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Yamakawa AC, Haisi A, Kmetiuk LB, Pellizzaro M, Mendes JCR, Canavessi AMO, Ullmann LS, de Castro WAC, Pessoa Araújo Júnior J, dos Santos AP, Biondo AW. Molecular detection of feline hemoplasmas and retroviruses in free-roaming and shelter cats within a university campus. JFMS Open Rep 2023; 9:20551169221148672. [PMID: 37223406 PMCID: PMC10201909 DOI: 10.1177/20551169221148672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Objectives The aim of the present study was to assess the frequency of hemoplasma, feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) infections in cats living in an on-campus shelter and free-roaming cats within a university campus in Brazil. Methods Blood samples were tested using quantitative PCR for hemoplasma, FIV and FeLV. Positive hemoplasma samples were sequenced. Associations between hemoplasma detection and living situation, sex, flea and/or tick parasitism, and coinfection with FIV and FeLV, were assessed using Fisher's exact test and the respective odds ratios were calculated. Results Overall, 6/45 (13.3%) cats tested positive: four (8.9%) were infected with 'Candidatus Mycoplasma haemominutum' and two (4.4%) with Mycoplasma haemofelis. All positive samples were from free-roaming cats (6/15; 40.0%) and had statistically significantly lower packed cell volumes (P = 0.037). Although 5/23 (21.7%) males and 1/22 (4.6%) females were positive, no statistically significant association between sex and hemoplasma infection was found (P = 0.19). Viral quantitative PCR (qPCR) was performed on 43/45 samples, among which 2/43 (4.7%) were positive for FIV and none for FeLV. Only one cat (2.3%) was coinfected with hemoplasma and FIV (P = 0.26). In addition, 4/6 (66.7%) cats that tested positive for hemoplasmas were infested by fleas (P = 0.0014) and/or ticks (P = 0.25). Conclusions and relevance These results show that even if the free-roaming cat population is clinically healthy and has adequate access to food, it may present flea infestation and hemoplasma infection with lower packed cell volume values.
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Affiliation(s)
| | - Amanda Haisi
- Biotechnology Institute, São Paulo
State University (UNESP), Botucatu, SP, Brazil
| | - Louise Bach Kmetiuk
- Graduate College of Cell and Molecular
Biology, Federal University of Paraná (UFPR), R dos Funcionários, Curitiba, PR,
Brazil
| | - Maysa Pellizzaro
- Institute of Collective Health, Federal
University of Bahia, Salvador, BA, Brazil
| | | | | | | | - Wagner Antônio Chiba de Castro
- Latin-American Institute of Life and
Nature Sciences, Federal University for Latin American Integration, Foz do Iguaçu,
PR, Brazil
| | | | | | - Alexander Welker Biondo
- Graduate College of Cell and Molecular
Biology, Federal University of Paraná (UFPR), R dos Funcionários, Curitiba, PR,
Brazil
- Department of Comparative Pathobiology,
Purdue University, West Lafayette, IN, USA
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Chauhan K, Aly SS, Lehenbauer TW, Tonooka KH, Glenn K, Rossitto P, Marco ML. Development of a multiplex qPCR assay for the simultaneous detection of Mycoplasma bovis, Mycoplasma species, and Acholeplasma laidlawii in milk. PeerJ 2021; 9:e11881. [PMID: 34447623 PMCID: PMC8364749 DOI: 10.7717/peerj.11881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/07/2021] [Indexed: 11/30/2022] Open
Abstract
Contagious bovine mastitis caused by Mycoplasma bovis and other Mycoplasma species including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma canadense is an economical obstacle affecting many dairy herds throughout California and elsewhere. Routine bacteriological culture-based assays for the pathogens are slow and subject to false-positive results due to the presence of the related, non-pathogenic species Acholeplasma laidlawii. To address the need for rapid and accurate detection methods, a new TaqMan multiplex, quantitative real-time PCR (qPCR) assay was developed that targets the 16S rRNA gene of Mycoplasma, rpoB gene of M. bovis, and the 16S to 23S rRNA intergenic transcribed spacer (ITS) region of A. laidlawii. qPCR amplification efficiency and range of detection were similar for individual assays in multiplex as when performed separately. The multiplex assay was able to distinguish between M. bovis and A. laidlawii as well as detect Mycoplasma spp. collectively, including Mycoplasma californicum, Mycoplasma bovigenitalium, Mycoplasma canadense, Mycoplasma arginini and Mycoplasma alkalescens. In milk, the lower limit of detection of M. bovis, M. californicum, and A. laidlawii with the multiplex assay was between 120 to 250 colony forming units (CFU) per mL. The assay was also able to simultaneously detect both M. bovis and A. laidlawii in milk when present in moderate (103 to 104 CFU/mL) to high (106 to 107 CFU/mL) quantities. Compared to laboratory culture-based methods, the multiplex qPCR diagnostic specificity (Sp) was 100% (95% CI [86.8-100]; n = 26) and diagnostic sensitivity (Se) was 92.3% (95% CI [74.9-99.1]; n = 26) for Mycoplasma species in milk samples collected from California dairy farms. Similarly, the Sp was 100% (95% CI [90.5-100]; n = 37) and Se was 93.3% (95% CI [68.1-99.8]; n = 15) for M. bovis. Our assay can detect and distinguish among M. bovis, other prevalent Mycoplasma spp., and non-pathogenic Acholeplasma laidlawii for effective identification and control of mycoplasma mastitis, ultimately supporting dairy cattle health and high-quality dairy products in California.
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Affiliation(s)
- Kanika Chauhan
- Veterinary Medicine Teaching & Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
- Department of Food Science and Technology, University of California, Davis, Davis, CA, United States
| | - Sharif S. Aly
- Veterinary Medicine Teaching & Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Terry W. Lehenbauer
- Veterinary Medicine Teaching & Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Karen H. Tonooka
- Veterinary Medicine Teaching & Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
| | - Kathy Glenn
- Veterinary Medicine Teaching & Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
| | - Paul Rossitto
- Veterinary Medicine Teaching & Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, United States
| | - Maria L. Marco
- Department of Food Science and Technology, University of California, Davis, Davis, CA, United States
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CHARACTERIZING THE EPIDEMIOLOGY OF HISTORIC AND NOVEL PATHOGENS IN BLANDING'S TURTLES ( EMYDOIDEA BLANDINGII). J Zoo Wildl Med 2021; 51:606-617. [PMID: 33480536 DOI: 10.1638/2019-0154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2020] [Indexed: 11/21/2022] Open
Abstract
Pathogens such as herpesviruses, Mycoplasma spp., and frog virus 3-like ranavirus have contributed to morbidity and mortality in many species of free-living and zoo-maintained chelonians. However, their prevalence is understudied in Blanding's turtles (Emydoidea blandingii) across North America. To assess the presence of these pathogens, Blanding's turtles were sampled in Lake County, Illinois, in 2017 (N = 213) and 2018 (N = 160). DNA from cloacal-oral swabs was assayed for four ranaviruses, three Mycoplasma spp., two Salmonella spp., Emydoidea herpesvirus 1 (EBHV1), and tortoise intranuclear coccidiosis (TINC) using a multiplex quantitative polymerase chain reaction (qPCR). Pathogens were most frequently detected in adult turtles (n = 25) and rarely in subadults (n = 2) or juveniles (n = 1). EBHV1 was detected in 22 individuals with no clinical signs of illness, most (n = 20) occurring in the month of May (P < 0.0001). EBHV1 cases at one study site significantly clustered within the same 0.64-km area from 17 to 22 May 2017 (P < 0.0001) and 14 to 15 May 2018 (P = 0.0006). Individuals were rarely positive for Salmonella typhimurium (n = 6). A novel Mycoplasma sp. sharing high homology with other emydid Mycoplasma spp. was detected in one turtle with nasal discharge. Neither TINC nor any ranaviruses were detected. Continued monitoring of this population and habitat may facilitate identification of risk factors for pathogen occurrence and clarify the impact of infectious diseases on Blanding's turtle conservation outcomes.
