Garry Myers completed his PhD on chlamydial biology in 1998 at the University of Sydney (Faculty of Medicine) via the Menzies School of Health Research (Darwin, NT). He did postdoctoral training at The Institute for Genome Research (TIGR) in Rockville, Maryland, working on microbial genomics and pathogenesis, with numerous high-impact publications, including Science, Nature Biotechnology and Genome Research. In 2005 he was invited to join the TIGR Faculty. In 2007, along with twelve other TIGR Faculty, he was a co-founder of the Institute for Genome Sciences at the University of Maryland School of Medicine (Baltimore, Maryland). In June 2014, he relocated to the ithree Institute at the University of Technology, Sydney.
Can supervise: YES
Garry's research interests are focused upon the application of genomic-scale tools to bacterial pathogens and the host response, specifically to Chlamydia.
Chlamydia are obligate intracellular bacterial pathogens that cause a range of mammalian diseases, including the most common human sexually transmitted infections and trachoma (infectious blindness). Human disease arises by adverse host inflammatory reactions that induce tissue damage & scarring. Despite the global morbidity caused by chlamydial infections, relatively little is known about disease mechanisms. Chlamydia are genetically intractable as replication outside of the host cell is not yet possible and there are no practical tools for routine genetic manipulation, making genome-scale approaches critical to the understanding of this major human and veterinary pathogen.
De Puysseleyr, K., Kieckens, E., De Puysseleyr, L., Van den Wyngaert, H., Ahmed, B., Van Lent, S., Creasy, H.H., Myers, G.S.A. & Vanrompay, D. 2018, 'Development of a Chlamydia suis-specific antibody enzyme-linked immunosorbent assay based on the use of a B-cell epitope of the polymorphic membrane protein C.', Transboundary and emerging diseases, vol. 65, no. 2, pp. e457-e469.View/Download from: UTS OPUS or Publisher's site
Chlamydia suis infections lead to economic loss in the pork industry. Chlamydia suis infections could be successfully treated with tetracyclines until the appearance of a tetracycline resistant phenotype, which was acquired via horizontal gene transfer of the tet(C) gene. Given the importance of C. suis as a swine pathogen and as a recently emerged tetracycline resistant pathogen with zoonotic potential, our aim was to develop a sensitive C. suis-specific antibody ELISA based on the polymorphic membrane proteins (Pmps). Chlamydia Pmps are important virulence factors and candidate antigens for serodiagnosis. We identified nine Pmps (PmpA to I) in C. suis strain MD56 using a recently developed Hidden-Markov model. PmpC was the most promising candidate for the development of a C. suis-specific antibody ELISA as the protein was absent in C. abortus, C. pecorum and C. psittaci which also infect pigs and as the protein contained C. suis-specific amino acid regions, absent in C. trachomatis PmpC. We identified an immunodominant B-cell epitope in C. suis PmpC using experimental porcine sera. The sensitivity and specificity of the PmpC ELISA was compared to the complement fixation test (CFT) and to a recombinant MOMP ELISA using experimental sera. The PmpC ELISA detected all positive control sera and was in contrast to CFT and the rMOMP ELISA 100% C. suis specific as positive control sera against other Chlamydia species did not react in the PmpC ELISA. The test was successfully validated using slaughterhouse sera and sera from clinically affected pigs. The PmpC ELISA could assist in diminishing the spread of C. suis infections in the pork industry.
Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA-Seq technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. We pioneered dRNA-Seq to simultaneously capture prokaryotic and eukaryotic expression profiles of cells infected with bacteria, using in vitro Chlamydia-infected epithelial cells as proof of principle. Here we provide a detailed laboratory and bioinformatics protocol for dRNA-seq that is readily adaptable to any host-bacteria system of interest.
