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Dekio I, Culak R, Misra R, Gaulton T, Fang M, Tanaka M, Klenk HP, Rajendram D, Gharbia SE, Shah HN. Dissecting out the taxonomic heterogeneity within Propionibacterium acnes and proposal for two novel subspecies of the species. J Dermatol Sci 2016. [DOI: 10.1016/j.jdermsci.2016.08.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Dekio I, Culak R, Misra R, Gaulton T, Fang M, Sakamoto M, Ohkuma M, Oshima K, Hattori M, Klenk HP, Rajendram D, Gharbia SE, Shah HN. Dissecting the taxonomic heterogeneity within Propionibacterium acnes: proposal for Propionibacterium acnes subsp. acnes subsp. nov. and Propionibacterium acnes subsp. elongatum subsp. nov. Int J Syst Evol Microbiol 2015; 65:4776-4787. [PMID: 26432704 DOI: 10.1099/ijsem.0.000648] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Propionibacterium acnes subsp. acnes subsp. nov. and Propionibacterium acnes subsp. elongatum subsp. nov. are described. These emanate from the three known phylotypes of P. acnes, designated types I, II and III. Electron microscopy confirmed the filamentous cell shape of type III, showing a striking difference from types I/II, which were short rods. Biochemical tests indicated that, in types I/II, either the pyruvate, l-pyrrolidonyl arylamidase or d-ribose 2 test was positive, whereas all of these were negative among type III strains. Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectra, which profile mainly their ribosomal proteins, were different between these two groups. Surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) spectra of all phylotypes revealed a specific protein biomarker that was overexpressed in type III strains compared with types I/II only when grown aerobically. Reference strains had high whole-genome similarity between types I (>91 %) and II (>75 %), but a considerably lower level of 72 % similarity with type III. recA and gyrB sequence dendrograms confirmed the distant relatedness of type III, indicating the presence of two distinct centres of variation within the species P. acnes. On the other hand, cellular fatty acid profiles and 16S rRNA gene sequence relatedness (>99.3 %) circumscribed the species. Thus, we propose two subspecies, Propionibacterium acnes subsp. acnes subsp. nov. for types I/II and Propionibacterium acnes subsp. elongatum subsp. nov. for type III. The type strain of Propionibacterium acnes subsp. acnes is NCTC 737T ( = ATCC 6919T = JCM 6425T = DSM 1897T = CCUG 1794T), while the type strain of Propionibacterium acnes subsp. elongatum is K124T ( = NCTC 13655T = JCM 18919T).
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Affiliation(s)
- Itaru Dekio
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan.,Proteomics Research Unit, Culture Collections, Public Health England, Colindale, London, UK.,Department of Dermatology, Medical Centre East, Tokyo Women's Medical University, Tokyo, Japan
| | - Renata Culak
- Proteomics Research Unit, Culture Collections, Public Health England, Colindale, London, UK
| | - Raju Misra
- Genomic Research Unit, Public Health England, Colindale, London, UK
| | - Tom Gaulton
- Proteomics Research Unit, Culture Collections, Public Health England, Colindale, London, UK
| | - Min Fang
- Proteomics Research Unit, Culture Collections, Public Health England, Colindale, London, UK
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan
| | - Kenshiro Oshima
- Hattori Lab, The University of Tokyo Kashiwa Campus, Kashiwa, Japan
| | - Masahira Hattori
- Hattori Lab, The University of Tokyo Kashiwa Campus, Kashiwa, Japan
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | | | - Saheer E Gharbia
- Genomic Research Unit, Public Health England, Colindale, London, UK
| | - Haroun N Shah
- Proteomics Research Unit, Culture Collections, Public Health England, Colindale, London, UK
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Chattaway MA, Jenkins C, Rajendram D, Cravioto A, Talukder KA, Dallman T, Underwood A, Platt S, Okeke IN, Wain J. Enteroaggregative Escherichia coli have evolved independently as distinct complexes within the E. coli population with varying ability to cause disease. PLoS One 2014; 9:e112967. [PMID: 25415318 PMCID: PMC4240581 DOI: 10.1371/journal.pone.0112967] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/16/2014] [Indexed: 01/01/2023] Open
Abstract
Enteroaggregative E. coli (EAEC) is an established diarrhoeagenic pathotype. The association with virulence gene content and ability to cause disease has been studied but little is known about the population structure of EAEC and how this pathotype evolved. Analysis by Multi Locus Sequence Typing of 564 EAEC isolates from cases and controls in Bangladesh, Nigeria and the UK spanning the past 29 years, revealed multiple successful lineages of EAEC. The population structure of EAEC indicates some clusters are statistically associated with disease or carriage, further highlighting the heterogeneous nature of this group of organisms. Different clusters have evolved independently as a result of both mutational and recombination events; the EAEC phenotype is distributed throughout the population of E. coli.