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Molecular Differentiation of Mycoplasma gallisepticum Outbreaks: A Last Decade Study on Italian Farms Using GTS and MLST. Vaccines (Basel) 2020; 8:vaccines8040665. [PMID: 33182244 PMCID: PMC7712042 DOI: 10.3390/vaccines8040665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 11/17/2022] Open
Abstract
Mycoplasma gallisepticum (MG) infects many avian species and leads to significant economic losses in the poultry industry. Transmission of this pathogen occurs both horizontally and vertically, and strategies to avoid the spread of MG rely on vaccination and the application of biosecurity measures to maintain breeder groups as pathogen-free. Two live attenuated MG vaccine strains are licensed in Italy: 6/85 and ts-11. After their introduction, the implementation of adequate genotyping tools became necessary to distinguish between field and vaccine strains and to guarantee proper infection monitoring activity. In this study, 40 Italian MG isolates collected between 2010–2019 from both vaccinated and unvaccinated farms were genotyped using gene-targeted sequencing (GTS) of the cythadesin gene mgc2 and multilocus sequence typing (MLST) based on six housekeeping genes. The discriminatory power of GTS typing ensures 6/85-like strain identification, but the technique does not allow the identification ts-11 strains; conversely, MLST differentiates both vaccine strains, describing more detailed interrelation structures. Our study describes MG genetic scenario within a mixed farming context. In conclusion, the use of adequate typing methods is essential to understand the evolutionary dynamics of MG strains in a particular area and to conduct epidemiological investigations in the avian population.
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Volokhov DV, Grózner D, Gyuranecz M, Ferguson-Noel N, Gao Y, Bradbury JM, Whittaker P, Chizhikov VE, Szathmary S, Stipkovits L. Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese ( Anser anser domesticus) with reproductive pathology. Int J Syst Evol Microbiol 2020; 70:2369-2381. [PMID: 32068526 DOI: 10.1099/ijsem.0.004052] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S-23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02-99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00-96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma. Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis. Based on the genetic data, we propose a novel species of the genus Mycoplasma, for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.
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Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Dénes Grózner
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, Budapest, 1143, Hungary.,Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Hungária krt. 23-25, Budapest, 1143, Hungary
| | - Miklós Gyuranecz
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Hungária krt. 23-25, Budapest, 1143, Hungary.,Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, Budapest, 1143, Hungary
| | - Naola Ferguson-Noel
- Poultry Diagnostic & Research Center, University of Georgia, 953 College Station Rd., Athens, GA 30602, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Janet M Bradbury
- University of Liverpool, School of Veterinary Science, Leahurst Campus, Neston, CH64 7TE, UK
| | - Paul Whittaker
- Present address: Currently retired from the US FDA, Maryland, USA.,Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Dr., College Park, MD 20740, USA
| | - Vladimir E Chizhikov
- Present address: Currently retired from the US FDA, Maryland, USA.,Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Susan Szathmary
- RT-Europe Research Center, 9200 Var 2, Mosonmagyaróvár, Hungary.,Galen Bio, Inc. Carlsbad, 5922 Farnsworth Ct Carlsbad, CA 92008, USA
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Volokhov DV, Gulland FM, Gao Y, Chizhikov VE. Ureaplasma miroungigenitalium sp. nov. isolated from northern elephant seals (Mirounga angustirostris) and Ureaplasma zalophigenitalium sp. nov. isolated from California sea lions (Zalophus californianus). Int J Syst Evol Microbiol 2020; 70:153-164. [DOI: 10.1099/ijsem.0.003729] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Dmitriy V. Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | | | - Yamei Gao
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Vladimir E. Chizhikov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
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7
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Volokhov DV, Batac F, Gao Y, Miller M, Chizhikov VE. Mycoplasma enhydrae sp. nov. isolated from southern sea otters (Enhydra lutris nereis). Int J Syst Evol Microbiol 2019; 69:363-370. [DOI: 10.1099/ijsem.0.003144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Dmitriy V. Volokhov
- 1Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Francesca Batac
- 2California Department of Fish and Wildlife, Marine Wildlife Veterinary Care and Research Center, 151 McAllister Way, Santa Cruz, CA 95060, USA
| | - Yamei Gao
- 1Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Melissa Miller
- 2California Department of Fish and Wildlife, Marine Wildlife Veterinary Care and Research Center, 151 McAllister Way, Santa Cruz, CA 95060, USA
| | - Vladimir E. Chizhikov
- 1Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
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A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera. Antonie van Leeuwenhoek 2018; 112:561-588. [PMID: 30392177 DOI: 10.1007/s10482-018-1188-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/14/2018] [Indexed: 01/01/2023]
Abstract
The "Spiroplasma cluster" is a taxonomically heterogeneous assemblage within the phylum Tenericutes encompassing different Entomoplasmatales species as well as the genus Mycoplasma, type genus of the order Mycoplasmatales. Within this cluster, the family Entomoplasmataceae contains two non-cohesive genera Entomoplasma and Mesoplasma with their members exhibiting extensive polyphyletic branching; additionally, the genus Mycoplasma is also embedded within this family. Genome sequences are now available for all 19 Entomoplasmataceae species with validly published names, as well as 6 of the 7 species from the genus Mycoplasma. With the aim of developing a reliable phylogenetic and taxonomic framework for the family Entomoplasmataceae, exhaustive phylogenetic and comparative genomic studies were carried out on these genome sequences. Phylogenetic trees were constructed based on concatenated sequences of 121 core proteins for this cluster, 67 conserved proteins shared with the phylum Firmicutes, 40 ribosomal proteins, three major subunits of RNA polymerase (RpoA, B and C) by different means and also for the 16S rRNA gene sequences. The interspecies relationships as well as different species groups observed in these trees were identical and robustly resolved. In all of these trees, members of the genera Mesoplasma and Entomoplasma formed three and two distinct clades, respectively, which were interspersed among the members of the other genus. The observed species groupings in the phylogenetic trees are independently strongly supported by our identification of 103 novel molecular markers or synapomorphies in the forms of conserved signature indels and conserved signature proteins, which are uniquely shared by the members of different observed species clades. To account for the different observed species clades, we are proposing a division of the genus Mesoplasma into an emended genus Mesoplasma and two new genera Tullyiplasma gen. nov. and Edwardiiplasma gen. nov. Likewise, to recognize the distinct species groupings of Entomoplasma, we are proposing its division into an emended genus Entomoplasma and a new genus Williamsoniiplasma gen. nov. Lastly, to rectify the long-existing taxonomic anomaly caused by the presence of genus Mycoplasma (order Mycoplasmatales) within the Entomoplasmatales, we are proposing an emendation of the family Mycoplasmataceae to include both Entomoplasmataceae plus Mycoplasma species and an emendation of the order Mycoplasmatales, which now comprises of the emended family Mycoplasmataceae and the family Spiroplasmataceae. The taxonomic reclassifications proposed here accurately reflect the species relationships within this group of Tenericutes and they should lead to a better understanding of their biological and pathogenic characteristics.