Marsh, J.W., Hayward, R.J., Shetty, A.C., Mahurkar, A., Humphrys, M.S. & Myers, G.S.A. 2018, 'Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments', Briefings in Bioinformatics.View/Download from: UTS OPUS or Publisher's site
Wee, B.A., Thomas, M., Sweeney, E.L., Frentiu, F.D., Samios, M., Ravel, J., Gajer, P., Myers, G., Timms, P., Allan, J.A. & Huston, W.M. 2018, 'A retrospective pilot study to determine whether the reproductive tract microbiota differs between women with a history of infertility and fertile women.', The Australian and New Zealand Journal of Obstetrics and Gynaecology (ANZJOG).View/Download from: UTS OPUS or Publisher's site
We know very little about the microbiota inhabiting the upper female reproductive tract and how it impacts on fertility.This pilot study aimed to examine the vaginal, cervical and endometrial microbiota for women with a history of infertility compared to women with a history of fertility.Using a retrospective case-control study design, women were recruited for collection of vaginal, cervical and endometrial samples. The microbiota composition was analysed by 16S ribosomal RNA (rRNA) gene amplification and endometrial expression of selected human genes by quantitative reverse transcription polymerase chain reaction.Sixty-five specimens from the reproductive tract of 31 women were successfully analysed using 16S rRNA gene amplicon sequencing (16 controls and 15 cases). The dominant microbial community members were consistent in the vagina and cervix, and generally consistent with the endometrium although the relative proportions varied. We detected three major microbiota clusters that did not group by tissue location or case-control status. There was a trend that infertile women more often had Ureaplasma in the vagina and Gardnerella in the cervix. Testing for the expression of selected genes in the endometrium did not show evidence of correlation with case-control status, or with microbial community composition, although Tenascin-C expression correlated with a history of miscarriage.There is a need for further exploration of the endometrial microbiota, and how the microbiota members or profile interplays with fertility or assisted reproductive technologies.
Marsh, J.W., Humphrys, M.S. & Myers, G.S.A. 2017, 'A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro', Frontiers in Microbiology, vol. 8.View/Download from: UTS OPUS or Publisher's site
Branley, J., Bachmann, N.L., Jelocnik, M., Myers, G.S.A. & Polkinghorne, A. 2016, 'Australian human and parrot Chlamydia psittaci strains cluster within the highly virulent 6BC clade of this important zoonotic pathogen.', Scientific reports, vol. 6, p. 30019.View/Download from: UTS OPUS or Publisher's site
Chlamydia psittaci is an avian pathogen and zoonotic agent of atypical pneumonia. The most pathogenic C. psittaci strains cluster into the 6BC clade, predicted to have recently emerged globally. Exposure to infected parrots is a risk factor with limited evidence also of an indirect exposure risk. Genome sequencing was performed on six Australian human and a single avian C. psittaci strain isolated over a 9 year period. Only one of the five human patients had explicit psittacine contact. Genomics analyses revealed that the Australian C. psittaci strains are remarkably similar, clustering tightly within the C. psittaci 6BC clade suggested to have been disseminated by South America parrot importation. Molecular clock analysis using the newly sequenced C. psittaci genomes predicted the emergence of the 6BC clade occurring approximately 2,000 years ago. These findings reveal the potential for an Australian natural reservoir of C. psittaci 6BC strains. These strains can also be isolated from seriously ill patients without explicit psittacine contact. The apparent recent and global spread of C. psittaci 6BC strains raises important questions over how this happened. Further studies may reveal whether the dissemination of this important zoonotic pathogen is linked to Australian parrot importation rather than parrots from elsewhere.
Van Lent, S., Creasy, H.H., Myers, G.S.A. & Vanrompay, D. 2016, 'The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences as well as the Most Conserved Pmp Protein Differ within and across Chlamydia Species', Journal of Molecular Microbiology and Biotechnology, vol. 26, no. 5, pp. 333-344.View/Download from: UTS OPUS or Publisher's site
Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of pmp coding sequences differs between Chlamydia species, but it is unknown whether the number of pmp coding sequences is constant within a Chlamydia species. The level of conservation of the Pmp proteins has previously only been determined for Chlamydia trachomatis. As different Pmp proteins might be indispensible for the pathogenesis of different Chlamydia species, this study investigated the conservation of Pmp proteins both within and across C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci. The pmp coding sequences were annotated in 16 C. trachomatis, 6 C. pneumoniae, 2 C. abortus, and 16 C. psittaci genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed Chlamydia species. The length of coding sequences of pmpA,pmpB, and pmpH was conserved among all analyzed genomes, while the length of pmpE/F and pmpG, and remarkably also of the subtype pmpD, differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci, respectively. PmpB was the most conserved Pmp across the 4 analyzed Chlamydia species.
