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Elrashedy A, Nayel M, Salama A, Zaghawa A, Abdelsalam NR, Hasan ME. Phylogenetic Analysis and Comparative Genomics of Brucella abortus and Brucella melitensis Strains in Egypt. J Mol Evol 2024; 92:338-357. [PMID: 38809331 PMCID: PMC11169049 DOI: 10.1007/s00239-024-10173-0] [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: 01/18/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Brucellosis is a notifiable disease induced by a facultative intracellular Brucella pathogen. In this study, eight Brucella abortus and eighteen Brucella melitensis strains from Egypt were annotated and compared with RB51 and REV1 vaccines respectively. RAST toolkit in the BV-BRC server was used for annotation, revealing genome length of 3,250,377 bp and 3,285,803 bp, 3289 and 3323 CDS, 48 and 49 tRNA genes, the same number of rRNA (3) genes, 583 and 586 hypothetical proteins, 2697 and 2726 functional proteins for B. abortus and B. melitensis respectively. B. abortus strains exhibit a similar number of candidate genes, while B. melitensis strains showed some differences, especially in the SRR19520422 Faiyum strain. Also, B. melitensis clarified differences in antimicrobial resistance genes (KatG, FabL, MtrA, MtrB, OxyR, and VanO-type) in SRR19520319 Faiyum and (Erm C and Tet K) in SRR19520422 Faiyum strain. Additionally, the whole genome phylogeny analysis proved that all B. abortus strains were related to vaccinated animals and all B. melitensis strains of Menoufia clustered together and closely related to Gharbia, Dameitta, and Kafr Elshiek. The Bowtie2 tool identified 338 (eight B. abortus) and 4271 (eighteen B. melitensis) single nucleotide polymorphisms (SNPs) along the genomes. These variants had been annotated according to type and impact. Moreover, thirty candidate genes were predicted and submitted at GenBank (24 in B. abortus) and (6 in B. melitensis). This study contributes significant insights into genetic variation, virulence factors, and vaccine-related associations of Brucella pathogens, enhancing our knowledge of brucellosis epidemiology and evolution in Egypt.
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Affiliation(s)
- Alyaa Elrashedy
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt.
| | - Mohamed Nayel
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Akram Salama
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Ahmed Zaghawa
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
| | - Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
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Maurin M, Pondérand L, Hennebique A, Pelloux I, Boisset S, Caspar Y. Tularemia treatment: experimental and clinical data. Front Microbiol 2024; 14:1348323. [PMID: 38298538 PMCID: PMC10827922 DOI: 10.3389/fmicb.2023.1348323] [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: 12/02/2023] [Accepted: 12/31/2023] [Indexed: 02/02/2024] Open
Abstract
Tularemia is a zoonosis caused by the Gram negative, facultative intracellular bacterium Francisella tularensis. This disease has multiple clinical presentations according to the route of infection, the virulence of the infecting bacterial strain, and the underlying medical condition of infected persons. Systemic infections (e.g., pneumonic and typhoidal form) and complications are rare but may be life threatening. Most people suffer from local infection (e.g., skin ulcer, conjunctivitis, or pharyngitis) with regional lymphadenopathy, which evolve to suppuration in about 30% of patients and a chronic course of infection. Current treatment recommendations have been established to manage acute infections in the context of a biological threat and do not consider the great variability of clinical situations. This review summarizes literature data on antibiotic efficacy against F. tularensis in vitro, in animal models, and in humans. Empirical treatment with beta-lactams, most macrolides, or anti-tuberculosis agents is usually ineffective. The aminoglycosides gentamicin and streptomycin remain the gold standard for severe infections, and the fluoroquinolones and doxycycline for infections of mild severity, although current data indicate the former are usually more effective. However, the antibiotic treatments reported in the literature are highly variable in their composition and duration depending on the clinical manifestations, the age and health status of the patient, the presence of complications, and the evolution of the disease. Many patients received several antibiotics in combination or successively. Whatever the antibiotic treatment administered, variable but high rates of treatment failures and relapses are still observed, especially in patients treated more then 2-3 weeks after disease onset. In these patients, surgical treatment is often necessary for cure, including drainage or removal of suppurative lymph nodes or other infectious foci. It is currently difficult to establish therapeutic recommendations, particularly due to lack of comparative randomized studies. However, we have attempted to summarize current knowledge through proposals for improving tularemia treatment which will have to be discussed by a group of experts. A major factor in improving the prognosis of patients with tularemia is the early administration of appropriate treatment, which requires better medical knowledge and diagnostic strategy of this disease.
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Affiliation(s)
- Max Maurin
- Centre National de Référence Francisella tularensis, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Translational Innovation in Medicine and Complexity (TIMC), Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Léa Pondérand
- Centre National de Référence Francisella tularensis, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Commissariat à l’énergie atomique (CEA), CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Aurélie Hennebique
- Centre National de Référence Francisella tularensis, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Translational Innovation in Medicine and Complexity (TIMC), Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Isabelle Pelloux
- Centre National de Référence Francisella tularensis, CHU Grenoble Alpes, Grenoble, France
| | - Sandrine Boisset
- Centre National de Référence Francisella tularensis, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Commissariat à l’énergie atomique (CEA), CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Yvan Caspar
- Centre National de Référence Francisella tularensis, CHU Grenoble Alpes, Grenoble, France
- Université Grenoble Alpes, Commissariat à l’énergie atomique (CEA), CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
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Chavarría-Bencomo IV, Nevárez-Moorillón GV, Espino-Solís GP, Adame-Gallegos JR. Antibiotic resistance in tick-borne bacteria: A One Health approach perspective. J Infect Public Health 2023; 16 Suppl 1:153-162. [PMID: 37945496 DOI: 10.1016/j.jiph.2023.10.027] [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: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
The emergence and re-emergence of tick-borne bacteria (TBB) as a public health problem raises the uncertainty of antibiotic resistance in these pathogens, which could be dispersed to other pathogens. The impact of global warming has led to the emergence of pathogenic TBB in areas where they were not previously present and is another risk that must be taken into account under the One Health guides. This review aimed to analyze the existing information regarding antibiotic-resistant TBB and antibiotic-resistance genes (ARG) present in the tick microbiome, considering the potential to be transmitted to pathogenic microorganisms. Several Ehrlichia species have been reported to exhibit natural resistance to fluoroquinolones and typhus group Rickettsiae are naturally susceptible to erythromycin. TBB have a lower risk of acquiring ARG due to their natural habitat, but there is still a probability of acquiring them; furthermore, studies of these pathogens are limited. Pathogenic and commensal bacteria coexist within the tick microbiome along with ARGs for antibiotic deactivation, cellular protection, and efflux pumps; these ARGs confer resistance to antibiotics such as aminoglycosides, beta-lactamase, diaminopyrimidines, fluoroquinolones, glycopeptides, sulfonamides, and tetracyclines. Although with low probability, TBB can be a reservoir of ARGs.
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Affiliation(s)
- Inés Valeria Chavarría-Bencomo
- Facultad de Ciencias Químicas. Universidad Autónoma de Chihuahua, Circuito Universitario s/n. Campus Universitario II., 31125 Chihuahua, Mexico
| | - Guadalupe Virginia Nevárez-Moorillón
- Facultad de Ciencias Químicas. Universidad Autónoma de Chihuahua, Circuito Universitario s/n. Campus Universitario II., 31125 Chihuahua, Mexico.
| | - Gerardo Pavel Espino-Solís
- Laboratorio Nacional de Citometría de Flujo. Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n. Campus Universitario II., 31125 Chihuahua, Mexico
| | - Jaime Raúl Adame-Gallegos
- Facultad de Ciencias Químicas. Universidad Autónoma de Chihuahua, Circuito Universitario s/n. Campus Universitario II., 31125 Chihuahua, Mexico
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You C, Liao M, Wang M, Zhao L, Li L, Ye X, Yang T. The Effect of Amoxicillin Pre-Exposure on Treatment Outcomes and Antimicrobial Susceptibility in Patients with Urogenital Chlamydia trachomatis Infection. Infect Drug Resist 2023; 16:3575-3587. [PMID: 37305735 PMCID: PMC10257477 DOI: 10.2147/idr.s410410] [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: 02/28/2023] [Accepted: 05/25/2023] [Indexed: 06/13/2023] Open
Abstract
Purpose We investigated the influence of amoxicillin pre-exposure on treatment outcomes, Chlamydia trachomatis (CT) culture, the presence of drug-resistant genes, minimum inhibitory concentrations (MICs), and fractional inhibitory concentrations (FICs) in CT clinical strains. Additionally, we explored the effect of different antimicrobial combinations on CT. Patients and Methods Clinical data of 62 patients with CT infection were recorded. Of these, 33 had pre-exposure to amoxicillin and 29 did not. Among patients with pre-exposure, 17 received azithromycin and 16 received minocycline. Among the patients without pre-exposure, 15 received azithromycin and 14 received minocycline. All patients underwent microbiological cure follow-ups one month after completing the treatment. 23S rRNA gene mutations, acquisition of tet(M) and tet(C) were detected using reverse transcription PCR (RT-PCR) and PCR, respectively. The MICs and FICs of azithromycin, minocycline, and moxifloxacin, alone or in combination, were determined using the microdilution and checkerboard methods, respectively. Results More cases of treatment failure occurred in pre-exposed patients, in both treatment groups (P <0.05). No 23S rRNA gene mutations or tet(M) and tet(C) acquisitions were found. More inclusion bodies were cultured from patients without amoxicillin pre-exposure than from those with pre-exposure (P <0.0001). The MICs of all antibiotics were higher in pre-exposed patients than in those without pre-exposure (P <0.01). The FICs of azithromycin plus moxifloxacin were lower than those of the other antibiotic combinations (P <0.0001). The synergy rate of azithromycin plus moxifloxacin was significantly higher than those of azithromycin plus minocycline and minocycline plus moxifloxacin (P <0.001). The FICs of all antibiotic combinations were comparable between isolates from the two patient groups (all P >0.05). Conclusion Pre-exposure to amoxicillin in CT patients may inhibit CT growth and decrease sensitivity of CT strains to antibiotics. Azithromycin plus moxifloxacin may be a promising treatment regimen for genital CT infections with treatment failure.