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Gupta RS, Sawnani S, Adeolu M, Alnajar S, Oren A. Phylogenetic framework for the phylum Tenericutes based on genome sequence data: proposal for the creation of a new order Mycoplasmoidales ord. nov., containing two new families Mycoplasmoidaceae fam. nov. and Metamycoplasmataceae fam. nov. harbouring Eperythrozoon, Ureaplasma and five novel genera. Antonie van Leeuwenhoek 2018; 111:1583-1630. [PMID: 29556819 DOI: 10.1007/s10482-018-1047-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/08/2018] [Indexed: 12/19/2022]
Abstract
The genus Mycoplasma, including species earlier classified in the genera Eperythrozoon and Haemobartonella, contains ~ 120 species and constitutes an extensively polyphyletic assemblage of bacteria within the phylum Tenericutes. Due to their small genome sizes and lack of unique characteristics, the relationships among the mycoplasmas/Tenericutes are not reliably discerned. Using genome sequences for 140 Tenericutes, their evolutionary relationships were examined using multiple independent approaches. Phylogenomic trees were constructed for 63 conserved proteins, 45 ribosomal proteins, three main subunits of RNA polymerase and 16S rRNA gene sequences. In all of these trees, Tenericutes species reliably grouped into four main clades designated as the "Acholeplasma", "Spiroplasma", "Pneumoniae" and "Hominis" clusters. These clades are also distinguished based on a similarity matrix constructed based on 16S rRNA gene sequences. Mycoplasma species were dispersed across 3 of these 4 clades highlighting their extensive polyphyly. In parallel, our comparative genomic analyses have identified > 100 conserved signature indels (CSIs) and 14 conserved signature proteins (CSPs), which are uniquely shared by the members of four identified clades, strongly supporting their monophyly and identifying them in molecular terms. Mycoplasma mycoides, the type species of the genus Mycoplasma, and a small number of other Mycoplasma species, formed a strongly supported clade within the "Spiroplasma" cluster. Nine CSIs and 14 CSPs reliably distinguish this clade from all other Mycoplasmatales species. The remainder of the Mycoplasmatales species are part of the "Pneumoniae" and "Hominis" clusters, which group together in phylogenetic trees. Here we are proposing that the order Mycoplasmatales should be emended to encompass only the Mycoplasma species within the "Spiroplasma" cluster and that a new order, Mycoplasmoidales ord. nov., should be created to encompass the other Mycoplasma species. The "Pneumoniae" and the "Hominis" clusters are proposed as two new families, Mycoplasmoidaceae fam. nov., which includes the genera Eperythrozoon, Ureaplasma, and the newly proposed genera Malacoplasma and Mycoplasmoides, and Metamycoplasmataceae fam. nov. to contain the newly proposed genera Metamycoplasma, Mycoplasmopsis, and Mesomycoplasma. The results presented here allow reliable discernment, both in phylogenetic and molecular terms, of the members of the two proposed families as well as different described genera within these families including members of the genus Eperythrozoon, which is comprised of uncultivable organisms. The taxonomic reclassifications proposed here, which more accurately portray the genetic diversity among the Tenericutes/Mycoplasma species, provide a new framework for understanding the biological and clinical aspects of these important microbes.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada.
| | - Sahil Sawnani
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Seema Alnajar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401, Jerusalem, Israel
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Yavari CA, Ramírez AS, Nicholas RAJ, Radford AD, Darby AC, Bradbury JM. Mycoplasma tullyi sp. nov., isolated from penguins of the genus Spheniscus. Int J Syst Evol Microbiol 2017; 67:3692-3698. [PMID: 28895509 DOI: 10.1099/ijsem.0.002052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mycoplasma isolated from the liver of a dead Humboldt penguin (Spheniscus humboldti) and designated strain 56A97T, was investigated to determine its taxonomic status. Complete 16S rRNA gene sequence analysis indicated that the organism was most closely related to Mycoplasma gallisepticum and Mycoplasma imitans(99.7 and 99.9 % similarity, respectively). The average DNA-DNA hybridization values between strain 56A97T and M. gallisepticum and M. imitans were 39.5 and 30 %, respectively and the Genome to Genome Distance Calculator gave results of 29.10 and 23.50 %, respectively. The 16S-23S rRNA intergenic spacer was 72-73 % similar to M. gallisepticum strains and 52.2 % to M. imitans. A partial sequence of rpoB was 91.1-92 % similar to M. gallisepticum strains and 84.7 % to M. imitans. Colonies possessed a typical fried-egg appearance and electron micrographs revealed the lack of a cell wall and a nearly spherical morphology, with an electron-dense tip-like structure on some flask-shaped cells. The isolate required sterol for growth, fermented glucose, adsorbed and haemolysed erythrocytes, but did not hydrolyse arginine or urea. The strain was compared serologically against 110 previously described Mycoplasma reference strains, showing that, except for M. gallisepticum, strain 56A97T is not related to any of the previously described species, although weak cross-reactions were evident. Genomic information, serological reactions and phenotypic properties demonstrate that this organism represents a novel species of the genus Mycoplasma, for which the name Mycoplasma tullyi sp. nov. is proposed; the type strain is 56A97T (ATCC BAA-1432T, DSM 21909T, NCTC 11747T).
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Affiliation(s)
- Christine A Yavari
- University of Liverpool, Institute of Infection and Global Health, Leahurst Campus, Neston, CH64 7TE, UK
| | - Ana S Ramírez
- Unidad de Epidemiología y Medicina Preventiva, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Islas Canarias, Spain
| | | | - Alan D Radford
- University of Liverpool, Institute of Infection and Global Health, Leahurst Campus, Neston, CH64 7TE, UK
| | - Alistair C Darby
- University of Liverpool, Institute of Integrative Biology, Liverpool, L69 7ZB, UK
| | - Janet M Bradbury
- University of Liverpool, Institute of Infection and Global Health, Leahurst Campus, Neston, CH64 7TE, UK
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MOLECULAR IDENTIFICATION AND SEQUENCE CHARACTERIZATION OF MYCOPLASMAS IN FREE-LIVING BIRDS OF PREY. J Zoo Wildl Med 2016; 47:917-922. [PMID: 27691956 DOI: 10.1638/2015-0259.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Mycoplasma spp. have been detected in birds of prey, but their prevalence in free living raptors and their significance to birds' health need further investigation. Molecular techniques have been increasingly used to identify mycoplasmas in various avian species, due to the fastidious nature of these pathogens hampering traditional bacteriologic tests. This study reports the identification of 23 novel mycoplasma sequences during the monitoring of 62 birds of prey on admission to wildlife centers in Sardinia, Italy. Molecular investigation performed on pharyngeal swabs revealed 26 birds positive to Mycoplasma (42%). Sequence analysis based on 16S rRNA, 16S-23S rRNA intergenic spacer, and RNA polymerase β subunit (rpoB) gene highlighted cluster assignment and phylogenetic relationships among the identified types, classified within the hominis group. Additionally, Ornithobacterium rhinotracheale , associated with respiratory disease in poultry, was identified in 17 birds (27%). Potential coinfection and mycoplasma opportunistic nature present implications for raptor species conservation.
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Edouard S, Courtois GD, Gautret P, Jouve JL, Minodier P, Noël G, Roch A, Brouqui P, Stein A, Drancourt M, Fournier PE, Raoult D. High Prevalence of Mycoplasma faucium DNA in the Human Oropharynx. J Clin Microbiol 2016; 54:194-6. [PMID: 26511735 PMCID: PMC4702739 DOI: 10.1128/jcm.02068-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/19/2015] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma faucium has recently been associated with brain abscesses and seems to originate from the mouth. We evaluated its prevalence by quantitative real-time PCR (qPCR) in the oropharynxes of 644 subjects and found that 25% harbored M. faucium, probably constituting the gateway for entrance of the bacteria into cerebral abscesses.
