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Belkhou C, Tadeo RT, Bacigalupe R, Valles-Colomer M, Chaffron S, Joossens M, Obregon A, Marín Reyes L, Trujillo O, Huys GRB, Raes J. Treponema peruense sp. nov., a commensal spirochaete isolated from human faeces. Int J Syst Evol Microbiol 2021; 71. [PMID: 34672919 PMCID: PMC8604162 DOI: 10.1099/ijsem.0.005050] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A Gram-stain-negative, obligatory anaerobic spirochaete (RCC2812T) was isolated from a faecal sample obtained from an individual residing in a remote Amazonian community in Peru. The bacterium showed highest 16S rRNA gene sequence similarity to the pig intestinal spirochete Treponema succinifaciens (89.48 %). Average nucleotide identity values between strain RCC2812T and all available Treponema genomes from validated type strains were all <73 %, thus clearly lower than the species delineation threshold. The DNA G+C content of RCC2812T was 41.24 mol%. Phenotypic characterization using the API-ZYM and API 20A systems confirmed the divergent position of this bacterium within the genus Treponema. Strain RCC2812T could be differentiated from the phylogenetically most closely related T. succinifaciens by the presence of alkaline phosphatase and α -glucosidase activities. Unlike T. succinifaciens, strain RCC2812T grew equally well with or without serum. Strain RCC2812T is the first commensal Treponema isolated from the human faecal microbiota of remote populations, and based on the collected data represents a novel Treponema species for which the name Treponema peruense sp. nov. is proposed. The type strain is RCC2812T (=LMG 31794T=CIP 111910T).
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Affiliation(s)
- Claire Belkhou
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Raul Tito Tadeo
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Rodrigo Bacigalupe
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Mireia Valles-Colomer
- Centre for Integrative Biology (CIBIO), Università degli Studi di Trento (UNITN), Trento, Italy
| | | | - Marie Joossens
- Department of Biochemistry and microbiology, Universiteit Gent, Gent, Belgium
| | - Alexandra Obregon
- Department of Genetic Counseling, College of Health Professions, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Luis Marín Reyes
- Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru
| | - Omar Trujillo
- Centro Nacional de Salud Intercultural, Instituto Nacional de Salud, Lima, Peru
| | - Geert R B Huys
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
| | - Jeroen Raes
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven, Belgium
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Resistance to rifampicin: a review. J Antibiot (Tokyo) 2014; 67:625-30. [PMID: 25118103 DOI: 10.1038/ja.2014.107] [Citation(s) in RCA: 217] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 06/28/2014] [Accepted: 07/04/2014] [Indexed: 11/08/2022]
Abstract
Resistance to rifampicin (RIF) is a broad subject covering not just the mechanism of clinical resistance, nearly always due to a genetic change in the β subunit of bacterial RNA polymerase (RNAP), but also how studies of resistant polymerases have helped us understand the structure of the enzyme, the intricacies of the transcription process and its role in complex physiological pathways. This review can only scratch the surface of these phenomena. The identification, in strains of Escherichia coli, of the positions within β of the mutations determining resistance is discussed in some detail, as are mutations in organisms that are therapeutic targets of RIF, in particular Mycobacterium tuberculosis. Interestingly, changes in the same three codons of the consensus sequence occur repeatedly in unrelated RIF-resistant (RIF(r)) clinical isolates of several different bacterial species, and a single mutation predominates in mycobacteria. The utilization of our knowledge of these mutations to develop rapid screening tests for detecting resistance is briefly discussed. Cross-resistance among rifamycins has been a topic of controversy; current thinking is that there is no difference in the susceptibility of RNAP mutants to RIF, rifapentine and rifabutin. Also summarized are intrinsic RIF resistance and other resistance mechanisms.
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Trad S, El Hajjam M, Dupin N, Emile JF, Hanslik T, Sène D. [Hepatomegaly in a 62-year-old woman]. Rev Med Interne 2012; 33:713-7. [PMID: 22974483 DOI: 10.1016/j.revmed.2012.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 07/05/2012] [Indexed: 10/27/2022]
Affiliation(s)
- S Trad
- Service de médecine interne, hôpital Ambroise-Paré, 92104 Boulogne-Billancourt, France.
