TY - JOUR ID - 1505 T1 - Diversity in a variable-number tandem repeat from Yersinia pestis A1 - Adair,D.M. A1 - Worsham,P.L. A1 - Hill,K.K. A1 - Klevytska,A.M. A1 - Jackson,P.J. A1 - Friedlander,A.M. A1 - Keim,P. Y1 - 2000/04// N1 - DA - 20000517 IS - 0095-1137 (Print) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S PT - Research Support, U.S. Gov't, P.H.S RN - 0 (Antigens, Bacterial) RN - 0 (DNA, Bacterial) RN - 0 (LcrV protein, Yersinia) RN - 0 (Pore Forming Cytotoxic Proteins) SB - IM KW - Alleles KW - Antigen KW - culture KW - dna KW - gene KW - Mutation KW - Open Reading Frames KW - Research KW - rev3 KW - strain KW - USA KW - yersinia KW - Yersinia pestis RP - NOT IN FILE SP - 1516 EP - 1519 JA - J Clin Microbiol. VL - 38 N2 - We have identified a tetranucleotide repeat sequence, (CAAA)(N), in the genome of Yersinia pestis, the causative agent of plague. This variable-number tandem repeat (VNTR) region has nine alleles and great diversity (calculated as 1 minus the sum of the squared allele frequencies) (diversity value, 0.82) within a set of 35 diverse Y. pestis strains. In contrast, the nucleotide sequence of the lcrV (low-calcium-response) gene differed only slightly among these strains, having a haplotype diversity value of 0.17. Replicated cultures, phenotypic variants of particular strains, and extensively cultured replicates within strains did not differ in VNTR allele type. Thus, while a high mutation rate must contribute to the great diversity of this locus, alleles appear stable under routine laboratory culture conditions. The classic three plague biovars did not have single identifying alleles, although there were allelic biases within biovar categories. The antiqua biovar was the most diverse, with four alleles observed in 5 strains, while the orientalis and mediaevalis biovars exhibited five alleles in 21 strains and three alleles in 8 strains, respectively. The CAAA VNTR is located immediately adjacent to the transcriptional promoters for flanking open reading frames and may affect their activity. This VNTR marker may provide a high-resolution tool for epidemiological analyses of plague AD - Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011-5640, USA UR - PM:10747136 ER - TY - BOOK ID - 1506 T1 - Techniques for the brucellosis laboratory A1 - Alton,G.G. A1 - Jones,L.M. A1 - Angus,R.D. A1 - Verger,J.M. Y1 - 1988/// KW - Brucellosis KW - rev3 RP - IN FILE SP - 169 EP - 173 CY - Paris PB - INRA, 20, 39  ER - TY - JOUR ID - 1507 T1 - Detection of Brucella melitensis and Brucella abortus by DNA amplification A1 - Baily,G.G. A1 - Krahn,J.B. A1 - Drasar,B.S. A1 - Stoker,N.G. Y1 - 1992/08// N1 - DA - 19920910 IS - 0022-5304 (Print) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't RN - 0 (DNA, Bacterial) SB - IM KW - ABORTUS KW - Antigen KW - Brucella KW - Brucella abortus KW - Brucella melitensis KW - Brucellosis KW - DIAGNOSIS KW - dna KW - gene KW - Medicine KW - MELITENSIS KW - Polymerase Chain Reaction KW - Research KW - rev3 KW - size RP - IN FILE SP - 271 EP - 275 JA - J Trop.Med Hyg. VL - 95 N2 - Suitable reaction conditions and oligonucleotide primers were sought for the detection of Brucella melitensis and Brucella abortus by the polymerase chain reaction. Primers were chosen from within the coding sequence of a gene encoding a 31 kDa B. abortus antigen. The test was shown to be sensitive, and specificity was demonstrated using DNA derived from a panel of Gram-negative pathogens. There was no detectable difference between B. melitensis and B. abortus in the sensitivity of the reaction or in the size of the amplification product. The technique should be applicable in the diagnosis of brucellosis AD - Department of Clinical Sciences, London School of Hygiene and Tropical Medicine, UK UR - PM:1495123 ER - TY - JOUR ID - 1514 T1 - Feeding habits and flight range of blow-flies (Chrysomyia spp.) in relation to anthrax transmission in the Kruger National Park, South Africa A1 - Braack,L.E. A1 - De,Vos,V Y1 - 1990/06// N1 - DA - 19901107 IS - 0030-2465 (Print) LA - eng PT - Journal Article SB - IM KW - AFRICA KW - analysis KW - Animal KW - Animals KW - Anthrax KW - Blood KW - density KW - Diptera KW - feeding KW - Feeding Behavior KW - Flight,Animal KW - fly KW - impala KW - Insect Vectors KW - mortality KW - physiology KW - Research KW - rev3 KW - SOUTH AFRICA KW - TRANSMISSION KW - veterinary RP - IN FILE SP - 141 EP - 142 JA - Onderstepoort J Vet Res. VL - 57 N2 - Carrion-frequenting blow-flies (Chrysomyia albiceps and C. marginalis) were allowed 4 days of feeding on 32P-orthophosphate-labelled blood or an impala carcass (Aepyceros melampus) in the northern Kruger National Park, South Africa. The dispersal and density of fly faecal and discard droplets were then established using a Geiger-Counter, indicating that most droplets occurred between a height of 1 and 3 m on nearby leaves and twigs. This coincides with the preferred feeding height of kudu (Tragelaphus strepsiceros). During a previous anthrax epizootic kudu comprised 73.15% of a total medium to large mammal mortality figure of 1054. Further analysis of mortality shows browsers to have been most severely affected, and it is suggested that this is correlated with feeding habits of these animals. Trapping also yielded radioactively labelled C. albiceps up to 32.5 km and C. marginalis up to 25 km from the isotope source AD - Research Department, National Parks Board, Skukuza UR - PM:2216348 ER - TY - JOUR ID - 1516 T1 - Differentiation of Brucella abortus bv. 1, 2, and 4, Brucella melitensis, Brucella ovis, and Brucella suis bv. 1 by PCR A1 - Bricker,B.J. A1 - Halling,S.M. Y1 - 1994/11// N1 - DA - 19950316 IS - 0095-1137 (Print) LA - eng PT - Journal Article RN - 0 (DNA, Bacterial) SB - IM KW - ABORTUS KW - agriculture KW - analysis KW - Animal KW - ASSAY KW - Bacteria KW - Base Sequence KW - Brucella KW - Brucella abortus KW - Brucella melitensis KW - cattle KW - DIFFERENTIATION KW - Disease KW - dna KW - DNA,Bacterial KW - Escherichia coli KW - ESCHERICHIA-COLI KW - field KW - genetics KW - identification KW - isolation & purification KW - MELITENSIS KW - Methods KW - Molecular Sequence Data KW - PCR ASSAY KW - Polymerase Chain Reaction KW - Research KW - rev3 KW - species KW - SUIS KW - United States RP - IN FILE SP - 2660 EP - 2666 JA - J Clin Microbiol. VL - 32 N2 - Several PCR assays which identify the genus Brucella but do not discriminate among species have been reported. We describe a PCR assay that comprises five oligonucleotide primers which can identify selected biovars of four species of Brucella. Individual biovars within a species are not differentiated. The assay can identify three biovars (1, 2, and 4) of B. abortus, all three biovars of B. melitensis, biovar 1 of B. suis, and all B. ovis biovars. These biovars include all of the Brucella species typically isolated from cattle in the United States, a goal of the present research. The assay exploits the polymorphism arising from species-specific localization of the genetic element IS711 in the Brucella chromosome. Identity is determined by the size(s) of the product(s) amplified from primers hybridizing at various distances from the element. The performance of the assay with U.S. field isolates was highly effective. When 107 field isolates were screened by the described method, there was 100% agreement with the identifications made by conventional methods. Six closely related bacteria (Agrobacterium radiobacter, Agrobacterium rhizogenes, Ochrobactrum anthropi, Rhizobium leguminosarum, Rhizobium meliloti, and Rhodospirillum rubrum) and two control bacteria (Bordetella bronchiseptica and Escherichia coli) tested negative by the assay AD - National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa 50010 UR - PM:7852552 ER - TY - JOUR ID - 1517 T1 - Enhancement of the Brucella AMOS PCR assay for differentiation of Brucella abortus vaccine strains S19 and RB51 A1 - Bricker,B.J. A1 - Halling,S.M. Y1 - 1995/06// N1 - DA - 19950922 IS - 0095-1137 (Print) LA - eng PT - Comparative Study PT - Journal Article RN - 0 (Bacterial Vaccines) RN - 0 (DNA Primers) RN - 0 (DNA, Bacterial) SB - IM KW - ABORTUS KW - Animal KW - Animals KW - ASSAY KW - Bacterial Vaccines KW - Base Sequence KW - benefit KW - Brucella KW - Brucella abortus KW - Brucellosis KW - Brucellosis,Bovine KW - cattle KW - classification KW - Comparative Study KW - DIFFERENTIATION KW - Disease KW - dna KW - DNA Primers KW - DNA,Bacterial KW - eradication KW - FEMALE KW - field KW - genetics KW - identification KW - IMMUNOLOGY KW - INFECTION KW - INFECTIONS KW - Methods KW - microbiology KW - Molecular Sequence Data KW - PCR ASSAY KW - Polymerase Chain Reaction KW - Polymorphism,Genetic KW - Pregnancy KW - prevention & control KW - PROGRAM KW - Quarantine KW - Research KW - rev3 KW - Species Specificity KW - strain KW - USA KW - vaccine KW - Vaccines KW - veterinary RP - IN FILE SP - 1640 EP - 1642 JA - J Clin Microbiol. VL - 33 N2 - Because the brucellosis eradication program uses slaughter and quarantine as control measures, it would benefit from faster methods of bacterial identification. Distinguishing vaccine strains from strains that cause infections among vaccinated herds in the field is essential. To accomplish this, our PCR-based, species-specific assay (B. J. Bricker and S. M. Halling, J. Clin. Microbiol. 