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Keim P, Gruendike JM, Klevytska AM, Schupp JM, Challacombe J, Okinaka R. The genome and variation of Bacillus anthracis. Mol Aspects Med 2009; 30:397-405. [PMID: 19729033 DOI: 10.1016/j.mam.2009.08.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 08/24/2009] [Indexed: 01/01/2023]
Abstract
The Bacillus anthracis genome reflects its close genetic ties to Bacillus cereus and Bacillus thuringiensis but has been shaped by its own unique biology and evolutionary forces. The genome is comprised of a chromosome and two large virulence plasmids, pXO1 and pXO2. The chromosome is mostly co-linear among B. anthracis strains and even with the closest near neighbor strains. An exception to this pattern has been observed in a large inversion in an attenuated strain suggesting that chromosome co-linearity is important to the natural biology of this pathogen. In general, there are few polymorphic nucleotides among B. anthracis strains reflecting the short evolutionary time since its derivation from a B. cereus-like ancestor. The exceptions to this lack of diversity are the variable number tandem repeat (VNTR) loci that exist in genic and non genic regions of the chromosome and both plasmids. Their variation is associated with high mutability that is driven by rapid insertion and deletion of the repeats within an array. A notable example is found in the vrrC locus which is homologous to known DNA translocase genes from other bacteria.
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Affiliation(s)
- Paul Keim
- The Microbial Genetics and Genomics Center, Northern Arizona University, Flagstaff AZ 86011-4073, USA.
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52
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Hugh-Jones M, Blackburn J. The ecology of Bacillus anthracis. Mol Aspects Med 2009; 30:356-67. [PMID: 19720074 DOI: 10.1016/j.mam.2009.08.003] [Citation(s) in RCA: 189] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 08/24/2009] [Indexed: 02/08/2023]
Abstract
The global distribution of anthrax is largely determined by soils with high calcium levels and a pH above 6.1, which foster spore survival. It is speculated that the spore exosporium probably plays a key part by restricting dispersal and thereby increasing the probability of a grazing animal acquiring a lethal dose. 'Anthrax Seasons' are characterized by hot-dry weather which stresses animals and reduces their innate resistance to infection allowing low doses of spores to be infective. Necrophagic flies act as case-multipliers and haemophagic flies as space-multipliers; the latter are aided by climatic factors which play a key part in whether epidemics occur. Host death is a function of species sensitivity to the toxins. The major function of scavengers is to open the carcass, spill fluids, and thereby aid bacilli dispersal and initiate sporulation. In the context of landscape ecology viable spore distribution is a function of mean annual temperature, annual precipitation, elevation, mean NDVI, annual NDVI amplitude, soil moisture content, and soil pH.
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Affiliation(s)
- Martin Hugh-Jones
- Department of Environmental Science, School of the Coast and Environment, Louisiana State University, Baton Rouge, LA 70803-5705, USA.
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53
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An extracytoplasmic function sigma factor controls beta-lactamase gene expression in Bacillus anthracis and other Bacillus cereus group species. J Bacteriol 2009; 191:6683-93. [PMID: 19717606 DOI: 10.1128/jb.00691-09] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The susceptibility of most Bacillus anthracis strains to beta-lactam antibiotics is intriguing considering that the closely related species Bacillus cereus and Bacillus thuringiensis typically produce beta-lactamases and the B. anthracis genome harbors two beta-lactamase genes, bla1 and bla2. We show that beta-lactamase activity associated with B. anthracis is affected by two genes, sigP (BA2502) and rsiP (BA2503), predicted to encode an extracytoplasmic function sigma factor and an anti-sigma factor, respectively. Deletion of the sigP-rsiP locus abolished beta-lactamase activity in a naturally occurring penicillin-resistant strain and had no effect on beta-lactamase activity in a prototypical penicillin-susceptible strain. Complementation with sigP and rsiP from the penicillin-resistant strain, but not with sigP and rsiP from the penicillin-susceptible strain, conferred constitutive beta-lactamase activity in both mutants. These results are attributed to a nucleotide deletion near the 5' end of rsiP in the penicillin-resistant strain that is predicted to result in a nonfunctional protein. B. cereus and B. thuringiensis sigP and rsiP homologues are required for inducible penicillin resistance in these species. Expression of the B. cereus or B. thuringiensis sigP and rsiP genes in a B. anthracis sigP-rsiP-null mutant confers inducible production of beta-lactamase activity, suggesting that while B. anthracis contains the genes necessary for sensing beta-lactam antibiotics, the B. anthracis sigP and rsiP gene products are not sufficient for bla induction.
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54
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Geographical distribution of genotypic and phenotypic markers among Bacillus anthracis isolates and related species by historical movement and horizontal transfer. Folia Microbiol (Praha) 2009; 53:472-8. [PMID: 19381470 DOI: 10.1007/s12223-008-0074-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 09/04/2008] [Indexed: 10/20/2022]
Abstract
The geographical distribution of Bacillus anthracis strains and isolates bearing some of the same genetic markers as the Amerithrax Ames isolate was examined and evaluated. At least one mechanism for the horizontal movement of genetic markers was shown amongst isolates and closely related species and the effect of such mixing was demonstrated on phenotype. The results provided potential mechanisms by which attempts to attribute isolates of Bacillus anthracis to certain geographical and isolate sources may be disrupted.
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55
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Porwal S, Lal S, Cheema S, Kalia VC. Phylogeny in aid of the present and novel microbial lineages: diversity in Bacillus. PLoS One 2009; 4:e4438. [PMID: 19212464 PMCID: PMC2639701 DOI: 10.1371/journal.pone.0004438] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 12/18/2008] [Indexed: 11/18/2022] Open
Abstract
Bacillus represents microbes of high economic, medical and biodefense importance. Bacillus strain identification based on 16S rRNA sequence analyses is invariably limited to species level. Secondly, certain discrepancies exist in the segregation of Bacillus subtilis strains. In the RDP/NCBI databases, out of a total of 2611 individual 16S rDNA sequences belonging to the 175 different species of the genus Bacillus, only 1586 have been identified up to species level. 16S rRNA sequences of Bacillus anthracis (153 strains), B. cereus (211 strains), B. thuringiensis (108 strains), B. subtilis (271 strains), B. licheniformis (131 strains), B. pumilus (83 strains), B. megaterium (47 strains), B. sphaericus (42 strains), B. clausii (39 strains) and B. halodurans (36 strains) were considered for generating species-specific framework and probes as tools for their rapid identification. Phylogenetic segregation of 1121, 16S rDNA sequences of 10 different Bacillus species in to 89 clusters enabled us to develop a phylogenetic frame work of 34 representative sequences. Using this phylogenetic framework, 305 out of 1025, 16S rDNA sequences presently classified as Bacillus sp. could be identified up to species level. This identification was supported by 20 to 30 nucleotides long signature sequences and in silico restriction enzyme analysis specific to the 10 Bacillus species. This integrated approach resulted in identifying around 30% of Bacillus sp. up to species level and revealed that B. subtilis strains can be segregated into two phylogenetically distinct groups, such that one of them may be renamed.
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Affiliation(s)
- Shalini Porwal
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
- Department of Biotechnology, University of Pune, Pune, India
| | - Sadhana Lal
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
| | - Simrita Cheema
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Delhi, India
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56
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Shaik R, Pillay D, Pillay B. Amplified fragment length polymorphisms reveal genetic differentiation among strains of Xanthomonas albilineans. J Microbiol Methods 2008; 76:43-51. [PMID: 18834907 DOI: 10.1016/j.mimet.2008.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 09/11/2008] [Accepted: 09/12/2008] [Indexed: 10/21/2022]
Abstract
Xanthomonas albilineans, the causative agent of leaf scald disease (LSD), colonizes the vascular system of sugarcane (Saccharum spp. hybrids). In this study X. albilineans strains from 28 countries were differentiated by using two methods of amplified fragment length polymorphism (AFLP). In the manual procedure, AFLP reactions were performed on 57 X. albilineans strains and after selective amplification using radiolabelled primers, the resulting products were separated using polyacrylamide gel electrophoresis. The autoradiographs were analyzed using GelCompar version 4.1 software (Applied Maths) to construct dendograms from similarity matrices. Fluorescent AFLP (FAFLP) was also employed on 52 X. albilineans strains using three fluorescently labelled primer combinations (automated AFLP). The FAFLP data was converted to a binary format using the Genemapper Software 3.7 (Applied Biosystems). Thereafter, dendograms were generated using the NTSYSpc. Software (USA). Distinct AFLP profiles were produced for the majority of the strains and were found to be useful in differentiating X. albilineans strains from various geographical locations. Fingerprints unique to each strain were reproducibly obtained and may be used to create a database for use in the identification of the various X. albilineans strains. It can be also concluded from the results obtained that the FAFLP has considerable technical advantages compared with the manual AFLP and also that the FAFLP is more sensitive than AFLP using radiolabelled primers in differentiating X. albilineans.
