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Yasi Huang
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Hong Zhou
- Key Laboratory of Basic Pharmacology, Ministry of Education and Joint Laboratory of International Cooperation, Ministry of Education of Characteristic Ethnic Medicine, School of Pharmacy, Zunyi Medical University, Zunyi, China
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25
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Antimicrobial Treatment Options for Difficult-to-Treat Resistant Gram-Negative Bacteria Causing Cystitis, Pyelonephritis, and Prostatitis: A Narrative Review. Drugs 2022; 82:407-438. [PMID: 35286622 PMCID: PMC9057390 DOI: 10.1007/s40265-022-01676-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 02/06/2023]
Abstract
Urinary tract infections, including cystitis, acute pyelonephritis, and prostatitis, are among the most common diagnoses prompting antibiotic prescribing. The rise in antimicrobial resistance over the past decades has led to the increasing challenge of urinary tract infections because of multidrug-resistant and "difficult-to-treat resistance" among Gram-negative bacteria. Recent advances in pharmacotherapy and medical microbiology are modernizing how these urinary tract infections are treated. Advances in pharmacotherapy have included not only the development and approval of novel antibiotics, such as ceftazidime/avibactam, meropenem/vaborbactam, imipenem/relebactam, ceftolozane/tazobactam, cefiderocol, plazomicin, and glycylcyclines, but also the re-examination of the potential role of legacy antibiotics, including older aminoglycosides and tetracyclines. Recent advances in medical microbiology allow phenotypic and molecular mechanism of resistance testing, and thus antibiotic prescribing can be tailored to the mechanism of resistance in the infecting pathogen. Here, we provide a narrative review on the clinical and pre-clinical studies of drugs that can be used for difficult-to-treat resistant Gram-negative bacteria, with a particular focus on data relevant to the urinary tract. We also offer a pragmatic framework for antibiotic selection when encountering urinary tract infections due to difficult-to-treat resistant Gram-negative bacteria based on the organism and its mechanism of resistance.
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26
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Tevyashova AN, Shapovalova KS. Potential for the Development of a New Generation of Aminoglycoside Antibiotics. Pharm Chem J 2022; 55:860-875. [PMID: 35039693 PMCID: PMC8754558 DOI: 10.1007/s11094-021-02510-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Indexed: 11/29/2022]
Abstract
The present review summarizes recent publications devoted to aminoglycosides that study the main types of resistance to antibiotics of this class and the main directions of chemical modification aimed at overcoming the resistance or changing the spectrum of biological activity. Conjugates of aminoglycosides with various pharmacophores including amino acids, peptides, peptide nucleic acids, nucleic bases, and several other biologically active molecules and modifications resulting in other types of biological activity of this class of antibiotics are described. It is concluded that a promising research direction aimed at increasing the activity of antibiotics against resistant strains is the search for selective inhibitors of aminoglycoside-modifying enzymes. This would allow renewal of the use of antibiotics already meeting widespread resistance and would increase the potential of a new generation of antibiotics.
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Affiliation(s)
- A. N. Tevyashova
- G. F. Gause Institute of New Antibiotics, 11/1 B. Pirogovskaya St, Moscow, 119021 Russia
| | - K. S. Shapovalova
- G. F. Gause Institute of New Antibiotics, 11/1 B. Pirogovskaya St, Moscow, 119021 Russia
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27
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Moser AI, Keller PM, Campos-Madueno EI, Poirel L, Nordmann P, Endimiani A. A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC bla NDM-1- and armA-carrying Plasmid. Pathog Immun 2022; 6:119-134. [PMID: 34988342 PMCID: PMC8714174 DOI: 10.20411/pai.v6i2.482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background. Patients colonized with multiple species of carbapenemase-producing Enterobacterales (CPE) are increasingly observed. This phenomenon can be due to the high local prevalence of these pathogens, the presence of important host risk factors, and the great genetic promiscuity of some carbapenemase genes. Methods. We analyzed 4 CPE (Escherichia coli, Klebsiella pneumoniae, Providencia stuartii, Citrobacter sedlakii), 1 extended-spectrum cephalosporin-resistant K. pneumoniae (ESC-R-Kp), and 1 carbapenemase-producing Acinetobacter baumannii simultaneously isolated from a patient transferred from Macedonia. Susceptibility tests were performed using a microdilution MIC system. The complete genome sequences were obtained by using both short-read and long-read whole-genome sequencing technologies. Results. All CPE presented high-level resistance to all aminoglycosides due to the expression of the armA 16S rRNA methylase. In C. sedlakii and E. coli (ST69), both the carbapenemase blaNDM-1 and armA genes were located on an identical IncC plasmid of type 1a. The K. pneumoniae (ST268) and P. stuartii carried chromosomal blaNDM-1 and blaOXA-48, respectively, while the ESC-R-Kp (ST395) harbored a plasmid-located blaCTX-M-15. In the latter 3 isolates, armA-harboring IncC plasmids similar to plasmids found in C. sedlakii and E. coli were also detected. The A. baumannii strain possessed the blaOXA-40 carbapenemase gene. Conclusions. The characterization of the genetic organization of IncC-type plasmids harbored by 3 different species from the same patient offered insights into the evolution of these broad-host-range plasmids. Moreover, we characterized here the first complete genome sequence of a carbapenemase-producing C. sedlakii strain, providing a reference for future studies on this rarely reported species.