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Affiliation(s)
- Sophie Edouard
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERM U 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Hôpital de la Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Gaëlle Denis Courtois
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Hôpital de la Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Gautret
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERM U 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Jean-Luc Jouve
- Urgence Pédiatrique, Hôpital de la Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Minodier
- Urgence Pédiatrique, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Guilhem Noël
- Urgence Pédiatrique, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Antoine Roch
- Urgence Adulte, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Brouqui
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERM U 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Andreas Stein
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Hôpital La Conception, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERM U 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Hôpital de la Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERM U 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Hôpital de la Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERM U 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Hôpital de la Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
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13
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Biogeography of Nocardiopsis strains from hypersaline environments of Yunnan and Xinjiang Provinces, western China. Sci Rep 2015; 5:13323. [PMID: 26289784 PMCID: PMC4542603 DOI: 10.1038/srep13323] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 07/23/2015] [Indexed: 12/19/2022] Open
Abstract
The genus Nocardiopsis is a widespread group within the phylum Actinobacteria and has been isolated from various salty environments worldwide. However, little is known about whether biogeography affects Nocardiopsis distribution in various hypersaline environments. Such information is essential for understanding the ecology of Nocardiopsis. Here we analyzed 16S rRNA, gyrB, rpoB and sodA genes of 78 Nocardiopsis strains isolated from hypersaline environments in Yunnan and Xinjiang Provinces of western China. The obtained Nocardiopsis strains were classified into five operational taxonomic units, each comprising location-specific phylo- and genotypes. Statistical analyses showed that spatial distance and environmental factors substantially influenced Nocardiopsis distribution in hypersaline environments: the former had stronger influence at large spatial scales, whereas the latter was more influential at small spatial scales.
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14
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Specificity and Strain-Typing Capabilities of Nanorod Array-Surface Enhanced Raman Spectroscopy for Mycoplasma pneumoniae Detection. PLoS One 2015; 10:e0131831. [PMID: 26121242 PMCID: PMC4487258 DOI: 10.1371/journal.pone.0131831] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 06/07/2015] [Indexed: 01/29/2023] Open
Abstract
Mycoplasma pneumoniae is a cell wall-less bacterial pathogen of the human respiratory tract that accounts for > 20% of all community-acquired pneumonia (CAP). At present the most effective means for detection and strain-typing is quantitative polymerase chain reaction (qPCR), which can exhibit excellent sensitivity and specificity but requires separate tests for detection and genotyping, lacks standardization between available tests and between labs, and has limited practicality for widespread, point-of-care use. We have developed and previously described a silver nanorod array-surface enhanced Raman Spectroscopy (NA-SERS) biosensing platform capable of detecting M. pneumoniae with statistically significant specificity and sensitivity in simulated and true clinical throat swab samples, and the ability to distinguish between reference strains of the two main genotypes of M. pneumoniae. Furthermore, we have established a qualitative lower endpoint of detection for NA-SERS of < 1 genome equivalent (cell/μl) and a quantitative multivariate detection limit of 5.3 ± 1 cells/μl. Here we demonstrate using partial least squares- discriminatory analysis (PLS-DA) of sample spectra that NA-SERS correctly identified M. pneumoniae clinical isolates from globally diverse origins and distinguished these from a panel of 12 other human commensal and pathogenic mycoplasma species with 100% cross-validated statistical accuracy. Furthermore, PLS-DA correctly classified by strain type all 30 clinical isolates with 96% cross-validated accuracy for type 1 strains, 98% cross-validated accuracy for type 2 strains, and 90% cross-validated accuracy for type 2V strains.
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15
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Jung LRC, Bomfim MRQ, Kroon EG, Nunes ÁC. Identification of Leptospira serovars by RFLP of the RNA polymerase beta subunit gene (rpoB). Braz J Microbiol 2015; 46:465-76. [PMID: 26273261 PMCID: PMC4507538 DOI: 10.1590/s1517-838246220120018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 10/29/2014] [Indexed: 11/30/2022] Open
Abstract
Leptospires are usually classified by methods based on DNA-DNA hybridization and
the conventional cross-agglutination absorption test, which uses polyclonal
antibodies against lipopolysaccharides. In this study, the amplification of the
rpoB gene, which encodes the beta-subunit of RNA
polymerase, was used as an alternative tool to identify
Leptospira. DNA extracts from sixty-eight serovars were
obtained, and the hypervariable region located between 1990 and 2500-bp in the
rpoB gene was amplified by polymerase chain reaction (PCR).
The 600-bp amplicons of the rpoB gene were digested with the
restriction endonucleases TaqI, Tru1I,
Sau3AI and MslI, and the restriction
fragments were separated by 6% polyacrylamide gel electrophoresis. Thirty-five
fragment patters were obtained from the combined data of restriction fragment
length polymorphism (PCR-RFLP) analysis and used to infer the phylogenetic
relationships among the Leptospira species and serovars. The
species assignments obtained were in full agreement with the established
taxonomic classifications. Twenty-two serovars were effectively identified based
on differences in their molecular profiles. However, the other 46 serovars
remained clustered in groups that included more than one serovar of different
species. This study demonstrates the value of RFLP analysis of PCR-amplified
rpoB as an initial method for identifying
Leptospira species and serovars.
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Affiliation(s)
- Lenice Roteia Cardoso Jung
- Universidade Federal de Minas Gerais, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maria Rosa Quaresma Bomfim
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil. ; Universidade do Ceuma, Departamento de Biologia Parasitária, Universidade Ceuma, São Luis, MA, Brasil, Universidade Ceuma, Departamento de Biologia Parasitária, São Luis, MA, Brazil
| | - Erna Geessien Kroon
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Álvaro Cantini Nunes
- Universidade Federal de Minas Gerais, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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16
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Evaluating the occurrence of Escherichia albertii in chicken carcass rinses by PCR, Vitek analysis, and sequencing of the rpoB gene. Appl Environ Microbiol 2014; 81:1727-34. [PMID: 25548040 DOI: 10.1128/aem.03681-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Escherichia albertii is a recently described species that has been associated with gastroenteritis in humans and with healthy and ill birds. Most recently, it has been identified as the causative agent in a food-borne outbreak in Japan. The distribution and clinical importance of E. albertii are not well studied because its importance is unclear. Culture methods for clinical isolation frequently miss E. albertii or incorrectly identify it as Shigella spp., Escherichia coli, or Hafnia alvei. This study was designed to determine if E. albertii could be recovered from chicken carcass rinses collected at slaughter during a 1-year period from November 2009 until October 2010. Colonies were isolated from chicken carcass rinses and tested by PCR for the presence or absence of clpX, lysP, mdh, intimin (eae), Shiga toxins 1 and 2 (stx1, stx2, and stx2f), heat-stable enterotoxin A (staA), and cytolethal distending toxins 1 and 2 (cdtB) genes. Sixty-five isolates were analyzed by sequencing a section of the rpoB gene. Analysis of the rpoB gene sequences revealed 14 fixed differences between E. albertii and other, closely related organisms. The fixed differences found in the rpoB gene could aid in future discrimination of E. albertii from closely related bacteria.