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Affiliation(s)
- Rehana Shaik
- Discipline of Microbiology, Faculty of Science and Agriculture, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa
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57
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SHRINIVAS K, KESTER K, MARTIN PAW, BROWN B. Molecular markers to determine the ecological fate ofBacillus thuringiensisssp.kurstaki. Mol Ecol Resour 2008; 8:1145-8. [DOI: 10.1111/j.1755-0998.2008.02207.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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58
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Okinaka RT, Henrie M, Hill KK, Lowery KS, Van Ert M, Pearson T, Schupp J, Kenefic L, Beaudry J, Hofstadler SA, Jackson PJ, Keim P. Single nucleotide polymorphism typing of Bacillus anthracis from Sverdlovsk tissue. Emerg Infect Dis 2008; 14:653-6. [PMID: 18394287 PMCID: PMC2570946 DOI: 10.3201/eid1404.070984] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A small number of conserved canonical single nucleotide polymorphisms (canSNP) that define major phylogenetic branches for Bacillus anthracis were used to place a Sverdlovsk patient’s B. anthracis genotype into 1 of 12 subgroups. Reconstruction of the pagA gene also showed a unique SNP that defines a new lineage for B. anthracis.
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59
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Carrera M, Zandomeni R, Sagripanti JL. Wet and dry density ofBacillus anthracisand otherBacillusspecies. J Appl Microbiol 2008; 105:68-77. [DOI: 10.1111/j.1365-2672.2008.03758.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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60
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Allender CJ, Clancy KM, Degomez TE, McMillin JD, Woolbright SA, Keim P, Wagner DM. Lack of genetic differentiation in aggressive and secondary bark beetles (Coleoptera: Curculionidae, Scolytinae) from Arizona. ENVIRONMENTAL ENTOMOLOGY 2008; 37:817-824. [PMID: 18559189 DOI: 10.1603/0046-225x(2008)37[817:logdia]2.0.co;2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Bark beetles (Coleoptera: Curculionidae, Scolytinae) play an important role as disturbance agents in ponderosa pine (Pinus ponderosa Douglas ex Lawson) forests of Arizona. However, from 2001 to 2003, elevated bark beetle activity caused unprecedented levels of ponderosa pine mortality. A better understanding of the population structure of these species will facilitate analysis of their dispersal patterns and improve management strategies. Here, we use fluorescently labeled amplified fragment length polymorphism (fAFLP) analysis to resolve genetic variation among and within sampling locations in northcentral Arizona of Ips pini (Say), Dendroctonus brevicomis LeConte, and D. frontalis Zimmermann. We generated genetic fingerprints for >500 beetle specimens and analyzed genetic diversity. For all species, gene flow estimates among sampling locations were high, and significant population subdivision was not discernible across a large portion of ponderosa pine forests in Arizona. However, a weak relationship was detected with I. pini population structure and elevation. Because of the lack of genetic differentiation detected throughout the large study area, our findings suggest these insects are capable of long distance dispersal and exhibit a high degree of gene flow across a broad region. We conclude that our results are consistent with strong dispersal patterns and large population sizes of all three species.
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Affiliation(s)
- Christopher J Allender
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640, USA
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61
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Gamma irradiation can be used to inactivate Bacillus anthracis spores without compromising the sensitivity of diagnostic assays. Appl Environ Microbiol 2008; 74:4427-33. [PMID: 18515484 DOI: 10.1128/aem.00557-08] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The use of Bacillus anthracis as a biological weapon in 2001 heightened awareness of the need for validated methods for the inactivation of B. anthracis spores. This study determined the gamma irradiation dose for inactivating virulent B. anthracis spores in suspension and its effects on real-time PCR and antigen detection assays. Strains representing eight genetic groups of B. anthracis were exposed to gamma radiation, and it was found that subjecting spores at a concentration of 10(7) CFU/ml to a dose of 2.5 x 10(6) rads resulted in a 6-log-unit reduction of spore viability. TaqMan real-time PCR analysis of untreated versus irradiated Ames strain (K1694) spores showed that treatment significantly enhanced the detection of B. anthracis chromosomal DNA targets but had no significant effect on the ability to detect targets on the pXO1 and pXO2 plasmids of B. anthracis. When analyzed by an enzyme-linked immunosorbent assay (ELISA), irradiation affected the detection of B. anthracis spores in a direct ELISA but had no effect on the limit of detection in a sandwich ELISA. The results of this study showed that gamma irradiation-inactivated spores can be tested by real-time PCR or sandwich ELISA without decreasing the sensitivity of either type of assay. Furthermore, the results suggest that clinical and public health laboratories which test specimens for B. anthracis could potentially incorporate gamma irradiation into sample processing protocols without compromising the sensitivity of the B. anthracis assays.
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62
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Koppisch AT, Dhungana S, Hill KK, Boukhalfa H, Heine HS, Colip LA, Romero RB, Shou Y, Ticknor LO, Marrone BL, Hersman LE, Iyer S, Ruggiero CE. Petrobactin is produced by both pathogenic and non-pathogenic isolates of the Bacillus cereus group of bacteria. Biometals 2008; 21:581-9. [PMID: 18459058 DOI: 10.1007/s10534-008-9144-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 04/23/2008] [Indexed: 11/28/2022]
Abstract
Petrobactin is the primary siderophore synthesized by Bacillus anthracis str Sterne and is required for virulence of this organism in a mouse model. The siderophore's biosynthetic machinery was recently defined and gene homologues of this operon exist in several other Bacillus strains known to be mammalian pathogens, but are absent in several known to be harmless such as B. subtilis and B. lichenformis. Thus, a common hypothesis regarding siderophore production in Bacillus species is that petrobactin production is exclusive to pathogenic isolates. In order to test this hypothesis, siderophores produced by 106 strains of an in-house library of the Bacillus cereus sensu lato group were isolated and identified using a MALDI-TOF-MS assay. Strains were selected from a previously defined phylogenetic tree of this group in order to include both known pathogens and innocuous strains. Petrobactin is produced by pathogenic strains and innocuous isolates alike, and thus is not itself indicative of virulence.
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Affiliation(s)
- Andrew T Koppisch
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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63
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Guinebretière MH, Thompson FL, Sorokin A, Normand P, Dawyndt P, Ehling-Schulz M, Svensson B, Sanchis V, Nguyen-The C, Heyndrickx M, De Vos P. Ecological diversification in the Bacillus cereus Group. Environ Microbiol 2008; 10:851-65. [DOI: 10.1111/j.1462-2920.2007.01495.x] [Citation(s) in RCA: 333] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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64
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Kim W, Kim JY, Cho SL, Nam SW, Shin JW, Kim YS, Shin HS. Glycosyltransferase: a specific marker for the discrimination of Bacillus anthracis from the Bacillus cereus group. J Med Microbiol 2008; 57:279-286. [PMID: 18287289 DOI: 10.1099/jmm.0.47642-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacillus anthracis, the aetiological agent of anthrax, has been taxonomically classified with the Bacillus cereus group, which comprises B. cereus, Bacillus thuringiensis, Bacillus mycoides, Bacillus pseudomycoides and Bacillus weihenstephanensis. Although the pathogenesis and ecological manifestations may be different, B. anthracis shares a high degree of DNA sequence similarity with its group member species. As a result, the discrimination of B. anthracis from its close relatives in the B. cereus group is still quite difficult. Suppression subtractive hybridization (SSH) was performed to search for genomic differences between a B. anthracis Korean isolate CR and the most closely related B. cereus type strain KCTC 3624(T). Two-hundred and five B. anthracis CR clones obtained by SSH underwent Southern hybridization, and comparative sequences were analysed using the blast program from the National Center for Biotechnology Information (NCBI). Subsequently, primer sets based on the glycosyltransferase group 1 family protein gene specific to B. anthracis were designed from the sequences of subtracted clones, and their specificities were evaluated using eight B. anthracis, 33 B. cereus, 10 B. thuringiensis, six B. mycoides, one B. pseudomycoides, one B. weihenstephanensis and 19 strains from 11 other representative Bacillus species. PCR primers specific for the glycosyltransferase group 1 family protein gene did not amplify the desired products from any of the Bacillus strains under examination, except B. anthracis alone. These findings may be useful in the future development of efficient diagnostic tools for the rapid identification of B. anthracis from other members of the B. cereus group.
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Affiliation(s)
- Wonyong Kim
- Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, Seoul, Republic of Korea.,Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yeon Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Sung-Lim Cho
- Research Institute for Translational System Biomics, Chung-Ang University College of Medicine, Seoul, Republic of Korea.,Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Sun-Woo Nam
- Korea Health Industry Development Institute, Seoul, Republic of Korea
| | - Jong-Wook Shin
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Yang-Soo Kim
- Department of Radiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Hyoung-Shik Shin
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
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65
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Assays for the rapid and specific identification of North American Yersinia pestis and the common laboratory strain CO92. Biotechniques 2008; 44:201, 203-4, 207. [PMID: 18330347 DOI: 10.2144/000112815] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We present TaqMan-minor groove binding (MGB) assays for an SNP that separates the Yersinia pestis strain CO92 from all other strains and for another SNP that separates North American strains from all other global strains.