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Affiliation(s)
- Cong You
- Department of Dermatology and Venereology; Candidate Branch of National Clinical Research Centre for Skin and Immune Diseases, the First Affiliated Hospital of Gannan Medical University, Ganzhou, People’s Republic of China
| | - Mingyi Liao
- Department of Dermatology and Venereology; Candidate Branch of National Clinical Research Centre for Skin and Immune Diseases, the First Affiliated Hospital of Gannan Medical University, Ganzhou, People’s Republic of China
| | - Mei Wang
- Department of Dermatology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Leran Zhao
- Department of Dermatology and Venereology, the General Hospital of Tianjin Medical University, Tianjin, People’s Republic of China
| | - Longnian Li
- Department of Dermatology and Venereology; Candidate Branch of National Clinical Research Centre for Skin and Immune Diseases, the First Affiliated Hospital of Gannan Medical University, Ganzhou, People’s Republic of China
| | - Xiaoying Ye
- Department of Dermatology and Venereology; Candidate Branch of National Clinical Research Centre for Skin and Immune Diseases, the First Affiliated Hospital of Gannan Medical University, Ganzhou, People’s Republic of China
| | - Tao Yang
- Department of Dermatology and Venereology; Candidate Branch of National Clinical Research Centre for Skin and Immune Diseases, the First Affiliated Hospital of Gannan Medical University, Ganzhou, People’s Republic of China
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Determination of Virulence-Associated Genes and Antimicrobial Resistance Profiles in Brucella Isolates Recovered from Humans and Animals in Iran Using NGS Technology. Pathogens 2023; 12:pathogens12010082. [PMID: 36678430 PMCID: PMC9865427 DOI: 10.3390/pathogens12010082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/25/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Brucellosis is a common zoonotic disease in Iran. Antimicrobial-resistant (AMR) Brucella isolates have been reported from different developing countries, posing an imminent health hazard. The objective of this study was to evaluate AMR and virulence-associated factors in Brucella isolates recovered from humans and animals in different regions of Iran using classical phenotyping and next generation sequencing (NGS) technology. Our findings revealed that B. melitensis is the most common species in bovines, small ruminants and camels. B. abortus was isolated only from one human case. Probable intermediate or resistant phenotype patterns for rifampicin, trimethoprim-sulfamethoxazole, ampicillin-sulbactam and colistin were found. Whole genome sequencing (WGS) identified mprF, bepG, bepF, bepC, bepE, and bepD in all isolates but failed to determine other classical AMR genes. Forty-three genes associated with five virulence factors were identified in the genomes of all Brucella isolates, and no difference in the distribution of virulence-associated genes was found. Of them, 27 genes were associated with lipopolysaccharide (LPS), 12 genes were related to a type IV secretion system (virB1-B12), two were associated with the toll-interleukin-1 receptor (TIR) domain-containing proteins (btpA, btpB), one gene encoded the Rab2 interacting conserved protein A (ricA) and one was associated with the production of cyclic β-1,2 glucans (cgs). This is the first investigation reporting the molecular-based AMR and virulence factors in brucellae isolated from different animal hosts and humans in Iran. Iranian B. abortus and B. melitensis isolates are still in vitro susceptible to the majority of antibiotics used for the treatment of human brucellosis. WGS failed to determine classical AMR genes and no difference was found in the distribution of virulence-associated genes in all isolates. Still, the absence of classical AMR genes in genomes of resistant strains is puzzling, and investigation of phenotypic resistance mechanisms at the proteomic and transcriptomic levels is needed.
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Wu Z, Wu Y, Gao H, He X, Yao Q, Yang Z, Zhou J, Ji L, Gao J, Jia X, Dou Y, Wang X, Shao P. Identification and whole-genome sequencing analysis of Vibrio vulnificus strains causing pearl gentian grouper disease in China. BMC Microbiol 2022; 22:200. [PMID: 35974308 PMCID: PMC9380395 DOI: 10.1186/s12866-022-02610-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/28/2022] Open
Abstract
Vibrio vulnificus is a pathogenic bacterium that causes disease in marine fish, affecting fish farming and human health worldwide. In May 2021, in the Bohai Bay region, a disease broke out in commercially farmed pearl gentian grouper (♀Epinephelus fuscoguttatus × ♂Epinephelus lanceolatus), causing huge economic losses. The diseased fish had skin lesions, water accumulation in their abdomens, and showed tissue and organ damage. V. vulnificus biotype 2 has been reported in eels and other marine fish, but it is less reported in pearl gentian grouper. In this study, the pathogenic strain isolated from diseased fish was identified as V. vulnificus EPL 0201 biotype 2 on the basis of physiological and biochemical characteristics and the results of 16S rRNA gene and gyrB sequencing, virulence gene detection, and recursive infection experiments. To gain a comprehensive understanding of the pathogenicity and drug resistance of this strain, whole-genome sequencing was performed. Whole-genome analysis showed that the gene map of this strain was complete. The Virulence Factor Database annotation results showed that this strain had the key virulence factor genes vvhA and rtxA, which cause host disease. In addition, this strain had genes conferring resistance against cephalosporins, aminoglycosides, tetracyclines, and sulfonamides. Antimicrobial susceptibility testing confirmed the presence of these resistance genes identified in the genome. The results of this study show that V. vulnificus EPL 0201 biotype 2 is a multi-drug resistant strain with high pathogenicity.
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Affiliation(s)
- Zun Wu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Yating Wu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Haofeng Gao
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Xuexin He
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Qiang Yao
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Zhanglei Yang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Jinyi Zhou
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Linting Ji
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Jinwei Gao
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Xuying Jia
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Yong Dou
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China
| | - Xiaoyu Wang
- Tianjin Fisheries Research Institute, 422 Jiefang Nan Road, He Xi District, Tianjin, 300221, People's Republic of China.
| | - Peng Shao
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, 300384, People's Republic of China.
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Chigwada AD, Mapholi NO, Ogola HJO, Mbizeni S, Masebe TM. Pathogenic and Endosymbiotic Bacteria and Their Associated Antibiotic Resistance Biomarkers in Amblyomma and Hyalomma Ticks Infesting Nguni Cattle (Bos spp.). Pathogens 2022; 11:pathogens11040432. [PMID: 35456107 PMCID: PMC9028808 DOI: 10.3390/pathogens11040432] [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: 03/01/2022] [Revised: 03/27/2022] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
Deciphering the interactions between ticks and their microbiome is key to revealing new insights on tick biology and pathogen transmission. However, knowledge on tick-borne microbiome diversity and their contribution to drug resistance is scarce in sub–Saharan Africa (SSA), despite endemism of ticks. In this study, high-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used to characterize the bacterial community structure and associated antibiotic resistance markers in Amblyomma variegatum, A. hebraeum, and Hyalomma truncatum ticks infesting Nguni cattle (Bos spp.). Twenty-one (seven families and fourteen genera) potentially pathogenic and endosymbiotic bacterial taxa were differentially enriched in two tick genera. In H. truncatum ticks, a higher abundance of Corynebacterium (35.6%), Porphyromonas (14.4%), Anaerococcus (11.1%), Trueperella (3.7%), and Helcococcus (4.7%) was detected. However, Rickettsia (38.6%), Escherichia (7%), and Coxiellaceae (2%) were the major differentially abundant taxa in A. variegatum and A. hebraeum. Further, an abundance of 50 distinct antibiotic resistance biomarkers relating to multidrug resistance (MDR) efflux pumps, drug detoxification enzymes, ribosomal protection proteins, and secretion systems, were inferred in the microbiome. This study provides theoretical insights on the microbiome and associated antibiotic resistance markers, important for the design of effective therapeutic and control decisions for tick-borne diseases in the SSA region.
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Affiliation(s)
- Aubrey Dickson Chigwada
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa (UNISA), Florida Campus, Roodepoort 1709, South Africa; (A.D.C.); (N.O.M.); (H.J.O.O.); (S.M.)
| | - Ntanganedzeni Olivia Mapholi
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa (UNISA), Florida Campus, Roodepoort 1709, South Africa; (A.D.C.); (N.O.M.); (H.J.O.O.); (S.M.)
| | - Henry Joseph Oduor Ogola
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa (UNISA), Florida Campus, Roodepoort 1709, South Africa; (A.D.C.); (N.O.M.); (H.J.O.O.); (S.M.)
- School of Agricultural and Food Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo P.O. Box 210-40601, Kenya
| | - Sikhumbuzo Mbizeni
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa (UNISA), Florida Campus, Roodepoort 1709, South Africa; (A.D.C.); (N.O.M.); (H.J.O.O.); (S.M.)
| | - Tracy Madimabi Masebe
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa (UNISA), Florida Campus, Roodepoort 1709, South Africa; (A.D.C.); (N.O.M.); (H.J.O.O.); (S.M.)
- Correspondence: ; Tel.: +27-11-471-2268
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Yang X, Wang Y, Li J, Chen J, Liu J, Tian G, Zhao H, Piao D, Fan Y, Jiang H. Genetic characteristics of an amikacin-resistant Brucella abortus strain first isolated from Marmota himalayana. Microb Pathog 2022; 164:105402. [PMID: 35038548 DOI: 10.1016/j.micpath.2022.105402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022]
Abstract
Brucella spp. are facultative intracellular pathogens that can persistently colonize animal host cells and cause zoonotic brucellosis. Brucellosis affects public health and safety and even affects economic development. Our lab found that a Brucella strain isolated from Marmota himalayana exhibited amikacin resistance. To annotate and analyze the potential resistance genes in this strain, we utilized sequencing platforms in this study and cloned potential resistance genes. The findings showed that the isolated strain belonged to B. abortus biovar 1 and was similar to B. abortus 2308. The isolate had amikacin resistance genes encoding aminoglycoside 3'-phosphotransferase. Based on the results of genome analysis, the isolated strain may have obtained amikacin resistance genes from Salmonella spp. through Tn3 family transposons. Notably, this study establishes a foundation for further research on the resistance mechanism of Brucella spp. and provides data that may be useful for the prevention and control of drug-resistant Brucella strains.