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17
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Liu BB, Zhao WY, Chu X, Hozzein WN, Prabhu DM, Wadaan MAM, Tang SK, Zhang LL, Li WJ. Haladaptatus pallidirubidus sp. nov., a halophilic archaeon isolated from saline soil samples in Yunnan and Xinjiang, China. Antonie van Leeuwenhoek 2014; 106:901-10. [PMID: 25190334 DOI: 10.1007/s10482-014-0259-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 08/11/2014] [Indexed: 10/24/2022]
Abstract
Two extremely halophilic archaea, designated YIM 90917 and YIM 93656(T), were isolated from saline soils in Yunnan province and Lup nur region in Xinjiang province, western China, respectively. Colonies of the two strains were observed to be pink-pigmented. The cells were found to be Gram-stain negative, coccoid and non-motile. The organisms were found to be aerobic and could grow in an NaCl range of 6-35 % (optimum 18 %), temperatures ranging from 25 to 50 °C (optimum 37-42 °C), pH range from 6.0-8.5 (optimum pH 7.0-7.5) and Mg(2+) range from 0 to 1.5 M (optimum 0.5-1.0 M); Mg(2+) was not necessary for growth. Cells were not observed to lyse in distilled water. Strains YIM 90917 and YIM 93656(T) showed the highest 16S rRNA gene sequence similarities to Haladaptatus cibarius JCM 15962(T) (97.6 and 97.9 %, respectively). In addition, the DNA-DNA hybridizations of strains YIM 90917 and YIM 93656(T) with type strains H. cibarius JCM 15962(T), Haladaptatus litoreus JCM 15771(T) and Haladaptatus paucihalophilus JCM 13897(T) were 37.2 and 38.2 %, 36.6 and 39.0 % and 27.9 and 27.7 %, respectively. The DNA G+C contents of strains YIM 90917 and YIM 93656(T) were determined to be 56.0 and 57.4 mol%. The major polar lipids of the two strains were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether and other four unidentified glycolipids. On the basis of physiological, chemotaxonomic data and phylogenetic analysis, the strains YIM 90917 and YIM 93656(T) can be classified as a novel species of the genus Haladaptatus, for which the name Haladaptatus pallidirubidus sp. nov. is proposed. The type strain is YIM 93656(T) (=JCM 17504(T) = CCTCC AB2010454(T)).
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Affiliation(s)
- Bing-Bing Liu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
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18
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Valiunas D, Jomantiene R, Davis RE. Evaluation of the DNA-dependent RNA polymerase β-subunit gene (rpoB) for phytoplasma classification and phylogeny. Int J Syst Evol Microbiol 2013; 63:3904-3914. [DOI: 10.1099/ijs.0.051912-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplasmas are classified into 16Sr groups and subgroups and ‘Candidatus
Phytoplasma
’ species, largely or entirely based on analysis of 16S rRNA gene sequences. Yet, distinctions among closely related ‘Ca.
Phytoplasma
’ species and strains based on 16S rRNA genes alone have limitations imposed by the high degree of rRNA nucleotide sequence conservation across diverse phytoplasma lineages and by the presence in a phytoplasma genome of two, sometimes sequence-heterogeneous, copies of the 16S rRNA gene. Since the DNA-dependent RNA polymerase (DpRp) β-subunit gene (rpoB) exists as a single copy in the phytoplasma genome, we explored the use of rpoB for phytoplasma classification and phylogenetic analysis. We sequenced a clover phyllody (CPh) phytoplasma genetic locus containing ribosomal protein genes, a complete rpoB gene and a partial rpoC gene encoding the β′-subunit of DpRp. Primers and reaction conditions were designed for PCR-mediated amplification of rpoB gene fragments from diverse phytoplasmas. The rpoB gene sequences from phytoplasmas classified in groups 16SrI, 16SrII, 16SrIII, 16SrX and 16SrXII were subjected to sequence similarity and phylogenetic analyses. The rpoB gene sequences were more variable than 16S rRNA gene sequences, more clearly distinguishing among phytoplasma lineages. Phylogenetic trees based on 16S rRNA and rpoB gene sequences had similar topologies, and branch lengths in the rpoB tree facilitated distinctions among closely related phytoplasmas. Virtual RFLP analysis of rpoB gene sequences also improved distinctions among closely related lineages. The results indicate that the rpoB gene provides a useful additional marker for phytoplasma classification that should facilitate studies of disease aetiology and epidemiology.
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Affiliation(s)
- Deividas Valiunas
- Phytovirus Laboratory, Institute of Botany, Nature Research Centre, Akademijos g. 2, Vilnius LT-08412, Lithuania
| | - Rasa Jomantiene
- Phytovirus Laboratory, Institute of Botany, Nature Research Centre, Akademijos g. 2, Vilnius LT-08412, Lithuania
| | - Robert Edward Davis
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
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19
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Seong WJ, Kwon HJ, Kim TE, Lee DY, Park MS, Kim JH. Molecular serotyping of Salmonella enterica by complete rpoB gene sequencing. J Microbiol 2012; 50:962-9. [DOI: 10.1007/s12275-012-2547-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 11/26/2012] [Indexed: 10/27/2022]
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20
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Fischer A, Shapiro B, Muriuki C, Heller M, Schnee C, Bongcam-Rudloff E, Vilei EM, Frey J, Jores J. The origin of the 'Mycoplasma mycoides cluster' coincides with domestication of ruminants. PLoS One 2012; 7:e36150. [PMID: 22558362 PMCID: PMC3338596 DOI: 10.1371/journal.pone.0036150] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 03/27/2012] [Indexed: 01/22/2023] Open
Abstract
The ‘Mycoplasma mycoides cluster’ comprises the ruminant pathogens Mycoplasma mycoides subsp. mycoides the causative agent of contagious bovine pleuropneumonia (CBPP), Mycoplasma capricolum subsp. capripneumoniae the agent of contagious caprine pleuropneumonia (CCPP), Mycoplasma capricolum subsp. capricolum, Mycoplasma leachii and Mycoplasma mycoides subsp. capri. CBPP and CCPP are major livestock diseases and impact the agricultural sector especially in developing countries through reduced food-supply and international trade restrictions. In addition, these diseases are a threat to disease-free countries. We used a multilocus sequence typing (MLST) approach to gain insights into the demographic history of and phylogenetic relationships among the members of the ‘M. mycoides cluster’. We collected partial sequences from seven housekeeping genes representing a total of 3,816 base pairs from 118 strains within this cluster, and five strains isolated from wild Caprinae. Strikingly, the origin of the ‘M. mycoides cluster’ dates to about 10,000 years ago, suggesting that the establishment and spread of the cluster coincided with livestock domestication. In addition, we show that hybridization and recombination may be important factors in the evolutionary history of the cluster.
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Affiliation(s)
- Anne Fischer
- Molecular Biology and Biotechnology Department, International Centre for Insect Physiology and Ecology, Nairobi, Kenya
- Biotechnology Department, International Livestock Research Institute, Nairobi, Kenya
| | - Beth Shapiro
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Cecilia Muriuki
- Biotechnology Department, International Livestock Research Institute, Nairobi, Kenya
| | - Martin Heller
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute, Jena, Germany
| | - Christiane Schnee
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute, Jena, Germany
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Edy M. Vilei
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Joerg Jores
- Biotechnology Department, International Livestock Research Institute, Nairobi, Kenya
- * E-mail:
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21
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RNA polymerase beta subunit (rpoB) gene and the 16S-23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene for phylogenetic analysis and identification of the species of the family Mycoplasmataceae. Mol Phylogenet Evol 2011; 62:515-28. [PMID: 22115576 DOI: 10.1016/j.ympev.2011.11.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 10/30/2011] [Accepted: 11/03/2011] [Indexed: 12/20/2022]
Abstract
Conventional classification of the species in the family Mycoplasmataceae is mainly based on phenotypic criteria, which are complicated, can be difficult to measure, and have the potential to be hampered by phenotypic deviations among the isolates. The number of biochemical reactions suitable for phenotypic characterization of the Mycoplasmataceae is also very limited and therefore the strategy for the final identification of the Mycoplasmataceae species is based on comparative serological results. However, serological testing of the Mycoplasmataceae species requires a performance panel of hyperimmune sera which contains anti-serum to each known species of the family, a high level of technical expertise, and can only be properly performed by mycoplasma-reference laboratories. In addition, the existence of uncultivated and fastidious Mycoplasmataceae species/isolates in clinical materials significantly complicates, or even makes impossible, the application of conventional bacteriological tests. The analysis of available genetic markers is an additional approach for the primary identification and phylogenetic classification of cultivable species and uncultivable or fastidious organisms in standard microbiological laboratories. The partial nucleotide sequences of the RNA polymerase β-subunit gene (rpoB) and the 16S-23S rRNA intergenic transcribed spacer (ITS) were determined for all known type strains and the available non-type strains of the Mycoplasmataceae species. In addition to the available 16S rRNA gene data, the ITS and rpoB sequences were used to infer phylogenetic relationships among these species and to enable identification of the Mycoplasmataceae isolates to the species level. The comparison of the ITS and rpoB phylogenetic trees with the 16S rRNA reference phylogenetic tree revealed a similar clustering patterns for the Mycoplasmataceae species, with minor discrepancies for a few species that demonstrated higher divergence of their ITS and rpoB in comparison to their neighbor species. Overall, our results demonstrated that the ITS and rpoB gene could be useful complementary phylogenetic markers to infer phylogenetic relationships among the Mycoplasmataceae species and provide useful background information for the choice of appropriate metabolic and serological tests for the final classification of isolates. In summary, three-target sequence analysis, which includes the ITS, rpoB, and 16S rRNA genes, was demonstrated to be a reliable and useful taxonomic tool for the species differentiation within the family Mycoplasmataceae based on their phylogenetic relatedness and pairwise sequence similarities. We believe that this approach might also become a valuable tool for routine analysis and primary identification of new isolates in medical and veterinary microbiological laboratories.