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66
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Analysis of a novel spore antigen in Bacillus anthracis that contributes to spore opsonization. Microbiology (Reading) 2008; 154:619-632. [DOI: 10.1099/mic.0.2007/008292-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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67
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Mechaly A, Zahavy E, Fisher M. Development and implementation of a single-chain Fv antibody for specific detection of Bacillus anthracis spores. Appl Environ Microbiol 2008; 74:818-22. [PMID: 17965209 PMCID: PMC2227706 DOI: 10.1128/aem.01244-07] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Accepted: 10/07/2007] [Indexed: 11/20/2022] Open
Abstract
A single-chain Fv (scFv) antibody was developed and applied for efficient and specific detection of Bacillus anthracis spores. The antibody was isolated from a phage display library prepared from spleens of mice immunized with a water-soluble extract of the outer membrane of the B. anthracis spore (exosporium). The library (7 x 10(6) PFU) was biopanned against live, native B. anthracis ATCC delta14185 spores suspended in solution, resulting in the isolation of a unique soluble scFv antibody. The antibody was affinity purified and its affinity constant (3 x 10(8) +/- 1 x 10(8) M(-1)) determined via flow cytometry (FCM). Preliminary characterization of scFv specificity indicated that the scFv antibody does not cross-react with representatives of some phylogenetically related Bacillus spores. The potential use of scFv antibodies in detection platforms was demonstrated by the successful application of the soluble purified scFv antibody in enzyme-linked immunosorbent assays, immunofluorescence assays, and FCM.
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Affiliation(s)
- A Mechaly
- Department of Infectious Diseases, Israel Institute for Biological Research, P.O. Box 19, Ness-Ziona 74100, Israel
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68
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Bavykin SG, Mikhailovich VM, Zakharyev VM, Lysov YP, Kelly JJ, Alferov OS, Gavin IM, Kukhtin AV, Jackman J, Stahl DA, Chandler D, Mirzabekov AD. Discrimination of Bacillus anthracis and closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microarray. Chem Biol Interact 2008; 171:212-35. [PMID: 17950718 PMCID: PMC3188417 DOI: 10.1016/j.cbi.2007.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 08/23/2007] [Accepted: 09/03/2007] [Indexed: 10/22/2022]
Abstract
Analysis of 16S rRNA sequences is a commonly used method for the identification and discrimination of microorganisms. However, the high similarity of 16S and 23S rRNA sequences of Bacillus cereus group organisms (up to 99-100%) and repeatedly failed attempts to develop molecular typing systems that would use DNA sequences to discriminate between species within this group have resulted in several suggestions to consider B. cereus and B. thuringiensis, or these two species together with B. anthracis, as one species. Recently, we divided the B. cereus group into seven subgroups, Anthracis, Cereus A and B, Thuringiensis A and B, and Mycoides A and B, based on 16S rRNA, 23S rRNA and gyrB gene sequences and identified subgroup-specific makers in each of these three genes. Here we for the first time demonstrated discrimination of these seven subgroups, including subgroup Anthracis, with a 3D gel element microarray of oligonucleotide probes targeting 16S and 23S rRNA markers. This is the first microarray enabled identification of B. anthracis and discrimination of these seven subgroups in pure cell cultures and in environmental samples using rRNA sequences. The microarray bearing perfect match/mismatch (p/mm) probe pairs was specific enough to discriminate single nucleotide polymorphisms (SNPs) and was able to identify targeted organisms in 5min. We also demonstrated the ability of the microarray to determine subgroup affiliations for B. cereus group isolates without rRNA sequencing. Correlation of these seven subgroups with groupings based on multilocus sequence typing (MLST), fluorescent amplified fragment length polymorphism analysis (AFLP) and multilocus enzyme electrophoresis (MME) analysis of a wide spectrum of different genes, and the demonstration of subgroup-specific differences in toxin profiles, psychrotolerance, and the ability to harbor some plasmids, suggest that these seven subgroups are not based solely on neutral genomic polymorphisms, but instead reflect differences in both the genotypes and phenotypes of the B. cereus group organisms.
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MESH Headings
- Bacillus anthracis/genetics
- Bacillus anthracis/isolation & purification
- Base Sequence
- Molecular Sequence Data
- Oligonucleotide Array Sequence Analysis
- Polymorphism, Single Nucleotide
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/analysis
- RNA, Ribosomal, 23S/genetics
- Sequence Homology, Nucleic Acid
- Species Specificity
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Affiliation(s)
- Sergei G Bavykin
- Center for Environmental and Security Science and Technology, Argonne National Laboratory, Argonne, IL 60439, USA.
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69
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Multiple-locus sequence typing and analysis of toxin genes in Bacillus cereus food-borne isolates. Appl Environ Microbiol 2007; 74:850-60. [PMID: 18083872 DOI: 10.1128/aem.01495-07] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the present study we characterized 47 food-borne isolates of Bacillus cereus using multilocus sequence typing (MLST). Newly determined sequences were combined with sequences available in public data banks in order to produce the largest data set possible. Phylogenetic analysis was performed on a total of 296 strains for which MLST sequence information is available, and three main lineages--I, II, and III--within the B. cereus complex were identified. With few exceptions, all food-borne isolates were in group I. The occurrence of horizontal gene transfer (HGT) among various strains was analyzed by several statistical methods, providing evidence of widespread lateral gene transfer within B. cereus. We also investigated the occurrence of toxin-encoding genes, focusing on their evolutionary history within B. cereus. Several patterns were identified, indicating a pivotal role of HGT in the evolution of toxin-encoding genes. Our results indicate that HGT is an important element in shaping the population structure of the B. cereus complex. The results presented here also provide strong evidence of reticulate evolution within the B. cereus complex.
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70
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Abstract
Fast-sequencing throughput methods have increased the number of completely sequenced bacterial genomes to about 400 by December 2006, with the number increasing rapidly. These include several strains. In silico methods of comparative genomics are of use in categorizing and phylogenetically sorting these bacteria. Various word-based tools have been used for quantifying the similarities and differences between entire genomes. The simple di-nucleotide frequency comparison, codon specificity and k-mer repeat detection are among some of the well-known methods. In this paper, we show that the Mutual Information function, which is a measure of correlations and a concept from Information Theory, is very effective in determining the similarities and differences among genome sequences of various strains of bacteria such as the plant pathogen Xylella fastidiosa, marine Cyanobacteria Prochlorococcus marinus or animal and human pathogens such as species of Ehrlichia and Legionella. The short-range three-base periodicity, small sequence repeats and long-range correlations taken together constitute a genome signature that can be used as a technique for identifying new bacterial strains with the help of strains already catalogued in the database. There have been several applications of using the Mutual Information function as a measure of correlations in genomics but this is the first whole genome analysis done to detect strain similarities and differences.
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Affiliation(s)
- D Swati
- Department of Physics, MMV, Banaras Hindu University, Varanasi 221005, India.
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71
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Genetic diversity of Actinobacillus pleuropneumoniae assessed by amplified fragment length polymorphism analysis. J Clin Microbiol 2007; 45:3921-9. [PMID: 17959758 DOI: 10.1128/jcm.00906-07] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Amplified fragment length polymorphism (AFLP) was evaluated as a method for genotypic characterization and subtyping within the bacterial species Actinobacillus pleuropneumoniae. A total of 155 isolates of A. pleuropneumoniae, representing the serotypic variation described to occur within this species, were analyzed. In order to elucidate the species boundaries, six strains of the phylogenetically closely related species Actinobacillus lignieresii were also included. Furthermore, the ability of AFLP to subtype was studied using 42 isolates of serovar 2 and the performance compared to that obtained by pulsed-field gel electrophoresis (PFGE). AFLP analysis provided a clear separation of A. lignieresii and A. pleuropneumoniae and divided the isolates of A. pleuropneumoniae into 20 clusters. Most of the serovars of A. pleuropneumoniae were represented by single and quite homogeneous clusters. The exceptions were serovars 10, K2:O7, and K1:O7, which were represented by two clusters each. In the cases where the serovars were represented by more than one cluster, the existence of these clusters was supported by additional phenotypic or genotypic properties. Furthermore, AFLP typing was able to allocate serologically nontypeable isolates to appropriate genetic groups within the species. Further investigations are needed to determine whether some of the clusters revealed through AFLP analysis represent additional serovars. When evaluated as a method for subtyping within serovar 2 of A. pleuropneumoniae, AFLP was found to achieve a degree of separation among isolates superior to that obtained by PFGE. However, a higher degree of separation between serovar 2 isolates was obtained by a combination of the two methods.