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Affiliation(s)
- Marie Anne Chattaway
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom
- * E-mail:
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom
| | | | - Alejandro Cravioto
- International Vaccine Institute, Gwanak-gu, Seoul, Republic of Korea
- Centre for Food and Water Borne Diseases, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Tim Dallman
- Gastrointestinal Bacteria Reference Unit, Public Health England, London, United Kingdom
| | | | | | - Iruka N. Okeke
- Haverford College, Haverford, Pennsylvania, United States of America
| | - John Wain
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
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Dekio I, Rajendram D, Morita E, Gharbia S, Shah HN. Genetic diversity of Propionibacterium acnes strains isolated from human skin in Japan and comparison with their distribution in Europe. J Med Microbiol 2012; 61:622-630. [DOI: 10.1099/jmm.0.040949-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Itaru Dekio
- Department for Bioanalysis and Horizon Technologies, Microbiology Services, Health Protection Agency, London, UK
- Skin Microbe Laboratory, Department of Dermatology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Dunstan Rajendram
- Department for Bioanalysis and Horizon Technologies, Microbiology Services, Health Protection Agency, London, UK
| | - Eishin Morita
- Skin Microbe Laboratory, Department of Dermatology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Saheer Gharbia
- Department for Bioanalysis and Horizon Technologies, Microbiology Services, Health Protection Agency, London, UK
| | - Haroun N. Shah
- Department for Bioanalysis and Horizon Technologies, Microbiology Services, Health Protection Agency, London, UK
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Jacinto RC, Gomes BPFA, Desai M, Rajendram D, Shah HN. Bacterial examination of endodontic infections by clonal analysis in concert with denaturing high-performance liquid chromatography. ACTA ACUST UNITED AC 2007; 22:403-10. [PMID: 17949344 DOI: 10.1111/j.1399-302x.2007.00378.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND/AIMS The aim of this study was to examine the diversity of bacterial species in the infected root canals of teeth associated with endodontic abscesses by cloning and sequencing techniques in concert with denaturing high-performance liquid chromatography. METHODS Samples collected from five infected root canals were subjected to polymerase chain reaction (PCR) with universal 16S ribosomal DNA primers. Products of these PCRs were cloned and sequenced. Denaturing high-performance liquid chromatography (DHPLC) was used as a screening method to reduce the number of clones necessary for DNA sequencing. RESULTS All samples were positive for the presence of bacteria and a range of 7-13 different bacteria were found per root canal sample. In total, 48 different oral clones were detected among the five root canal samples. Olsenella profusa was the only species present in all samples. Porphyromonas gingivalis, Dialister pneumosintes, Dialister invisus, Lachnospiraceae oral clone, Staphylococcus aureus, Pseudoramibacter alactolyticus, Peptostreptococcus micros and Enterococcus faecalis were found in two of the five samples. The majority of the taxa were present in only one sample, for example Tannerella forsythia, Shuttleworthia satelles and Filifactor alocis. Some facultative anaerobes that are frequently isolated from endodontic infections such as E. faecalis, Streptococcus anginosus and Lactobacillus spp. were also found in this study. CONCLUSION Clonal analysis of the microflora associated with endodontic infections revealed a wide diversity of oral species.