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Affiliation(s)
- Xiaowen Yang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuanzhi Wang
- School of Medicine, Shihezi University, Shihezi, Xinjiang Uygur Autonomous Region, China
| | - Jiquan Li
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Junjie Chen
- Tongliao Institute of Mongolian Medicine, Tongliao, Inner Mongolia, China
| | - Jiayin Liu
- School of Public Health, Baotou Medical College, Baotou, Inner Mongolia, China
| | - Guozhong Tian
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongyan Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongri Piao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Fan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hai Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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Uddin TM, Chakraborty AJ, Khusro A, Zidan BRM, Mitra S, Emran TB, Dhama K, Ripon MKH, Gajdács M, Sahibzada MUK, Hossain MJ, Koirala N. Antibiotic resistance in microbes: History, mechanisms, therapeutic strategies and future prospects. J Infect Public Health 2021; 14:1750-1766. [PMID: 34756812 DOI: 10.1016/j.jiph.2021.10.020] [Citation(s) in RCA: 276] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/04/2021] [Accepted: 10/14/2021] [Indexed: 12/22/2022] Open
Abstract
Antibiotics have been used to cure bacterial infections for more than 70 years, and these low-molecular-weight bioactive agents have also been used for a variety of other medicinal applications. In the battle against microbes, antibiotics have certainly been a blessing to human civilization by saving millions of lives. Globally, infections caused by multidrug-resistant (MDR) bacteria are on the rise. Antibiotics are being used to combat diversified bacterial infections. Synthetic biology techniques, in combination with molecular, functional genomic, and metagenomic studies of bacteria, plants, and even marine invertebrates are aimed at unlocking the world's natural products faster than previous methods of antibiotic discovery. There are currently only few viable remedies, potential preventive techniques, and a limited number of antibiotics, thereby necessitating the discovery of innovative medicinal approaches and antimicrobial therapies. MDR is also facilitated by biofilms, which makes infection control more complex. In this review, we have spotlighted comprehensively various aspects of antibiotics viz. overview of antibiotics era, mode of actions of antibiotics, development and mechanisms of antibiotic resistance in bacteria, and future strategies to fight the emerging antimicrobial resistant threat.
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Affiliation(s)
- Tanvir Mahtab Uddin
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh.
| | - Arka Jyoti Chakraborty
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh.
| | - Ameer Khusro
- Research Department of Plant Biology and Biotechnology, Loyola College, Nungambakkam, Chennai, Tamil Nadu, India.
| | - Bm Redwan Matin Zidan
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh.
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh.
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh.
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India.
| | - Md Kamal Hossain Ripon
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh.
| | - Márió Gajdács
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, 6720 Szeged, Hungary.
| | | | - Md Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, 77 Satmasjid Road, Dhanmondi, Dhaka 1205, Bangladesh.
| | - Niranjan Koirala
- Department of Natural Products Research, Dr. Koirala Research Institute for Biotechnology and Biodiversity, Kathmandu 44600, Nepal.
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10
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Mala L, Lalouckova K, Skrivanova E. Bacterial Skin Infections in Livestock and Plant-Based Alternatives to Their Antibiotic Treatment. Animals (Basel) 2021; 11:2473. [PMID: 34438930 PMCID: PMC8388705 DOI: 10.3390/ani11082473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 12/16/2022] Open
Abstract
Due to its large surface area, the skin is susceptible to various injuries, possibly accompanied by the entrance of infective agents into the body. Commensal organisms that constitute the skin microbiota play important roles in the orchestration of cutaneous homeostasis and immune competence. The opportunistic pathogen Staphylococcus aureus is present as part of the normal biota of the skin and mucous membranes in both humans and animals, but can cause disease when it invades the body either due to trauma or because of the impaired immune response of the host. Colonization of livestock skin by S. aureus is a precursor for majority of bacterial skin infections, which range from boils to sepsis, with the best-characterized being bovine mastitis. Antibiotic treatment of these infections can contribute to the promotion of resistant bacterial strains and even to multidrug resistance. The development of antibiotic resistance to currently available antibiotics is a worldwide problem. Considering the increasing ability of bacteria to effectively resist antibacterial agents, it is important to reduce the livestock consumption of antibiotics to preserve antibiotic effectiveness in the future. Plants are recognized as sources of various bioactive substances, including antibacterial activity towards clinically important microorganisms. This review provides an overview of the current knowledge on the major groups of phytochemicals with antibacterial activity and their modes of action. It also provides a list of currently known and used plant species aimed at treating or preventing bacterial skin infections in livestock.
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Affiliation(s)
- Lucie Mala
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (L.M.); (K.L.)
- Department of Nutritional Physiology and Animal Product Quality, Institute of Animal Science, Pratelstvi 815, 104 00 Prague, Czech Republic
| | - Klara Lalouckova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (L.M.); (K.L.)
- Department of Nutritional Physiology and Animal Product Quality, Institute of Animal Science, Pratelstvi 815, 104 00 Prague, Czech Republic
| | - Eva Skrivanova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (L.M.); (K.L.)
- Department of Nutritional Physiology and Animal Product Quality, Institute of Animal Science, Pratelstvi 815, 104 00 Prague, Czech Republic
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11
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Whole-Genome Sequencing for Tracing the Genetic Diversity of Brucella abortus and Brucella melitensis Isolated from Livestock in Egypt. Pathogens 2021; 10:pathogens10060759. [PMID: 34208761 PMCID: PMC8235727 DOI: 10.3390/pathogens10060759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 02/03/2023] Open
Abstract
Brucellosis is a highly contagious zoonosis that occurs worldwide. Whole-genome sequencing (WGS) has become a widely accepted molecular typing method for outbreak tracing and genomic epidemiology of brucellosis. Twenty-nine Brucella spp. (eight B. abortus biovar 1 and 21 B. melitensis biovar 3) were isolated from lymph nodes, milk, and fetal abomasal contents of infected cattle, buffaloes, sheep, and goats originating from nine districts in Egypt. The isolates were identified by microbiological methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Differentiation and genotyping were confirmed using multiplex PCR. Illumina MiSeq® was used to sequence the 29 Brucella isolates. Using MLST typing, ST11 and ST1 were identified among B. melitensis and B. abortus, respectively. Brucella abortus and B. melitensis isolates were divided into two main clusters (clusters 1 and 2) containing two and nine distinct genotypes by core-genome SNP analysis, respectively. The genotypes were irregularly distributed over time and space in the study area. Both Egyptian B. abortus and B. melitensis isolates proved to be genomically unique upon comparison with publicly available sequencing from strains of neighboring Mediterranean, African, and Asian countries. The antimicrobial resistance mechanism caused by mutations in rpoB, gyrA, and gyrB genes associated with rifampicin and ciprofloxacin resistance were identified. To the best of our knowledge, this is the first study investigating the epidemiology of Brucella isolates from livestock belonging to different localities in Egypt based on whole genome analysis.
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12
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Kassinger SJ, van Hoek ML. Genetic Determinants of Antibiotic Resistance in Francisella. Front Microbiol 2021; 12:644855. [PMID: 34054749 PMCID: PMC8149597 DOI: 10.3389/fmicb.2021.644855] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/25/2021] [Indexed: 12/21/2022] Open
Abstract
Tularemia, caused by Francisella tularensis, is endemic to the northern hemisphere. This zoonotic organism has historically been developed into a biological weapon. For this Tier 1, Category A select agent, it is important to expand our understanding of its mechanisms of antibiotic resistance (AMR). Francisella is unlike many Gram-negative organisms in that it does not have significant plasmid mobility, and does not express AMR mechanisms on plasmids; thus plasmid-mediated resistance does not occur naturally. It is possible to artificially introduce plasmids with AMR markers for cloning and gene expression purposes. In this review, we survey both the experimental research on AMR in Francisella and bioinformatic databases which contain genomic and proteomic data. We explore both the genetic determinants of intrinsic AMR and naturally acquired or engineered antimicrobial resistance as well as phenotypic resistance in Francisella. Herein we survey resistance to beta-lactams, monobactams, carbapenems, aminoglycosides, tetracycline, polymyxins, macrolides, rifampin, fosmidomycin, and fluoroquinolones. We also highlight research about the phenotypic AMR difference between planktonic and biofilm Francisella. We discuss newly developed methods of testing antibiotics against Francisella which involve the intracellular nature of Francisella infection and may better reflect the eventual clinical outcomes for new antibiotic compounds. Understanding the genetically encoded determinants of AMR in Francisella is key to optimizing the treatment of patients and potentially developing new antimicrobials for this dangerous intracellular pathogen.
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Affiliation(s)
| | - Monique L. van Hoek
- School of Systems Biology, George Mason University, Manassas, VA, United States
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13
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Lee MM, Yan D, Chau JH, Park H, Ma CC, Kwok RT, Lam JW, Wang D, Tang BZ. Highly efficient phototheranostics of macrophage-engulfed Gram-positive bacteria using a NIR luminogen with aggregation-induced emission characteristics. Biomaterials 2020; 261:120340. [DOI: 10.1016/j.biomaterials.2020.120340] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/30/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022]
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14
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Baquero F, F Lanza V, Duval M, Coque TM. Ecogenetics of antibiotic resistance in Listeria monocytogenes. Mol Microbiol 2020; 113:570-579. [PMID: 32185838 DOI: 10.1111/mmi.14454] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/25/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022]
Abstract
The acquisition process of antibiotic resistance in an otherwise susceptible organism is shaped by the ecology of the species. Unlike other relevant human pathogens, Listeria monocytogenes has maintained a high rate of susceptibility to the antibiotics used for decades to treat human and animal infections. However, L. monocytogenes can acquire antibiotic resistance genes from other organisms' plasmids and conjugative transposons. Ecological factors could account for its susceptibility. L. monocytogenes is ubiquitous in nature, most frequently including reservoirs unexposed to antibiotics, including intracellular sanctuaries. L. monocytogenes has a remarkably closed genome, reflecting limited community interactions, small population sizes and high niche specialization. The L. monocytogenes species is divided into variants that are specialized in small specific niches, which reduces the possibility of coexistence with potential donors of antibiotic resistance. Interactions with potential donors are also hampered by interspecies antagonism. However, occasional increases in population sizes (and thus the possibility of acquiring antibiotic resistance) can derive from selection of the species based on intrinsic or acquired resistance to antibiotics, biocides, heavy metals or by a natural tolerance to extreme conditions. High-quality surveillance of the emergence of resistance to the key drugs used in primary therapy is mandatory.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal Institute for Health Research, Ramón y Cajal University Hospital, Madrid, Spain
| | - Val F Lanza
- Department of Microbiology, Ramón y Cajal Institute for Health Research, Ramón y Cajal University Hospital, Madrid, Spain.,Bioinformatics Unit, Ramón y Cajal Institute for Health Research, Ramón y Cajal University Hospital, Madrid, Spain
| | - Mélodie Duval
- Département de Biologie Cellulaire et Infection, Unité des interactions Bactéries-Cellules, Institut Pasteur, and Inserm, Paris, France
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research, Ramón y Cajal University Hospital, Madrid, Spain
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15
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Xu X, Biswas S, Gu G, Elbediwi M, Li Y, Yue M. Characterization of Multidrug Resistance Patterns of Emerging Salmonella enterica Serovar Rissen along the Food Chain in China. Antibiotics (Basel) 2020; 9:antibiotics9100660. [PMID: 33007986 PMCID: PMC7600917 DOI: 10.3390/antibiotics9100660] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 11/25/2022] Open
Abstract
Salmonella spp. are recognized as important foodborne pathogens globally. Salmonella enterica serovar Rissen is one of the important Salmonella serovars linked with swine products in numerous countries and can transmit to humans by food chain contamination. Worldwide emerging S. Rissen is considered as one of the most common pathogens to cause human salmonellosis. The objective of this study was to determine the antimicrobial resistance properties and patterns of Salmonella Rissen isolates obtained from humans, animals, animal-derived food products, and the environment in China. Between 2016 and 2019, a total of 311 S. Rissen isolates from different provinces or province-level cities in China were included here. Bacterial isolates were characterized by serotyping and antimicrobial susceptibility testing. Minimum inhibitory concentration (MIC) values of 14 clinically relevant antimicrobials were obtained by broth microdilution method. S. Rissen isolates from humans were found dominant (67%; 208/311). S. Rissen isolates obtained from human patients were mostly found with diarrhea. Other S. Rissen isolates were acquired from food (22%; 69/311), animals (8%; 25/311), and the environment (3%; 9/311). Most of the isolates were resistant to tetracycline, trimethoprim-sulfamethoxazole, chloramphenicol, streptomycin, sulfisoxazole, and ampicillin. The S. Rissen isolates showed susceptibility against ceftriaxone, ceftiofur, gentamicin, nalidixic acid, ciprofloxacin, and azithromycin. In total, 92% of the S. Rissen isolates were multidrug-resistant and ASSuT (27%), ACT (25%), ACSSuT (22%), ACSSuTAmc (11%), and ACSSuTFox (7%) patterns were among the most prevalent antibiotic resistance patterns found in this study. The widespread dissemination of antimicrobial resistance could have emerged from misuse of antimicrobial agents in animal husbandry in China. These findings could be useful for rational antimicrobial usage against Salmonella Rissen infections.