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72
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Teramoto K, Sato H, Sun L, Torimura M, Tao H, Yoshikawa H, Hotta Y, Hosoda A, Tamura H. Phylogenetic Classification of Pseudomonas putida Strains by MALDI-MS Using Ribosomal Subunit Proteins as Biomarkers. Anal Chem 2007; 79:8712-9. [DOI: 10.1021/ac701905r] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kanae Teramoto
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Hiroaki Sato
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Liwei Sun
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Masaki Torimura
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Hiroaki Tao
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Hiromichi Yoshikawa
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Yudai Hotta
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Akifumi Hosoda
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
| | - Hiroto Tamura
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan, Fukuoka Institute of Technology, 3-30-1 Wajirohigashi, Higashi-ku, Fukuoka 811-0295, Japan, and Department of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi 468-8502, Japan
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73
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Olsen JS, Skogan G, Fykse EM, Rawlinson EL, Tomaso H, Granum PE, Blatny JM. Genetic distribution of 295 Bacillus cereus group members based on adk-screening in combination with MLST (Multilocus Sequence Typing) used for validating a primer targeting a chromosomal locus in B. anthracis. J Microbiol Methods 2007; 71:265-74. [PMID: 17997177 DOI: 10.1016/j.mimet.2007.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 09/21/2007] [Accepted: 10/01/2007] [Indexed: 10/22/2022]
Abstract
The genetic distribution of 295 Bacillus cereus group members has been investigated by using a modified Multilocus Sequence Typing method (MLST). By comparing the nucleic acid sequence of the adk gene fragment, isolates of B. cereus group members most related to B. anthracis may be easily identified. The genetic distribution, with focus on the B. anthracis close neighbours, was used to evaluate a new primer set for specific identification of B. anthracis. This primer set, BA5510-1/2, targeted the putative B. anthracis specific gene BA5510. Real-time PCR using BA5510-1/2 amplified the target fragment from all B. anthracis strains tested and only two (of 289) non-B. anthracis strains analysed. This is one of the most thoroughly validated chromosomal B. anthracis markers for real-time PCR identification, in which the screened collection contained several very closely related B. anthracis strains.
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Affiliation(s)
- Jaran S Olsen
- Forsvarets forskningsinstitutt FFI, Norwegian Defence Research Establishment, P. O. Box 25, N-2027 Kjeller, Norway.
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74
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Sagripanti JL, Carrera M, Insalaco J, Ziemski M, Rogers J, Zandomeni R. Virulent spores of Bacillus anthracis and other Bacillus species deposited on solid surfaces have similar sensitivity to chemical decontaminants. J Appl Microbiol 2007; 102:11-21. [PMID: 17184315 DOI: 10.1111/j.1365-2672.2006.03235.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS To compare the relative sensitivity of Bacillus anthracis and spores of other Bacillus spp. deposited on different solid surfaces to inactivation by liquid chemical disinfecting agents. METHODS AND RESULTS We prepared under similar conditions spores from five different virulent and three attenuated strains of B. anthracis, as well as spores of Bacillus subtilis, Bacillus atrophaeus (previously known as Bacillus globigii), Bacillus cereus, Bacillus thuringiensis and Bacillus megaterium. As spore-surface interactions may bias inactivation experiments, we evaluated the relative binding of different spores to carrier materials. The survival of spores deposited on glass, metallic or polymeric surfaces were quantitatively measured by ASTM standard method E-2414-05 which recovers spores from surfaces by increasing stringency. The number of spores inactivated by each decontaminant was similar and generally within 1 log among the 12 different Bacillus strains tested. This similarity among Bacillus strains and species was observed through a range of sporicidal efficacy on spores deposited on painted metal, polymeric rubber or glass. CONCLUSIONS The data obtained indicate that the sensitivity of common simulants (B. atrophaeus and B. subtilis), as well as spores of B. cereus, B. thuringiensis, and B. megaterium, to inactivation by products that contain either: peroxide, chlorine or oxidants is similar to that shown by spores from all eight B. anthracis strains studied. SIGNIFICANCE AND IMPACT OF THE STUDY The comparative results of the present study suggest that decontamination and sterilization data obtained with simulants can be safely extrapolated to virulent spores of B. anthracis. Thus, valid conclusions on sporicidal efficacy could be drawn from safer and less costly experiments employing non-pathogenic spore simulants.
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Affiliation(s)
- J-L Sagripanti
- Edgewood Chemical Biological Center, Research, Development and Engineering Command, Army Materiel Command, US Army, Aberdeen Proving Ground, MD 21010, USA.
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75
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Pfaller SL, Aronson TW, Holtzman AE, Covert TC. Amplified fragment length polymorphism analysis of Mycobacterium avium complex isolates recovered from southern California. J Med Microbiol 2007; 56:1152-1160. [PMID: 17761476 DOI: 10.1099/jmm.0.47075-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fine-scale genotyping methods are necessary in order to identify possible sources of human exposure to opportunistic pathogens belonging to the Mycobacterium avium complex (MAC). In this study, amplified fragment length polymorphism (AFLP) analysis was evaluated for fingerprinting 159 patient and environmental MAC isolates from southern California. AFLP analysis accurately identified strains belonging to M. avium and Mycobacterium intracellulare and differentiated between strains within each species. The method was also able to differentiate strains that were presumed to be genetically identical in two previous studies using large RFLP analysis with PFGE, or PCR-amplification of DNA segments located between insertion sequences IS1245 and IS1311. For M. avium, drinking-water isolates clustered more closely with each other than with patient or food isolates. Patient isolates were more genetically diverse. None of the environmental isolates shared identical AFLP patterns with patient isolates for either species. There were, however, environmental isolates that shared identical patterns, and patient isolates that shared identical patterns. A subset of the isolates, which are referred to as MX isolates due to their ambiguous identification with the Gen-Probe system, produced AFLP patterns similar to those obtained from M. intracellulare isolates. Sequence analysis of 16S rDNA obtained from the MX isolates suggests that they are strains of M. intracellulare that were not correctly identified by the M. intracellulare AccuProbe from Gen-Probe.
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Affiliation(s)
- Stacy L Pfaller
- National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, OH, USA
| | - Timothy W Aronson
- Education and Research Institute, Olive View - University of California Los Angeles (UCLA), Medical Center, Sylmar, Los Angeles, CA, USA
| | - Alan E Holtzman
- Education and Research Institute, Olive View - University of California Los Angeles (UCLA), Medical Center, Sylmar, Los Angeles, CA, USA
| | - Terry C Covert
- SHAW Environmental and Infrastructure, Inc., Cincinnati, OH, USA
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76
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Auerbach RK, Tuanyok A, Probert WS, Kenefic L, Vogler AJ, Bruce DC, Munk C, Brettin TS, Eppinger M, Ravel J, Wagner DM, Keim P. Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America. PLoS One 2007; 2:e770. [PMID: 17712418 PMCID: PMC1940323 DOI: 10.1371/journal.pone.0000770] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Accepted: 07/25/2007] [Indexed: 11/29/2022] Open
Abstract
Background Yersinia pestis, the etiologic agent of plague, was responsible for several devastating epidemics throughout history and is currently of global importance to current public heath and biodefense efforts. Y. pestis is widespread in the Western United States. Because Y. pestis was first introduced to this region just over 100 years ago, there has been little time for genetic diversity to accumulate. Recent studies based upon single nucleotide polymorphisms have begun to quantify the genetic diversity of Y. pestis in North America. Methodology/Principal Findings To examine the evolution of Y. pestis in North America, a gapped genome sequence of CA88-4125 was generated. Sequence comparison with another North American Y. pestis strain, CO92, identified seven regions of difference (six inversions, one rearrangement), differing IS element copy numbers, and several SNPs. Conclusions/Significance The relatively large number of inverted/rearranged segments suggests that North American Y. pestis strains may be undergoing inversion fixation at high rates over a short time span, contributing to higher-than-expected diversity in this region. These findings will hopefully encourage the scientific community to sequence additional Y. pestis strains from North America and abroad, leading to a greater understanding of the evolutionary history of this pathogen.
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Affiliation(s)
- Raymond K. Auerbach
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - William S. Probert
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Leo Kenefic
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Amy J. Vogler
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David C. Bruce
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christine Munk
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Thomas S. Brettin
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Mark Eppinger
- J. Craig Venter Institute, The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Jacques Ravel
- J. Craig Venter Institute, The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - David M. Wagner
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * To whom correspondence should be addressed. E-mail:
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77
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Budowle B, Beaudry JA, Barnaby NG, Giusti AM, Bannan JD, Keim P. Role of law enforcement response and microbial forensics in investigation of bioterrorism. Croat Med J 2007; 48:437-49. [PMID: 17696298 PMCID: PMC2080552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
The risk and threat of bioterrorism and biocrime have become a large concern and challenge for governments and society to enhance biosecurity. Law enforcement plays an important role in assessing and investigating activities involved in an event of bioterrorism or biocrime. Key to a successful biosecurity program is increased awareness and early detection of threats facilitated by an integrated network of responsibilities and capabilities from government, academic, private, and public assets. To support an investigation, microbial forensic sciences are employed to analyze and characterize forensic evidence with the goal of attribution or crime scene reconstruction. Two different molecular biology-based assays--real time polymerase chain reaction (PCR) and repetitive element PCR--are described and demonstrate how molecular biology tools may be utilized to aid in the investigative process. Technologies relied on by microbial forensic scientists need to be properly validated so that the methods used are understood and so that interpretation of results is carried out within the limitations of the assays. The three types of validation are preliminary, developmental, and internal. The first is necessary for rapid response when a threat is imminent or an attack has recently occurred. The latter two apply to implementation of routinely used procedures.