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22
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Use of rpoB sequences and rep-PCR for phylogenetic study of Anoxybacillus species. J Microbiol 2011; 49:782-90. [DOI: 10.1007/s12275-011-1136-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/07/2011] [Indexed: 11/26/2022]
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Perumbakkam S, Craig AM. Design and in vitro evaluation of new rpoB-DGGE primers for ruminants. FEMS Microbiol Ecol 2011; 76:156-69. [PMID: 21223335 DOI: 10.1111/j.1574-6941.2011.01042.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Two new primer sets based on the rpoB gene were designed and evaluated with bovine and ovine rumen samples. The newly developed rpoB-DGGE primer set was used along with the 16S rRNA gene-V3, and another (old) rpoB-DGGE-based primer set from a previous study to in vitro compare the bovine and ovine rumen ecosystems. The results indicate a significant (P<0.001) difference in the microbial population between the two ruminants irrespective of the primers used in the analysis. Qualitative comparison of the data provides evidence for the presence of similar phyla profiles between the 16S rRNA gene and the newly developed rpoB primers. A comparison between the two rpoB-based primer sets (old and new) showed that the old rpoB-based primers failed to amplify phylum Bacteroidetes (a common phylum in the rumen) in both bovine and ovine rumen samples. The old and new rpoB-DGGE-based primers amplified a large number of clones belonging to phylum Proteobacteria, providing a useful insight into the microbial structure of the rumen. ChaoI, ACE, Simpson, and Shannon-Weaver index analysis estimated the bovine rumen to be more diverse than the ovine rumen for all three primer sets. These results provide a new insight into the community structure among ruminants using the newly developed primers in this study.
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Affiliation(s)
- Sudeep Perumbakkam
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.
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24
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Adékambi T, Drancourt M, Raoult D. The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 2008; 17:37-45. [PMID: 19081723 DOI: 10.1016/j.tim.2008.09.008] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 09/24/2008] [Accepted: 09/25/2008] [Indexed: 11/16/2022]
Abstract
The rpoB gene, encoding the beta-subunit of RNA polymerase, has emerged as a core gene candidate for phylogenetic analyses and identification of bacteria, especially when studying closely related isolates. Together with the 16S rRNA gene, rpoB has helped to delineate new bacterial species and refine bacterial community analysis, as well as enabling the monitoring of rifampicin resistance-conferring mutations. Sequencing of rpoB enables efficient estimation of bacterial G+C% content, DNA-DNA hybridization value and average nucleotide identity (percentage of the total genomic sequence shared between two strains) when taxonomic relationships have been firmly established. New identification tools targeting a rpoB gene fragment located between positions 2300 and 3300 have been developed recently. Therefore, inclusion of the rpoB gene sequence would be useful when describing new bacterial species.
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Affiliation(s)
- Toïdi Adékambi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS IRD UMR 6236 IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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25
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Adekambi T, Shinnick TM, Raoult D, Drancourt M. Complete rpoB gene sequencing as a suitable supplement to DNA-DNA hybridization for bacterial species and genus delineation. Int J Syst Evol Microbiol 2008; 58:1807-14. [DOI: 10.1099/ijs.0.65440-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Pineiro SA, Williams HN, Stine OC. Phylogenetic relationships amongst the saltwater members of the genus Bacteriovorax using rpoB sequences and reclassification of Bacteriovorax stolpii as Bacteriolyticum stolpii gen. nov., comb. nov. Int J Syst Evol Microbiol 2008; 58:1203-9. [DOI: 10.1099/ijs.0.65710-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Meintanis C, Chalkou K, Kormas KA, Lymperopoulou D, Katsifas E, Hatzinikolaou D, Karagouni A. Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus. Lett Appl Microbiol 2008; 46:395-401. [DOI: 10.1111/j.1472-765x.2008.02328.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mayor D, Jores J, Korczak BM, Kuhnert P. Multilocus sequence typing (MLST) of Mycoplasma hyopneumoniae: A diverse pathogen with limited clonality. Vet Microbiol 2008; 127:63-72. [PMID: 17884308 DOI: 10.1016/j.vetmic.2007.08.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Revised: 07/31/2007] [Accepted: 08/06/2007] [Indexed: 11/15/2022]
Abstract
A multilocus sequence typing (MLST) scheme was established and evaluated for Mycoplasma hyopneumoniae, the etiologic agent of enzootic pneumonia in swine with the aim of defining strains. Putative target genes were selected by genome sequence comparisons. Out of 12 housekeeping genes chosen and experimentally validated, the 7 genes efp, metG, pgiB, recA, adk, rpoB, and tpiA were finally used to establish the MLST scheme. Their usefulness was assessed individually and in combination using a set of well-defined field samples and strains of M. hyopneumoniae. A reduction to the three targets showing highest variation (adk, rpoB, and tpiA) was possible resulting in the same number of sequence types as using the seven targets. The established MLST approach was compared with the recently described typing method using the serine-rich repeat motif-encoding region of the p146 gene. There was coherence between the two methods, but MLST resulted in a slightly higher resolution. Farms recognized to be affected by enzootic pneumonia were always associated with a single M. hyopneumoniae clone, which in most cases differed from farm to farm. However, farms in close geographic or operational contact showed identical clones as defined by MLST typing. Population analysis showed that recombination in M. hyopneumoniae occurs and that strains are very diverse with only limited clonality observed. Elaborate classical MLST schemes using multiple targets for M. hyopneumoniae might therefore be of limited value. In contrast, MLST typing of M. hyopneumoniae using the three genes adk, rpoB, and tpiA seems to be sufficient for epidemiological investigations by direct amplification of target genes from lysate of clinical material without prior cultivation.
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Affiliation(s)
- Désirée Mayor
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
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Manso-Silván L, Perrier X, Thiaucourt F. Phylogeny of the Mycoplasma mycoides cluster based on analysis of five conserved protein-coding sequences and possible implications for the taxonomy of the group. Int J Syst Evol Microbiol 2008; 57:2247-2258. [PMID: 17911291 DOI: 10.1099/ijs.0.64918-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A phylogenetic tree of the Mycoplasma mycoides cluster was inferred from a set of concatenated sequences from five housekeeping genes (fusA, glpQ, gyrB, lepA and rpoB). The relevance of this phylogeny was reinforced by detailed analysis of the congruence of the phylogenies derived from each of the five individual gene sequences. Two subclusters were distinguished. The M. mycoides subcluster comprised M. mycoides subsp. mycoides biotypes Small Colony (SC) and Large Colony (LC) and M. mycoides subsp. capri. The latter two groups could not be clearly separated, which supports previous proposals that they be united into a single taxonomic entity. The Mycoplasma capricolum subcluster included M. capricolum subsp. capricolum, M. capricolum subsp. capripneumoniae and Mycoplasma sp. bovine group 7 of Leach, a group of strains that remains unassigned. This group constituted a distinct branch within this cluster, supporting its classification as a subspecies of M. capricolum. Mycoplasma cottewii and Mycoplasma yeatsii clustered in a group that was distinct from Mycoplasma putrefaciens and they were all clearly separated from the M. mycoides cluster. In conclusion, this approach has allowed us to assign phylogenetic positions to all members of the M. mycoides cluster and related species and has proved the need to adjust the existing taxonomy. Furthermore, this method may be used as a reference technique to assign an unequivocal position to any particular strain related to this cluster and may lead to the development of new techniques for rapid species identification.