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Affiliation(s)
- Xuebin Xu
- Department of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China;
| | - Silpak Biswas
- Institute of Veterinary Sciences & Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (S.B.); (M.E.); (Y.L.)
| | - Guimin Gu
- Guangxi Institute for Product Quality Inspection, Nanning 530007, China;
| | - Mohammed Elbediwi
- Institute of Veterinary Sciences & Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (S.B.); (M.E.); (Y.L.)
- Animal Health Research Institute, Agriculture Research Centre, Cairo 11435, Egypt
| | - Yan Li
- Institute of Veterinary Sciences & Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (S.B.); (M.E.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
| | - Min Yue
- Institute of Veterinary Sciences & Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (S.B.); (M.E.); (Y.L.)
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
- Correspondence: ; Tel./Fax: +86-0571-8898-2832
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Ermakova AY, Beletsky AV, Mardanov AV, Petrova MA, Ravin NV, Rakitin AL. A Novel Plasmid pALWVS1.4 from Acinetobacter lwoffii Strain VS15, Carrying the Chloramphenicol Resistance Gene. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720050070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Pérez VKC, Costa GMD, Guimarães AS, Heinemann MB, Lage AP, Dorneles EMS. Relationship between virulence factors and antimicrobial resistance in Staphylococcus aureus from bovine mastitis. J Glob Antimicrob Resist 2020; 22:792-802. [PMID: 32603906 DOI: 10.1016/j.jgar.2020.06.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 05/10/2020] [Accepted: 06/09/2020] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES This review summarizes the literature on the role of virulence and antimicrobial resistance genes of Staphylococcus aureus in bovine mastitis, focusing on the association between these characteristics and their implications for public and animal health. CONCLUSIONS There is the possibility of antimicrobial resistance gene exchange among different bacteria, which is of serious concern in livestock husbandry, as well as in the treatment of human staphylococcal infections.
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Affiliation(s)
- Verónica Karen Castro Pérez
- Departamento de Medicina Veterinária, Universidade Federal de Lavras, Lavras 37200-000, Minas Gerais, Brazil
| | - Geraldo Márcio da Costa
- Departamento de Medicina Veterinária, Universidade Federal de Lavras, Lavras 37200-000, Minas Gerais, Brazil
| | - Alessandro Sá Guimarães
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Gado de Leite, Juiz de Fora 36038-330, Minas Gerais, Brazil
| | - Marcos Bryan Heinemann
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo 05508-900, São Paulo, Brazil
| | - Andrey Pereira Lage
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Elaine Maria Seles Dorneles
- Departamento de Medicina Veterinária, Universidade Federal de Lavras, Lavras 37200-000, Minas Gerais, Brazil.
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18
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Ndagi U, Falaki AA, Abdullahi M, Lawal MM, Soliman ME. Antibiotic resistance: bioinformatics-based understanding as a functional strategy for drug design. RSC Adv 2020; 10:18451-18468. [PMID: 35685616 PMCID: PMC9122625 DOI: 10.1039/d0ra01484b] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022] Open
Abstract
The use of antibiotics to manage infectious diseases dates back to ancient civilization, but the lack of a clear distinction between the therapeutic and toxic dose has been a major challenge. This precipitates the notion that antibiotic resistance was from time immemorial, principally because of a lack of adequate knowledge of therapeutic doses and continuous exposure of these bacteria to suboptimal plasma concentration of antibiotics. With the discovery of penicillin by Alexander Fleming in 1924, a milestone in bacterial infections' treatment was achieved. This forms the foundation for the modern era of antibiotic drugs. Antibiotics such as penicillins, cephalosporins, quinolones, tetracycline, macrolides, sulphonamides, aminoglycosides and glycopeptides are the mainstay in managing severe bacterial infections, but resistant strains of bacteria have emerged and hampered the progress of research in this field. Recently, new approaches to research involving bacteria resistance to antibiotics have appeared; these involve combining the molecular understanding of bacteria systems with the knowledge of bioinformatics. Consequently, many molecules have been developed to curb resistance associated with different bacterial infections. However, because of increased emphasis on the clinical relevance of antibiotics, the synergy between in silico study and in vivo study is well cemented and this facilitates the discovery of potent antibiotics. In this review, we seek to give an overview of earlier reviews and molecular and structural understanding of bacteria resistance to antibiotics, while focusing on the recent bioinformatics approach to antibacterial drug discovery. Understanding the evolution of antibiotic resistance at the molecular level as a functional tool for bioinformatic-based drug design.![]()
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Affiliation(s)
- Umar Ndagi
- Centre for Trans-Sahara Disease, Vaccine and Drug Research
- Ibrahim Badamasi Babangida University
- Lapai
- Nigeria
| | - Abubakar A. Falaki
- Department of Microbiology
- School of Agriculture and Applied Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Maryam Abdullahi
- Faculty of Pharmaceutical Sciences
- Ahmadu Bello University Zaria
- Nigeria
| | - Monsurat M. Lawal
- School of Laboratory Medicine and Medical Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Mahmoud E. Soliman
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences
- University of KwaZulu Natal
- Durban 4001
- South Africa
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Guliy OI, Zaitsev BD, Borodina IA. New approach for determination of antimicrobial susceptibility to antibiotics by an acoustic sensor. Appl Microbiol Biotechnol 2019; 104:1283-1290. [PMID: 31865437 DOI: 10.1007/s00253-019-10295-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 12/19/2022]
Abstract
For the first time, a rapid method was proposed to determine the susceptibility of Escherichia coli cells to antibiotics by the example of ampicillin by using a biological sensor based on a slot mode in an acoustic delay line. It has been established that an indicator of the antibiotic activity to microbial cells is the difference between the recorded sensor's signal before and after exposure cells with antibiotic. The depth and frequency of the peaks of resonant absorption in the frequency dependence of the insertion loss of sensor varied after adding an antibiotic with different concentrations to the microbial cells. By using the acoustic sensor based on slot-mode a criterion of E. coli sensitivity to ampicillin was established. The advantages of this method are the ability to carry out the analysis directly in the liquid, the short analysis time (within 10-15 min), and the possibility to reusable sensor.
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Affiliation(s)
- O I Guliy
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov, 410049, Russia.
| | - B D Zaitsev
- Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Saratov Branch, Saratov, 410019, Russia
| | - I A Borodina
- Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Saratov Branch, Saratov, 410019, Russia
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20
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Khan AU, Shell WS, Melzer F, Sayour AE, Ramadan ES, Elschner MC, Moawad AA, Roesler U, Neubauer H, El-Adawy H. Identification, Genotyping and Antimicrobial Susceptibility Testing of Brucella spp. Isolated from Livestock in Egypt. Microorganisms 2019; 7:microorganisms7120603. [PMID: 31766725 PMCID: PMC6955977 DOI: 10.3390/microorganisms7120603] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/14/2019] [Accepted: 11/16/2019] [Indexed: 02/07/2023] Open
Abstract
Brucellosis is a highly contagious zoonosis worldwide with economic and public health impacts. The aim of the present study was to identify Brucella (B.) spp. isolated from animal populations located in different districts of Egypt and to determine their antimicrobial resistance. In total, 34-suspected Brucella isolates were recovered from lymph nodes, milk, and fetal abomasal contents of infected cattle, buffaloes, sheep, and goats from nine districts in Egypt. The isolates were identified by microbiological methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Differentiation and genotyping were confirmed using multiplex PCR for B. abortus, Brucella melitensis, Brucella ovis, and Brucella suis (AMOS) and Bruce-ladder PCR. Antimicrobial susceptibility testing against clinically used antimicrobial agents (chloramphenicol, ciprofloxacin, erythromycin, gentamicin, imipenem, rifampicin, streptomycin, and tetracycline) was performed using E-Test. The antimicrobial resistance-associated genes and mutations in Brucella isolates were confirmed using molecular tools. In total, 29 Brucella isolates (eight B. abortus biovar 1 and 21 B. melitensis biovar 3) were identified and typed. The resistance of B. melitensis to ciprofloxacin, erythromycin, imipenem, rifampicin, and streptomycin were 76.2%, 19.0%, 76.2%, 66.7%, and 4.8%, respectively. Whereas, 25.0%, 87.5%, 25.0%, and 37.5% of B. abortus were resistant to ciprofloxacin, erythromycin, imipenem, and rifampicin, respectively. Mutations in the rpoB gene associated with rifampicin resistance were identified in all phenotypically resistant isolates. Mutations in gyrA and gyrB genes associated with ciprofloxacin resistance were identified in four phenotypically resistant isolates of B. melitensis. This is the first study highlighting the antimicrobial resistance in Brucella isolated from different animal species in Egypt. Mutations detected in genes associated with antimicrobial resistance unravel the molecular mechanisms of resistance in Brucella isolates from Egypt. The mutations in the rpoB gene in phenotypically resistant B. abortus isolates in this study were reported for the first time in Egypt.