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Affiliation(s)
- R C Jacinto
- Department of Restorative Dentistry, Endodontic Area, Piracicaba Dental School, State University of Campinas-UNICAMP, Piracicaba, SP, Brazil
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Rajendram D, Ayenza R, Holder FM, Moran B, Long T, Shah HN. Long-term storage and safe retrieval of DNA from microorganisms for molecular analysis using FTA matrix cards. J Microbiol Methods 2006; 67:582-92. [PMID: 16859786 DOI: 10.1016/j.mimet.2006.05.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Revised: 05/12/2006] [Accepted: 05/22/2006] [Indexed: 11/19/2022]
Abstract
We assessed the potential use of Whatman FTA paper as a device for archiving and long-term storage of bacterial cell suspensions of over 400 bacterial strains representing 61 genera, the molecular applications of immobilised DNA on FTA paper, and tested its microbial inactivation properties. The FTA paper extracted bacterial DNA is of sufficiently high quality to successfully carryout the molecular detection of several key genes including 16S rRNA, esp (Enterococcus surface protein), Bft (Bacteroides fragilis enterotoxin) and por (porin protein) by PCR and for DNA fingerprinting by random amplified polymorphic DNA-PCR (RAPD-PCR). To test the long-term stability of the FTA immobilised DNA, 100 of the 400 archived bacterial samples were randomly selected following 3 years of storage at ambient temperature and PCR amplification was used to monitor its success. All of the 100 samples were successfully amplified using the 16S rDNA gene as a target and confirmed by DNA sequencing. Furthermore, the DNA was eluted into solution from the FTA cards using a new alkaline elution procedure for evaluation by real-time PCR-based assays. The viability of cells retained on the FTA cards varied among broad groups of bacteria. For the more fragile gram-negative species, no viable cells were retained even at high cell densities of between 10(7) and 10(8) colony forming units (cfu) ml(-1), and for the most robust species such as spore-formers and acid-fast bacteria, complete inactivation was achieved at cell densities ranging between 10(1) and 10(4) cfu ml(-1). The inactivation of bacterial cells on FTA cards suggest that this is a safe medium for the storage and transport of bacterial nucleic acids.
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Affiliation(s)
- D Rajendram
- Molecular Identification Services Unit, Health Protection Agency Centre For Infections, 61 Colindale Avenue, London, UK
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Ulger Toprak N, Rajendram D, Yagci A, Gharbia S, Shah HN, Gulluoglu BM, Akin LM, Demirkalem P, Celenk T, Soyletir G. The distribution of the bft alleles among enterotoxigenic Bacteroides fragilis strains from stool specimens and extraintestinal sites. Anaerobe 2005; 12:71-4. [PMID: 16701617 DOI: 10.1016/j.anaerobe.2005.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Accepted: 11/08/2005] [Indexed: 10/25/2022]
Abstract
Enterotoxigenic Bacteroides fragilis (ETBF) has been implicated in diarrhoeal illness in animals and humans. Recent data suggest that ETBF is associated with flares of inflammatory bowel disease. Toxigenicity is attributed to expression of a toxin referred to as fragilysin, which stimulates fluid accumulation in ligated intestinal segments and alter the morphology of human intestinal cells. Three different isoforms or variants of the enterotoxin gene, designated bft-1, bft-2, and bft-3, have been identified. In this study we investigated the distribution of bft alleles among ETBF strains in stool specimens from patients with colon cancer (n: 31), the control patients (n: 8) and extraintestinal sources (n: 15). We used restriction fragment length polymorphism analysis of the PCR-amplified enterotoxin gene and sequencing the PCR-product to detect the isoforms of bft gene. Among the stool strains, bft-1 was found to be more common than bft-2; as it was detected 27 of 31 strains from colon cancer patients and 7 of 8 control strains. The bft-1 isoform was also found in almost all isolates from extraintestinal sites. No bft-3 subtype was detected among all tested strains.
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Affiliation(s)
- Nurver Ulger Toprak
- Medical School, Department of Clinical Microbiology, Marmara University, Haydarpasa, Tibbiye Cad, Istanbul, Turkey.
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Williams JC, Gharbia SE, Gulabivala K, Rajendram D, Mehta N, Huttson R, Collins MD, Shah HN. Noncultivable microbial communities in dentine and cementum: a molecular analytical approach. Clin Infect Dis 1997; 25 Suppl 2:S233-4. [PMID: 9310689 DOI: 10.1086/516203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- J C Williams
- Eastman Dental Institute, University of London, United Kingdom
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