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Characterization of a rifampin-inactivating glycosyltransferase from a screen of environmental actinomycetes. Antimicrob Agents Chemother 2012; 56:5061-9. [PMID: 22802246 DOI: 10.1128/aac.01166-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Identifying and understanding the collection of all antibiotic resistance determinants presented in the global microbiota, the antibiotic resistome, provides insight into the evolution of antibiotic resistance and critical information for the development of future antimicrobials. The rifamycins are broad-spectrum antibiotics that target bacterial transcription by inhibition of RNA polymerase. Although mutational alteration of the drug target is the predominant mechanism of resistance to this family of antibiotics in the clinic, a number of diverse inactivation mechanisms have also been reported. In this report, we investigate a subset of environmental rifampin-resistant actinomycete isolates and identify a diverse collection of rifampin inactivation mechanisms. We describe a single isolate, WAC1438, capable of inactivating rifampin by glycosylation. A draft genome sequence of WAC1438 (most closely related to Streptomyces speibonae, according to a 16S rRNA gene comparison) was assembled, and the associated rifampin glycosyltransferase open reading frame, rgt1438, was identified. The role of rgt1438 in rifampin resistance was confirmed by its disruption in the bacterial chromosome, resulting in a loss of antibiotic inactivation and a 4-fold decrease in MIC. Interestingly, examination of the RNA polymerase β-subunit sequence of WAC1438 suggests that it harbors a resistant target and thus possesses dual mechanisms of rifamycin resistance. Using an in vitro assay with purified enzyme, Rgt1438 could inactivate a variety of rifamycin antibiotics with comparable steady-state kinetics constants. Our results identify rgt1438 as a rifampin resistance determinant from WAC1438 capable of inactivating an assortment of rifamycins, adding a new element to the rifampin resistome.
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Cayrou C, Raoult D, Drancourt M. Broad-spectrum antibiotic resistance of Planctomycetes organisms determined by Etest. J Antimicrob Chemother 2010; 65:2119-22. [PMID: 20699245 DOI: 10.1093/jac/dkq290] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES The in vitro susceptibility of Planctomycetes organisms to antibiotics has seldom been studied and when it has, a variety of methods have been used. The objective of the study was to expand the knowledge of Planctomycetes antibiotic susceptibility patterns. METHODS Planctomyces maris, Planctomyces brasiliensis, Blastopirellula marina, Planctomyces limnophilus, Gemmata obscuriglobus and Rhodopirellula baltica reference strains were tested for in vitro susceptibility to 18 antibiotics, representing 11 antibiotic families, using the Etest method. RESULTS All Planctomycetes organisms were found to be resistant to β-lactams, with MICs of > 32 mg/L for penicillin G and imipenem, and MICs of > 256 mg/L for ampicillin, cefalotin and ceftriaxone. The organisms were resistant to nalidixic acid and vancomycin (MIC > 256 mg/L), but susceptible to tetracycline (MICs < 0.016-0.5 mg/L) and doxycycline (MICs < 0.016-1 mg/L). The MIC of gentamicin ranged from 1 mg/L (P. limnophilus) to > 256 mg/L (B. marina and P. brasiliensis); the MIC of erythromycin ranged from 0.032 mg/L (P. limnophilus) to 2 mg/L (P. brasiliensis); the MIC for ciprofloxacin ranged from 0.008 mg/L (R. baltica) to > 32 mg/L (P. brasiliensis); and the MIC for colistin ranged from 0.125 mg/L (P. limnophilus) to 96 mg/L (B. marina). CONCLUSIONS In addition to shedding new light on the biology of Planctomycetes organisms, these data could be used for the further phenotypic characterization of Planctomycetes organisms, and for the optimization of culture media for the primary isolation and growth of Planctomycetes organisms from contaminated specimens.