Bachmann, N.L., Sullivan, M.J., Jelocnik, M., Myers, G.S.A., Timms, P. & Polkinghorne, A. 2015, 'Culture-independent genome sequencing of clinical samples reveals an unexpected heterogeneity of infections by Chlamydia pecorum.', Journal of clinical microbiology, vol. 53, no. 5, pp. 1573-1581.View/Download from: UTS OPUS or Publisher's site
Chlamydia pecorum is an important global pathogen of livestock, and it is also a significant threat to the long-term survival of Australia's koala populations. This study employed a culture-independent DNA capture approach to sequence C. pecorum genomes directly from clinical swab samples collected from koalas with chlamydial disease as well as from sheep with arthritis and conjunctivitis. Investigations into single-nucleotide polymorphisms within each of the swab samples revealed that a portion of the reads in each sample belonged to separate C. pecorum strains, suggesting that all of the clinical samples analyzed contained mixed populations of genetically distinct C. pecorum isolates. This observation was independent of the anatomical site sampled and the host species. Using the genomes of strains identified in each of these samples, whole-genome phylogenetic analysis revealed that a clade containing a bovine and a koala isolate is distinct from other clades comprised of livestock or koala C. pecorum strains. Providing additional evidence to support exposure of koalas to Australian livestock strains, two minor strains assembled from the koala swab samples clustered with livestock strains rather than koala strains. Culture-independent probe-based genome capture and sequencing of clinical samples provides the strongest evidence yet to suggest that naturally occurring chlamydial infections are comprised of multiple genetically distinct strains.
Jelocnik, M., Bachmann, N.L., Kaltenboeck, B., Waugh, C., Woolford, L., Speight, K.N., Gillett, A., Higgins, D.P., Flanagan, C., Myers, G.S.A., Timms, P. & Polkinghorne, A. 2015, 'Genetic diversity in the plasticity zone and the presence of the chlamydial plasmid differentiates Chlamydia pecorum strains from pigs, sheep, cattle, and koalas.', BMC genomics, vol. 16, p. 893.View/Download from: UTS OPUS or Publisher's site
Chlamydia pecorum is a globally recognised pathogen of livestock and koalas. To date, comparative genomics of C. pecorum strains from sheep, cattle and koalas has revealed that only single nucleotide polymorphisms (SNPs) and a limited number of pseudogenes appear to contribute to the genetic diversity of this pathogen. No chlamydial plasmid has been detected in these strains despite its ubiquitous presence in almost all other chlamydial species. Genomic analyses have not previously included C. pecorum from porcine hosts. We sequenced the genome of three C. pecorum isolates from pigs with differing pathologies in order to re-evaluate the genetic differences and to update the phylogenetic relationships between C. pecorum from each of the hosts.Whole genome sequences for the three porcine C. pecorum isolates (L1, L17 and L71) were acquired using C. pecorum-specific sequence capture probes with culture-independent methods, and assembled in CLC Genomics Workbench. The pairwise comparative genomic analyses of 16 pig, sheep, cattle and koala C. pecorum genomes were performed using several bioinformatics platforms, while the phylogenetic analyses of the core C. pecorum genomes were performed with predicted recombination regions removed. Following the detection of a C. pecorum plasmid, a newly developed C. pecorum-specific plasmid PCR screening assay was used to evaluate the plasmid distribution in 227 C. pecorum samples from pig, sheep, cattle and koala hosts.Three porcine C. pecorum genomes were sequenced using C. pecorum-specific sequence capture probes with culture-independent methods. Comparative genomics of the newly sequenced porcine C. pecorum genomes revealed an increased average number of SNP differences (~11 500) between porcine and sheep, cattle, and koala C. pecorum strains, compared to previous C. pecorum genome analyses. We also identified a third copy of the chlamydial cytotoxin gene, found only in porcine C. pecorum isolates. Phylogenetic analyses cluster...
Neuendorf, E., Gajer, P., Bowlin, A.K., Marques, P.X., Ma, B., Yang, H., Fu, L., Humphrys, M.S., Forney, L.J., Myers, G.S., Bavoil, P.M., Rank, R.G. & Ravel, J. 2015, 'Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota.', Pathogens and Disease, vol. 73, no. 4, pp. 1-12.View/Download from: UTS OPUS or Publisher's site
In humans, the vaginal microbiota is thought to be the first line of defense again pathogens including Chlamydia trachomatis. The guinea pig has been extensively used as a model to study chlamydial infection because it shares anatomical and physiological similarities with humans, such as a squamous vaginal epithelium as well as some of the long-term outcomes caused by chlamydial infection. In this study, we aimed to evaluate the guinea pig-C. caviae model of genital infection as a surrogate for studying the role of the vaginal microbiota in the early steps of C. trachomatis infection in humans. We used culture-independent molecular methods to characterize the relative and absolute abundance of bacterial phylotypes in the guinea pig vaginal microbiota in animals non-infected, mock-infected or infected by C. caviae. We showed that the guinea pig and human vaginal microbiotas are of different bacterial composition and abundance. Chlamydia caviae infection had a profound effect on the absolute abundance of bacterial phylotypes but not on the composition of the guinea pig vaginal microbiota. Our findings compromise the validity of the guinea pig-C. caviae model to study the role of the vaginal microbiota during the early steps of sexually transmitted infection.