32:2660-2666, 1994) was updated to identify Brucella abortus vaccine strains S19 and RB51. Three new oligonucleotide primers were added to the five-primer multiplex Brucella AMOS PCR assay. Identification is based on the number and sizes of six products amplified by PCR AD - National Animal Disease Center, Agricultural Research Service, Ames, Iowa 50010, USA UR - PM:7650203 ER - TY - JOUR ID - 1515 T1 - Brucella 'HOOF-Prints': strain typing by multi-locus analysis of variable number tandem repeats (VNTRs) A1 - Bricker,B.J. A1 - Ewalt,D.R. A1 - Halling,S.M. Y1 - 2003/07/11/ N1 - DA - 20040129 IS - 1471-2180 (Electronic) LA - eng PT - Journal Article RN - 0 (DNA, Bacterial) SB - IM KW - ABORTUS KW - agriculture KW - Alleles KW - analysis KW - Animal KW - Animals KW - Bacterial Typing Techniques KW - Brucella KW - Brucellosis KW - cattle KW - characterization KW - classification KW - Disease KW - dna KW - DNA,Bacterial KW - epidemiology KW - Evolution KW - field KW - genetics KW - identification KW - In vitro KW - IN-VITRO KW - INFECTION KW - INFECTIONS KW - Methods KW - microbiology KW - Minisatellite Repeats KW - Molecular Sequence Data KW - Polymerase Chain Reaction KW - POPULATION KW - Research KW - rev3 KW - species KW - strain KW - Tandem Repeat Sequences KW - United States KW - USA RP - IN FILE SP - 15 JA - BMC.Microbiol. VL - 3 N2 - BACKGROUND: Currently, there are very few tools available for subtyping Brucella isolates for epidemiological trace-back. Subtyping is difficult because of the genetic homogeneity within the genus. Sequencing of the genomes from three Brucella species has facilitated the search for DNA sequence variability. Recently, hypervariability among short tandem repeat sequences has been exploited for strain-typing of several bacterial pathogens. RESULTS: An eight-base pair tandem repeat sequence was discovered in nine genomic loci of the B. abortus genome. Eight loci were hypervariable among the three Brucella species. A PCR-based method was developed to identify the number of repeat units (alleles) at each locus, generating strain-specific fingerprints. None of the loci exhibited species- or biovar-specific alleles. Sometimes, a species or biovar contained a specific allele at one or more loci, but the allele also occurred in other species or biovars. The technique successfully differentiated the type strains for all Brucella species and biovars, among unrelated B. abortus biovar 1 field isolates in cattle, and among B. abortus strains isolated from bison and elk. Isolates from the same herd or from short-term in vitro passage exhibited little or no variability in fingerprint pattern. Sometimes, isolates from an animal would have multiple alleles at a locus, possibly from mixed infections in enzootic areas, residual disease from incomplete depopulation of an infected herd or molecular evolution within the strain. Therefore, a mixed population or a pool of colonies from each animal and/or tissue was tested. CONCLUSION: This paper describes a new method for fingerprinting Brucella isolates based on multi-locus characterization of a variable number, eight-base pair, tandem repeat. We have named this technique "HOOF-Prints" for Hypervariable Octameric Oligonucleotide Finger-Prints. The technique is highly discriminatory among Brucella species, among previously characterized Brucella strains, and among unrelated field isolates that could not be differentiated by classical methods. The method is rapid and the results are reproducible. HOOF-Printing will be most useful as a follow-up test after identification by established methods since we did not find species-specific or biovar-specific alleles. Nonetheless, this technology provides a significant advancement in brucellosis epidemiology, and consequently, will help to eliminate this disease worldwide AD - United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, 2300 Dayton Rd, Ames, IA 50010, USA. bbricker@nadc.ars.usda.gov UR - PM:12857351 ER - TY - CHAP ID - 1508 T1 - Molecular Diagnostics of Animal Brucellosis: A Review of PCR-Based Assays and Approaches A1 - Bricker,B.J.; Y1 - 2004/// KW - Animal KW - ASSAY KW - Brucella KW - Brucellosis KW - rev3 KW - review RP - IN FILE SP - 25 EP - 51 T2 - Brucella: Molecular and Cellular Biology A2 - Lopez-Goni,I. A2 - Moriyon,I. CY - England PB - Horizon Bioscience ER - TY - JOUR ID - 1518 T1 - Detection of Brucella species DNA in the stomach content of aborted sheep fetuses by PCR A1 - Cetinkaya,B. A1 - Ongor,H. A1 - Muz,A. A1 - Ertas,H.B. A1 - Kalender,H. A1 - Erdogan,H.M. Y1 - 1999/02/27/ N1 - DA - 19990609 IS - 0042-4900 (Print) LA - eng PT - Journal Article RN - 0 (DNA, Bacterial) SB - IM KW - Abortion,Veterinary KW - analysis KW - Animals KW - Brucella KW - Brucella abortus KW - Cells,Cultured KW - dna KW - DNA,Bacterial KW - FEMALE KW - Fetus KW - genetics KW - isolation & purification KW - microbiology KW - Polymerase Chain Reaction KW - Pregnancy KW - rev3 KW - SHEEP KW - Sheep Diseases KW - species KW - Stomach KW - Turkey RP - IN FILE SP - 239 EP - 240 JA - Vet Rec. VL - 144 AD - FU Veteriner Fakultesi, Mikrobiyoloji Anabilim Dali, Elazig, Turkey UR - PM:10189677 ER - TY - JOUR ID - 1519 T1 - Brucellosis: an overview A1 - Corbel,M.J. Y1 - 1997/04// N1 - DA - 19970724 IS - 1080-6040 (Print) LA - eng PT - Journal Article PT - Review RN - 0 (Antigens, Bacterial) SB - IM KW - ABORTUS KW - analysis KW - Animals KW - Antibodies KW - antibody KW - Antigen KW - Antigens,Bacterial KW - Brucella KW - Brucella abortus KW - Brucella melitensis KW - Brucellosis KW - cattle KW - development KW - DIAGNOSIS KW - epidemiology KW - gene KW - genetics KW - GOAT KW - Goats KW - human KW - Humans KW - IMMUNITY KW - Immunoassay KW - IMMUNOLOGY KW - INFECTION KW - Lipopolysaccharides KW - MELITENSIS KW - Methods KW - PATHOGENICITY KW - Polymerase Chain Reaction KW - prevention & control KW - production KW - rev3 KW - review KW - SHEEP KW - species KW - standards KW - strain KW - SUIS KW - survival KW - Tetracycline KW - therapy KW - UNITED-KINGDOM KW - VACCINATION KW - vaccine KW - Vaccines RP - IN FILE SP - 213 EP - 221 JF - Emerging Infectious Diseases JA - Emerg.Infect.Dis. VL - 3 N2 - Brucellosis remains a major zoonosis worldwide. Although many countries have eradicated Brucella abortus from cattle, in some areas Brucella melitensis has emerged as a cause of infection in this species as well as in sheep and goats. Despite vaccination campaigns with the Rev 1 strain, B. melitensis remains the principal cause of human brucellosis. Brucella suis is also emerging as an agent of infection in cattle, thus extending its opportunities to infect humans. The recent isolation of distinctive strains of Brucella from marine mammals has extended its ecologic range. Molecular genetic studies have demonstrated phylogenetic affiliation to Agrobacterium, Phyllobacterium, Ochrobactrum, and Rhizobium. Polymerase chain reaction and gene probe development may provide more effective typing methods. Pathogenicity is related to production of lipopolysaccharides containing a poly N-formyl perosamine O chain, CuZn superoxide dismutase, erythrlose phosphate dehydrogenase, stress-induced proteins related to intracellular survival, and adenine and guanine monophosphate inhibitors of phagocyte functions. Protective immunity is conferred by antibody to lipopolysaccharide and T-cell-mediated macrophage activation triggered by protein antigens. Diagnosis still centers on isolation of the organism and serologic test results, especially enzyme immunoassay, which is replacing other methods. Polymerase chain reaction is also under evaluation. Therapy is based on tetracyclines with or without rifampicin, aminoglycosides, or quinolones. No satisfactory vaccines against human brucellosis are available, although attenuated purE mutants appear promising AD - National Institute of Biological Standards and Control, South Mimmas, Potters Bar, Hertfordshire, United Kingdom. mcorbel@nibsc.ac.uk UR - PM:9204307 ER - TY - JOUR ID - 1520 T1 - Detection of Brucella DNA from aborted bovine foetuses by polymerase chain reaction A1 - Cortez,A. A1 - Scarcelli,E. A1 - Soares,R.M. A1 - Heinemann,M.B. A1 - Sakamoto,S.M. A1 - Genovez,M.E. A1 - Ferreira,F. A1 - Richtzenhain,L.J. Y1 - 2001/07// N1 - DA - 20010910 IS - 0005-0423 (Print) LA - eng PT - Evaluation Studies PT - Journal Article PT - Research Support, Non-U.S. Gov't RN - 0 (DNA, Bacterial) SB - IM KW - Abortion,Veterinary KW - Animals KW - bovine KW - Brazil KW - Brucella KW - Brucella abortus KW - Brucellosis,Bovine KW - cattle KW - DIAGNOSIS KW - dna KW - DNA,Bacterial KW - Evaluation Studies KW - FEMALE KW - Fetus KW - genetics KW - isolation & purification KW - microbiology KW - Polymerase Chain Reaction KW - Predictive Value of Tests KW - Pregnancy KW - Research KW - rev3 KW - standards KW - veterinary RP - IN FILE SP - 500 EP - 501 JA - Aust.Vet J VL - 79 AD - Faculdade de Medicina Veterinaria e Zootecnia, University of Sao Paulo, Brazil UR - PM:11549051 ER - TY - JOUR ID - 1521 T1 - Phenotypic and molecular characterisation of Brucella isolates from marine mammals A1 - Dawson,C.E. A1 - Stubberfield,E.J. A1 - Perrett,L.L. A1 - King,A.C. A1 - Whatmore,A.M. A1 - Bashiruddin,J.B. A1 - Stack,J.A. A1 - Macmillan,A.P. Y1 - 2008/// N1 - DA - 20090226 IS - 1471-2180 (Electronic) LA - eng PT - Journal Article RN - 0 (DNA, Bacterial) SB - IM KW - analysis KW - Animal KW - Animals KW - Bacteria KW - Bacterial Typing Techniques KW - Brucella KW - Brucellosis KW - Cetacea KW - classification KW - Disease KW - dna KW - DNA Fingerprinting KW - DNA,Bacterial KW - gene KW - genetics KW - HOST KW - isolation & purification KW - man KW - microbiology KW - phenotype KW - Pinnipedia KW - Polymerase Chain Reaction KW - Polymorphism,Restriction Fragment Length KW - RESTRICTION KW - rev3 KW - species KW - Species Specificity KW - strain KW - veterinary RP - IN FILE SP - 224 JA - BMC.Microbiol. VL - 8 N2 - BACKGROUND: Bacteria of the genus Brucella are the causative organisms of brucellosis in animals and man. Previous characterisation of Brucella strains originating from marine mammals showed them to be distinct from the terrestrial species and likely to comprise one or more new taxa. Recently two new species comprising Brucella isolates from marine mammals, B. pinnipedialis and B. ceti, were validly published. Here we report on an extensive study of the molecular and phenotypic characteristics of marine mammal Brucella isolates and on how these characteristics relate to the newly described species. RESULTS: In this study, 102 isolates of Brucella originating from eleven species of marine mammals were characterised. Results obtained by analysis using the Infrequent Restriction Site (IRS)-Derivative PCR, PCR-RFLP of outer membrane protein genes (omp) and IS711 fingerprint profiles showed good consistency with isolates originating from cetaceans, corresponding to B. ceti, falling into two clusters. These correspond to isolates with either dolphins or porpoises as their preferred host. Isolates originating predominantly from seals, and corresponding to B. pinnipedialis, cluster separately on the basis of IS711 fingerprinting and other molecular approaches and can be further subdivided, with isolates from hooded seals comprising a distinct group. There was little correlation between phenotypic characteristics used in classical Brucella biotyping and these groups. CONCLUSION: Molecular approaches are clearly valuable in the division of marine mammal Brucella into subtypes that correlate with apparent ecological divisions, whereas conventional bioyping is of less value. The data presented here