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Affiliation(s)
- Aman Ullah Khan
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
- Institute for Animal Hygiene and Environmental Health, Free University of Berlin, 14163 Berlin, Germany;
- Department of Pathobiology, College of Veterinary and Animal Sciences, 35200 Jhang, Pakistan
| | - Waleed S. Shell
- Central Laboratory for Evaluation of Veterinary Biologics, Agricultural Research Center, 11517 Abbasaia-Cairo, Egypt;
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
| | - Ashraf E. Sayour
- Department of Brucellosis, Animal Health Research Institute, Agricultural Research Center, 12618 Dokki-Giza, Egypt;
| | - Eman Shawkat Ramadan
- Animal Reproduction Research Institute, Agricultural Research Center, 12556 Al Ahram-Giza, Egypt;
| | - Mandy C. Elschner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
| | - Amira A. Moawad
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
- Institute for Animal Hygiene and Environmental Health, Free University of Berlin, 14163 Berlin, Germany;
- Provincial Laboratory, Institute of Animal Health Research, 35516 Mansoura, Egypt
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Free University of Berlin, 14163 Berlin, Germany;
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
| | - Hosny El-Adawy
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany; (A.U.K.); (F.M.); (M.C.E.); (A.A.M.); (H.N.)
- Faculty of Veterinary Medicine, Kafr Elsheikh University, 33516 Kafr El-Sheikh, Egypt
- Correspondence:
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22
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Johansen TB, Scheffer L, Jensen VK, Bohlin J, Feruglio SL. Whole-genome sequencing and antimicrobial resistance in Brucella melitensis from a Norwegian perspective. Sci Rep 2018; 8:8538. [PMID: 29867163 PMCID: PMC5986768 DOI: 10.1038/s41598-018-26906-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/17/2018] [Indexed: 11/09/2022] Open
Abstract
Brucellosis is a rarely encountered infection in Norway. The aim of this study was to explore all Brucella melitensis isolates collected in Norway from 1999 to 2016 in relation to origin of infection and antimicrobial resistance patterns. A total of 23 isolates were analysed by whole-genome sequencing and compared with selected sequences of B. melitensis available from NCBI. Additionally, SNP analysis in antibiotic resistance determining genes was performed. The majority belonged to the East Mediterranean clade (genotype II), while the remaining isolates belonged to the African clade (genotype III). These results indicate that human brucellosis in Norway is related to travels or migration from the Middle East, Asia or Africa, in accordance with results from Germany, Denmark and Sweden. Antibiotic susceptibility patterns were determined by broth microdilution method and/or gradient strip method. All isolates were susceptible for all tested antibiotics, except for rifampicin where phenotypical results indicated resistance or intermediate resistance in all isolates based on broth microdilution method, and in four isolates based on gradient strip testing. In contrast, screening of the rpoB gene did not reveal any mutations in the previously described rpoB "hot spot" regions related to rifampicin resistance, indicating overestimation of resistance based on phenotypical results.
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Affiliation(s)
- Tone B Johansen
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, PO Box 4404 Nydalen, N-0403, Oslo, Norway.
| | - Lonneke Scheffer
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, PO Box 4404 Nydalen, N-0403, Oslo, Norway
- Hanze University of Applied Sciences, Zernikeplein 7, 9747 AS, Groningen, The Netherlands
- Department of Informatics, University of Oslo, P.O. Box 1072 Blindern, 0316, Oslo, Norway
| | - Veronica K Jensen
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, PO Box 4404 Nydalen, N-0403, Oslo, Norway
| | - Jon Bohlin
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, PO Box 4404 Nydalen, N-0403, Oslo, Norway
| | - Siri L Feruglio
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, PO Box 4404 Nydalen, N-0403, Oslo, Norway
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23
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Spidlova P, Stojkova P, Dankova V, Senitkova I, Santic M, Pinkas D, Philimonenko V, Stulik J. Francisella tularensis D-Ala D-Ala Carboxypeptidase DacD Is Involved in Intracellular Replication and It Is Necessary for Bacterial Cell Wall Integrity. Front Cell Infect Microbiol 2018; 8:111. [PMID: 29692981 PMCID: PMC5903032 DOI: 10.3389/fcimb.2018.00111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/21/2018] [Indexed: 12/16/2022] Open
Abstract
D-alanyl-D-alanine carboxypeptidase, product of dacD gene in Francisella, belongs to penicillin binding proteins (PBPs) and is involved in remodeling of newly synthetized peptidoglycan. In E. coli, PBPs are synthetized in various growth phases and they are able to substitute each other to a certain extent. The DacD protein was found to be accumulated in fraction enriched in membrane proteins from severely attenuated dsbA deletion mutant strain. It has been presumed that the DsbA is not a virulence factor by itself but that its substrates, whose correct folding and topology are dependent on the DsbA oxidoreductase and/or isomerase activities, are the primary virulence factors. Here we demonstrate that Francisella DacD is required for intracellular replication and virulence in mice. The dacD insertion mutant strain showed higher sensitivity to acidic pH, high temperature and high osmolarity when compared to the wild-type. Eventually, transmission electron microscopy revealed differences in mutant bacteria in both the size and defects in outer membrane underlying its SDS and serum sensitivity. Taken together these results suggest DacD plays an important role in Francisella pathogenicity.
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Affiliation(s)
- Petra Spidlova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
| | - Pavla Stojkova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
| | - Vera Dankova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
| | - Iva Senitkova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
| | - Marina Santic
- Department of Microbiology and Parasitology, Medical Faculty, University of Rijeka, Rijeka, Croatia
| | - Dominik Pinkas
- Microscopy Center, Institute of Molecular Genetics ASCR v.v.i., Electron Microscopy Core Facility, Prague, Czechia
| | - Vlada Philimonenko
- Microscopy Center, Institute of Molecular Genetics ASCR v.v.i., Electron Microscopy Core Facility, Prague, Czechia
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics ASCR v.v.i., Prague, Czechia
| | - Jiri Stulik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Hradec Kralove, Czechia
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24
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Khan R, Roy N, Choi K, Lee SW. Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis. PLoS One 2018; 13:e0192277. [PMID: 29420585 PMCID: PMC5805296 DOI: 10.1371/journal.pone.0192277] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/18/2018] [Indexed: 12/11/2022] Open
Abstract
The substantial use of triclosan (TCS) has been aimed to kill pathogenic bacteria, but TCS resistance seems to be prevalent in microbial species and limited knowledge exists about TCS resistance determinants in a majority of pathogenic bacteria. We aimed to evaluate the distribution of TCS resistance determinants in major pathogenic bacteria (N = 231) and to assess the enrichment of potentially pathogenic genera in TCS contaminated environments. A TCS-resistant gene (TRG) database was constructed and experimentally validated to predict TCS resistance in major pathogenic bacteria. Genome-wide in silico analysis was performed to define the distribution of TCS-resistant determinants in major pathogens. Microbiome analysis of TCS contaminated soil samples was also performed to investigate the abundance of TCS-resistant pathogens. We experimentally confirmed that TCS resistance could be accurately predicted using genome-wide in silico analysis against TRG database. Predicted TCS resistant phenotypes were observed in all of the tested bacterial strains (N = 17), and heterologous expression of selected TCS resistant genes from those strains conferred expected levels of TCS resistance in an alternative host Escherichia coli. Moreover, genome-wide analysis revealed that potential TCS resistance determinants were abundant among the majority of human-associated pathogens (79%) and soil-borne plant pathogenic bacteria (98%). These included a variety of enoyl-acyl carrier protein reductase (ENRs) homologues, AcrB efflux pumps, and ENR substitutions. FabI ENR, which is the only known effective target for TCS, was either co-localized with other TCS resistance determinants or had TCS resistance-associated substitutions. Furthermore, microbiome analysis revealed that pathogenic genera with intrinsic TCS-resistant determinants exist in TCS contaminated environments. We conclude that TCS may not be as effective against the majority of bacterial pathogens as previously presumed. Further, the excessive use of this biocide in natural environments may selectively enrich for not only TCS-resistant bacterial pathogens, but possibly for additional resistance to multiple antibiotics.
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Affiliation(s)
- Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Nazish Roy
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Kihyuck Choi
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
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25
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Luce-Fedrow A, Lehman ML, Kelly DJ, Mullins K, Maina AN, Stewart RL, Ge H, John HS, Jiang J, Richards AL. A Review of Scrub Typhus (Orientia tsutsugamushi and Related Organisms): Then, Now, and Tomorrow. Trop Med Infect Dis 2018; 3:E8. [PMID: 30274407 PMCID: PMC6136631 DOI: 10.3390/tropicalmed3010008] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 12/26/2022] Open
Abstract
Scrub typhus and the rickettsial diseases represent some of the oldest recognized vector-transmitted diseases, fraught with a rich historical aspect, particularly as applied to military/wartime situations. The vectors of Orientia tsutsugamushi were once thought to be confined to an area designated as the Tsutsugamushi Triangle. However, recent reports of scrub typhus caused by Orientia species other than O. tsutsugamushi well beyond the limits of the Tsutsugamushi Triangle have triggered concerns about the worldwide presence of scrub typhus. It is not known whether the vectors of O. tsutsugamushi will be the same for the new Orientia species, and this should be a consideration during outbreak/surveillance investigations. Additionally, concerns surrounding the antibiotic resistance of O. tsutsugamushi have led to considerations for the amendment of treatment protocols, and the need for enhanced public health awareness in both the civilian and medical professional communities. In this review, we discuss the history, outbreaks, antibiotic resistance, and burgeoning genomic advances associated with one of the world's oldest recognized vector-borne pathogens, O. tsutsugamushi.
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Affiliation(s)
- Alison Luce-Fedrow
- Department of Biology, Shippensburg University, Shippensburg, PA 17202, USA.
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA.
| | - Marcie L Lehman
- Department of Biology, Shippensburg University, Shippensburg, PA 17202, USA.
| | - Daryl J Kelly
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA.
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Kristin Mullins
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA.
| | - Alice N Maina
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA.
| | - Richard L Stewart
- Department of Biology, Shippensburg University, Shippensburg, PA 17202, USA.
| | - Hong Ge
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA.
| | - Heidi St John
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA.
| | - Ju Jiang
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA.
| | - Allen L Richards
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD 20910, USA.