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Affiliation(s)
- Bruce Budowle
- Scientific Analysis Section, Federal Bureau of Investigation, Quantico, Va, USA.
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78
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Vilas-Bôas GT, Peruca APS, Arantes OMN. Biology and taxonomy ofBacillus cereus,Bacillus anthracis, andBacillus thuringiensis. Can J Microbiol 2007; 53:673-87. [PMID: 17668027 DOI: 10.1139/w07-029] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three species of the Bacillus cereus group (Bacillus cereus, Bacillus anthracis , and Bacillus thuringiensis ) have a marked impact on human activity. Bacillus cereus and B. anthracis are important pathogens of mammals, including humans, and B. thuringiensis is extensively used in the biological control of insects. The microbiological, biochemical, and genetic characteristics of these three species are reviewed, together with a discussion of several genomic studies conducted on strains of B. cereus group. Using bacterial systematic concepts, we speculate that to understand the taxonomic relationship within this group of bacteria, special attention should be devoted also to the ecology and the population genetics of these species.
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Affiliation(s)
- G T Vilas-Bôas
- Departamento de Biologia Geral, CCB, UEL, CP 6001, Londrina/PR, 86051-990, Brazil.
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79
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Tourasse NJ, Helgason E, Økstad OA, Hegna IK, Kolstø AB. The Bacillus cereus group: novel aspects of population structure and genome dynamics. J Appl Microbiol 2007; 101:579-93. [PMID: 16907808 DOI: 10.1111/j.1365-2672.2006.03087.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
AIMS To provide new insights into the population and genomic structure of the Bacillus cereus group of bacteria. METHODS AND RESULTS The genetic relatedness among B. cereus group strains was assessed by multilocus sequence typing (MLST) using an optimized scheme based on seven chromosomal housekeeping genes. A set of 48 strains from different clinical sources was included, and six clonal complexes containing several genetically similar isolates from unrelated patients were identified. Interestingly, several clonal groups contained strains that were isolated from similar human sources. Furthermore, comparative whole genome sequence analysis of 16 strains led to the discovery of novel ubiquitous genome features of the B. cereus group, such as atypical group II introns, IStrons, and hitherto uncharacterized repeated elements. CONCLUSIONS The B. cereus group constitutes a coherent population unified by the presence of ubiquitous and specific genetic elements which do not show any pattern, either in their sequences or genomic locations, which allows to differentiate between the member species of the group. Nevertheless, the population is very dynamic, as particular lineages of clinical origin can evolve to form clonal complexes. At the genome level, the dynamic behaviour is indicated by the presence of numerous mobile and repeated elements. SIGNIFICANCE AND IMPACT OF THE STUDY The B. cereus group of bacteria comprises species that are of medical and economic importance. The MLST data, along with the primers and protocols used, will be available in a public, web-accessible database (http://mlstoslo.uio.no).
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Affiliation(s)
- N J Tourasse
- Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Norway
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80
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Zhong W, Shou Y, Yoshida TM, Marrone BL. Differentiation of Bacillus anthracis, B. cereus, and B. thuringiensis by using pulsed-field gel electrophoresis. Appl Environ Microbiol 2007; 73:3446-9. [PMID: 17400781 PMCID: PMC1907107 DOI: 10.1128/aem.02478-06] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A pulsed-field gel electrophoresis (PFGE) method was developed for discriminating Bacillus anthracis from B. cereus and B. thuringiensis. A worldwide collection of 25 B. anthracis isolates showed high-profile homology, and these isolates were unambiguously distinguished from B. cereus and B. thuringiensis isolates by cluster analysis of the whole-genome macrorestriction enzyme digestion patterns generated by NotI.
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Affiliation(s)
- Wenwan Zhong
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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81
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Sue D, Marston CK, Hoffmaster AR, Wilkins PP. Genetic diversity in a Bacillus anthracis historical collection (1954 to 1988). J Clin Microbiol 2007; 45:1777-82. [PMID: 17392445 PMCID: PMC1933066 DOI: 10.1128/jcm.02488-06] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis, the etiologic agent of anthrax, has been widely described as a genetically monomorphic species. We used both multiple-locus variable-number tandem-repeat analysis (MLVA) and pagA gene sequencing to determine the genetic diversity of a historical collection of B. anthracis isolates collected from the 1950s to the 1980s from various geographic locations and sources. We sequenced the pagA gene of 124 diverse B. anthracis isolates and found all previously identified B. anthracis pagA types except type 4. Sixty-three of the 124 B. anthracis strains were identified as pagA type 6, while 44 were pagA type 5, 12 were pagA type 1, and individual isolates were identified for types 2 and 3, respectively. Two new pagA genotypes were discovered in three environmental isolates within the historical collection. Two isolates had the same new genotype, and an additional isolate produced a second new genotype. MLVA detected 22 previously described genotypes in the historical collection. In addition, 33 new MLVA genotypes were found. For 11 isolates, an MLVA genotype could not be assigned because one or more alleles did not amplify. While only two additional B. anthracis pagA types were identified, in two instances, the use of pagA sequencing discriminated isolates with the same MLVA genotype. MLVA revealed that 39 of the 124 isolates were previously undocumented genotypes and that 1 isolate was found to be in the C cluster when it was subtyped by MLVA.
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Affiliation(s)
- David Sue
- Bacterial Zoonoses Branch, Division of Foodborne, Bacterial and Mycotic Diseases, National Center for Zoonotic, Vector-Borne and Enteric Diseases, Centers for Disease Control and Prevention, NE, Atlanta, Georgia 30333, USA
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82
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Vogler AJ, Keys CE, Allender C, Bailey I, Girard J, Pearson T, Smith KL, Wagner DM, Keim P. Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis. Mutat Res 2007; 616:145-58. [PMID: 17161849 DOI: 10.1016/j.mrfmmm.2006.11.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
VNTRs are able to discriminate among closely related isolates of recently emerged clonal pathogens, including Yersinia pestis the etiologic agent of plague, because of their great diversity. Diversity is driven largely by mutation but little is known about VNTR mutation rates, factors affecting mutation rates, or the mutational mechanisms. The molecular epidemiological utility of VNTRs will be greatly enhanced when this foundational knowledge is available. Here, we measure mutation rates for 43 VNTR loci in Y. pestis using an in vitro generated population encompassing approximately 96,000 generations. We estimate the combined 43-locus rate and individual rates for 14 loci. A comparison of Y. pestis and Escherichia coli O157:H7 VNTR mutation rates and products revealed a similar relationship between diversity and mutation rate in these two species. Likewise, the relationship between repeat copy number and mutation rate is nearly identical between these species, suggesting a generalized relationship that may be applicable to other species. The single- versus multiple-repeat mutation ratios and the insertion versus deletion mutation ratios were also similar, providing support for a general model for the mutations associated with VNTRs. Finally, we use two small sets of Y. pestis isolates to show how this general model and our estimated mutation rates can be used to compare alternate phylogenies, and to evaluate the significance of genotype matches, near-matches, and mismatches found in empirical comparisons with a reference database.
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Affiliation(s)
- Amy J Vogler
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640, USA
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83
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Curtin CD, Bellon JR, Henschke PA, Godden PW, de Barros Lopes MA. Genetic diversity of Dekkera bruxellensis yeasts isolated from Australian wineries. FEMS Yeast Res 2007; 7:471-81. [PMID: 17233769 DOI: 10.1111/j.1567-1364.2006.00183.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Yeasts of the genus Dekkera and its anamorph Brettanomyces represent a significant spoilage issue for the global wine industry. Despite this, there is limited knowledge of genetic diversity and strain distribution within wine and winery-related environments. In this study, amplified fragment length polymorphism (AFLP) analysis was conducted on 244 Dekkera bruxellensis isolates from red wine made in 31 winemaking regions of Australia. The results indicated there were eight genotypes among the isolates, and three of these were commonly found across multiple winemaking regions. Analysis of 26S rRNA gene sequences provided further evidence of three common, conserved groups, whereas a phylogeny based upon the AFLP data demonstrated that the most common D. bruxellensis genotype (I) in Australian red wine was highly divergent from the D. bruxellensis type strain (CBS 74).
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Affiliation(s)
- Chris D Curtin
- The Australian Wine Research Institute, Glen Osmond, Adelaide, Australia
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84
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Abstract
Genome sequences from several blood borne and respiratory viruses have recently been recovered directly from clinical specimens by variants of a technique known as sequence‐independent single primer amplification. This and related methods are increasingly being used to search for the causes of diseases of presumed infectious aetiology, but for which no agent has yet been found. Other methods that do not require prior knowledge of the genome sequence of any virus that may be present in the patient specimen include whole genome amplification, random PCR and subtractive hybridisation and differential display. This review considers the development and application of these techniques. Copyright © 2006 John Wiley & Sons, Ltd.