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Affiliation(s)
- Lucía Manso-Silván
- CIRAD BIOS, UPR15, Control of Exotic and Emerging Animal Diseases, TA A-15/G, Campus International Baillarguet, 34398 Montpellier Cedex 5, France
| | - Xavier Perrier
- CIRAD BIOS, UPR75, Biomathematics, Genetic Improvement of Vegetatively Propagated Crops, TA 71/09, Campus Lavalette, 34398 Montpellier Cedex 5, France
| | - François Thiaucourt
- CIRAD BIOS, UPR15, Control of Exotic and Emerging Animal Diseases, TA A-15/G, Campus International Baillarguet, 34398 Montpellier Cedex 5, France
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Tran-Hung L, Tran-Thi N, Aboudharam G, Raoult D, Drancourt M. A new method to extract dental pulp DNA: application to universal detection of bacteria. PLoS One 2007; 2:e1062. [PMID: 17957246 PMCID: PMC2031827 DOI: 10.1371/journal.pone.0001062] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Accepted: 10/01/2007] [Indexed: 11/21/2022] Open
Abstract
Background Dental pulp is used for PCR-based detection of DNA derived from host and bacteremic microorganims. Current protocols require odontology expertise for proper recovery of the dental pulp. Dental pulp specimen exposed to laboratory environment yields contaminants detected using universal 16S rDNA-based detection of bacteria. Methodology/Principal Findings We developed a new protocol by encasing decontaminated tooth into sterile resin, extracting DNA into the dental pulp chamber itself and decontaminating PCR reagents by filtration and double restriction enzyme digestion. Application to 16S rDNA-based detection of bacteria in 144 teeth collected in 86 healthy people yielded a unique sequence in only 14 teeth (9.7%) from 12 individuals (14%). Each individual yielded a unique 16S rDNA sequence in 1–2 teeth per individual. Negative controls remained negative. Bacterial identifications were all confirmed by amplification and sequencing of specific rpoB sequence. Conclusions/Significance The new protocol prevented laboratory contamination of the dental pulp. It allowed the detection of bacteria responsible for dental pulp colonization from blood and periodontal tissue. Only 10% such samples contained 16S rDNA. It provides a new tool for the retrospective diagnostic of bacteremia by allowing the universal detection of bacterial DNA in animal and human, contemporary or ancient tooth. It could be further applied to identification of host DNA in forensic medicine and anthropology.
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Affiliation(s)
- Lam Tran-Hung
- Unité des Rickettsies, CNRS UMR 6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Ny Tran-Thi
- Unité des Rickettsies, CNRS UMR 6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Gérard Aboudharam
- Unité des Rickettsies, CNRS UMR 6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Didier Raoult
- Unité des Rickettsies, CNRS UMR 6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
- * To whom correspondence should be addressed. E-mail:
| | - Michel Drancourt
- Unité des Rickettsies, CNRS UMR 6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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Oshima K, Nishida H. Phylogenetic relationships among mycoplasmas based on the whole genomic information. J Mol Evol 2007; 65:249-58. [PMID: 17687503 DOI: 10.1007/s00239-007-9010-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Accepted: 04/17/2007] [Indexed: 10/23/2022]
Abstract
With the rapid increase in available bacterial whole-genome information, comparison of bacteria at the whole-genome level has proven to be highly useful in microbial phylogenetic research. Here we constructed a phylogenetic tree based on 15 whole genomes of Mycoplasma and the related bacteria. First, 143 orthologous gene families that are shared by all of the 15 bacteria were selected and 143 multiple alignments were generated. Next, a concatenated multiple alignment inferred from the 143 multiple alignments was generated. A total of 43,370 amino acid sites were considered in the neighbor-joining analysis. The phylogenetic tree based on the whole-genomic information indicated that the 15 bacteria were divided into four major groups with 100% bootstrap support, i.e., the M. hyopneumoniae (Mhy) group, the M. mycoides (Mmy) group, the M. pneumoniae (Mpn) group, and the Bacillus-Phytoplasma (BP) group. In the phylogenetic tree, the Mhy group was more closely related to the Mpn group than the Mmy group. The relationships among the Mhy, Mmy, Mpn, and BP groups were supported with 100% in bootstrap analysis. The phylogenetic tree based on the whole-genome comparison is different from the 16S rRNA tree. Thirty-nine of the 143 phylogenetic trees had the same type of the topology based on the whole-genome comparison. However, we could not identify a gene family contributing or solely belonging to the topology of the 39 proteins. In this study, we showed that some proteins, such as RpoA, RpoB, RpoC, and RpoD, are not suitable for evolutionary studies on relationships among major groups of mycoplasmas. We also showed that glycolysis-related genes of Ureaplasma have a higher substitution rate than the other bacteria. The phylogenetic approaches at the whole-genome level are very important and will be essential for microbial evolutionary studies.
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Affiliation(s)
- Kenro Oshima
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Volokhov DV, Neverov AA, George J, Kong H, Liu SX, Anderson C, Davidson MK, Chizhikov V. Genetic analysis of housekeeping genes of members of the genus Acholeplasma: Phylogeny and complementary molecular markers to the 16S rRNA gene. Mol Phylogenet Evol 2007; 44:699-710. [PMID: 17267242 DOI: 10.1016/j.ympev.2006.12.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Revised: 11/29/2006] [Accepted: 12/01/2006] [Indexed: 11/27/2022]
Abstract
The partial nucleotide sequences of the rpoB and gyrB genes as well as the complete sequence of the 16S-23S rRNA intergenic transcribed spacer (ITS) were determined for all known Acholeplasma species. The same genes of Mesoplasma and Entomoplasma species were also sequenced and used to infer phylogenetic relationships among the species within the orders Entomoplasmatales and Acholeplasmatales. The comparison of the ITS, rpoB, and gyrB phylogenetic trees with the 16S rRNA phylogenetic tree revealed a similar branch topology suggesting that the ITS, rpoB, and gyrB could be useful complementary phylogenetic markers for investigation of evolutionary relationships among Acholeplasma species. Thus, the multilocus phylogenetic analysis of Acholeplasma multilocale sequence data (ATCC 49900 (T) = PN525 (NCTC 11723)) strongly indicated that this organism is most closely related to the genera Mesoplasma and Entomoplasma (family Entomoplasmataceae) and form the branch with Mesoplasma seiffertii, Mesoplasma syrphidae, and Mesoplasma photuris. The closest genetic relatedness of this species to the order Entomoplasmatales was additionally supported by the finding that A. multilocale uses UGA as the tryptophan codon in its gyrB and gyrA sequences. Use of the UGA codon for encoding tryptophan was previously reported as a unique genetic feature of Entomoplasmatales and Mycoplasmatales but not of Acholeplasmatales. These data, as well as previously published data on metabolic features of A. multilocale, leads to the proposal to reclassify A. multilocale as a member of the family Entomoplasmataceae.
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Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, HFM-470, Rockville, MD 20852, USA.