Roulis, E., Bachmann, N., Humphrys, M., Myers, G., Huston, W., Polkinghorne, A. & Timms, P. 2015, 'Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent.', BMC Genomics, vol. 16, pp. 1-15.View/Download from: UTS OPUS or Publisher's site
The obligate intracellular bacterium Chlamydia pneumoniae is a common respiratory pathogen, which has been found in a range of hosts including humans, marsupials and amphibians. Whole genome comparisons of human C. pneumoniae have previously highlighted a highly conserved nucleotide sequence, with minor but key polymorphisms and additional coding capacity when human and animal strains are compared.In this study, we sequenced three Australian human C. pneumoniae strains, two of which were isolated from patients in remote indigenous communities, and compared them to all available C. pneumoniae genomes. Our study demonstrated a phylogenetically distinct human C. pneumoniae clade containing the two indigenous Australian strains, with estimates that the most recent common ancestor of these strains predates the arrival of European settlers to Australia. We describe several polymorphisms characteristic to these strains, some of which are similar in sequence to animal C. pneumoniae strains, as well as evidence to suggest that several recombination events have shaped these distinct strains.Our study reveals a greater sequence diversity amongst both human and animal C. pneumoniae strains, and suggests that a wider range of strains may be circulating in the human population than current sampling indicates.
Roulis, E., Bachmann, N.L., Myers, G.S.A., Huston, W., Summersgill, J., Hudson, A., Dreses-Werringloer, U., Polkinghorne, A. & Timms, P. 2015, 'Comparative genomic analysis of human Chlamydia pneumoniae isolates from respiratory, brain and cardiac tissues.', Genomics, vol. 106, no. 6, pp. 373-383.View/Download from: UTS OPUS or Publisher's site
Chlamydia pneumoniae is an obligate intracellular bacterium implicated in a wide range of human diseases including atherosclerosis and Alzheimer's disease. Efforts to understand the relationships between C. pneumoniae detected in these diseases have been hindered by the availability of sequence data for non-respiratory strains. In this study, we sequenced the whole genomes for C. pneumoniae isolates from atherosclerosis and Alzheimer's disease, and compared these to previously published C. pneumoniae genomes. Phylogenetic analyses of these new C. pneumoniae strains indicate two sub-groups within human C. pneumoniae, and suggest that both recombination and mutation events have driven the evolution of human C. pneumoniae. Further fine-detailed analyses of these new C. pneumoniae sequences show several genetically variable loci. This suggests that similar strains of C. pneumoniae are found in the brain, lungs and cardiovascular system and that only minor genetic differences may contribute to the adaptation of particular strains in human disease.
Bachmann, N.L., Fraser, T.A., Bertelli, C., Jelocnik, M., Gillett, A., Funnell, O., Flanagan, C., Myers, G.S.A., Timms, P. & Polkinghorne, A. 2014, 'Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum.', BMC Genomics, vol. 15, pp. 1-14.View/Download from: UTS OPUS or Publisher's site
BACKGROUND: Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koalas. The genome of the C. pecorum VR629 (IPA) strain, isolated from a sheep with polyarthritis, was also sequenced. RESULTS: Comparisons of the draft C. pecorum genomes against the complete genomes of livestock C. pecorum isolates revealed that these strains have a conserved gene content and order, sharing a nucleotide sequence similarity>98%. Single nucleotide polymorphisms (SNPs) appear to be key factors in understanding the adaptive process. Two regions of the chromosome were found to be accumulating a large number of SNPs within the koala strains. These regions include the Chlamydia plasticity zone, which contains two cytotoxin genes (toxA and toxB), and a 77 kbp region that codes for putative type III effector proteins. In one koala strain (MC/MarsBar), the toxB gene was truncated by a premature stop codon but is full-length in IPTaLE and DBDeUG. Another five pseudogenes were also identified, two unique to the urogenital strains C. pecorum MC/MarsBar and C. pecorum DBDeUG, respectively, while three were unique to the koala C. pecorum conjunctival isolate IPTaLE. An examination of the distribution of these pseudogenes in C. pecorum strains from a variety of koala populations, alongside a number of sheep and cattle C. pecorum positive samples from Australian livestock, confirmed the presence of four predicted pseudogenes in koala C. pecorum clinical samples. Consistent with our genomics analyses, none of these pseudogenes were observed in the livestock C. pecorum samples examined. Interestingly, three SNPs resulting in pseudogenes identified in the IPTaLE isolate were not found in any other C. pecorum strain analysed, raising questions over the ...