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
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26
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Gupta SK, Drancourt M, Rolain JM. In Silico Prediction of Antibiotic Resistance in Mycobacterium ulcerans Agy99 through Whole Genome Sequence Analysis. Am J Trop Med Hyg 2017; 97:810-814. [PMID: 28749770 DOI: 10.4269/ajtmh.16-0478] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Buruli ulcer is an emerging infectious disease caused by Mycobacterium ulcerans that has been reported from 33 countries. Antimicrobial agents either alone or in combination with surgery have been proved to be clinically relevant and therapeutic strategies have been deduced mainly from the empirical experience. The genome sequences of M. ulcerans strain AGY99, M. ulcerans ecovar liflandii, and three Mycobacterium marinum strains were analyzed to predict resistance in these bacteria. Fourteen putative antibiotic resistance genes from different antibiotics classes were predicted in M. ulcerans and mutation in katG (R431G) and pncA (T47A, V125I) genes were detected, that confer resistance to isoniazid and pyrazinamide, respectively. No mutations were detected in rpoB, gyrA, gyrB, rpsL, rrs, emb, ethA, 23S ribosomal RNA genes and promoter region of inhA and ahpC genes associated with resistance. Our results reemphasize the usefulness of in silico analysis for the prediction of antibiotic resistance in fastidious bacteria.
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Affiliation(s)
- Sushim Kumar Gupta
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278-IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278-IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278-IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
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27
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Whipple's disease. J Neurol Sci 2017; 377:197-206. [DOI: 10.1016/j.jns.2017.01.048] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/16/2016] [Accepted: 01/15/2017] [Indexed: 11/24/2022]
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28
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Marti H, Kim H, Joseph SJ, Dojiri S, Read TD, Dean D. Tet(C) Gene Transfer between Chlamydia suis Strains Occurs by Homologous Recombination after Co-infection: Implications for Spread of Tetracycline-Resistance among Chlamydiaceae. Front Microbiol 2017; 8:156. [PMID: 28223970 PMCID: PMC5293829 DOI: 10.3389/fmicb.2017.00156] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/20/2017] [Indexed: 11/13/2022] Open
Abstract
Chlamydia suis is a swine pathogen that has also recently been found to cause zoonotic infections of the human eye, pharynx, and gastrointestinal tract. Many strains contain a tetracycline class C gene [tet(C)] cassette that confers tetracycline resistance. The cassette was likely originally acquired by horizontal gene transfer from a Gram-negative donor after the introduction of tetracycline into animal feed in the 1950s. Various research groups have described the capacity for different Chlamydia species to exchange DNA by homologous recombination. Since over 90% of C. suis strains are tetracycline resistant, they represent a potential source for antibiotic-resistance spread within and between Chlamydiaceae species. Here, we examined the genetics of tet(C)-transfer among C. suis strains. Tetracycline-sensitive C. suis strain S45 was simultaneously or sequentially co-infected with tetracycline-resistant C. suis strains in McCoy cells. Potential recombinants were clonally purified by a harvest assay derived from the classic plaque assay. C. suis strain Rogers132, lacking transposases IS200 and IS605, was the most efficient donor, producing two unique recombinants detected in three of the 56 (5.4%) clones screened. Recombinants were found to have a minimal inhibitory concentration (MIC) of 8-16 μg/mL for tetracycline. Resistance remained stable over 10 passages as long as recombinants were initially grown in tetracycline at twice the MIC of S45 (0.032 μg/mL). Genomic analysis revealed that tet(C) had integrated into the S45 genome by homologous recombination at two unique sites depending on the recombinant: a 55 kb exchange between nrqF and pckG, and a 175 kb exchange between kdsA and cysQ. Neither site was associated with inverted repeats or motifs associated with recombination hotspots. Our findings show that cassette transfer into S45 has low frequency, does not require IS200/IS605 transposases, is stable if initially grown in tetracycline, and results in multiple genomic configurations. We provide a model for stable cassette transfer to better understand the capability for cassette acquisition by Chlamydiaceae species that infect humans, a matter of public health importance.
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Affiliation(s)
- Hanna Marti
- Center for Immunobiology and Vaccine Development, University of California at San Francisco/Benioff Children's Hospital Oakland Research Institute, Oakland CA, USA
| | - Hoyon Kim
- Center for Immunobiology and Vaccine Development, University of California at San Francisco/Benioff Children's Hospital Oakland Research Institute, Oakland CA, USA
| | - Sandeep J Joseph
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, AtlantaGA, USA; Department of Human Genetics, Emory University School of Medicine, AtlantaGA, USA
| | - Stacey Dojiri
- Center for Immunobiology and Vaccine Development, University of California at San Francisco/Benioff Children's Hospital Oakland Research Institute, Oakland CA, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, AtlantaGA, USA; Department of Human Genetics, Emory University School of Medicine, AtlantaGA, USA
| | - Deborah Dean
- Center for Immunobiology and Vaccine Development, University of California at San Francisco/Benioff Children's Hospital Oakland Research Institute, OaklandCA, USA; Joint Graduate Program in Bioengineering, University of California, San Francisco, San FranciscoCA, USA; Joint Graduate Program in Bioengineering, University of California, Berkeley, BerkeleyCA, USA; Departments of Medicine and Pediatrics, University of California, San Francisco, San FranciscoCA, USA
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Cimmino T, Le Page S, Raoult D, Rolain JM. Contemporary challenges and opportunities in the diagnosis and outbreak detection of multidrug-resistant infectious disease. Expert Rev Mol Diagn 2016; 16:1163-1175. [PMID: 27690721 DOI: 10.1080/14737159.2016.1244005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The dissemination of multi-drug resistant bacteria (MDRB) has become a major public health concern worldwide because of the increase in infections caused by MDRB, the difficulty in treating them, and expenditures in patient care. Areas covered: We have reviewed challenges and contemporary opportunities for rapidly confronting infections caused by MDRB in the 21st century, including surveillance, detection, identification of resistance mechanisms, and action steps. Expert commentary: In this context, the first critical point for clinical microbiologists is to be able to rapidly detect an abnormal event, an outbreak and/or the spread of a MDRB with surveillance tools so that healthcare policies and therapies adapted to a new stochastic event that will certainly occur again in the future can be implemented.
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Affiliation(s)
- Teresa Cimmino
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Stéphanie Le Page
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Didier Raoult
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Jean-Marc Rolain
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
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30
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Jaing CJ, McLoughlin KS, Thissen JB, Zemla A, Gardner SN, Vergez LM, Bourguet F, Mabery S, Fofanov VY, Koshinsky H, Jackson PJ. Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing. PLoS One 2016; 11:e0163458. [PMID: 27668749 PMCID: PMC5036845 DOI: 10.1371/journal.pone.0163458] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/08/2016] [Indexed: 11/19/2022] Open
Abstract
Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. Genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms.
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Affiliation(s)
- Crystal J. Jaing
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
- * E-mail:
| | - Kevin S. McLoughlin
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - James B. Thissen
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Adam Zemla
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Shea N. Gardner
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Lisa M. Vergez
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Feliza Bourguet
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Shalini Mabery
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | | | | | - Paul J. Jackson
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
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Karlsson E, Golovliov I, Lärkeryd A, Granberg M, Larsson E, Öhrman C, Niemcewicz M, Birdsell D, Wagner DM, Forsman M, Johansson A. Clonality of erythromycin resistance in Francisella tularensis. J Antimicrob Chemother 2016; 71:2815-23. [PMID: 27334667 DOI: 10.1093/jac/dkw235] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/17/2016] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVES We analysed diverse strains of Francisella tularensis subsp. holarctica to assess if its division into biovars I and II is associated with specific mutations previously linked to erythromycin resistance and to determine the distribution of this resistance trait across this subspecies. METHODS Three-hundred and fourteen F. tularensis subsp. holarctica strains were tested for erythromycin susceptibility and whole-genome sequences for these strains were examined for SNPs in genes previously associated with erythromycin resistance. Each strain was assigned to a global phylogenetic framework using genome-wide canonical SNPs. The contribution of a specific SNP to erythromycin resistance was examined using allelic exchange. The geographical distribution of erythromycin-resistant F. tularensis strains was further investigated by literature search. RESULTS There was a perfect correlation between biovar II strains (erythromycin resistance) and the phylogenetic group B.12. Only B.12 strains had an A → C SNP at position 2059 in the three copies of the rrl gene. Introducing 2059C into an rrl gene of an erythromycin-susceptible F. tularensis strain resulted in resistance. An additional 1144 erythromycin-resistant strains were identified from the scientific literature, all of them from Eurasia. CONCLUSIONS Erythromycin resistance in F. tularensis is caused by an A2059C rrl gene mutation, which exhibits a strictly clonal inheritance pattern found only in phylogenetic group B.12. This group is an extremely successful clone, representing the most common type of F. tularensis throughout Eurasia.
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Affiliation(s)
- Edvin Karlsson
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Igor Golovliov
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Adrian Lärkeryd
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Malin Granberg
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Eva Larsson
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Caroline Öhrman
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Marcin Niemcewicz
- Wojskowy Instytut Higieny i Epidemioligii, Biological Threat Identification and Countermeasure Center, Warsaw, Poland
| | - Dawn Birdsell
- Department of Biological Sciences and Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - David M Wagner
- Department of Biological Sciences and Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Mats Forsman
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
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32
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Aloni-Grinstein R, Shifman O, Lazar S, Steinberger-Levy I, Maoz S, Ber R. A rapid real-time quantitative PCR assay to determine the minimal inhibitory extracellular concentration of antibiotics against an intracellular Francisella tularensis Live Vaccine Strain. Front Microbiol 2015; 6:1213. [PMID: 26579112 PMCID: PMC4630301 DOI: 10.3389/fmicb.2015.01213] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/19/2015] [Indexed: 12/17/2022] Open
Abstract
Francisella tularensis is a highly virulent facultative intracellular bacterium. The lack of a safe and efficient vaccine makes antibiotics the preferred treatment. F. tularensis antibiotic susceptibility tests are based on the in vitro standard CLSI-approved microdilution method for determining the MIC. However, limited data are available regarding the minimal inhibitory extracellular concentration (MIEC) needed to eradicate intracellular bacteria. Here, we evaluated the MIEC values of various WHO-recommended antibiotics and compared the MIEC values to the established MICs. We describe a rapid 3-h quantitative PCR (qPCR) intracellular antibiogram assay, which yields comparable MIEC values to those obtained by the classical 72-h cfu assay. This rapid qPCR assay is highly advantageous in light of the slow growth rates of F. tularensis. Our results showed that the MIECs obtained for doxycycline, chloramphenicol and ciprofloxacin were indicative of intracellular activity. Gentamicin was not effective against intracellular bacteria for at least 32 h post treatment, raising the question of whether slow-penetrating gentamicin should be used for certain stages of the disease. We suggest that the qPCR intracellular antibiogram assay may be used to screen for potentially active antibiotics against intracellular F. tularensis as well as to detect strains with acquired resistance to recommended antibiotics.