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Korczak BM, Stieber R, Emler S, Burnens AP, Frey J, Kuhnert P. Genetic relatedness within the genus Campylobacter inferred from rpoB sequences. Int J Syst Evol Microbiol 2006; 56:937-945. [PMID: 16627635 DOI: 10.1099/ijs.0.64109-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Campylobacter comprises 17 species, some of which are important animal and human pathogens. To gain more insight into the genetic relatedness of this genus and to improve the molecular tools available for diagnosis, a universal sequencing approach was established for the gene encoding the beta-subunit of RNA polymerase (rpoB) for the genus Campylobacter. A total of 59 strains, including the type strains of currently recognized species as well as field isolates, were investigated in the study. A primer set specific for Campylobacter species enabled straightforward amplification and sequencing of a 530 bp fragment of the rpoB gene. The 16S rRNA gene sequences of all of the strains were determined in parallel. A good congruence was obtained between 16S rRNA and rpoB gene sequence-based trees within the genus Campylobacter. The branching of the rpoB tree was similar to that of the 16S rRNA gene tree, even though a few discrepancies were observed for certain species. The resolution of the rpoB gene within the genus Campylobacter was generally much higher than that of the 16S rRNA gene sequence, resulting in a clear separation of most species and even some subspecies. The universally applicable amplification and sequencing approach for partial rpoB gene sequence determination provides a powerful tool for DNA sequence-based discrimination of Campylobacter species.
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Affiliation(s)
- Bożena M Korczak
- Institute of Veterinary Bacteriology, University of Bern, CH-3012 Bern, Switzerland
| | - Regina Stieber
- Institute of Veterinary Bacteriology, University of Bern, CH-3012 Bern, Switzerland
| | | | - André P Burnens
- Institute of Veterinary Bacteriology, University of Bern, CH-3012 Bern, Switzerland
| | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, CH-3012 Bern, Switzerland
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, University of Bern, CH-3012 Bern, Switzerland
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Vilei EM, Korczak BM, Frey J. Mycoplasma mycoides subsp. capri and Mycoplasma mycoides subsp. mycoides LC can be grouped into a single subspecies. Vet Res 2006; 37:779-90. [PMID: 16973118 DOI: 10.1051/vetres:2006037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Accepted: 05/10/2006] [Indexed: 11/14/2022] Open
Abstract
Mycoplasma mycoides subsp. capri and Mycoplasma mycoides subsp. mycoides LC can be combined into one taxon on the basis of several contributions on both DNA sequence and protein analyses reported in the literature. Moreover, for the differentiation and identification of mycoplasmas of the "mycoides cluster", we investigated the rpoB gene, encoding the beta-subunit of the RNA polymerase. A segment of 527 bp of the rpoB gene was amplified from 31 strains of ruminant mycoplasmas by PCR. The nucleotide sequences were determined and aligned, and accurate genetic relationships were calculated. Cluster analysis of rpoB DNA allowed species differentiation within the "mycoides cluster" and confirmed that M. mycoides subsp. capri and M. mycoides subsp. mycoides LC cannot be distinguished from each other. "Mycoplasma mycoides subsp. capri" is proposed as a common name for both subspecies.
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Affiliation(s)
- Edy M Vilei
- Institute of Veterinary Bacteriology, Universität Bern, Länggass-Strasse 122, Postfach, 3001 Bern, Switzerland.
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Volokhov DV, George J, Liu SX, Ikonomi P, Anderson C, Chizhikov V. Sequencing of the intergenic 16S-23S rRNA spacer (ITS) region ofMollicutes species and their identification using microarray-based assay and DNA sequencing. Appl Microbiol Biotechnol 2006; 71:680-98. [PMID: 16470366 DOI: 10.1007/s00253-005-0280-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 11/20/2005] [Accepted: 11/27/2005] [Indexed: 10/25/2022]
Abstract
We have completed sequencing the 16S-23S rRNA intergenic transcribed spacer (ITS) region of most known Mycoplasma , Acholeplasma , Ureaplasma , Mesoplasma , and Spiroplasma species. Analysis of the sequence data revealed a significant interspecies variability and low intraspecies polymorphism of the ITS region among Mollicutes . This finding enabled the application of a combined polymerase chain reaction-microarray technology for identifying Mollicutes species. The microarray included individual species-specific oligonucleotide probes for characterizing human Mollicutes species and other species known to be common cell line contaminants. Evaluation of the microarray was conducted using multiple, previously characterized, Mollicutes species. The microarray analysis of the samples used demonstrated a highly specific assay, which is capable of rapid and accurate discrimination among Mollicutes species.
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Affiliation(s)
- Dmitriy V Volokhov
- Center of Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Viral Products, Laboratory of Methods Development, US Food and Drug Administration, Rockville, MD 20852, USA.
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Carvalho FM, Fonseca MM, Batistuzzo De Medeiros S, Scortecci KC, Blaha CAG, Agnez-Lima LF. DNA repair in reduced genome: the Mycoplasma model. Gene 2005; 360:111-9. [PMID: 16153783 DOI: 10.1016/j.gene.2005.06.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 03/31/2005] [Accepted: 06/03/2005] [Indexed: 11/30/2022]
Abstract
The occurrence of bacteria with a reduced genome, such as that found in Mycoplasmas, raises the question as to which genes should be enough to guarantee the genomic stability indispensable for the maintenance of life. The aim of this work was to compare nine Mycoplasma genomes in regard to DNA repair genes. An in silico analysis was done using six Mycoplasma species, whose genomes are accessible at GenBank, and M. synoviae, and two strains of M. hyopneumoniae, whose genomes were recently sequenced by The Brazilian National Genome Project Consortium and Southern Genome Investigation Program (Brazil) respectively. Considering this reduced genome model, our comparative analysis suggests that the DNA integrity necessary for life can be primarily maintained by nucleotide excision repair (NER), which is the only complete repair pathway. Furthermore, some enzymes involved with base excision repair (BER) and recombination are also present and can complement the NER activity. The absence of RecR and RecO-like ORFs was observed only in M. genitalium and M. pneumoniae, which can be involved with the conservation of gene order observed between these two species. We also obtained phylogenetic evidence for the recent acquisition of the ogt gene in M. pulmonis and M. penetrans by a lateral transference event. In general, the presence or nonexistence of repair genes is shared by all species analyzed, suggesting that the loss of the majority of repair genes was an ancestral event, which occurred before the divergence of the Mycoplasma species.
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Affiliation(s)
- Fabíola Marques Carvalho
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
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Yun YJ, Lee KH, Haihua L, Ryu YJ, Kim BJ, Lee YH, Baek GH, Kim HJ, Chung MS, Lee MC, Lee SH, Choi IH, Cho TJ, Chang BS, Kook YH. Detection and identification of Mycobacterium tuberculosis in joint biopsy specimens by rpoB PCR cloning and sequencing. J Clin Microbiol 2005; 43:174-8. [PMID: 15634968 PMCID: PMC540102 DOI: 10.1128/jcm.43.1.174-178.2005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Osteoarticular tuberculosis (OAT) is an extrapulmonary tuberculosis and accounts for 1 to 3% of all tuberculosis cases. We used an rpoB PCR-plasmid TA cloning-sequencing method to detect and identify tubercle bacilli in surgical specimens from patients suspected of having OAT. By comparing the similarities of the rpoB sequences determined with those in GenBank, Mycobacterium tuberculosis was detected in 23 of 43 samples. Three of the 23 positive samples had mutations at codon 531, which are commonly observed in rifampin-resistant M. tuberculosis strains. Our results suggest that the rpoB PCR-TA cloning-sequencing method developed, which detects M. tuberculosis and which simultaneously determines its rifampin susceptibility, can also be used efficiently for the diagnosis of OAT.
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Affiliation(s)
- Yeo-Jun Yun
- Department of Microbiology and Cancer Research Institute, Seoul National University College of Medicine, Seoul National Research Hospital, Korea
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