Crabtree, J., Agrawal, S., Mahurkar, A., Myers, G.S., Rasko, D.A. & White, O. 2014, 'Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG.', Bioinformatics (Oxford, England), vol. 30, no. 21, pp. 3125-3127.View/Download from: UTS OPUS or Publisher's site
Circleator is a Perl application that generates circular figures of genome-associated data. It leverages BioPerl to support standard annotation and sequence file formats and produces publication-quality SVG output. It is designed to be both flexible and easy to use. It includes a library of circular track types and predefined configuration files for common use-cases, including. (i) visualizing gene annotation and DNA sequence data from a GenBank flat file, (ii) displaying patterns of gene conservation in related microbial strains, (iii) showing Single Nucleotide Polymorphisms (SNPs) and indels relative to a reference genome and gene set and (iv) viewing RNA-Seq plots.Circleator is freely available under the Artistic License 2.0 from http://jonathancrabtree.github.io/Circleator/ and is integrated with the CloVR cloud-based sequence analysis Virtual Machine (VM), which can be downloaded from http://clovr.org or run on Amazon EC2.
Donati, M., Huot-Creasy, H., Humphrys, M., Di Paolo, M., Di Francesco, A. & Myers, G.S.A. 2014, 'Genome Sequence of Chlamydia suis MD56, Isolated from the Conjunctiva of a Weaned Piglet.', Genome Announcements, vol. 2, no. 3, pp. e00425-14-e00425-14.View/Download from: UTS OPUS or Publisher's site
Chlamydia suis is a natural pathogen of pigs (Sus scrofa) and causes conjunctivitis, pneumonia, enteritis, and various reproductive disorders that adversely impact this economically important animal. Here, we report the first C. suis genome, that of C. suis MD56, isolated from a conjunctival swab of a weaned piglet.
Dugan, V.G., Emrich, S.J., Giraldo-Calderón, G.I., Harb, O.S., Newman, R.M., Pickett, B.E., Schriml, L.M., Stockwell, T.B., Stoeckert, C.J., Sullivan, D.E., Singh, I., Ward, D.V., Yao, A., Zheng, J., Barrett, T., Birren, B., Brinkac, L., Bruno, V.M., Caler, E., Chapman, S., Collins, F.H., Cuomo, C.A., Di Francesco, V., Durkin, S., Eppinger, M., Feldgarden, M., Fraser, C., Fricke, W.F., Giovanni, M., Henn, M.R., Hine, E., Hotopp, J.D., Karsch-Mizrachi, I., Kissinger, J.C., Lee, E.M., Mathur, P., Mongodin, E.F., Murphy, C.I., Myers, G., Neafsey, D.E., Nelson, K.E., Nierman, W.C., Puzak, J., Rasko, D., Roos, D.S., Sadzewicz, L., Silva, J.C., Sobral, B., Squires, R.B., Stevens, R.L., Tallon, L., Tettelin, H., Wentworth, D., White, O., Will, R., Wortman, J., Zhang, Y. & Scheuermann, R.H. 2014, 'Standardized metadata for human pathogen/vector genomic sequences.', PLoS ONE, vol. 9, no. 6, pp. 1-11.View/Download from: UTS OPUS or Publisher's site
High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consi...
Sachse, K., Laroucau, K., Riege, K., Wehner, S., Dilcher, M., Creasy, H.H., Weidmann, M., Myers, G., Vorimore, F., Vicari, N., Magnino, S., Liebler-Tenorio, E., Ruettger, A., Bavoil, P.M., Hufert, F.T., Rosselló-Móra, R. & Marz, M. 2014, 'Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov.', Systematic and applied microbiology, vol. 37, no. 2, pp. 79-88.View/Download from: UTS OPUS or Publisher's site
The family Chlamydiaceae with the recombined single genus Chlamydia currently comprises nine species, all of which are obligate intracellular organisms distinguished by a unique biphasic developmental cycle. Anecdotal evidence from epidemiological surveys in flocks of poultry, pigeons and psittacine birds have indicated the presence of non-classified chlamydial strains, some of which may act as pathogens. In the present study, phylogenetic analysis of ribosomal RNA and ompA genes, as well as multi-locus sequence analysis of 11 field isolates were conducted. All independent analyses assigned the strains into two different clades of monophyletic origin corresponding to pigeon and psittacine strains or poultry isolates, respectively. Comparative genome analysis involving the type strains of currently accepted Chlamydiaceae species and the designated type strains representing the two new clades confirmed that the latter could be classified into two different species as their average nucleotide identity (ANI) values were always below 94%, both with the closest relative species and between themselves. In view of the evidence obtained from the analyses, we propose the addition of two new species to the current classification: Chlamydia avium sp. nov. comprising strains from pigeons and psittacine birds (type strain 10DC88(T); DSMZ: DSM27005(T), CSUR: P3508(T)) and Chlamydia gallinacea sp. nov. comprising strains from poultry (type strain 08-1274/3(T); DSMZ: DSM27451(T), CSUR: P3509(T)).