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Affiliation(s)
- Helen E. Ambrose
- Virus Reference Department, Centre for Infections, Health Protection Agency, London NW9 5EQ, UK
| | - Jonathan P. Clewley
- Virus Reference Department, Centre for Infections, Health Protection Agency, London NW9 5EQ, UK
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85
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Van Ert MN, Easterday WR, Simonson TS, U'Ren JM, Pearson T, Kenefic LJ, Busch JD, Huynh LY, Dukerich M, Trim CB, Beaudry J, Welty-Bernard A, Read T, Fraser CM, Ravel J, Keim P. Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain. J Clin Microbiol 2006; 45:47-53. [PMID: 17093023 PMCID: PMC1828967 DOI: 10.1128/jcm.01233-06] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Highly precise diagnostics and forensic assays can be developed through a combination of evolutionary analysis and the exhaustive examination of genomic sequences. In Bacillus anthracis, whole-genome sequencing efforts revealed ca. 3,500 single-nucleotide polymorphisms (SNPs) among eight different strains and evolutionary analysis provides the identification of canonical SNPs. We have previously shown that SNPs are highly evolutionarily stable, and the clonal nature of B. anthracis makes them ideal signatures for subtyping this pathogen. Here we identified SNPs that define the lineage of B. anthracis that contains the Ames strain, the strain used in the 2001 bioterrorist attacks in the United States. Sequencing and real-time PCR were used to validate these SNPs across B. anthracis strains, including (i) 88 globally and genetically diverse isolates; (ii) isolates that were shown to be genetic relatives of the Ames strain by multiple-locus variable number tandem repeat analysis (MLVA); and (iii) several different lab stocks of the Ames strain, including a clinical isolate from the 2001 letter attack. Six SNPs were found to be highly specific for the Ames strain; four on the chromosome, one on the pX01 plasmid, and one on the pX02 plasmid. All six SNPs differentiated the B. anthracis Ames strain from the 88 unique B. anthracis strains, while five of the six separated Ames from its close genetic relatives. The use of these SNPs coupled with real-time PCR allows specific and sensitive (<100 fg of template DNA) identification of the Ames strain. This evolutionary and genomics-based approach provides an effective means for the discovery of strain-specific SNPs in B. anthracis.
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Affiliation(s)
- Matthew N Van Ert
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640, USA
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86
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Affiliation(s)
| | | | - Paul Keim
- Scripps Research Institute, United States of America
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87
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Hoffmaster AR, Hill KK, Gee JE, Marston CK, De BK, Popovic T, Sue D, Wilkins PP, Avashia SB, Drumgoole R, Helma CH, Ticknor LO, Okinaka RT, Jackson PJ. Characterization of Bacillus cereus isolates associated with fatal pneumonias: strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes. J Clin Microbiol 2006; 44:3352-60. [PMID: 16954272 PMCID: PMC1594744 DOI: 10.1128/jcm.00561-06] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacillus cereus is ubiquitous in nature, and while most isolates appear to be harmless, some are associated with food-borne illnesses, periodontal diseases, and other more serious infections. In one such infection, B. cereus G9241 was identified as the causative agent of a severe pneumonia in a Louisiana welder in 1994. This isolate was found to harbor most of the B. anthracis virulence plasmid pXO1 (13). Here we report the characterization of two clinical and one environmental B. cereus isolate collected during an investigation of two fatal pneumonia cases in Texas metal workers. Molecular subtyping revealed that the two cases were not caused by the same strain. However, one of the three isolates was indistinguishable from B. cereus G9241. PCR analysis demonstrated that both clinical isolates contained B. anthracis pXO1 toxin genes. One clinical isolate and the environmental isolate collected from that victim's worksite contained the cap A, B, and C genes required for capsule biosynthesis in B. anthracis. Both clinical isolates expressed a capsule; however, neither was composed of poly-D-glutamic acid. Although most B. cereus isolates are not opportunistic pathogens and only a limited number cause food-borne illnesses, these results demonstrate that some B. cereus strains can cause severe and even fatal infections in patients who appear to be otherwise healthy.
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Affiliation(s)
- Alex R Hoffmaster
- Epidemiologic Investigations Laboratory, Meningitis and Special Pathogens Branch, MS G34, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30333, USA.
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88
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Merabishvili M, Natidze M, Rigvava S, Brusetti L, Raddadi N, Borin S, Chanishvili N, Tediashvili M, Sharp R, Barbeschi M, Visca P, Daffonchio D. Diversity of Bacillus anthracis strains in Georgia and of vaccine strains from the former Soviet Union. Appl Environ Microbiol 2006; 72:5631-6. [PMID: 16885320 PMCID: PMC1538727 DOI: 10.1128/aem.00440-06] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the increased number of anthrax outbreaks in Georgia and the other Caucasian republics of the former Soviet Union, no data are available on the diversity of the Bacillus anthracis strains involved. There is also little data available on strains from the former Soviet Union, including the strains previously used for vaccine preparation. In this study we used eight-locus variable-number tandem repeat analyses to genotype 18 strains isolated from infected animals and humans at different sites across Georgia, where anthrax outbreaks have occurred in the last 10 years, and 5 strains widely used for preparation of human and veterinary vaccines in the former Soviet Union. Three different genotypes affiliated with the A3.a cluster were detected for the Georgian isolates. Two genotypes were previously shown to include Turkish isolates, indicating that there is a regional strain pattern in the South Caucasian-Turkish region. Four of the vaccine strains were polymorphic, exhibiting three different patterns of the cluster A1.a genotype and the cluster A3.b genotype. The genotype of vaccine strain 71/12, which is considered an attenuated strain in spite of the presence of both of the virulence pXO plasmids, appeared to be a novel genotype in the A1.a cluster.
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Affiliation(s)
- Maya Merabishvili
- The G.Eliava Institute of Bacteriophage, Microbiology and Virology, 0160 Tbilisi, Georgia
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89
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Klee SR, Ozel M, Appel B, Boesch C, Ellerbrok H, Jacob D, Holland G, Leendertz FH, Pauli G, Grunow R, Nattermann H. Characterization of Bacillus anthracis-like bacteria isolated from wild great apes from Cote d'Ivoire and Cameroon. J Bacteriol 2006; 188:5333-44. [PMID: 16855222 PMCID: PMC1540047 DOI: 10.1128/jb.00303-06] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the microbiological and molecular characterization of bacteria isolated from four chimpanzees and one gorilla thought to have died of an anthrax-like disease in Côte d'Ivoire and Cameroon. These isolates differed significantly from classic Bacillus anthracis by the following criteria: motility, resistance to the gamma phage, and, for isolates from Cameroon, resistance to penicillin G. A capsule was expressed not only after induction by CO(2) and bicarbonate but also under normal growth conditions. Subcultivation resulted in beta-hemolytic activity and gamma phage susceptibility in some subclones, suggesting differences in gene regulation compared to classic B. anthracis. The isolates from Côte d'Ivoire and Cameroon showed slight differences in their biochemical characteristics and MICs of different antibiotics but were identical in all molecular features and sequences analyzed. PCR and Southern blot analyses confirmed the presence of both the toxin and the capsule plasmid, with sizes corresponding to the B. anthracis virulence plasmids pXO1 and pXO2. Protective antigen was expressed and secreted into the culture supernatant. The isolates possessed variants of the Ba813 marker and the SG-749 fragment differing from that of classic B. anthracis strains. Multilocus sequence typing revealed a close relationship of our atypical isolates with both classic B. anthracis strains and two uncommonly virulent Bacillus cereus and Bacillus thuringiensis isolates. We propose that the newly discovered atypical B. anthracis strains share a common ancestor with classic B. anthracis or that they emerged recently by transfer of the B. anthracis plasmids to a strain of the B. cereus group.
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Affiliation(s)
- Silke R Klee
- Robert Koch Institut, Centre for Biological Safety 2, Nordufer 20, 13353 Berlin, Germany.
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90
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Morse SA, Budowle B. Microbial forensics: application to bioterrorism preparedness and response. Infect Dis Clin North Am 2006; 20:455-73, xi. [PMID: 16762747 DOI: 10.1016/j.idc.2006.03.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Stephen A Morse
- Bioterrorism Preparedness and Response Program, Centers for Disease Control and Prevention, 1600 Clifton Road, MS C-12, Atlanta, GA 30333, USA.
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91
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Stratilo CW, Lewis CT, Bryden L, Mulvey MR, Bader D. Single-nucleotide repeat analysis for subtyping Bacillus anthracis isolates. J Clin Microbiol 2006; 44:777-82. [PMID: 16517854 PMCID: PMC1393151 DOI: 10.1128/jcm.44.3.777-782.2006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Single-nucleotide repeats (SNRs) are variable-number tandem repeats that display very high mutation rates. In an outbreak situation, the use of a marker system that exploits regions with very high mutation rates, such as SNRs, allows the differentiation of isolates with extremely low levels of genetic diversity. This report describes the identification and analysis of SNR loci of Bacillus anthracis. SNR loci were selected in silico, and the loci with the highest diversity were used to design and test locus-specific primers against a number of B. anthracis strains with the same multilocus variable-number tandem repeat analysis (MLVA) genotype. SNR markers that allowed strains with the same MLVA genotype to be differentiated from each other were identified. The resulting SNR marker system can be used as a molecular epidemiological tool in a natural outbreak or bioterrorism event, offering the best chance of distinguishing very closely related isolates.