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Affiliation(s)
- Ronit Aloni-Grinstein
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness Ziona, Israel
| | - Shlomi Lazar
- Department of Pharmacology, Israel Institute for Biological Research Ness Ziona, Israel
| | - Ida Steinberger-Levy
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness Ziona, Israel
| | - Sharon Maoz
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness Ziona, Israel
| | - Raphael Ber
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research Ness Ziona, Israel
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de Barsy M, Bertelli C, Jacquier N, Kebbi-Beghdadi C, Greub G. ESCCAR international congress on Rickettsia and other intracellular bacteria. Microbes Infect 2015; 17:680-8. [PMID: 26297854 DOI: 10.1016/j.micinf.2015.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 07/08/2015] [Indexed: 11/17/2022]
Abstract
The European Society for the study of Chlamydia, Coxiella, Anaplasma and Rickettsia (ESCCAR) held his triennial international meeting in Lausanne. This meeting gathered 165 scientists from 28 countries and all 5 continents, allowing efficient networking and major scientific exchanges. Topics covered include molecular and cellular microbiology, genomics, as well as epidemiology, veterinary and human medicine. Several breakthroughs have been revealed at the meeting, such as (i) the presence of CRISPR (the "prokaryotic immune system") in chlamydiae, (ii) an Anaplasma effector involved in host chromatin remodelling, (iii) the polarity of the type III secretion system of chlamydiae during the entry process revealed by cryo-electron tomography. Moreover, the ESCCAR meeting was a unique opportunity to be exposed to cutting-edge science and to listen to comprehensive talks on current hot topics.
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Affiliation(s)
- Marie de Barsy
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Nicolas Jacquier
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Carole Kebbi-Beghdadi
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland.
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Li XZ, Plésiat P, Nikaido H. The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria. Clin Microbiol Rev 2015; 28:337-418. [PMID: 25788514 PMCID: PMC4402952 DOI: 10.1128/cmr.00117-14] [Citation(s) in RCA: 924] [Impact Index Per Article: 102.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The global emergence of multidrug-resistant Gram-negative bacteria is a growing threat to antibiotic therapy. The chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. Multidrug pumps, particularly those represented by the clinically relevant AcrAB-TolC and Mex pumps of the resistance-nodulation-division (RND) superfamily, not only mediate intrinsic and acquired multidrug resistance (MDR) but also are involved in other functions, including the bacterial stress response and pathogenicity. Additionally, efflux pumps interact synergistically with other resistance mechanisms (e.g., with the outer membrane permeability barrier) to increase resistance levels. Since the discovery of RND pumps in the early 1990s, remarkable scientific and technological advances have allowed for an in-depth understanding of the structural and biochemical basis, substrate profiles, molecular regulation, and inhibition of MDR pumps. However, the development of clinically useful efflux pump inhibitors and/or new antibiotics that can bypass pump effects continues to be a challenge. Plasmid-borne efflux pump genes (including those for RND pumps) have increasingly been identified. This article highlights the recent progress obtained for organisms of clinical significance, together with methodological considerations for the characterization of MDR pumps.
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Affiliation(s)
- Xian-Zhi Li
- Human Safety Division, Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Patrick Plésiat
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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Modulation of Bacterial Multidrug Resistance Efflux Pumps of the Major Facilitator Superfamily. INTERNATIONAL JOURNAL OF BACTERIOLOGY 2013; 2013. [PMID: 25750934 PMCID: PMC4347946 DOI: 10.1155/2013/204141] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacterial infections pose a serious public health concern, especially when an infectious disease has a multidrug resistant causative agent. Such multidrug resistant bacteria can compromise the clinical utility of major chemotherapeutic antimicrobial agents. Drug and multidrug resistant bacteria harbor several distinct molecular mechanisms for resistance. Bacterial antimicrobial agent efflux pumps represent a major mechanism of clinical resistance. The major facilitator superfamily (MFS) is one of the largest groups of solute transporters to date and includes a significant number of bacterial drug and multidrug efflux pumps. We review recent work on the modulation of multidrug efflux pumps, paying special attention to those transporters belonging primarily to the MFS.
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Lagier JC, Fenollar F, Lepidi H, Giorgi R, Million M, Raoult D. Treatment of classic Whipple's disease: from in vitro results to clinical outcome. J Antimicrob Chemother 2013; 69:219-27. [PMID: 23946319 DOI: 10.1093/jac/dkt310] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Patients with classic Whipple's disease have a lifetime defect in immunity to Tropheryma whipplei and frequently develop treatment failures, relapses or reinfections. Empirical treatments were tested before culture was possible, but the only in vitro bactericidal treatment consists of a combination of doxycycline and hydroxychloroquine. METHODS Our laboratory has been a reference centre since the first culturing of Tropheryma whipplei, and we have tested 27,000 samples by PCR and diagnosed 250 cases of classic Whipple's disease. We report here the clinical course of patients who were followed by one of our group. RESULTS Of 29 patients, 22 (76%) were previously treated with immunosuppressive drugs, 26 (90%) suffered from arthralgias and 22 (76%) exhibited weight loss. Intravenous initial treatment was paradoxically associated with an increased risk of failure (P = 0.0282). Treatment with doxycycline and hydroxychloroquine (± sulfadiazine or trimethoprim/sulfamethoxazole) was associated with a better outcome (0/13 failures), whereas all 14 patients who were first treated with trimethoprim/sulfamethoxazole and referred to us (P < 0.0001) experienced failure. Among the patients treated with doxycycline and hydroxychloroquine after previous antibiotic treatments, two presented with a reinfection caused by different T. whipplei strains. Finally, serum therapeutic drug monitoring allowed us to detect a lack of compliance in the only patient with failure among the 22 patients treated with lifetime doxycycline. CONCLUSIONS In vitro results were confirmed by clinical outcomes and trimethoprim/sulfamethoxazole was associated with failures. The recommended management is a combination of doxycycline and hydroxychloroquine for 1 year, followed by doxycycline for the patient's lifetime along with stringent therapeutic drug monitoring.
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Affiliation(s)
- Jean-Christophe Lagier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 13005 Marseille, France
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Müller W, Hotzel H, Otto P, Karger A, Bettin B, Bocklisch H, Braune S, Eskens U, Hörmansdorfer S, Konrad R, Nesseler A, Peters M, Runge M, Schmoock G, Schwarz BA, Sting R, Myrtennäs K, Karlsson E, Forsman M, Tomaso H. German Francisella tularensis isolates from European brown hares (Lepus europaeus) reveal genetic and phenotypic diversity. BMC Microbiol 2013; 13:61. [PMID: 23517149 PMCID: PMC3663675 DOI: 10.1186/1471-2180-13-61] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 03/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tularemia is a zoonotic disease caused by Francisella tularensis that has been found in many different vertebrates. In Germany most human infections are caused by contact with infected European brown hares (Lepus europaeus). The aim of this study was to elucidate the epidemiology of tularemia in hares using phenotypic and genotypic characteristics of F. tularensis. RESULTS Cultivation of F. tularensis subsp. holarctica bacteria from organ material was successful in 31 of 52 hares that had a positive PCR result targeting the Ft-M19 locus. 17 isolates were sensitive to erythromycin and 14 were resistant. Analysis of VNTR loci (Ft-M3, Ft-M6 and Ft-M24), INDELs (Ftind33, Ftind38, Ftind49, RD23) and SNPs (B.17, B.18, B.19, and B.20) was shown to be useful to investigate the genetic relatedness of Francisella strains in this set of strains. The 14 erythromycin resistant isolates were assigned to clade B.I, and 16 erythromycin sensitive isolates to clade B.IV and one isolate was found to belong to clade B.II. MALDI-TOF mass spectrometry (MS) was useful to discriminate strains to the subspecies level. CONCLUSIONS F. tularensis seems to be a re-emerging pathogen in Germany. The pathogen can easily be identified using PCR assays. Isolates can also be identified within one hour using MALDI-TOF MS in laboratories where specific PCR assays are not established. Further analysis of strains requires genotyping tools. The results from this study indicate a geographical segregation of the phylogenetic clade B.I and B.IV, where B.I strains localize primarily within eastern Germany and B.IV strains within western Germany. This phylogeographical pattern coincides with the distribution of biovar I (erythromycin sensitive) and biovar II (erythromycin resistance) strains. When time and costs are limiting parameters small numbers of isolates can be analysed using PCR assays combined with DNA sequencing with a focus on genetic loci that are most likely discriminatory among strains found in a specific area. In perspective, whole genome data will have to be investigated especially when terrorist attack strains need to be tracked to their genetic and geographical sources.
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Affiliation(s)
- Wolfgang Müller
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Str. 96A, Jena D-07743, Germany
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Mackie RS, McKenney ES, van Hoek ML. Resistance of Francisella novicida to fosmidomycin associated with mutations in the glycerol-3-phosphate transporter. Front Microbiol 2012; 3:226. [PMID: 22905031 PMCID: PMC3417576 DOI: 10.3389/fmicb.2012.00226] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/01/2012] [Indexed: 01/23/2023] Open
Abstract
The methylerythritol phosphate (MEP) pathway is essential in most prokaryotes and some lower eukaryotes but absent from human cells, and is a validated target for antimicrobial drug development. The formation of MEP is catalyzed by 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR). MEP pathway genes have been identified in many category A and B biothreat agents, including Francisella tularensis, which causes the zoonosis tularemia. Fosmidomycin (Fos) inhibits purified Francisella DXR. This compound also inhibits the growth of F. tularensis NIH B38, F. novicida and F. tularensis subsp. holarctica LVS bacteria. Related compounds such as FR900098 and the lipophilic prodrug of FR900098 (compound 1) have been developed to improve the bioavailability of these DXR inhibitors. In performing disk-inhibition assays with these compounds, we observed breakthrough colonies of F. novicida in the presence of Fos, suggesting spontaneous development of Fos resistance (Fos(R)). Fos(R) bacteria had decreased sensitivity to both Fos and FR900098. The two most likely targets for the development of mutants would be the DXR enzyme itself or the glycerol-3-phosphate transporter (GlpT) that allows entry of Fos into the bacteria. Sensitivity of Fos(R)F. novicida bacteria to compound 1 was not abated suggesting that spontaneous resistance is not due to mutation of DXR. We thus predicted that the glpT transporter may be mutated leading to this resistant phenotype. Supporting this, transposon insertion mutants at the glpT locus were also found to be resistant to Fos. DNA sequencing of four different spontaneous Fos(R) colonies demonstrated a variety of deletions in the glpT coding region. The overall frequency of Fos(R) mutations in F. novicida was determined to be 6.3 × 10(-8). Thus we conclude that one mechanism of resistance of F. novicida to Fos is caused by mutations in GlpT. This is the first description of spontaneous mutations in Francisella leading to Fos(R).