Sait, M., Livingstone, M., Clark, E.M., Wheelhouse, N., Spalding, L., Markey, B., Magnino, S., Lainson, F.A., Myers, G.S.A. & Longbottom, D. 2014, 'Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes.', BMC Genomics, vol. 15, pp. 1-15.View/Download from: UTS OPUS or Publisher's site
BACKGROUND: Chlamydia pecorum is the causative agent of a number of acute diseases, but most often causes persistent, subclinical infection in ruminants, swine and birds. In this study, the genome sequences of three C. pecorum strains isolated from the faeces of a sheep with inapparent enteric infection (strain W73), from the synovial fluid of a sheep with polyarthritis (strain P787) and from a cervical swab taken from a cow with metritis (strain PV3056/3) were determined using Illumina/Solexa and Roche 454 genome sequencing. RESULTS: Gene order and synteny was almost identical between C. pecorum strains and C. psittaci. Differences between C. pecorum and other chlamydiae occurred at a number of loci, including the plasticity zone, which contained a MAC/perforin domain protein, two copies of a >3400 amino acid putative cytotoxin gene and four (PV3056/3) or five (P787 and W73) genes encoding phospholipase D. Chlamydia pecorum contains an almost intact tryptophan biosynthesis operon encoding trpABCDFR and has the ability to sequester kynurenine from its host, however it lacks the genes folA, folKP and folB required for folate metabolism found in other chlamydiae. A total of 15 polymorphic membrane proteins were identified, belonging to six pmp families. Strains possess an intact type III secretion system composed of 18 structural genes and accessory proteins, however a number of putative inc effector proteins widely distributed in chlamydiae are absent from C. pecorum. Two genes encoding the hypothetical protein ORF663 and IncA contain variable numbers of repeat sequences that could be associated with persistence of infection. CONCLUSIONS: Genome sequencing of three C. pecorum strains, originating from animals with different disease manifestations, has identified differences in ORF663 and pseudogene content between strains and has identified genes and metabolic traits that may influence intracellular survival, pathogenicity and evasion of the host immune system.
Yeruva, L., Myers, G.S.A., Spencer, N., Creasy, H.H., Adams, N.E., Maurelli, A.T., McChesney, G.R., Cleves, M.A., Ravel, J., Bowlin, A. & Rank, R.G. 2014, 'Early microRNA expression profile as a prognostic biomarker for the development of pelvic inflammatory disease in a mouse model of chlamydial genital infection.', mBio, vol. 5, no. 3, pp. e01241-e01214.View/Download from: UTS OPUS or Publisher's site
It is not currently possible to predict the probability of whether a woman with a chlamydial genital infection will develop pelvic inflammatory disease (PID). To determine if specific biomarkers may be associated with distinct chlamydial pathotypes, we utilized two Chlamydia muridarum variants (C. muridarum Var001 [CmVar001] and CmVar004) that differ in their abilities to elicit upper genital tract pathology in a mouse model. CmVar004 has a lower growth rate in vitro and induces pathology in only 20% of C57BL/6 mouse oviducts versus 83.3% of oviducts in CmVar001-infected mice. To determine if chemokine and cytokine production within 24 h of infection is associated with the outcome of pathology, levels of 15 chemokines and cytokines were measured. CmVar004 infection induced significantly lower levels of CXCL1, CXCL2, tumor necrosis factor alpha (TNF-), and CCL2 in comparison to CmVar001 infection with similar rRNA (rs16) levels for Chlamydiae. A combination of microRNA (miRNA) sequencing and quantitative real-time PCR (qRT-PCR) analysis of 134 inflammation-related miRNAs was performed 24 h postinfection to determine if the chemokine/cytokine responses would also be reflected in miRNA expression profiles. Interestingly, 12 miRNAs (miR-135a-5p, miR298-5p, miR142-3p, miR223-3p, miR299a-3p, miR147-3p, miR105, miR325-3p, miR132-3p, miR142-5p, miR155-5p, and miR-410-3p) were overexpressed during CmVar004 infection compared to CmVar001 infection, inversely correlating with the respective chemokine/cytokine responses. To our knowledge, this is the first report demonstrating that early biomarkers elicited in the host can differentiate between two pathological variants of chlamydiae and be predictive of upper tract disease.It is apparent that an infecting chlamydial population consists of multiple genetic variants with differing capabilities of eliciting a pathological response; thus, it may be possible to identify biomarkers specific for a given virulence pathotype. miRNA...