confirm that there are significant subtypes within the newly described marine mammal Brucella species and add to a body of evidence that could lead to the recognition of additional species or sub-species within this group AD - Department of Statutory and Exotic Bacterial Diseases, Veterinary Laboratories Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK. c.e.dawson@vla.defra.gsi.gov.uk UR - PM:19091076 ER - TY - JOUR ID - 1522 T1 - Anthrax A1 - Dixon,T.C. A1 - Meselson,M. A1 - Guillemin,J. A1 - Hanna,P.C. Y1 - 1999/09/09/ N1 - DA - 19990914 IS - 0028-4793 (Print) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S PT - Review RN - 0 (Anti-Bacterial Agents) RN - 0 (Glucocorticoids) SB - AIM SB - IM KW - Anthrax KW - Anti-Bacterial Agents KW - Bacillus anthracis KW - DIAGNOSIS KW - Diagnosis,Differential KW - drug therapy KW - Gastrointestinal Diseases KW - Glucocorticoids KW - Humans KW - Mediastinal Diseases KW - Meningitis,Bacterial KW - microbiology KW - Mouth Diseases KW - PATHOGENICITY KW - pathology KW - Pharyngeal Diseases KW - physiopathology KW - prevention & control KW - Research KW - rev3 KW - review KW - Skin Diseases,Bacterial KW - therapeutic use KW - USA KW - virulence RP - IN FILE SP - 815 EP - 826 JA - N.Engl.J Med VL - 341 AD - Department of Microbiology, Duke University Medical Center, Durham, NC, USA UR - PM:10477781 ER - TY - JOUR ID - 1523 T1 - Brucella ceti sp. nov. and Brucella pinnipedialis sp. nov. for Brucella strains with cetaceans and seals as their preferred hosts A1 - Foster,G. A1 - Osterman,B.S. A1 - Godfroid,J. A1 - Jacques,I. A1 - Cloeckaert,A. Y1 - 2007/11// N1 - DA - 20071105 IS - 1466-5026 (Print) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't SB - IM KW - Animals KW - Bacterial Typing Techniques KW - Brucella KW - Carbohydrates KW - Cetacea KW - classification KW - genetics KW - Genotype KW - HOST KW - Lysogeny KW - metabolism KW - Methods KW - microbiology KW - Nucleic Acid Hybridization KW - Oxidation-Reduction KW - phenotype KW - physiology KW - Pinnipedia KW - Research KW - rev3 KW - species KW - Species Specificity KW - strain KW - TESTS KW - veterinary KW - veterinary services RP - IN FILE SP - 2688 EP - 2693 JA - Int J Syst.Evol.Microbiol. VL - 57 N2 - Small Gram-negative cocco-bacilli resembling Brucella strains have been reported from marine mammals since the mid-1990s. Their placement in the genus Brucella has been supported by the following characteristics: they are aerobic, non-motile and catalase-positive, do not produce acid from carbohydrates and have a DNA-DNA relatedness value of >77% with the six established members of the genus. Twenty-eight European isolates of the genus Brucella from marine mammals were distinguished from the six recognized species by their pattern of utilization of eleven substrates in oxidative metabolism tests and phage lysis. The 28 strains could be further separated into two groups with cetaceans and seals as their respective preferred hosts on the basis of molecular methods and on differences in the metabolism of l-arabinose, d-galactose and d-xylose. The names Brucella ceti sp. nov. and Brucella pinnipedialis sp. nov. are proposed for the isolates from cetaceans and seals, respectively. The type strain of Brucella ceti sp. nov. is NCTC 12891T (=BCCN 94-74T) and the type strain of Brucella pinnipedialis sp. nov. is NCTC 12890T (=BCCN 94-73T) AD - SAC Veterinary Services, Inverness IV2 4JZ, UK. Geoffrey.Foster@sac.co.uk UR - PM:17978241 ER - TY - JOUR ID - 1524 T1 - Identification of Brucella by ribosomal-spacer-region PCR and differentiation of Brucella canis from other Brucella spp. pathogenic for humans by carbohydrate profiles A1 - Fox,K.F. A1 - Fox,A. A1 - Nagpal,M. A1 - Steinberg,P. A1 - Heroux,K. Y1 - 1998/11// N1 - DA - 19981211 IS - 0095-1137 (Print) LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S RN - 0 (Carbohydrates) RN - 0 (DNA Primers) RN - 0 (DNA, Bacterial) RN - 0 (DNA, Ribosomal) RN - 0 (RNA, Bacterial) RN - 0 (RNA, Ribosomal, 16S) RN - 0 (RNA, Ribosomal, 23S) SB - IM KW - ABORTUS KW - analysis KW - Bacteria KW - Base Sequence KW - Brucella KW - Brucella abortus KW - Brucella melitensis KW - Brucellosis KW - canis KW - Carbohydrates KW - chemistry KW - classification KW - Comparative Study KW - DIAGNOSIS KW - DIFFERENTIATION KW - dna KW - DNA Primers KW - DNA,Bacterial KW - DNA,Ribosomal KW - genetics KW - human KW - Humans KW - identification KW - IMMUNOLOGY KW - information KW - Medicine KW - MELITENSIS KW - Methods KW - microbiology KW - Polymerase Chain Reaction KW - Research KW - rev3 KW - RNA,Bacterial KW - RNA,Ribosomal,16S KW - RNA,Ribosomal,23S KW - Serology KW - species KW - Species Specificity KW - sugar KW - SUIS KW - USA KW - virulence RP - IN FILE SP - 3217 EP - 3222 JA - J Clin Microbiol. VL - 36 N2 - Molecular and chemical characteristics often provide complementary information in the differentiation of closely related organisms. The genus Brucella consists of a highly conserved group of organisms. Identification of the four species pathogenic in humans (Brucella melitensis, Brucella abortus, Brucella suis, and Brucella canis) is problematic for many clinical laboratories that depend primarily on serology and phenotypic characteristics to differentiate species. PCR amplification of the 16S-23S ribosomal DNA interspace region was evaluated for species-specific polymorphism. B. abortus, B. melitensis, B. suis, and B. canis produced identical PCR interspace profiles. However, these PCR products were unique to brucellae, allowing them to be readily distinguished from other gram-negative bacteria (including Bartonella spp. and Agrobacterium spp.). Carbohydrate profiles differentiated B. canis from the other three Brucella species due to the absence of the rare amino sugar quinovosamine in the three other species. PCR of the rRNA interspace region is useful in identification of the genus Brucella, while carbohydrate profiling is capable of differentiating B. canis from the other Brucella species AD - Department of Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, South Carolina 29208, USA UR - PM:9774568 ER - TY - JOUR ID - 1525 T1 - Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats A1 - Frothingham,R. A1 - Meeker-O'Connell,W.A. Y1 - 1998/05// N1 - DA - 19980707 IS - 1350-0872 (Print) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S RN - 0 (DNA, Bacterial) SB - IM KW - Alleles KW - analysis KW - Animals KW - Bacteria KW - Bacterial Typing Techniques KW - Base Sequence KW - BCG KW - BCG Vaccine KW - bovis KW - classification KW - DIFFERENTIATION KW - dna KW - DNA,Bacterial KW - gene KW - Gene Dosage KW - Gene Frequency KW - Genetic Variation KW - genetics KW - human KW - Humans KW - identification KW - MICROTI KW - Minisatellite Repeats KW - Molecular Sequence Data KW - Mycobacterium KW - Mycobacterium tuberculosis KW - Polymerase Chain Reaction KW - Polymorphism,Restriction Fragment Length KW - reference KW - Research KW - rev3 KW - Sequence Analysis,DNA KW - Species Specificity KW - strain KW - tuberculosis KW - USA KW - vaccine KW - VARIATION RP - IN FILE SP - 1189 EP - 1196 JA - Microbiology VL - 144 ( Pt 5) N2 - Genetic loci containing variable numbers of tandem repeats (VNTR loci) form the basis for human gene mapping and identification, forensic analysis and paternity testing. The variability of bacterial tandem repeats has not been systematically studied. Eleven tandem repeat loci in the M. tuberculosis genome were analysed. Five major polymorphic tandem repeat (MPTR) loci contained 15-bp repeats with substantial sequence variation in adjacent copies. Six exact tandem repeat (ETR) loci contained large DNA repeats with identical sequences in adjacent repeats. These 11 loci were amplified in 48 strains to determine the number of tandem repeats at each locus. The strains analysed included 25 wild-type strains of M. tuberculosis, M. bovis, M. africanum and M. microti and 23 substrains of the attenuated M. bovis BCG vaccine. One of the five MPTR loci and all six ETR loci had length polymorphisms corresponding to insertions or deletions of tandem repeats. Most ETR loci were located in intergenic regions where copy number may influence expression of downstream genes. Each ETR locus had multiple alleles in the panel. Combined analysis identified 22 distinct allele profiles in 25 wild-type strains of the M. tuberculosis complex and five allele profiles in 23 M. bovis BCG substrains. Allele profiles were reproducible and stable, as demonstrated by analyses of multiple isolates of particular reference strains obtained from different laboratories. VNTR typing may be generally useful for strain differentiation and evolutionary studies in bacteria AD - Veterans Affairs Medical Center, Durham, NC 27705, USA. richard.frothingham@duke.edu UR - PM:9611793 ER - TY - JOUR ID - 1526 T1 - Serological diagnosis of bovine brucellosis: a review of test performance and cost comparison A1 - Gall,D. A1 - Nielsen,K. Y1 - 2004/12// N1 - DA - 20050502 IS - 0253-1933 (Print) LA - eng PT - Comparative Study PT - Journal Article PT - Review SB - IM KW - ABORTUS KW - Agglutination Tests KW - Animal KW - Animal Diseases KW - Animals KW - Antigen KW - ASSAY KW - bovine KW - BOVINE BRUCELLOSIS KW - Brucella KW - Brucella abortus KW - Brucellosis KW - Brucellosis,Bovine KW - cattle KW - Comparative Study KW - cost KW - Cost-Benefit Analysis KW - DIAGNOSIS KW - Disease KW - economics KW - Enzyme Linked Immunosorbent Assay KW - Enzyme-Linked Immunosorbent Assay KW - Fluorescence Polarization Immunoassay KW - IMMUNOLOGY KW - isolation & purification KW - Methods KW - Reproducibility of Results KW - Research KW - rev3 KW - review KW - Rose Bengal KW - Sensitivity and Specificity KW - Serologic Tests KW - SEROLOGICAL DIAGNOSIS KW - TESTS KW - veterinary RP - IN FILE SP - 989 EP - 1002 JA - Rev.Sci.Tech. VL - 23 N2 - The authors reviewed over 50 publications in which the sensitivity and specificity values of assays used for the detection of exposure to Brucella abortus had been examined. The sum of the sensitivity and specificity values for each test was averaged to give a performance index (PI) and allow for a comparison between the different methodologies. A score of 200 was perfect. Based on the PI, the buffered antigen plate agglutination test (BPAT) rated highest (PI = 193.1) among the conventional tests. This indicates better accuracy than the other conventional tests including the Rose Bengal test (PI = 167.6) and the complement fixation test (PI = 172.5). Overall, the primary binding assays, including the fluorescence polarisation assay (PI = 196.4), the indirect enzyme-linked immunosorbent assay (PI = 189.8) and the competitive enzyme-linked immunosorbent assay (PI = 188.2), were more accurate than the conventional tests, except for the BPAT. In addition, a fee comparison suggested that the primary binding tests were price competitive with conventional tests for the diagnosis of brucellosis and, therefore, had a better combined cost/efficiency rating AD - Canadian Food Inspection Agency, Animal Diseases Research Institute, Brucellosis Centre of Expertise, Ottawa, Ontario, K2H 8P9, Canada UR - PM:15861895 ER - TY - JOUR ID - 1527 T1 - Multiplex PCR assay for the identification and differentiation of all Brucella species and the vaccine strains Brucella abortus S19 and RB51 and Brucella melitensis Rev1 A1 - Garcia-Yoldi,D. A1 - Marin,C.M. A1 - de Miguel,M.J. A1 - Munoz,P.M. A1 - Vizmanos,J.L. A1 - Lopez-Goni,I. Y1 - 2006/04// N1 - DA - 20060405 IS - 0009-9147 (Print) LA - eng PT - Letter RN - 0 (Brucella Vaccine) SB - IM KW - ABORTUS KW - ASSAY KW - Bacterial Typing Techniques KW - Brucella KW - Brucella abortus KW - Brucella melitensis KW - Brucella Vaccine KW - classification KW - DIFFERENTIATION KW - genetics KW - identification KW - MELITENSIS KW - PCR ASSAY KW - Polymerase Chain Reaction KW - rev1 KW - rev3 KW - species KW - strain KW - vaccine RP - IN FILE SP - 779 EP - 781 JA - Clin Chem. VL - 52 UR - PM:16595839 ER - TY - JOUR ID - 1528 T1 - Sequence and characterization of an insertion sequence, IS711, from Brucella ovis A1 - Halling,S.M. A1 - Tatum,F.M. A1 - Bricker,B.J. Y1 - 1993/10/29/ N1 - DA - 19931217 IS - 0378-1119 (Print) LA - eng PT - Journal Article RN - 0 (DNA Transposable Elements) RN - 0 (DNA, Bacterial) SB - IM KW - agriculture KW - Amino Acid Sequence KW - Animal KW - Base Sequence KW - Brucella KW - characterization KW - Disease KW - dna KW - DNA Transposable Elements KW - DNA,Bacterial KW - entry KW - gene KW - Genetic Variation KW - genetics KW - Molecular Sequence Data KW - Open Reading Frames KW - Repetitive Sequences,Nucleic Acid KW - rev3 KW - Sequence Homology,Nucleic Acid KW - United States KW - VARIATION RP - IN FILE SP - 123 EP - 127 JF - Gene VL - 133 N2 - The nucleotide (nt) sequence of a previously discovered insertion in Brucella ovis was determined and found to have the hallmarks of an insertion sequence (IS). The element, designated IS711, of 842 bp, is similar in G + C content to that of the Brucella genome and is bounded by 20-bp imperfect inverted repeats (IR). The element appears to duplicate the nt TA of a consensus target site, YTAR (R, purines; Y, pyrimidines). When the complete nt sequence of four elements and 300 bp of the 3' ends of five other elements were compared to IS711 and to each other, minor nt sequence variations were found amongst most of them. Similar to several other transposable elements, IS711 has overlapping ORFs rather than one long ORF extending the length of the element. Even though only ten B. ovis IS711 elements were characterized, in three cases we found these elements flanked by either identical or similar nt sequences. This suggests that some target sites are hot spots for insertion and that some of the elements may be duplicated by mechanisms other than transposition. No DNA or protein database entries had an obvious resemblance to either IS711 or its deduced gene products AD - National Animal Disease Center, United States Department of Agriculture, Ames, IA 50010 UR - PM:8224885 ER - TY - JOUR ID - 1529 T1 - Anthrax: the disease in relation to vaccines A1 - Hambleton,P. A1 - Carman,J.A. A1 - Melling,J. Y1 - 1984/06// N1 - DA - 19850430 IS - 0264-410X (Print) LA - eng PT - Journal Article PT - Review RN - 0 (Antigens, Bacterial) RN - 0 (Bacterial Vaccines) RN - 0 (Vaccines, Attenuated) SB - IM KW - administration & dosage KW - Animals KW - Anthrax KW - Antigen KW - Antigens,Bacterial KW - Bacillus anthracis KW - Bacterial Vaccines KW - development KW - Disease KW - efficacy KW - etiology KW - Great Britain KW - history KW - Humans KW - IMMUNOLOGY KW - INFECTION KW - Lung Diseases KW - Pathogenesis KW - PATHOGENICITY KW - physiology KW - prevention & control KW - rev3 KW - review KW - Skin Diseases KW - Spores,Bacterial KW - United States KW - Ussr KW - vaccine KW - Vaccines KW - Vaccines,Attenuated KW - veterinary RP - IN FILE SP - 125 EP - 132 JF - Vaccine VL - 2 N2 - The authors trace the origins and history of anthrax and anthrax vaccines. They describe the aetiology and pathogenesis of the disease and the variety of symptoms which result from infection. The authors relate the early work performed by Pasteur, the development of existing vaccines and the efficacy of these vaccines, and predict the type of non-living vaccines which may be used to combat anthrax in the future UR - PM:6442500 ER - TY - JOUR ID - 1510 T1 - Ticks, mites and insects infesting domestic animals in South Africa; Part 1: Descriptions and biology A1 - Howell,C.J. A1 - Walker,J.B. A1 - Nevill,E.M. Y1 - 1978/// N1 - ISBN 0621038482 KW - AFRICA KW - Animal KW - Animals KW - rev3 KW - SOUTH AFRICA RP - IN FILE SP - 59 EP - 60 JF - Science Bulletin Department of Agricultural Technical Services Republic of South Africa VL - 393 ER - TY - INPR ID - 1511 T1 - Development of a PCR assay for typing and subtyping of Brucella species A1 - Huber,B. A1 - Scholz,H.C. A1 - Lucero,N. A1 - Buss,H.-J. Y1 - 2009/// KW - ASSAY KW - Brucella KW - development KW - PCR ASSAY KW - rev3 KW - species RP - IN FILE JF - International Journal of Medical Microbiology ER - TY - JOUR ID - 1530 T1 - Anthrax and wildlife A1 - Hugh-Jones,M.E. A1 - De,Vos,V Y1 - 2002/08// N1 - DA - 20020426 IS - 0253-1933 (Print) LA - eng PT - Journal Article PT - Review SB - IM KW - AFRICA KW - Animals KW - Animals,Wild KW - Animals,Zoo KW - Anthrax KW - buffalo KW - Deer KW - DIAGNOSIS KW - Diagnosis,Differential KW - Disease KW - Disease Outbreaks KW - ecology KW - epidemiology KW - field KW - GAME KW - HEALTH KW - Humans KW - LIVESTOCK KW - Medicine KW - North America KW - oral KW - prevention & control KW - procedure KW - Public Health KW - Research KW - rev3 KW - review KW - risk KW - survival KW - United States KW - USA KW - vaccine KW - Vaccines KW - veterinary KW - Veterinary Medicine KW - wildlife RP - IN FILE SP - 359 EP - 383 JA - Rev.Sci.Tech. VL - 21 N2 - Although livestock anthrax is declining in many parts of the world, with an increasing number of countries probably truly free of the disease, anthrax remains enzootic in many national parks and even in some game ranching areas. These infected areas can present a persistent risk to surrounding livestock, which may otherwise be free of the disease, as well as a public health risk. The authors use as examples the national parks in southern Africa, the Wood Buffalo National Park in northern Alberta, Canada, and the deer ranching counties in south-west Texas, United States of America, to present the range of problems, epidemiology, and control procedures. While many advances have been achieved in the understanding of this disease, research is required into the genotypic grouping of anthrax isolates, improved field diagnostic techniques, and oral vaccines, as well as to provide a better understanding of spore survival in soil and the ecology of the disease under natural conditions AD - Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana 70803, USA UR - PM:11974621 ER - TY - JOUR ID - 1531 T1 - Comparison of culture and PCR for the detection of Brucella melitensis in blood and lymphoid tissues of serologically positive and negative slaughtered sheep A1 - Ilhan,Z. A1 - Aksakal,A. A1 - Ekin,I.H. A1 - Gulhan,T. A1 - Solmaz,H. A1 - Erdenlig,S. Y1 - 2008/03// N1 - DA - 20080222 IS - 1472-765X (Electronic) LA - eng PT - Comparative Study PT - Evaluation Studies PT - Journal Article RN - 0 (Antibodies, Bacterial) RN - 0 (Culture Media) RN - 0 (DNA, Bacterial) SB - IM KW - Abattoirs KW - analysis KW - Animal KW - Animals KW - Antibodies KW - Antibodies,Bacterial KW - antibody KW - ASSAY KW - Bacteriological Techniques KW - Blood KW - Brucella KW - Brucella melitensis KW - Brucellosis KW - Comparative Study KW - culture KW - Culture Media KW - dna KW - DNA,Bacterial KW - Evaluation Studies KW - FEMALE KW - genetics KW - IMMUNOLOGY KW - isolation & purification KW - Lymphoid Tissue KW - Mammary Glands,Animal KW - Medicine KW - MELITENSIS KW - Methods KW - microbiology KW - PCR ASSAY KW - Polymerase Chain Reaction KW - rev3 KW - Rose Bengal KW - SAMPLES KW - Sensitivity and Specificity KW - SHEEP KW - Sheep Diseases KW - size KW - Species Specificity KW - TESTS KW - Turkey KW - veterinary KW - Veterinary Medicine RP - IN FILE SP - 301 EP - 306 JA - Lett.Appl.Microbiol. VL - 46 N2 - AIMS: To compare the culture and PCR methods for detection of Brucella melitensis in blood and lymphoid tissue samples obtained from slaughtered sheep (n = 162) testing positive/negative in serological tests (Rose Bengal test and serum agglutination test). METHODS AND RESULTS: Of 162 sheep examined, 45 were positive and 117 negative in serological tests. A PCR assay based on a pair of Br. melitensis-specific primers was used to detect DNA in blood and lymphoid tissue. Brucella melitensis was isolated from 1.2% (2/162) and 17.2% (28/162) of the blood and lymphoid tissue samples respectively. Positive PCR products with a molecular size of 731 bp were obtained from 27.7% (45/162) of blood and 29.0% (47/162) of lymphoid tissue samples. CONCLUSIONS: The species-specific PCR assay detected a higher number of Br. melitensis DNA both from serologically positive (P < 0.01 in blood PCR, P < 0.001 in tissue PCR) and serologically negative (P < 0.001 in both blood PCR and tissue PCR) sheep compared with classical bacteriological culture methods. SIGNIFICANCE AND IMPACT OF THE STUDY: The results emphasize the importance of using more than one type of diagnostic technique for the detection of animals positive for brucellosis, especially with epidemiological purposes AD - Department of Microbiology, Faculty of Veterinary Medicine, Yuzuncu Yil University, Van, Turkey. zilhan@yyu.edu.tr UR - PM:18179446 ER - TY - JOUR ID - 1532 T1 - Validation of serological assays for diagnosis of infectious diseases A1 - Jacobson,R.H. Y1 - 1998/08// N1 - DA - 19980914 IS - 0253-1933 (Print) LA - eng LA - fre LA - spa PT - Journal Article PT - Review SB - IM KW - Animal KW - Animals KW - ASSAY KW - classification KW - Communicable Diseases KW - DIAGNOSIS KW - Disease KW - epidemiology KW - INFECTION KW - maintenance KW - Medicine KW - movement KW - POPULATION KW - POPULATIONS KW - Predictive Value of Tests KW - Prevalence KW - Quality Control KW - reference KW - Reference Standards KW - Reference Values KW - Reproducibility of Results KW - rev3 KW - review KW - Roc Curve KW - Sample Size KW - SAMPLES KW - Sensitivity and Specificity KW - Serologic Tests KW - standards KW - USA KW - veterinary KW - Veterinary Medicine RP - IN FILE SP - 469 EP - 526 JA - Rev.Sci.Tech. VL - 17 N2 - Assay validation is a series of the following interrelated processes: an experimental process: reagents and protocols are optimised by experimentation to detect the analyte with accuracy and precision, and to ensure repeatability and reproducibility in the assay. a relative process: its diagnostic sensitivity and diagnostic specificity are calculated relative to test results obtained from reference animal populations of known infection/exposure status. a conditional process: classification of animals in the target population as infected or uninfected is conditional upon how well the reference animal population used to validate the assay represents the population to which the assay will be applied (accurate predictions of the infection status of animals from test results and predictive values of positive and negative test results are conditional upon the estimated prevalence of disease/infection in the target population) an incremental process: confidence in the validity of an assay increases over time when use confirms that it is robust as demonstrated by accurate and precise results (the assay may also achieve increasing levels of validity as it is upgraded and extended by adding reference populations of known infection status) a continuous process: the assay remains valid only insofar as the assay continues to provide accurate and precise results as proved through statistical verification. Therefore, validation of diagnostic assays for infectious diseases does not end with a time-limited series of experiments based on a few reference samples. Rather, it is a process that also requires constant vigilance and maintenance, along with reassessment of its performance characteristics for each population of animals to which it is applied. It is certain that the current movement to develop and implement accreditation criteria for veterinary diagnostic laboratories may be of little worth unless there is some assurance that the assays conducted in such laboratories are properly validated. Fully accredited laboratories may generate highly reproducible test results, but the results may still misclassify animals as to their infection status due to an improper assay validation process. Therefore, assay validation is foundational to the core product of veterinary diagnostic laboratories--test results and their interpretation AD - Diagnostic Laboratory, College of Veterinary Medicine, Cornell University, Ithaca, NY 14852-5786, USA UR - PM:9713892 ER - TY - JOUR ID - 1533 T1 - Molecular diversity in Bacillus anthracis A1 - Keim,P. A1 - Klevytska,A.M. A1 - Price,L.B. A1 - Schupp,J.M. A1 - Zinser,G. A1 - Smith,K.L. A1 - Hugh-Jones,M.E. A1 - Okinaka,R. A1 - Hill,K.K. A1 - Jackson,P.J. Y1 - 1999/08// N1 - DA - 19991104 IS - 1364-5072 (Print) LA - eng PT - Journal Article SB - IM KW - Animals KW - Anthrax KW - Bacillus anthracis KW - dna KW - Evolution KW - FRAGMENT LENGTH POLYMORPHISM KW - gene KW - Genetic Variation KW - genetics KW - Genome,Bacterial KW - Humans KW - MARKERS KW - microbiology KW - Polymorphism,Genetic KW - rev3 KW - USA KW - VARIATION RP - IN FILE SP - 215 EP - 217 JA - J Appl.Microbiol. VL - 87 N2 - Molecular typing of Bacillus anthracis has been extremely difficult due to the lack of polymorphic DNA markers. We have identified nine novel variable number tandemly repeated loci from previously known amplified fragment length polymorphism markers or from the DNA sequence. In combination with the previously known vrrA locus, these markers provide discrimination power to genetically characterize B. anthracis isolates. The variable number tandem repeat (VNTR) loci are found in both gene coding (genic) and non-coding (non-genic) regions. The genic differences are 'in frame' and result in additions or deletion of amino acids to the predicted proteins. Due the rarity of molecular differences, the VNTR changes represent a significant portion of the genetic variation found within B. anthracis. This variation could represent an important adaptive mechanism. Marker similarity and differences among diverse isolates have identified seven major diversity groups that may represent the only world-wide B. anthracis clones. The lineages reconstructed using these data may reflect the dispersal and evolution of this pathogen AD - Department of Biological Sciences, Northern Arizona University, Flagstaff 86011-5640, USA. Paul.Keim@nau.edu UR - PM:10475952 ER - TY - JOUR ID - 1534 T1 - Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis A1 - Keim,P. A1 - Price,L.B. A1 - Klevytska,A.M. A1 - Smith,K.L. A1 - Schupp,J.M. A1 - Okinaka,R. A1 - Jackson,P.J. A1 - Hugh-Jones,M.E. Y1 - 2000/05// N1 - DA - 20000612 IS - 0021-9193 (Print) LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S PT - Research Support, U.S. Gov't, P.H.S RN - 0 (DNA, Bacterial) RN - 0 (Genetic Markers) SB - IM KW - Alleles KW - analysis KW - Bacillus anthracis KW - characterization KW - classification KW - Cluster Analysis KW - dna KW - DNA,Bacterial KW - Genetic Markers KW - Genetic Variation KW - genetics KW - Genotype KW - human KW - Humans KW - MARKERS KW - Minisatellite Repeats KW - Phylogeny KW - Research KW - rev3 KW - strain KW - USA RP - IN FILE SP - 2928 EP - 2936 JA - J Bacteriol. VL - 182 N2 - Bacillus anthracis is one of the most genetically homogeneous pathogens described, making strain discrimination particularly difficult. In this paper, we present a novel molecular typing system based on rapidly evolving variable-number tandem repeat (VNTR) loci. Multiple-locus VNTR analysis (MLVA) uses the combined power of multiple alleles at several marker loci. In our system, fluorescently labeled PCR primers are used to produce PCR amplification products from eight VNTR regions in the B. anthracis genome. These are detected and their sizes are determined using an ABI377 automated DNA sequencer. Five of these eight loci were discovered by sequence characterization of molecular markers (vrrC(1), vrrC(2), vrrB(1), vrrB(2), and CG3), two were discovered by searching complete plasmid nucleotide sequences (pXO1-aat and pXO2-at), and one was known previously (vrrA). MLVA characterization of 426 B. anthracis isolates identified 89 distinct genotypes. VNTR markers frequently identified multiple alleles (from two to nine), with Nei's diversity values between 0.3 and 0.8. Unweighted pair-group method arithmetic average cluster analysis identified six genetically distinct groups that appear to be derived from clones. Some of these clones show worldwide distribution, while others are restricted to particular geographic regions. Human commerce doubtlessly has contributed to the dispersal of particular clones in ancient and modern times AD - Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011-5640, USA. Paul.Keim@nau.edu UR - PM:10781564 ER - TY - JOUR ID - 1535 T1 - Molecular investigation of the Aum Shinrikyo anthrax release in Kameido, Japan A1 - Keim,P. A1 - Smith,K.L. A1 - Keys,C. A1 - Takahashi,H. A1 - Kurata,T. A1 - Kaufmann,A. Y1 - 2001/12// N1 - DA - 20020111 IS - 0095-1137 (Print) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S PT - Research Support, U.S. Gov't, P.H.S RN - 0 (Aerosols) SB - IM KW - Aerosols KW - Animal KW - Anthrax KW - Bacillus anthracis KW - Bacterial Typing Techniques KW - Bioterrorism KW - classification KW - genetics KW - Japan KW - Minisatellite Repeats KW - physiology KW - Polymerase Chain Reaction KW - prophylaxis KW - Religion KW - Research KW - rev3 KW - SAMPLES KW - Spores,Bacterial KW - strain KW - USA RP - IN FILE SP - 4566 EP - 4567 JA - J Clin Microbiol. VL - 39 N2 - In 1993, the Aum Shinrikyo cult aerosolized Bacillus anthracis spores over Kameido, Japan. Spore samples were obtained from the release site, cultured, and characterized by molecular genetic typing. The isolates were consistent with strain Sterne 34F2, which is used in Japan for animal prophylaxis against anthrax AD - Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011-5640, USA. Paul.Keim@NAU.EDU UR - PM:11724885 ER - TY - JOUR ID - 1536 T1 - Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales A1 - Keim,P. A1 - Van Ert,M.N. A1 - Pearson,T. A1 - Vogler,A.J. A1 - Huynh,L.Y. A1 - Wagner,D.M. Y1 - 2004/09// N1 - DA - 20040928 IS - 1567-1348 (Print) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S PT - Research Support, U.S. Gov't, P.H.S PT - Review RN - 0 (Genetic Markers) SB - IM KW - Animals KW - Anthrax KW - ASSAY KW - Bacillus anthracis KW - Bioterrorism KW - classification KW - epidemiology KW - Epidemiology,Molecular KW - Evolution KW - Forensic Sciences KW - Genetic Markers KW - genetics KW - Humans KW - identification KW - Key KW - MARKERS KW - Mutation KW - Phylogeny KW - Polymorphism,Genetic KW - PROGRAM KW - Research KW - rev3 KW - review KW - Selection KW - strain KW - USA KW - VARIATION RP - IN FILE SP - 205 EP - 213 JA - Infect.Genet.Evol. VL - 4 N2 - Precise identification of Bacillus anthracis isolates has aided forensic and epidemiological analyses of natural anthrax cases, bioterrorism acts and industrial scale accidents by state-sponsored bioweapons programs. Because there is little molecular variation among B. anthracis isolates, identifying and using rare variation is crucial for precise strain identification. We think that mutation is the primary diversifying force in a clonal, recently emerged pathogen, such as B. anthracis, since mutation rate is correlated with diversity on a per locus basis. While single nucleotide polymorphisms (SNPs) are rare, their detection is facilitated by whole genome discovery approaches. As highly stable phylogenetic markers, SNPs are useful for identifying long branches or key phylogenetic positions. Selection of single, diagnostic "Canonical SNPs" (canSNPs) for these phylogenetic positions allows for efficient and defining assays. We have taken a nested hierarchal strategy for subtyping B. anthracis, which is consistent with traditional diagnostics and