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Affiliation(s)
- Ryan S Mackie
- School of Systems Biology, George Mason University Manassas, VA, USA
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Biswas S, Rolain JM. Bartonella infection: treatment and drug resistance. Future Microbiol 2011; 5:1719-31. [PMID: 21133691 DOI: 10.2217/fmb.10.133] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bartonella species, which belong to the α-2 subgroup of Proteobacteria, are fastidious Gram-negative bacteria that are highly adapted to their mammalian host reservoirs. Bartonella species are responsible for different clinical conditions affecting humans, including Carrion's disease, cat scratch disease, trench fever, bacillary angiomatosis, endocarditis and peliosis hepatis. While some of these diseases can resolve spontaneously without treatment, in other cases, the disease is fatal without antibiotic treatment. In this article, we discuss the antibiotic susceptibility patterns of Bartonella species, detected using several methods. We also provide an overview of Bartonella infection in humans and animals and discuss the antibiotic treatment recommendations for the different infections, treatment failure and the molecular mechanism of antibiotic resistance in these bacteria.
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Affiliation(s)
- Silpak Biswas
- CNRS-IRD, UMR 6236, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, 27 boulevard Jean-Moulin, Marseille cedex 05, France
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Li D, Liu Q, Zhao F, Hu Y, Xiao D, Gu Y, Song X, Zhang J. Proteomic and bioinformatic analysis of outer membrane proteins of the protobacterium Bartonella henselae (Bartonellaceae). GENETICS AND MOLECULAR RESEARCH 2011; 10:1789-818. [DOI: 10.4238/vol10-3gmr1153] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Martínez-Martínez L, Calvo J. Desarrollo de las resistencias a los antibióticos: causas, consecuencias y su importancia para la salud pública. Enferm Infecc Microbiol Clin 2010; 28 Suppl 4:4-9. [DOI: 10.1016/s0213-005x(10)70035-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Vranakis I, Sandalakis V, Chochlakis D, Tselentis Y, Psaroulaki A. DNA gyrase and topoisomerase IV mutations in an in vitro fluoroquinolone-resistant Coxiella burnetii strain. Microb Drug Resist 2010; 16:111-7. [PMID: 20438350 DOI: 10.1089/mdr.2010.0015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The etiological agent of Q fever, Coxiella burnetii, is an obligate intracellular bacterium that multiplies within a vacuole with lysosomal characteristics. Quinolones have been used as an alternative therapy for Q fever. In this study, quinolone-resistance-determining regions of the genes coding for DNA gyrase and topoisomerase IV were analyzed by DNA sequencing from an in vitro fluoroquinolone-resistant C. burnetii strain (Q212). Sequencing and aligning of DNA gyrase encoding genes (gyrA and gyrB) and topoisomerase IV genes (parC and parE) revealed one gyrA mutation leading to the amino acid substitution Asp87Gly (Escherichia coli numbering), two gyrB mutations leading to the amino acid substitutions Ser431Pro and Met518Ile, and three parC mutations leading to the amino acid substitutions Asp69Asn, Thr80Ile, and Gly104Ser. The corresponding alignment of the C. burnetii Q212 reference strain, the in vitro developed fluoroquinolone-resistant C. burnetii Q212 strain, and E. coli resulted in the identification of several other naturally occurring mutations within and outside the quinolone-resistance-determining regions of C. burnetii providing indications of possible natural resistance to fluoroquinolones. The present study adds additional potential mutations in the DNA topoisomerases that may be involved in fluoroquinolone resistance in C. burnetii due to their previous characterization in other bacterial species.
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Affiliation(s)
- Iosif Vranakis
- Laboratory of Clinical Bacteriology, Parasitology, Zoonoses, and Geographical Medicine (WHO Collaborating Center), Medical School, University of Crete, Heraklion, Greece
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Tantibhedhyangkul W, Angelakis E, Tongyoo N, Newton PN, Moore CE, Phetsouvanh R, Raoult D, Rolain JM. Intrinsic fluoroquinolone resistance in Orientia tsutsugamushi. Int J Antimicrob Agents 2010; 35:338-41. [PMID: 20138477 DOI: 10.1016/j.ijantimicag.2009.11.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 11/27/2009] [Accepted: 11/27/2009] [Indexed: 10/19/2022]
Abstract
Scrub typhus is a public health concern for a population of over a billion humans, with an estimated incidence of one million cases/year in endemic areas. Although doxycycline remains the standard therapy, fluoroquinolones have been used successfully in a few patients. However, there is also clinical evidence that fluoroquinolones are ineffective in the treatment of scrub typhus. To clarify this matter, we determined the in vitro susceptibility of Orientia tsutsugamushi strain Kato to ciprofloxacin and ofloxacin and sequenced the quinolone resistance-determining region (QRDR) of the gyrA gene, the target of fluoroquinolones, of 18 fresh isolates from the Lao PDR. Orientia tsutsugamushi strain Kato was resistant to ciprofloxacin and ofloxacin in vitro (minimum inhibitory concentration=8 microg/mL). All sequences obtained, including those from the two available genomes of O. tsutsugamushi (strains Boryong and Ikeda), had a Ser83Leu mutation in their QRDR domain that is known to be associated with fluoroquinolone resistance. These findings re-emphasise the usefulness of in silico analysis for the prediction of antibiotic resistance and suggest that fluoroquinolones should not be used in the treatment of scrub typhus.
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Affiliation(s)
- Wiwit Tantibhedhyangkul
- URMITE CNRS-IRD UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille Cedex 05, France
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Ahmad S, Hunter L, Qin A, Mann BJ, van Hoek ML. Azithromycin effectiveness against intracellular infections of Francisella. BMC Microbiol 2010; 10:123. [PMID: 20416090 PMCID: PMC2881020 DOI: 10.1186/1471-2180-10-123] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 04/23/2010] [Indexed: 12/27/2022] Open
Abstract
Background Macrolide antibiotics are commonly administered for bacterial respiratory illnesses. Azithromycin (Az) is especially noted for extremely high intracellular concentrations achieved within macrophages which is far greater than the serum concentration. Clinical strains of Type B Francisella (F.) tularensis have been reported to be resistant to Az, however our laboratory Francisella strains were found to be sensitive. We hypothesized that different strains/species of Francisella (including Type A) may have different susceptibilities to Az, a widely used and well-tolerated antibiotic. Results In vitro susceptibility testing of Az confirmed that F. tularensis subsp. holarctica Live Vaccine Strain (LVS) (Type B) was not sensitive while F. philomiragia, F. novicida, and Type A F. tularensis (NIH B38 and Schu S4 strain) were susceptible. In J774A.1 mouse macrophage cells infected with F. philomiragia, F. novicida, and F. tularensis LVS, 5 μg/ml Az applied extracellularly eliminated intracellular Francisella infections. A concentration of 25 μg/ml Az was required for Francisella-infected A549 human lung epithelial cells, suggesting that macrophages are more effective at concentrating Az than epithelial cells. Mutants of RND efflux components (tolC and ftlC) in F. novicida demonstrated less sensitivity to Az by MIC than the parental strain, but the tolC disc-inhibition assay demonstrated increased sensitivity, indicating a complex role for the outer-membrane transporter. Mutants of acrA and acrB mutants were less sensitive to Az than the parental strain, suggesting that AcrAB is not critical for the efflux of Az in F. novicida. In contrast, F. tularensis Schu S4 mutants ΔacrB and ΔacrA were more sensitive than the parental strain, indicating that the AcrAB may be important for Az efflux in F. tularensis Schu S4. F. novicida LPS O-antigen mutants (wbtN, wbtE, wbtQ and wbtA) were found to be less sensitive in vitro to Az compared to the wild-type. Az treatment prolonged the survival of Galleria (G.) mellonella infected with Francisella. Conclusion These studies demonstrate that Type A Francisella strains, as well as F. novicida and F. philomiragia, are sensitive to Az in vitro. Francisella LPS and the RND efflux pump may play a role in Az sensitivity. Az also has antimicrobial activity against intracellular Francisella, suggesting that the intracellular concentration of Az is high enough to be effective against multiple strains/species of Francisella, especially in macrophages. Az treatment prolonged survival an in vivo model of Francisella-infection.
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Affiliation(s)
- Saira Ahmad
- Department of Molecular and Microbiology, National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20120, USA
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Sintchenko V. Informatics for Infectious Disease Research and Control. INFECTIOUS DISEASE INFORMATICS 2010. [PMCID: PMC7120928 DOI: 10.1007/978-1-4419-1327-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The goal of infectious disease informatics is to optimize the clinical and public health management of infectious diseases through improvements in the development and use of antimicrobials, the design of more effective vaccines, the identification of biomarkers for life-threatening infections, a better understanding of host-pathogen interactions, and biosurveillance and clinical decision support. Infectious disease informatics can lead to more targeted and effective approaches for the prevention, diagnosis and treatment of infections through a comprehensive review of the genetic repertoire and metabolic profiles of a pathogen. The developments in informatics have been critical in boosting the translational science and in supporting both reductionist and integrative research paradigms.
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Biswas S, Maggi RG, Papich MG, Breitschwerdt EB. Molecular mechanisms of Bartonella henselae resistance to azithromycin, pradofloxacin and enrofloxacin. J Antimicrob Chemother 2009; 65:581-2. [DOI: 10.1093/jac/dkp459] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Biswas S, Raoult D, Rolain JM. Molecular mechanism of gentamicin resistance in Bartonella henselae. Clin Microbiol Infect 2009; 15 Suppl 2:98-9. [DOI: 10.1111/j.1469-0691.2008.02178.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mapping simocyclinone D8 interaction with DNA gyrase: evidence for a new binding site on GyrB. Antimicrob Agents Chemother 2009; 54:213-20. [PMID: 19858260 DOI: 10.1128/aac.00972-09] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simocyclinone D8, a coumarin derivative isolated from Streptomyces antibioticus Tü 6040, represents an interesting new antiproliferative agent. It was originally suggested that this drug recognizes the GyrA subunit and interferes with the gyrase catalytic cycle by preventing its binding to DNA. To further characterize the mode of action of this antibiotic, we investigated its binding to the reconstituted DNA gyrase (A(2)B(2)) as well as to its GyrA and GyrB subunits and the individual domains of these proteins, by performing protein melting and proteolytic digestion studies as well as inhibition assays. Two binding sites were identified, one (anticipated) in the N-terminal domain of GyrA (GyrA59) and the other (unexpected) at the C-terminal domain of GyrB (GyrB47). Stabilization of the A subunit appears to be considerably more effective than stabilization of the B subunit. Our data suggest that these two distinct sites could cooperate in the reconstituted enzyme.
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