Zapata, J.C., Goicochea, M., Nadai, Y., Eyzaguirre, L.M., Carr, J.K., Tallon, L.J., Sadzewicz, L., Myers, G., Fraser, C.M., Su, Q., Djavani, M., Lukashevich, I.S. & Salvato, M.S. 2014, 'Genetic Variation In Vitro and In Vivo of an Attenuated Lassa Vaccine Candidate', JOURNAL OF VIROLOGY, vol. 88, no. 6, pp. 3058-3066.View/Download from: UTS OPUS or Publisher's site
Zapata, J.C., Goicochea, M., Nadai, Y., Eyzaguirre, L.M., Carr, J.K., Tallon, L.J., Sadzewicz, L., Myers, G., Fraser, C.M., Su, Q., Djavani, M., Lukashevich, I.S. & Salvato, M.S. 2014, 'Genetic variation in vitro and in vivo of an attenuated Lassa vaccine candidate.', Journal of virology, vol. 88, no. 6, pp. 3058-3066.View/Download from: UTS OPUS or Publisher's site
The attenuated Lassa vaccine candidate ML29 is a laboratory-produced reassortant between Lassa and Mopeia viruses, two Old World arenaviruses that differ by 40% in nucleic acid sequence. In our previous studies, ML29 elicited sterilizing immunity against Lassa virus challenge in guinea pigs and marmosets and virus-specific cell-mediated immunity in both simian immunodeficiency virus (SIV)-infected and uninfected rhesus macaques. Here, we show that ML29 is stable after 12 passages in vitro without losing its plaque morphology or its attenuated phenotype in suckling mice. Additionally, we used deep sequencing to characterize the viral population comprising the original stock of ML29, the stock of ML29 after 12 passages in Vero cells, and the ML29 isolates obtained from vaccinated animals. Twenty-seven isolates bore approximately 77 mutations that exceeded 20% of the single-nucleotide polymorphism (SNP) changes at any single locus. Of these 77 mutations, 5 appeared to be host specific, for example, appearing in mice but not in primates. None of these mutations were reversions of ML29 to the sequences of the parental Lassa and Mopeia viruses. The host-specific mutations indicate viral adaptations to virus-host interactions, and such interactions make reasonable targets for antiviral approaches. Variants capable of chronic infection did not emerge from any of the primate infections, even in immune-deficient animals, indicating that the ML29 reassortant is reasonably stable in vivo. In conclusion, the preclinical studies of ML29 as a Lassa virus vaccine candidate have been advanced, showing high levels of protection in nonhuman primates and acceptable stability both in vitro and in vivo.
Hovis, K.M., Mojica, S., McDermott, J.E., Pedersen, L., Simhi, C., Rank, R.G., Myers, G.S.A., Ravel, J., Hsia, R.-.C. & Bavoil, P.M. 2013, 'Genus-optimized strategy for the identification of chlamydial type III secretion substrates.', Pathogens and disease, vol. 69, no. 3, pp. 213-222.View/Download from: UTS OPUS or Publisher's site
Among chlamydial virulence factors are the type III secretion (T3S) system and its effectors. T3S effectors target host proteins to benefit the infecting chlamydiae. The assortment of effectors, each with a unique function, varies between species. This variation likely contributes to differences in host specificity and disease severity. A dozen effectors of Chlamydia trachomatis have been identified; however, estimates suggest that more exist. A T3S prediction algorithm, SVM-based Identification and Evaluation of Virulence Effectors (SIEVE), along with a Yersinia surrogate secretion system helped to identify a new T3S substrate, CT082, which rather than functioning as an effector associates with the chlamydial envelope after secretion. SIEVE was modified to improve/expand effector predictions to include all sequenced genomes. Additional adjustments were made to the existing surrogate system whereby the N terminus of putative effectors was fused to a known effector lacking its own N terminus and was tested for secretion. Expansion of effector predictions by cSIEVE and modification of the surrogate system have also assisted in identifying a new T3S substrate from C. psittaci. The expanded predictions along with modifications to improve the surrogate secretion system have enhanced our ability to identify novel species-specific effectors, which upon characterization should provide insight into the unique pathogenic properties of each species.