applicable to a wide range of pathogens. Progressive hierarchical resolving assays using nucleic acids (PHRANA) uses a progression of diagnostic genomic loci that are initially highly stable but with low resolution and, ultimately, very unstable but with high resolution. This approach mitigates the need for data weighting and provides both a deeply rooted phylogenetic hypothesis and high resolution discrimination among closely related isolates AD - Keim Genetics Laboratory, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640, USA. paul.keim@nau.edu UR - PM:15450200 ER - TY - JOUR ID - 1537 T1 - A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis A1 - Le Fleche,P. A1 - Hauck,Y. A1 - Onteniente,L. A1 - Prieur,A. A1 - Denoeud,F. A1 - Ramisse,V. A1 - Sylvestre,P. A1 - Benson,G. A1 - Ramisse,F. A1 - Vergnaud,G. Y1 - 2001/// N1 - DA - 20020923 IS - 1471-2180 (Electronic) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't RN - 0 (DNA, Bacterial) SB - IM KW - Alleles KW - analysis KW - Bacillus anthracis KW - Bacteria KW - characterization KW - classification KW - Databases,Factual KW - density KW - dna KW - DNA,Bacterial KW - Evolution KW - France KW - genetics KW - GENOME SEQUENCE KW - Genome,Bacterial KW - Genotype KW - human KW - identification KW - information KW - MARKERS KW - Minisatellite Repeats KW - Polymerase Chain Reaction KW - Polymorphism,Genetic KW - Research KW - rev3 KW - Selection KW - size KW - Statistics as Topic KW - strain KW - Tandem Repeat Sequences KW - yersinia KW - Yersinia pestis RP - IN FILE SP - 2 JA - BMC.Microbiol. VL - 1 N2 - BACKGROUND: Some pathogenic bacteria are genetically very homogeneous, making strain discrimination difficult. In the last few years, tandem repeats have been increasingly recognized as markers of choice for genotyping a number of pathogens. The rapid evolution of these structures appears to contribute to the phenotypic flexibility of pathogens. The availability of whole-genome sequences has opened the way to the systematic evaluation of tandem repeats diversity and application to epidemiological studies. RESULTS: This report presents a database (http://minisatellites.u-psud.fr) of tandem repeats from publicly available bacterial genomes which facilitates the identification and selection of tandem repeats. We illustrate the use of this database by the characterization of minisatellites from two important human pathogens, Yersinia pestis and Bacillus anthracis. In order to avoid simple sequence contingency loci which may be of limited value as epidemiological markers, and to provide genotyping tools amenable to ordinary agarose gel electrophoresis, only tandem repeats with repeat units at least 9 bp long were evaluated. Yersinia pestis contains 64 such minisatellites in which the unit is repeated at least 7 times. An additional collection of 12 loci with at least 6 units, and a high internal conservation were also evaluated. Forty-nine are polymorphic among five Yersinia strains (twenty-five among three Y. pestis strains). Bacillus anthracis contains 30 comparable structures in which the unit is repeated at least 10 times. Half of these tandem repeats show polymorphism among the strains tested. CONCLUSIONS: Analysis of the currently available bacterial genome sequences classifies Bacillus anthracis and Yersinia pestis as having an average (approximately 30 per Mb) density of tandem repeat arrays longer than 100 bp when compared to the other bacterial genomes analysed to date. In both cases, testing a fraction of these sequences for polymorphism was sufficient to quickly develop a set of more than fifteen informative markers, some of which show a very high degree of polymorphism. In one instance, the polymorphism information content index reaches 0.82 with allele length covering a wide size range (600-1950 bp), and nine alleles resolved in the small number of independent Bacillus anthracis strains typed here AD - Centre d'Etudes du Bouchet, BP3, 91710 Vert le Petit, France. lefleche@igmors.u-psud.fr UR - PM:11299044 ER - TY - JOUR ID - 1538 T1 - Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay A1 - Le Fleche,P. A1 - Jacques,I. A1 - Grayon,M. A1 - Al Dahouk,S. A1 - Bouchon,P. A1 - Denoeud,F. A1 - Nockler,K. A1 - Neubauer,H. A1 - Guilloteau,L.A. A1 - Vergnaud,G. Y1 - 2006/// N1 - DA - 20060721 IS - 1471-2180 (Electronic) LA - eng PT - Evaluation Studies PT - Journal Article PT - Research Support, Non-U.S. Gov't RN - 0 (DNA, Bacterial) RN - 0 (Genetic Markers) SB - IM KW - analysis KW - Animals KW - ASSAY KW - Bacterial Typing Techniques KW - Brucella KW - Brucellosis KW - classification KW - dna KW - DNA,Bacterial KW - Evaluation Studies KW - France KW - Genetic Markers KW - genetics KW - GENOME SEQUENCE KW - Genotype KW - Humans KW - identification KW - MARKERS KW - Methods KW - Minisatellite Repeats KW - Polymerase Chain Reaction KW - Polymorphism,Genetic KW - procedure KW - reference KW - Research KW - rev3 KW - Selection KW - species KW - standardization KW - strain RP - IN FILE SP - 9 JA - BMC.Microbiol. VL - 6 N2 - BACKGROUND: The classification of Brucella into species and biovars relies on phenotypic characteristics and sometimes raises difficulties in the interpretation of the results due to an absence of standardization of the typing reagents. In addition, the resolution of this biotyping is moderate and requires the manipulation of the living agent. More efficient DNA-based methods are needed, and this work explores the suitability of multiple locus variable number tandem repeats analysis (MLVA) for both typing and species identification. RESULTS: Eighty tandem repeat loci predicted to be polymorphic by genome sequence analysis of three available Brucella genome sequences were tested for polymorphism by genotyping 21 Brucella strains (18 reference strains representing the six 'classical' species and all biovars as well as 3 marine mammal strains currently recognized as members of two new species). The MLVA data efficiently cluster the strains as expected according to their species and biovar. For practical use, a subset of 15 loci preserving this clustering was selected and applied to the typing of 236 isolates. Using this MLVA-15 assay, the clusters generated correspond to the classical biotyping scheme of Brucella spp. The 15 markers have been divided into two groups, one comprising 8 user-friendly minisatellite markers with a good species identification capability (panel 1) and another complementary group of 7 microsatellite markers with higher discriminatory power (panel 2). CONCLUSION: The MLVA-15 assay can be applied to large collections of Brucella strains with automated or manual procedures, and can be proposed as a complement, or even a substitute, of classical biotyping methods. This is facilitated by the fact that MLVA is based on non-infectious material (DNA) whereas the biotyping procedure itself requires the manipulation of the living agent. The data produced can be queried on a dedicated MLVA web service site AD - Centre d'Etudes du Bouchet BP3, 91710 Vert le Petit, France. lefleche@igmors.u-psud.fr UR - PM:16469109 ER - TY - JOUR ID - 1539 T1 - Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis A1 - Lista,F. A1 - Faggioni,G. A1 - Valjevac,S. A1 - Ciammaruconi,A. A1 - Vaissaire,J. A1 - le Doujet,C. A1 - Gorge,O. A1 - De Santis,R. A1 - Carattoli,A. A1 - Ciervo,A. A1 - Fasanella,A. A1 - Orsini,F. A1 - D'Amelio,R. A1 - Pourcel,C. A1 - Cassone,A. A1 - Vergnaud,G. Y1 - 2006/// N1 - DA - 20060615 IS - 1471-2180 (Electronic) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't RN - 0 (DNA, Bacterial) RN - 0 (Genetic Markers) SB - IM KW - Alleles KW - analysis KW - Anthrax KW - ASSAY KW - Automation KW - Bacillus anthracis KW - Bioterrorism KW - classification KW - cost KW - DIFFERENTIATION KW - dna KW - DNA,Bacterial KW - Electrophoresis,Capillary KW - Evolution KW - France KW - Genetic Markers KW - genetics KW - Genotype KW - Italy KW - MARKERS KW - Methods KW - Phylogeny KW - reference KW - Research KW - rev3 KW - standardization KW - strain KW - Tandem Repeat Sequences RP - IN FILE SP - 33 JA - BMC.Microbiol. VL - 6 N2 - BACKGROUND: The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR) Analysis (MLVA) assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary. RESULTS : Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats. CONCLUSION: In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the B branch was described, and two new branches, D and E, are proposed. Owing to the upgrading achieved here, precise genotyping can now be produced either by automated capillary electrophoresis, or by the more accessible but slower and for some markers slightly less accurate agarose gel methodology AD - Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy). florigio.lista@esercito.difesa.it UR - PM:16600037 ER - TY - JOUR ID - 1540 T1 - The nature and dynamics of bacterial genomes A1 - Ochman,H. A1 - Davalos,L.M. Y1 - 2006/03/24/ N1 - DA - 20060324 IS - 1095-9203 (Electronic) LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review RN - 0 (Escherichia coli Proteins) SB - IM KW - Amino Acid Substitution KW - Bacteria KW - Cell KW - chemistry KW - Computational Biology KW - dna KW - Dynamic KW - Escherichia coli KW - Escherichia coli K12 KW - Escherichia coli Proteins KW - ESCHERICHIA-COLI KW - gene KW - Genes,Bacterial KW - genetics KW - Genome,Bacterial KW - Genomics KW - identification KW - Molecular Sequence Data KW - Mutation KW - phenotype KW - Pseudogenes KW - Research KW - rev3 KW - review KW - Selection (Genetics) KW - Transcription,Genetic KW - USA RP - IN FILE SP - 1730 EP - 1733 JF - Science VL - 311 N2 - Though generally small and gene rich, bacterial genomes are constantly subjected to both mutational and population-level processes that operate to increase amounts of functionless DNA. As a result, the coding potential of bacterial genomes can be substantially lower than originally predicted. Whereas only a single pseudogene was included in the original annotation of the bacterium Escherichia coli, we estimate that this genome harbors hundreds of inactivated and otherwise functionless genes. Such regions will never yield a detectable phenotype, but their identification is vital to efforts to elucidate the biological role of all the proteins within the cell AD - Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA. hochman@email.arizona.edu UR - PM:16556833 ER - TY - JOUR ID - 1541 T1 - The antibiotic sensitivity patterns of Bacillus anthracis isolated