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Affiliation(s)
- Chad W Stratilo
- Chemical and Biological Defence Section, Defence R&D Canada--Suffield Medicine Hat, AB, CBDS, P.O. Box 4000, Station Main, Medicine Hat, Alberta T1A 8K6, Canada.
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92
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Daffonchio D, Raddadi N, Merabishvili M, Cherif A, Carmagnola L, Brusetti L, Rizzi A, Chanishvili N, Visca P, Sharp R, Borin S. Strategy for identification of Bacillus cereus and Bacillus thuringiensis strains closely related to Bacillus anthracis. Appl Environ Microbiol 2006; 72:1295-301. [PMID: 16461679 PMCID: PMC1392923 DOI: 10.1128/aem.72.2.1295-1301.2006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus cereus strains that are genetically closely related to B. anthracis can display anthrax-like virulence traits (A. R. Hoffmaster et al., Proc. Natl. Acad. Sci. USA 101:8449-8454, 2004). Hence, approaches that rapidly identify these "near neighbors" are of great interest for the study of B. anthracis virulence mechanisms, as well as to prevent the use of such strains for B. anthracis-based bioweapon development. Here, a strategy is proposed for the identification of near neighbors of B. anthracis based on single nucleotide polymorphisms (SNP) in the 16S-23S rRNA intergenic spacer (ITS) containing tRNA genes, characteristic of B. anthracis. By using restriction site insertion-PCR (RSI-PCR) the presence of two SNP typical of B. anthracis was screened in 126 B. cereus group strains of different origin. Two B. cereus strains and one B. thuringiensis strain showed RSI-PCR profiles identical to that of B. anthracis. The sequencing of the entire ITS containing tRNA genes revealed two of the strains to be identical to B. anthracis. The strict relationship with B. anthracis was confirmed by multilocus sequence typing (MLST) of four other independent loci: cerA, plcR, AC-390, and SG-749. The relationship to B. anthracis of the three strains described by MLST was comparable and even higher to that of four B. cereus strains associated with periodontitis in humans and previously reported as the closest known strains to B. anthracis. SNP in ITS containing tRNA genes combined with RSI-PCR provide a very efficient tool for the identification of strains closely related to B. anthracis.
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Affiliation(s)
- Daniele Daffonchio
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, via Celoria 2, 20133 Milan, Italy.
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93
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Lista F, Faggioni G, Valjevac S, Ciammaruconi A, Vaissaire J, le Doujet C, Gorgé O, De Santis R, Carattoli A, Ciervo A, Fasanella A, Orsini F, D'Amelio R, Pourcel C, Cassone A, Vergnaud G. Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis. BMC Microbiol 2006; 6:33. [PMID: 16600037 PMCID: PMC1479350 DOI: 10.1186/1471-2180-6-33] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Accepted: 04/06/2006] [Indexed: 11/10/2022] Open
Abstract
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.
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Affiliation(s)
- Florigio Lista
- Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy), Via Santo Stefano Rotondo 4 00184 Rome, Italy
- Cattedra di Allergologia e Immunologia Clinica, II Facoltà di Medicina, Università di Roma "La Sapienza", Roma, Italy
| | - Giovanni Faggioni
- Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy), Via Santo Stefano Rotondo 4 00184 Rome, Italy
| | - Samina Valjevac
- Division of Analytical Microbiology, Centre d'Etudes du Bouchet, BP3, 91710 Vert le Petit, France
- Institut de Génétique et Microbiologie, Université Paris Sud, 91405 Orsay Cedex, France
| | - Andrea Ciammaruconi
- Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy), Via Santo Stefano Rotondo 4 00184 Rome, Italy
| | - Josée Vaissaire
- AFSSA/LERPAZ, LNR/CNR associé Laboratoire du Charbon, 23 avenue du Général de Gaulle, 94700 Maisons-Alfort, France
| | - Claudine le Doujet
- AFSSA/LERPAZ, LNR/CNR associé Laboratoire du Charbon, 23 avenue du Général de Gaulle, 94700 Maisons-Alfort, France
| | - Olivier Gorgé
- Division of Analytical Microbiology, Centre d'Etudes du Bouchet, BP3, 91710 Vert le Petit, France
- Institut de Génétique et Microbiologie, Université Paris Sud, 91405 Orsay Cedex, France
| | - Riccardo De Santis
- Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy), Via Santo Stefano Rotondo 4 00184 Rome, Italy
| | | | - Alessandra Ciervo
- Istituto Superiore di Sanità, Viale Regina Elena 299 00161 Rome, Italy
| | - Antonio Fasanella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata – Anthrax Reference Institute of Italy, Foggia 71100, Italy
| | - Francesco Orsini
- Army Medical Research Center, Via Santo Stefano Rotondo 4 00184 Rome (Italy), Via Santo Stefano Rotondo 4 00184 Rome, Italy
| | - Raffaele D'Amelio
- Cattedra di Allergologia e Immunologia Clinica, II Facoltà di Medicina, Università di Roma "La Sapienza", Roma, Italy
- Direzione Generale della Sanità Militare, Via Santo Stefano Rotondo 4 00184 Rome, Italy
| | - Christine Pourcel
- Institut de Génétique et Microbiologie, Université Paris Sud, 91405 Orsay Cedex, France
| | - Antonio Cassone
- Istituto Superiore di Sanità, Viale Regina Elena 299 00161 Rome, Italy
| | - Gilles Vergnaud
- Division of Analytical Microbiology, Centre d'Etudes du Bouchet, BP3, 91710 Vert le Petit, France
- Institut de Génétique et Microbiologie, Université Paris Sud, 91405 Orsay Cedex, France
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94
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Sozhamannan S, Chute MD, McAfee FD, Fouts DE, Akmal A, Galloway DR, Mateczun A, Baillie LW, Read TD. The Bacillus anthracis chromosome contains four conserved, excision-proficient, putative prophages. BMC Microbiol 2006; 6:34. [PMID: 16600039 PMCID: PMC1475869 DOI: 10.1186/1471-2180-6-34] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 04/06/2006] [Indexed: 11/17/2022] Open
Abstract
Background Bacillus anthracis is considered to be a recently emerged clone within the Bacillus cereus sensu lato group. The B. anthracis genome sequence contains four putative lambdoid prophages. We undertook this study in order to understand whether the four prophages are unique to B. anthracis and whether they produce active phages. Results More than 300 geographically and temporally divergent isolates of B. anthracis and its near neighbors were screened by PCR for the presence of specific DNA sequences from each prophage region. Every isolate of B. anthracis screened by PCR was found to produce all four phage-specific amplicons whereas none of the non-B. anthracis isolates, produced more than one phage-specific amplicon. Excision of prophages could be detected by a PCR based assay for attP sites on extra-chromosomal phage circles and for attB sites on phage-excised chromosomes. SYBR-green real-time PCR assays indicated that prophage excision occurs at very low frequencies (2 × 10-5 - 8 × 10-8/cell). Induction with mitomycin C increased the frequency of excision of one of the prophages by approximately 250 fold. All four prophages appear to be defective since, mitomycin C induced culture did not release any viable phage particle or lyse the cells or reveal any phage particle under electron microscopic examination. Conclusion The retention of all four putative prophage regions across all tested strains of B. anthracis is further evidence of the very recent emergence of this lineage and the prophage regions may be useful for differentiating the B. anthracis chromosome from that of its neighbors. All four prophages can excise at low frequencies, but are apparently defective in phage production.
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Affiliation(s)
- Shanmuga Sozhamannan
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20852, USA
| | - Michael D Chute
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20852, USA
| | - Farrell D McAfee
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20852, USA
| | - Derrick E Fouts
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
| | - Arya Akmal
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20852, USA
| | - Darrell R Galloway
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20852, USA
- University of Maryland Medical Biotechnology Center, Baltimore, Maryland 21201, USA
| | - Alfred Mateczun
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20852, USA
| | - Leslie W Baillie
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20852, USA
- University of Maryland Medical Biotechnology Center, Baltimore, Maryland 21201, USA
| | - Timothy D Read
- Biological Defense Research Directorate, Naval Medical Research Center, 503 Robert Grant Avenue, Silver Spring, Maryland 20852, USA
- University of Maryland Medical Biotechnology Center, Baltimore, Maryland 21201, USA
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95
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Fang SW, Yang CJ, Shih DYC, Chou CC, Yu RC. Amplified fragment length polymorphism, serotyping, and quinolone resistance of Campylobacter jejuni and Campylobacter coli strains from chicken-related samples and humans in Taiwan. J Food Prot 2006; 69:775-83. [PMID: 16629019 DOI: 10.4315/0362-028x-69.4.775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The high-resolution genotyping method of amplified fragment length polymorphism (AFLP) analysis was used to study the genetic relationships between Campylobacter jejuni isolates from chicken-related samples (n = 32) and humans (n = 27) as well as between Campylobacter coli isolates from chicken-related samples (n = 27) and humans (n = 5). These isolates were collected between 1994 and 2003 in Taiwan. All C. jejuni and C. coli isolates showed highly heterogeneous fingerprints. C. jejuni isolates were separated in two distinct genetic clusters (A and B) at 40% genetic similarity and 42 different AFLP types at 90% similarity. However, three clusters at 40% genetic similarity and 33 different AFLP types at 90% similarity were observed in C. coli isolates. These results showed that AFLP analysis could be used to identify individual isolates of two Campylobacter species. Among C. jejuni isolates, the predominant AFLP type 1 was observed in five (7.9%) isolates, and types 5 and 12 in four (6.3%) isolates each. Cluster B consisted of 10 isolates, while the majority of isolates (n = 53) belonged to cluster A. In some AFLP types (1, 5, 12, 14 and 31), AFLP fingerprints of chicken-related isolates were closely related genetically to those of isolates from humans with gastroenteritis. The predominant serotypes in C. jejuni isolates were B:2 and Y:37. All isolates belonging to serotype O:19 grouped into one single AFLP type. Some chicken samples yielded multiple isolates of Campylobacter harboring simultaneously quinolone-resistant and quinolone-sensitive isolates attributed to the same species, or harboring C. jejuni and C. coli that have the characteristics of quinolone resistance.