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Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Peter M Keller
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland.,French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland.,National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland.,French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland.,National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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28
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El-Badawy MF, Abou-Elazm FI, Omar MS, El-Naggar ME, Maghrabi IA. The First Saudi Study Investigating the Plasmid-borne Aminoglycoside and Sulfonamide Resistance among Acinetobacter baumannii Clinical Isolates Genotyped by RAPD-PCR: the Declaration of a Novel Allelic Variant Called aac(6')-SL and Three Novel Mutations in the sul1 Gene in the Acinetobacter Plasmid (s). Infect Drug Resist 2021; 14:4739-4756. [PMID: 34795490 PMCID: PMC8594745 DOI: 10.2147/idr.s324707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022] Open
Abstract
Background Acinetobacter baumannii (A. baumannii) is one of the most important nosocomial pathogens responsible for a wide range of infections. Aim This study aimed to investigate the existence of the plasmidic genes encoding for aminoglycoside modifying enzymes (AMEs), 16S rRNA methyltransferases (RMT), and the altered dihydropetroate synthase (DHPS) encoded by the sul1 gene among A. baumannii clinical isolates collected from Taif, Kingdom of Saudi Arabia (KSA). The mutations in aac(6ʹ)-Ib and sul1 genes were also investigated. Methods Forty A. baumannii clinical isolates were investigated for their susceptibility to ten antibiotics. The plasmid DNA was extracted and screened for nine genes encoding for aminoglycoside resistance in addition to the sul1 gene. The clonal relatedness was determined by random amplified polymorphic DNA (RAPD)-PCR. Mutation in aac(6ʹ)-Ib and the sul1 genes were detected by capillary electrophoresis sequencing (CES). Results All isolates were A. baumannii in which 42.5% of them exhibited a high level of aminoglycoside resistance (HLAR). The most prevalent AMEs and RMT encoding genes were aph(3ʹ)-VI, the two aac(6ʹ) gene variants [aac(6ʹ)-Ib and aac(6ʹ)-SL], ant(3ʹʹ)-I, and armA in which 90%, 87.5%, 85%, and 45% of isolates tested positive, respectively. The other investigated aminoglycoside resistant encoding genes, namely aac(3)-II, aac(6ʹ)-II, and rmtB, were not detected. Only 15% of isolates harbored the sul1 gene. RAPD-PCR classified the 40 isolates into three clusters in which cluster II was the main cluster. DNA sequencing revealed that 34.29% (12/35) of isolates tested positive for aac(6ʹ)-Ib were found to harbor a common missense mutation in position 102 indicating a novel allelic variant named aac(6ʹ)-SL. Also, DNA sequencing revealed three missense mutations in the sul1 gene. Conclusion This is the first Saudi study to investigate the plasmid borne aminoglycoside and sulfonamide resistance genes among A. baumannii clinical isolates. A novel allelic variant for aac(6ʹ)-Ib was detected in addition to novel mutations in the sul1 gene.