from the Kruger National Park A1 - Odendaal,M.W. A1 - Pieterson,P.M. A1 - De,Vos,V A1 - Botha,A.D. Y1 - 1991/03// N1 - DA - 19910722 IS - 0030-2465 (Print) LA - eng PT - Journal Article SB - IM KW - AFRICA KW - Animals KW - Anthrax KW - Bacillus anthracis KW - concentration KW - drug effects KW - Drug Resistance,Microbial KW - human KW - isolation & purification KW - Methods KW - Microbial Sensitivity Tests KW - physiology KW - Research KW - RESISTANCE KW - rev3 KW - SOUTH AFRICA KW - Streptomycin KW - Susceptibility KW - Tetracycline KW - therapeutic use KW - veterinary RP - IN FILE SP - 17 EP - 19 JA - Onderstepoort J Vet Res. VL - 58 N2 - Forty-four isolates of Bacillus anthracis made from carcasses and soil in different localities of an endemic anthrax area in the Kruger National Park, South Africa, were tested by standard disc diffusion for their susceptibility to 18 different antibiotics. These were ampicillin, penicillin G, sulphatriad, streptomycin, clindamycin, gentamicin, fusidic acid, trimethoprim, sulphamethoxazole, chloramphenicol, erythromycin, methicillin, tetracycline (2 different concentrations), novobiocin, cefotaxime, netilmicin, cefamandole and cefoxitin. All the isolates were susceptible to ampicillin, streptomycin, chloramphenicol, erythromycin, tetracycline, methicillin and netilmicin. More than 90% of the isolates were sensitive to clindamycin, gentamicin and cefoxitin, whereas only 84.1% of the isolates were sensitive to penicillin G, 86.4% to novobiocin and 68.18% to cefamandole. Complete resistance in 100% of the isolates was encountered with trimethoprim and sulphamethoxazole, with 95.45% for sulphatriad. Moderate sensitivity occurred with penicillin G (15.9% of the isolates), clindamycin (6.8%), novobiocin (13.6%), fusidic acid (84.1%), cefotaxime (100%), cefamandole (31.8%) and cefoxitin (6.8%). The relevance of the findings to the therapeutic uses of different types of antibiotic in human clinical cases referred to in the literature is discussed AD - Roodeplaat Research Laboratories, Sinoville UR - PM:1905000 ER - TY - JOUR ID - 1542 T1 - Brucellosis A1 - Pappas,G. A1 - Akritidis,N. A1 - Bosilkovski,M. A1 - Tsianos,E. Y1 - 2005/06/02/ N1 - DA - 20050602 IS - 1533-4406 (Electronic) LA - eng PT - Journal Article PT - Review RN - 0 (Antibodies, Bacterial) RN - 13292-46-1 (Rifampin) RN - 564-25-0 (Doxycycline) RN - 57-92-1 (Streptomycin) SB - AIM SB - IM KW - Antibodies KW - Antibodies,Bacterial KW - antibody KW - Brucella KW - Brucella melitensis KW - Brucellosis KW - classification KW - Dairy Products KW - DIAGNOSIS KW - Doxycycline KW - drug therapy KW - Drug Therapy,Combination KW - genetics KW - Genome,Bacterial KW - greece KW - Humans KW - IMMUNOLOGY KW - microbiology KW - PATHOGENICITY KW - Prevalence KW - Recurrence KW - rev3 KW - review KW - Rifampin KW - Streptomycin KW - therapeutic use KW - TRANSMISSION RP - IN FILE SP - 2325 EP - 2336 JA - N.Engl.J Med VL - 352 AD - Brucellosis Unit, University Hospital of Ioannina, Ioannina, Greece. gpele@otenet.gr UR - PM:15930423 ER - TY - JOUR ID - 1543 T1 - Evaluation of PCR and indirect enzyme-linked immunosorbent assay on milk samples for diagnosis of brucellosis in dairy cattle A1 - Romero,C. A1 - Pardo,M. A1 - Grillo,M.J. A1 - Diaz,R. A1 - Blasco,J.M. A1 - Lopez-Goni,I. Y1 - 1995/12// N1 - DA - 19960327 IS - 0095-1137 (Print) LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't RN - 0 (Antibodies, Bacterial) RN - 0 (DNA, Bacterial) SB - IM KW - analysis KW - Animals KW - Antibodies KW - Antibodies,Bacterial KW - antibody KW - ASSAY KW - Bacteriological Techniques KW - Brucella KW - Brucellosis KW - Brucellosis,Bovine KW - cattle KW - Comparative Study KW - DAIRY-CATTLE KW - DIAGNOSIS KW - dna KW - DNA,Bacterial KW - ELISA KW - Enzyme Linked Immunosorbent Assay KW - Enzyme-Linked Immunosorbent Assay KW - Evaluation Studies as Topic KW - FEMALE KW - genetics KW - IMMUNOLOGY KW - isolation & purification KW - Methods KW - microbiology KW - Milk KW - Polymerase Chain Reaction KW - Research KW - rev3 KW - SAMPLES KW - Sensitivity and Specificity KW - statistics & numerical data KW - TESTS RP - IN FILE SP - 3198 EP - 3200 JA - J Clin Microbiol. VL - 33 N2 - A study was performed to evaluate the previously described PCR (C. Romero, C. Gamazo, M. Pardo, and I. Lopez-Goni, J. Clin. Microbiol. 33:615-617, 1995) for the diagnosis of brucellosis in dairy cattle. Milk samples from 56 Brucella milk culture-positive cattle and from 37 cattle from Brucella-free herds were examined for Brucella DNA by PCR and for specific antibodies by an indirect enzyme-linked immunosorbent assay (ELISA). The specificities of both tests were 100% when testing the milk samples from Brucella-free cattle. The milk samples from 49 infected cattle were positive by PCR (87.5% sensitivity), and 55 were positive by ELISA (98.2% sensitivity). A PCR-positive sample was negative by ELISA, and 7 ELISA-positive samples were PCR negative, yielding an observed proportion of agreement of 0.91 for the two tests. Although the results suggest that ELISA is a better screening test than PCR, the combined sensitivity of the two assays was 100%, and their simultaneous application could be more useful than one test alone for a rapid screening of brucellosis in dairy cattle AD - Departamento de Microbiologia, Universidad de Navarra, Pamplona, Spain UR - PM:8586702 ER - TY - JOUR ID - 1544 T1 - Brucella microti sp. nov., isolated from the common vole Microtus arvalis A1 - Scholz,H.C. A1 - Hubalek,Z. A1 - Sedlacek,I. A1 - Vergnaud,G. A1 - Tomaso,H. A1 - Al Dahouk,S. A1 - Melzer,F. A1 - Kampfer,P. A1 - Neubauer,H. A1 - Cloeckaert,A. A1 - Maquart,M. A1 - Zygmunt,M.S. A1 - Whatmore,A.M. A1 - Falsen,E. A1 - Bahn,P. A1 - Gollner,C. A1 - Pfeffer,M. A1 - Huber,B. A1 - Busse,H.J. A1 - Nockler,K. Y1 - 2008/02// N1 - DA - 20080125 IS - 1466-5026 (Print) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (DNA, Bacterial) RN - 0 (RNA, Ribosomal, 16S) RN - EC 2.7.7.- (Rec A Recombinases) SB - IM KW - analysis KW - Animals KW - Arvicolinae KW - Bacteria KW - Bacterial Outer Membrane Proteins KW - Bacterial Typing Techniques KW - Brucella KW - Brucellosis KW - classification KW - dna KW - DNA,Bacterial KW - gene KW - Genes,rRNA KW - genetics KW - Genotype KW - Germany KW - isolation & purification KW - microbiology KW - MICROTI KW - Minisatellite Repeats KW - Molecular Sequence Data KW - Nucleic Acid Hybridization KW - phenotype KW - Phylogeny KW - physiology KW - Rec A Recombinases KW - Research KW - rev3 KW - RNA,Ribosomal,16S KW - Rodent Diseases KW - Sequence Analysis,DNA KW - species KW - Species Specificity KW - strain KW - veterinary RP - IN FILE SP - 375 EP - 382 JA - Int J Syst.Evol.Microbiol. VL - 58 N2 - Two Gram-negative, non-motile, non-spore-forming, coccoid bacteria (strains CCM 4915(T) and CCM 4916), isolated from clinical specimens of the common vole Microtus arvalis during an epizootic in the Czech Republic in 2001, were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA (rrs) and recA gene sequence similarities, both isolates were allocated to the genus Brucella. Affiliation to Brucella was confirmed by DNA-DNA hybridization studies. Both strains reacted equally with Brucella M-monospecific antiserum and were lysed by the bacteriophages Tb, Wb, F1 and F25. Biochemical profiling revealed a high degree of enzyme activity and metabolic capabilities not observed in other Brucella species. The omp2a and omp2b genes of isolates CCM 4915(T) and CCM 4916 were indistinguishable. Whereas omp2a was identical to omp2a of brucellae from certain pinniped marine mammals, omp2b clustered with omp2b of terrestrial brucellae. Analysis of the bp26 gene downstream region identified strains CCM 4915(T) and CCM 4916 as Brucella of terrestrial origin. Both strains harboured five to six copies of the insertion element IS711, displaying a unique banding pattern as determined by Southern blotting. In comparative multilocus VNTR (variable-number tandem-repeat) analysis (MLVA) with 296 different genotypes, the two isolates grouped together, but formed a separate cluster within the genus Brucella. Multilocus sequence typing (MLST) analysis using nine different loci also placed the two isolates separately from other brucellae. In the IS711-based AMOS PCR, a 1900 bp fragment was generated with the Brucella ovis-specific primers, revealing that the insertion element had integrated between a putative membrane protein and cboL, encoding a methyltransferase, an integration site not observed in other brucellae. Isolates CCM 4915(T) and CCM 4916 could be clearly distinguished from all known Brucella species and their biovars by means of both their phenotypic and molecular properties, and therefore represent a novel species within the genus Brucella, for which the name Brucella microti sp. nov. with the type strain CCM 4915(T) (=BCCN 07-01(T)=CAPM 6434(T)) is proposed AD - Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, D-80937 Munich, Germany. Holger1Scholz@bundeswehr.org UR - PM:18218934 ER - TY - JOUR ID - 1545 T1 - Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome A1 - Supply,P. A1 - Mazars,E. A1 - Lesjean,S. A1 - Vincent,V. A1 - Gicquel,B. A1 - Locht,C. Y1 - 2000/05// N1 - DA - 20000829 IS - 0950-382X (Print) LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't SB - IM KW - Base Sequence KW - BCG KW - Chromosome Mapping KW - Chromosomes,Bacterial KW - Consensus Sequence KW - dna KW - France KW - Genetic Variation KW - genetics KW - Genome,Bacterial KW - human KW - Humans KW - Minisatellite Repeats KW - Molecular Sequence Data KW - Mycobacterium KW - Mycobacterium tuberculosis KW - Polymerase Chain Reaction KW - POPULATION KW - POPULATIONS KW - Research KW - rev3 KW - strain KW - tuberculosis KW - VARIATION RP - IN FILE SP - 762 EP - 771 JA - Mol.Microbiol. VL - 36 N2 - Mycobacterial interspersed repetitive units (MIRUs) are 40-100 bp DNA elements often found as tandem repeats and dispersed in intergenic regions of the Mycobacterium tuberculosis complex genomes. The M. tuberculosis H37Rv chromosome contains 41 MIRU loci. After polymerase chain reaction (PCR) and sequence analyses of these loci in 31 M. tuberculosis complex strains, 12 of them were found to display variations in tandem repeat copy numbers and, in most cases, sequence variations between repeat units as well. These features are reminiscent of those of certain human variable minisatellites. Of the 12 variable loci, only one was found to vary among genealogically distant BCG