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Affiliation(s)
- C Cayrou
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 IRD 3R198, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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YANO T, MOE KK, CHUMA T, MISAWA N. Antimicrobial Susceptibility of Treponema phagedenis-Like Spirochetes Isolated from Dairy Cattle with Papillomatous Digital Dermatitis Lesions in Japan. J Vet Med Sci 2010; 72:379-82. [DOI: 10.1292/jvms.09-0418] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Takahisa YANO
- Laboratory of Veterinary Public Health, Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki
| | - Kyaw Kyaw MOE
- Laboratory of Veterinary Public Health, Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki
| | - Takehisa CHUMA
- Laboratory of Veterinary Public Health, Department of Veterinary Science, Faculty of Agriculture, Kagoshima University
| | - Naoaki MISAWA
- Laboratory of Veterinary Public Health, Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki
- Project for Zoonoses Education and Research, University of Miyazaki
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Abstract
Syphilis is a multistage infectious disease that is usually transmitted through contact with active lesions of a sexual partner or from an infected pregnant woman to her fetus. Despite elimination efforts, syphilis remains endemic in many developing countries and has reemerged in several developed countries, including China, where a widespread epidemic recently occurred. In the absence of a vaccine, syphilis control is largely dependent upon identification of infected individuals and treatment of these individuals and their contacts with antibiotics. Although penicillin is still effective, clinically significant resistance to macrolides, a second-line alternative to penicillin, has emerged. Macrolide-resistant strains of Treponema pallidum are now prevalent in several developed countries. An understanding of the genetic basis of T. pallidum antibiotic resistance is essential to enable molecular surveillance. This review discusses the genetic basis of T. pallidum macrolide resistance and the potential of this spirochete to develop additional antibiotic resistance that could seriously compromise syphilis treatment and control.
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Pringle M, Bergsten C, Fernström LL, Höök H, Johansson KE. Isolation and characterization of Treponema phagedenis-like spirochetes from digital dermatitis lesions in Swedish dairy cattle. Acta Vet Scand 2008; 50:40. [PMID: 18937826 PMCID: PMC2576277 DOI: 10.1186/1751-0147-50-40] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 10/20/2008] [Indexed: 11/10/2022] Open
Abstract
Background Digital dermatitis in cattle is an emerging infectious disease. Ulcerative lesions are typically located on the plantar skin between the heel bulbs and adjacent to the coronet. Spirochetes of the genus Treponema are found in high numbers in the lesions and are likely to be involved in the pathogenesis. The aim of this study was to obtain pure cultures of spirochetes from cattle with digital dermatitis and to describe them further. Methods Tissue samples and swabs from active digital dermatitis lesions were used for culturing. Pure isolates were subjected to, molecular typing through 16S rRNA gene sequencing, pulsed-field gel electrophoresis (PFGE), random amplified polymorphic DNA (RAPD) and an intergenic spacer PCR developed for Treponema spp. as well as API-ZYM and antimicrobial susceptibility tests. The antimicrobial agents used were tiamulin, valnemulin, tylosin, aivlosin, lincomycin and doxycycline. Results Seven spirochete isolates from five herds were obtained. Both 16S rRNA gene sequences, which were identical except for three polymorphic nucleotide positions, and the intergenic spacer PCR indicated that all isolates were of one yet unnamed species, most closely related to Treponema phagedenis. The enzymatic profile and antimicrobial susceptibility pattern were also similar for all isolates. However it was possible to separate the isolates through their PFGE and RAPD banding pattern. Conclusion This is the first report on isolation of a Treponema sp. from cattle with digital dermatitis in Scandinavia. The phylotype isolated has previously been cultured from samples from cattle in the USA and the UK and is closely related to T. phagedenis. While very similar, the isolates in this study were possible to differentiate through PFGE and RAPD indicating that these methods are suitable for subtyping of this phylotype. No antimicrobial resistance could be detected among the tested isolates.