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Affiliation(s)
- Shao W Fang
- Division of Food Microbiology, Bureau of Food and Drug Analysis, Department of Health, Executive Yuan, Taipei, Taiwan, Republic of China.
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96
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Edwards KA, Clancy HA, Baeumner AJ. Bacillus anthracis: toxicology, epidemiology and current rapid-detection methods. Anal Bioanal Chem 2005; 384:73-84. [PMID: 16283259 DOI: 10.1007/s00216-005-0090-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 08/18/2005] [Accepted: 08/18/2005] [Indexed: 01/27/2023]
Abstract
B. anthracis, the causative agent for anthrax, has been well studied for over 150 years. Due to the genetic similarities among various Bacillus species, as well as its existence in both a spore form and a vegetative state, the detection and specific identification of B. anthracis have been proven to require complex techniques and/or laborious methods. With the heightened interest in the organism as a potential biological threat agent, a large number of interesting detection technologies have recently been developed, including methods involving immunological and nucleic acid-based assay formats. The technologies range from culture-based methods to portable Total Analysis Systems based on real-time PCR. This review with 170 references provides a brief background on the toxicology and epidemiology of B. anthracis, discusses challenges associated with its detection related to genetic similarities to other species, and reviews immunological and, with greater emphasis, nucleic acid-based detection systems.
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Affiliation(s)
- Katie A Edwards
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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97
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Ryu C, Lee K, Hawng HJ, Yoo CK, Seong WK, Oh HB. Molecular characterization of Korean Bacillus anthracis isolates by amplified fragment length polymorphism analysis and multilocus variable-number tandem repeat analysis. Appl Environ Microbiol 2005; 71:4664-71. [PMID: 16085861 PMCID: PMC1183344 DOI: 10.1128/aem.71.8.4664-4671.2005] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed the genetic relationships and molecular characteristics of 34 Bacillus anthracis isolates from soil and clinical samples in various regions of Korea and 17 related Bacillus species, using the amplified fragment length polymorphism (AFLP) and multilocus variable-number tandem repeat (MLVA) approaches. Triplicate AFLP profiles of these strains showed high reproducibility and identified 376 polymorphisms. AFLP phylogenetic analysis of B. anthracis isolates showed a high level of similarity, 0.93, and this monomorphic fragment profile proved to be useful to differentiate B. anthracis strains from other Bacillus species. The B. cereus group was separated from other Bacillus species at a level of similarity of 0.68. Among them, some B. cereus strains showed genetic interspersion with B. thuringiensis strains. The evolutionary pattern of nucleotide differences among B. anthracis strains with the eight MLVA markers showed nine MLVA types. Three MLVA types, M1 to M3, were pathogenic B. anthracis isolates and were assigned as new genotypes belonging to the A4 and B3 clusters, compared with 89 genotypes deduced from previous data. This indicates that differences in cluster prevalence and distribution may be influenced more by MLVA markers on two plasmids loci and human activity. Consequently, we suggest that the novel MLVA type may represent significant evidence for historic adaptation to environmental conditions of the Asian continent, particularly Korea. Therefore, MLVA techniques may be available for molecular monitoring on anthrax-release-related bioterrorism and further study is required for the continuous epidemiological study of variable anthrax collections.
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Affiliation(s)
- Chunsun Ryu
- Department of Bacteriology, National Institute of Health, 5-Nokbeon-dong, Eunpyeong-gu, Seoul 122-701, South Korea
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98
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Muscillo M, La Rosa G, Sali M, De Carolis E, Adone R, Ciuchini F, Fasanella A. Validation of a pXO2-A PCR assay to explore diversity among Italian isolates of Bacillus anthracis strains closely related to the live, attenuated Carbosap vaccine. J Clin Microbiol 2005; 43:4758-65. [PMID: 16145138 PMCID: PMC1234070 DOI: 10.1128/jcm.43.9.4758-4765.2005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several circulating Bacillus anthracis strains isolated in Italy and belonging to the A1.a cluster, genotype 3 (A1.a-3) are genotypically indistinguishable from Carbosap, a live attenuated vaccine strain, containing both pXO1 and pXO2 plasmids. The genotype was assessed by using eight-locus multilocus variable-number tandem repeat analysis. We describe here the use of a ninth locus able to explore variability among strains that have the same genotype. It is important to be able to genotype the wild isolate of B. anthracis strains from outbreaks of anthrax in areas where Carbosap vaccination of cattle and sheep is common practice. A total of 27 representative field strains isolated in Italy and four vaccinal strains, namely, Carbosap, Sterne, Pasteur I, and Pasteur II, were characterized by a ninth marker, called pXO2-A. Twenty-three field strains were genotype 3 and therefore identical to Carbosap. The marker was in the pXO2 plasmid and is based on the polymorphism of the already-known VX2-3 locus. Detection was obtained by PCR with fluorescence-labeled forward primers in order to produce appropriate fragments for capillary electrophoresis with an ABI 310 genetic analyzer. Genetic relationships showed heterogeneity in all of the examined samples. Interestingly, with respect to genotype 3, samples grouped into eight different subtypes, A to H, and the subtype G, had only two samples indistinguishable from Carbosap. The results of the present study confirm the validity of a hierarchical progressive protocol for discrimination among closely related isolates.
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Affiliation(s)
- M Muscillo
- Department of Environment and Primary Prevention, Istituto Superiore Sanità Roma, Rome.
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Sawires YS, Songer JG. Multiple-locus variable-number tandem repeat analysis for strain typing of Clostridium perfringens. Anaerobe 2005; 11:262-72. [PMID: 16701582 DOI: 10.1016/j.anaerobe.2005.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Revised: 02/23/2005] [Accepted: 03/31/2005] [Indexed: 10/25/2022]
Abstract
Clostridium perfringens is ubiquitous in the environment and causes diseases in man and animals, with syndromes ranging from enteritis, enterotoxemia, and sudden death to food poisoning and gas gangrene. Understanding the epidemiology of these infections and of the evolution of virulence in C. perfringens necessitate an efficient, time and cost effective strain typing method. Multiple-locus variable-number tandem repeat analysis (MLVA) has been applied to typing of other pathogens and we describe here the development of a MLVA scheme for C. perfringens. We characterized five variable tandem repeat (VNTR) loci, four of which are contained within protein encoding genes and screened 112 C. perfringens isolates to evaluate typability, reproducibility, and discriminatory power of the scheme. All the isolates were assigned a MLVA genotype and the technique has excellent reproducibility, with a numerical index of discrimination for the five VNTR loci of 0.995. Thus MLVA is an efficient tool for C. perfringens strain typing, and being PCR based makes it rapid, easy, and cost effective. In addition, it can be employed in epidemiological, ecological, and evolutionary investigations of the organism.
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Affiliation(s)
- Youhanna S Sawires
- Department of Veterinary Science and Microbiology, University of Arizona, Room 201, 1117 East Lowelll Street, Tucson, AZ 85721, USA
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100
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Lindstedt BA. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 2005; 26:2567-82. [PMID: 15937984 DOI: 10.1002/elps.200500096] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA fingerprinting has attracted considerable interest as means for identifying, tracing and preventing the dissemination of infectious agents. Various methods have been developed for typing of pathogenic bacteria, which differ in discriminative power, reproducibility and ease of interpretation. During recent years a typing method, which uses the information provided by whole genome sequencing of bacterial species, has gained increased attention. Short sequence repeat (SSR) motifs are known to undergo frequent variation in the number of repeated units through cellular mechanisms most commonly active during chromosome replication. A class of SSRs, named variable number of tandem repeats (VNTRs), has proven to be a suitable target for assessing genetic polymorphisms within bacterial species. This review attempts to give an overview of bacterial agents where VNTR-based typing, or multiple-locus variant-repeat analysis (MLVA) has been developed for typing purposes, together with addressing advantages and drawbacks associated with the use of tandem repeated DNA motifs as targets for bacterial typing and identification.
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Affiliation(s)
- Bjørn-Arne Lindstedt
- Norwegian Institute of Public Health, Division for Infectious Diseases Control, Oslo, Norway.
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