substrains, suggesting that these interspersed bacterial minisatellite-like structures evolve slowly in mycobacterial populations AD - Laboratoire des Mecanismes Moleculaires de la Pathogenese Bacterienne, INSERM U447, France. philip.supply@pasteur-lille.fr UR - PM:10844663 ER - TY - JOUR ID - 1547 T1 - Antibodies to anthrax toxin in humans and guinea pigs and their relevance to protective immunity A1 - Turnbull,P.C. A1 - Leppla,S.H. A1 - Broster,M.G. A1 - Quinn,C.P. A1 - Melling,J. Y1 - 1988/// N1 - DA - 19881121 IS - 0300-8584 (Print) LA - eng PT - Journal Article RN - 0 (Antibodies, Bacterial) RN - 0 (Antigens, Bacterial) RN - 0 (Bacterial Toxins) RN - 0 (anthrax toxin) SB - IM KW - administration & dosage KW - analysis KW - Animals KW - Anthrax KW - Antibodies KW - Antibodies,Bacterial KW - antibody KW - Antigen KW - Antigens,Bacterial KW - Bacillus anthracis KW - Bacterial Toxins KW - biosynthesis KW - Enzyme-Linked Immunosorbent Assay KW - guinea pig KW - Guinea Pigs KW - HEALTH KW - history KW - human KW - Humans KW - IMMUNITY KW - Immunity,Innate KW - Immunization Schedule KW - IMMUNOLOGY KW - PIGS KW - production KW - PROTECTION KW - Public Health KW - reference KW - rev3 KW - strain RP - IN FILE SP - 293 EP - 303 JA - Med Microbiol.Immunol. VL - 177 N2 - A forerunning study on the relationship between antibodies to the protective antigen (PA) and lethal factor (LF) components of anthrax toxin and protective immunity has been expanded and extended to include the third toxin component, the edema factor (EF). It was found that protection against the "vaccine resistant" Ames strain was possible in the absence of detectable anti-LF and anti-EF antibodies. Evidence is given that PA may be the essential anthrax-derived antigen for protection, but that equally essential is that it be presented to the host's immune system in such a manner as to provide stimulation of more than just production of antibody to PA. Titers to the three components in sera of individuals with histories of clinically diagnosed anthrax as well as from human vaccinees are included in the report AD - Anthrax Reference Laboratory, Public Health Laboratory Service Centre, Salisbury, Wiltshire, UK UR - PM:3139974 ER - TY - JOUR ID - 1546 T1 - Current status of immunization against anthrax: old vaccines may be here to stay for a while A1 - Turnbull,P.C. Y1 - 2000/04// N1 - DA - 20020419 IS - 1535-3877 (Electronic) LA - ENG PT - JOURNAL ARTICLE KW - Anthrax KW - efficacy KW - IMMUNIZATION KW - live KW - production KW - PROTECTION KW - rev3 KW - Safety KW - VACCINATION KW - vaccine KW - Vaccines KW - War RP - IN FILE SP - 113 EP - 120 JA - Curr.Opin.Infect.Dis. VL - 13 N2 - Anthrax vaccination has become a 'hot' topic. On the one hand, fears that Iraq holds secret caches of anthrax-based weaponry, that other countries may be developing or may have developed similar devices, or that hard-line groups may make their own anthrax-based devices for bioterrorist attacks have focused official attention on the need for means of protection, principally, though, for the military. On the other hand, the unsolved issues of the Gulf War illnesses have left elements of doubt in the minds of some as to the possible role of anthrax (among other) vaccines in this syndrome, and have drawn attention to the shortage of pre-clinical, clinical, pharmacological and safety data on the existing UK and US anthrax vaccines. In the middle are those hotly debating the US and Canadian policies of mandatory anthrax immunization for military personnel or, in the case of the UK policy of voluntary immunization, simply voting with their feet. Compounding matters have been the publicized failures of the US vaccine production facility and the less publicized UK problems of supply. Meanwhile, those in genuine at-risk occupations are left unsure whether, if they can get the vaccine at all, they really want it. Despite two decades of elegant science aimed at formulating alternative vaccines to overcome all the problems of efficacy, safety and supply, such an alternative is at least five years away, and the current status is that we must live with the old vaccines or not vaccinate AD - Arjemptur Technology Ltd, Porton Down Science Park, Salisbury, UK UR - PM:11964777 ER - TY - JOUR ID - 1549 T1 - Short-sequence DNA repeats in prokaryotic genomes A1 - van Belkum,A. A1 - Scherer,S. A1 - van Alphen,L. A1 - Verbrugh,H. Y1 - 1998/06// N1 - DA - 19980709 IS - 1092-2172 (Print) LA - eng PT - Journal Article PT - Review RN - 0 (Adhesins, Bacterial) RN - 0 (DNA, Bacterial) RN - 0 (DNA, Protozoan) SB - IM KW - Adhesins,Bacterial KW - analysis KW - Animals KW - Bacteria KW - Base Sequence KW - Cell KW - Cell Division KW - Disease KW - dna KW - DNA Repair KW - DNA,Bacterial KW - DNA,Protozoan KW - epidemiology KW - Evolution KW - gene KW - Gene Expression Regulation KW - Gene Expression Regulation,Bacterial KW - genetics KW - Genome,Bacterial KW - Genome,Protozoan KW - Genotype KW - Methods KW - microbiology KW - Netherlands KW - Pathogenesis KW - PATHOGENICITY KW - pressure KW - Repetitive Sequences,Nucleic Acid KW - rev3 KW - review KW - VARIATION KW - virulence RP - IN FILE SP - 275 EP - 293 JA - Microbiol.Mol.Biol.Rev. VL - 62 N2 - Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10(-4) per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant AD - Department of Medical Microbiology & Infectious Diseases, Erasmus Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands. vanbelkum@bacl.azr.nl UR - PM:9618442 ER - TY - JOUR ID - 1548 T1 - Tracing isolates of bacterial species by multilocus variable number of tandem repeat analysis (MLVA) A1 - van Belkum,A. Y1 - 2007/02// N1 - DA - 20070201 IS - 0928-8244 (Print) LA - eng PT - Journal Article PT - Review RN - 0 (DNA, Bacterial) SB - IM KW - analysis KW - Bacillus anthracis KW - Bacteria KW - Bioterrorism KW - classification KW - Disease KW - dna KW - DNA,Bacterial KW - genetics KW - Genome,Bacterial KW - Humans KW - isolation & purification KW - microbiology KW - Minisatellite Repeats KW - Mutation KW - Mycobacterium tuberculosis KW - Netherlands KW - outbreak KW - rev3 KW - review KW - species KW - Staphylococcus aureus KW - strain RP - IN FILE SP - 22 EP - 27 JA - FEMS Immunol.Med Microbiol. VL - 49 N2 - All bacterial genomes contain multiple loci of repetitive DNA. Repeat unit sizes and repeat sequences may vary when multiple loci are considered for different isolates of an individual microbial species. Moreover, it has been documented on many occasions that the number of repeat units per locus is a strain-defining parameter. Consequently, there is isolate-specificity in the number of repeats per locus when different strains of a given bacterial species are compared. The experimental assessment of this variability for a number of different loci has been called 'multilocus variable number of tandem repeat analysis' (MLVA). The approach can be supported or extended by locus-specific DNA sequencing for establishing mutations in the individual repeat units, which usually enhances the resolution of the approach considerably. Essentially, MLVA with or without supportive sequencing has been developed for all of the medically relevant bacterial species and can be used effectively for tracing outbreaks or other forms of bacterial dissemination. MLVA is a modern, timely and versatile bacterial typing methodology AD - Department of Medical Microbiology and Infectious Diseases, Rotterdam, The Netherlands. a.vanbelkum@erasmusmc.nl UR - PM:17266711 ER - TY - JOUR ID - 1550 T1 - Global genetic population structure of Bacillus anthracis A1 - Van Ert,M.N. A1 - Easterday,W.R. A1 - Huynh,L.Y. A1 - Okinaka,R.T. A1 - Hugh-Jones,M.E. A1 - Ravel,J. A1 - Zanecki,S.R. A1 - Pearson,T. A1 - Simonson,T.S. A1 - U'Ren,J.M. A1 - Kachur,S.M. A1 - Leadem-Dougherty,R.R. A1 - Rhoton,S.D. A1 - Zinser,G. A1 - Farlow,J. A1 - Coker,P.R. A1 - Smith,K.L. A1 - Wang,B. A1 - Kenefic,L.J. A1 - Fraser-Liggett,C.M. A1 - Wagner,D.M. A1 - Keim,P. Y1 - 2007/// N1 - DA - 20070523 IS - 1932-6203 (Electronic) LA - eng PT - Journal Article KW - analysis KW - Animal KW - Anthrax KW - Bacillus anthracis KW - Bacteria KW - Disease KW - Evolution KW - Genotype KW - human KW - Humans KW - MARKERS KW - model KW - outbreak KW - POPULATION KW - rev3 KW - species KW - strain KW - TRANSMISSION KW - United States KW - VARIATION RP - IN FILE SP - e461 JA - PLoS One. VL - 2 N2 - Anthrax, caused by the bacterium Bacillus anthracis, is a disease of historical and current importance that is found throughout the world. The basis of its historical transmission is anecdotal and its true global population structure has remained largely cryptic. Seven diverse B. anthracis strains were whole-genome sequenced to identify rare single nucleotide polymorphisms (SNPs), followed by phylogenetic reconstruction of these characters onto an evolutionary model. This analysis identified SNPs that define the major clonal lineages within the species. These SNPs, in concert with 15 variable number tandem repeat (VNTR) markers, were used to subtype a collection of 1,033 B. anthracis isolates from 42 countries to create an extensive genotype data set. These analyses subdivided the isolates into three previously recognized major lineages (A, B, and C), with further subdivision into 12 clonal sub-lineages or sub-groups and, finally, 221 unique MLVA15 genotypes. This rare genomic variation was used to document the evolutionary progression of B. anthracis and to establish global patterns of diversity. Isolates in the A lineage are widely dispersed globally, whereas the B and C lineages occur on more restricted spatial scales. Molecular clock models based upon genome-wide synonymous substitutions indicate there was a massive radiation of the A lineage that occurred in the mid-Holocene (3,064-6,127 ybp). On more recent temporal scales, the global population structure of B. anthracis reflects colonial-era importation of specific genotypes from the Old World into the New World, as well as the repeated industrial importation of diverse genotypes into developed countries via spore-contaminated animal products. These findings indicate humans have played an important role in the evolution of anthrax by increasing the proliferation and dispersal of this now global disease. Finally, the value of global genotypic analysis for investigating bioterrorist-mediated outbreaks of anthrax is demonstrated AD - Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America UR - PM:17520020 ER -