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Kim H, Kim SH, Ying YH, Kim HJ, Koh YH, Kim CJ, Lee SH, Cha CY, Kook YH, Kim BJ. Mechanism of natural rifampin resistance of Streptomyces spp. Syst Appl Microbiol 2005; 28:398-404. [PMID: 16094866 DOI: 10.1016/j.syapm.2005.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a previous phylogenetic study of the genus Streptomyces using the rpoB gene, N531, which stands for an aspargine residue in position 531 of RpoB instead of serine (S531), known to be associated with natural rifampin resistance in several organisms, was also observed in the RpoB of several Streptomyces species. To determine whether N531 is associated with the rifampin resistance of Streptomyces strains, we analyzed the rifampin minimum inhibitory concentrations (MICs) of 11 strains of the N531 RpoB type (putative rifampin resistant strains) and of 12 strains of the S531 RpoB type. (putative rifampin susceptible strains). In general, the N531 RpoB types showed higher MIC levels (16-128 microg/ml) than the S531 RpoB types (0-8 microg/ml). To determine the isolation frequencies of N531 RpoB types versus rifampin concentration, we applied screening methods involving different rifampin concentrations (0, 20 and 100 microg/ml) to Korean soils. Higher isolation frequencies of the N531 RpoB types were observed at the higher rifampin concentrations. In addition, during the course of this study we developed an allele specific PCR method to detect rifampin resistant Streptomyces strains. Our results strongly suggested that N531 might be involved in a major mechanism of natural rifampin resistance in strains of the genus Streptomyces.
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Affiliation(s)
- Hong Kim
- Department of Microbiology, College of Medicine, Seoul National University, 28 Yongon-dong, Chongno-gu, Seoul 110-799, Republic of Korea
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Kim BJ, Kim CJ, Chun J, Koh YH, Lee SH, Hyun JW, Cha CY, Kook YH. Phylogenetic analysis of the genera Streptomyces and Kitasatospora based on partial RNA polymerase beta-subunit gene (rpoB) sequences. Int J Syst Evol Microbiol 2004; 54:593-598. [PMID: 15023980 DOI: 10.1099/ijs.0.02941-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The RNA polymerase beta-subunit genes (rpoB) of 67 Streptomyces strains, representing 57 species, five Kitasatospora strains and Micromonospora echinospora KCTC 9549 were partially sequenced using a pair of rpoB PCR primers. Among the streptomycetes, 99.7-100 % similarity within the same species and 90.2-99.3 % similarity at the interspecific level were observed by analysis of the determined rpoB sequences. The topology of the phylogenetic tree based on rpoB sequences was similar to that of 16S rDNA. The five Kitasatospora strains formed a stable monophyletic clade and a sister group to the clade comprising all Streptomyces species. Although there were several discrepancies in the details, considerable agreement was found between the results of rpoB analysis and those of numerical phenetic classification. This study demonstrates that analysis of rpoB can be used as an alternative genetic method in parallel to conventional taxonomic methods, including numerical phenetic and 16S rDNA analyses, for the phylogenetic analyses of the genera Streptomyces and Kitasatospora.
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Affiliation(s)
- Bum-Joon Kim
- Department of Microbiology, College of Medicine, Seoul National University, Seoul 110-799, Korea
| | - Chang-Jin Kim
- Korea Research Institute of Bioscience and Biotechnology, Yusung, Taejon 305-600, Korea
| | - Jongsik Chun
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Young-Hwan Koh
- Department of Food Science and Engineering, Cheju National University, Jeju 690-756, Korea
| | - Sueng-Hyun Lee
- Department of Microbiology, College of Medicine, Konkuk University, Chungju 380-230, Korea
| | - Jin-Won Hyun
- Department of Biochemistry, College of Medicine, Cheju National University, Jeju 690-756, Korea
| | - Chang-Yong Cha
- Department of Microbiology, College of Medicine, Seoul National University, Seoul 110-799, Korea
| | - Yoon-Hoh Kook
- Department of Microbiology, College of Medicine, Seoul National University, Seoul 110-799, Korea
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