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Affiliation(s)
- Mohamed F El-Badawy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Menoufia, 32897, Egypt
| | - Fatma I Abou-Elazm
- Department of Microbiology and Immunology, Faculty of Pharmacy, Misr University for Science and Technology, 6th of October City, Egypt
| | - Mohamed S Omar
- Department of Chemistry, Faculty of Science, Benha University, Benha, 13508, Egypt
| | - Mostafa E El-Naggar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Sadat City, Sadat City, Menoufia, 32897, Egypt
| | - Ibrahim A Maghrabi
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, Taif, 21974, Saudi Arabia
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29
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Uechi K, Tohya M, Tada T, Tome T, Takahashi A, Kinjo T, Maeda S, Kirikae T, Fujita J. Emergence of a multidrug-resistant plasmid encoding bla NDM-1, bla OXA-420 and armA in a clinical isolate of Acinetobacter variabilis in Japan. J Med Microbiol 2021; 70. [PMID: 34431761 DOI: 10.1099/jmm.0.001395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter variabilis (formerly genospecies 15 sensu Tjernberg and Ursing) has been isolated from humans and animals and was proposed to be a novel species in 2015. A multidrug-resistant A. variabilis isolate, RYU24, was obtained in 2012 from an inpatient in Okinawa, Japan, with no record of overseas travel. The isolate was resistant to carbapenems, aminoglycosides and ciprofloxacin, with minimum inhibitory concentrations (MICs) of 32 µg ml-1 for imipenem and meropenem; > 1024 µg ml-1 for amikacin, arbekacin, gentamicin and tobramycin; and 8 µg ml-1 for ciprofloxacin. The isolate was found to harbour a 68-kbp plasmid carrying bla NDM-1, which encodes New Delhi metallo-β-lactamase-1 (NDM-1); bla OXA-420, which encodes an OXA-58-like carbapenemase and; armA, which encodes ArmA 16S rRNA methylase conferring pan-aminoglycoside resistance. To our knowledge, this is the first report of a plasmid harbouring the three major drug-resistance genes, bla NDM-1, bla OXA-420 and armA.
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Affiliation(s)
- Kohei Uechi
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan.,Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Mari Tohya
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Takaaki Tome
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Ami Takahashi
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Takeshi Kinjo
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Shiro Maeda
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Okinawa, Japan
| | - Teruo Kirikae
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Jiro Fujita
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
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30
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Chen HL, Jiang Y, Li MM, Sun Y, Cao JM, Zhou C, Zhang XX, Qu Y, Zhou TL. Acquisition of Tigecycline Resistance by Carbapenem-Resistant Klebsiella pneumoniae Confers Collateral Hypersensitivity to Aminoglycosides. Front Microbiol 2021; 12:674502. [PMID: 34276606 PMCID: PMC8284424 DOI: 10.3389/fmicb.2021.674502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022] Open
Abstract
Tigecycline is a last-resort antibiotic for infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP). This study aimed to broaden our understanding of the acquisition of collateral hypersensitivity by CRKP, as an evolutionary trade-off of developing resistance to tigecycline. Experimental induction of tigecycline resistance was conducted with tigecycline-sensitive CRKP clinical isolates. Antimicrobial susceptibility testing, microbial fitness assessment, genotypic analysis and full-genome sequencing were carried out for these clinical isolates and their resistance-induced descendants. We found that tigecycline resistance was successfully induced after exposing CRKP clinical isolates to tigecycline at gradually increased concentrations, at a minor fitness cost of bacterial cells. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) found higher expression of the efflux pump gene acrB (5.3–64.5-fold) and its regulatory gene ramA (7.4–65.8-fold) in resistance-induced strains compared to that in the tigecycline-sensitive clinical isolates. Stable hypersensitivities to aminoglycosides and other antibiotics were noticed in resistance-induced strains, showing significantly lowered MICs (X 4 – >500 times). Full genome sequencing and plasmid analysis suggested the induced collateral hypersensitivity might be multifaceted, with the loss of an antimicrobial resistance (AMR) plasmid being a possible major player. This study rationalized the sequential combination of tigecycline with aminoglycosides for the treatment of CRKP infections.
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Affiliation(s)
- Hua-le Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Laboratory Medicine, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mei-Mei Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yao Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jian-Ming Cao
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Cui Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao-Xiao Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yue Qu
- Biomedicine Discovery Institute, Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Tie-Li Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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31
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Moser AI, Viaggi V, Mauri C, Carattoli A, Luzzaro F, Endimiani A. An XDR Proteus vulgaris isolate hosting a novel blaNDM-1- and armA-carrying plasmid. J Antimicrob Chemother 2021; 76:1938-1941. [PMID: 33891008 DOI: 10.1093/jac/dkab111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Valentina Viaggi
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Carola Mauri
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | | | - Francesco Luzzaro
- Clinical Microbiology and Virology Unit, A. Manzoni Hospital, Lecco, Italy
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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