Humphrys, M.S., Creasy, T., Sun, Y., Shetty, A.C., Chibucos, M.C., Drabek, E.F., Fraser, C.M., Farooq, U., Sengamalay, N., Ott, S., Shou, H., Bavoil, P.M., Mahurkar, A. & Myers, G.S.A. 2013, 'Simultaneous transcriptional profiling of bacteria and their host cells.', PLoS ONE, vol. 8, no. 12, pp. 1-13.View/Download from: UTS OPUS or Publisher's site
We developed an RNA-Seq-based method to simultaneously capture prokaryotic and eukaryotic expression profiles of cells infected with intracellular bacteria. As proof of principle, this method was applied to Chlamydia trachomatis-infected epithelial cell monolayers in vitro, successfully obtaining transcriptomes of both C. trachomatis and the host cells at 1 and 24 hours post-infection. Chlamydiae are obligate intracellular bacterial pathogens that cause a range of mammalian diseases. In humans chlamydiae are responsible for the most common sexually transmitted bacterial infections and trachoma (infectious blindness). Disease arises by adverse host inflammatory reactions that induce tissue damage & scarring. However, little is known about the mechanisms underlying these outcomes. Chlamydia are genetically intractable as replication outside of the host cell is not yet possible and there are no practical tools for routine genetic manipulation, making genome-scale approaches critical. The early timeframe of infection is poorly understood and the host transcriptional response to chlamydial infection is not well defined. Our simultaneous RNA-Seq method was applied to a simplified in vitro model of chlamydial infection. We discovered a possible chlamydial strategy for early iron acquisition, putative immune dampening effects of chlamydial infection on the host cell, and present a hypothesis for Chlamydia-induced fibrotic scarring through runaway positive feedback loops. In general, simultaneous RNA-Seq helps to reveal the complex interplay between invading bacterial pathogens and their host mammalian cells and is immediately applicable to any bacteria/host cell interaction.
Vorimore, F., Hsia, R.-.C., Huot-Creasy, H., Bastian, S., Deruyter, L., Passet, A., Sachse, K., Bavoil, P., Myers, G. & Laroucau, K. 2013, 'Isolation of a New Chlamydia species from the Feral Sacred Ibis (Threskiornis aethiopicus): Chlamydia ibidis.', PloS one, vol. 8, no. 9, p. e74823.View/Download from: UTS OPUS or Publisher's site
Investigations conducted on feral African Sacred Ibises (Threskiornisaethiopicus) in western France led to the isolation of a strain with chlamydial genetic determinants. Ultrastructural analysis, comparative sequence analysis of the 16S rRNA gene, ompA, and of a concatenate of 31 highly conserved genes, as well as determination of the whole genome sequence confirmed the relatedness of the new isolate to members of the Chlamydiaceae, while, at the same time demonstrating a unique position outside the currently recognized species of this family. We propose to name this new chlamydial species Chlamydiaibidis .
Van Lent, S., Piet, J.R., Beeckman, D., van der Ende, A., Van Nieuwerburgh, F., Bavoil, P., Myers, G., Vanrompay, D. & Pannekoek, Y. 2012, 'Full genome sequences of all nine Chlamydia psittaci genotype reference strains.', Journal of bacteriology, vol. 194, no. 24, pp. 6930-6931.View/Download from: UTS OPUS or Publisher's site
Chlamydia psittaci primarily infects birds, but zoonotic transmission occurs in people in close contact with infected birds. The clinical outcome ranges from inapparent disease to pneumonia. Here we report the genome sequences of all 9 Chlamydia psittaci genotype reference strains.
Collingro, A., Tischler, P., Weinmaier, T., Penz, T., Heinz, E., Brunham, R.C., Read, T.D., Bavoil, P.M., Sachse, K., Kahane, S., Friedman, M.G., Rattei, T., Myers, G.S.A. & Horn, M. 2011, 'Unity in variety--the pan-genome of the Chlamydiae.', Molecular biology and evolution, vol. 28, no. 12, pp. 3253-3270.View/Download from: UTS OPUS or Publisher's site
Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic host cells. They include important human pathogens such as Chlamydia trachomatis as well as symbionts of protozoa. As these bacteria are experimentally challenging and genetically intractable, our knowledge about them is still limited. In this study, we obtained the genome sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99, and Parachlamydia acanthamoebae UV-7. This enabled us to perform the first comprehensive comparative and phylogenomic analysis of representative members of four major families of the Chlamydiae, including the Chlamydiaceae. We identified a surprisingly large core gene set present in all genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV secretion system. In S. negevensis, the type IV secretion system is encoded on a large conjugative plasmid (pSn, 132 kb). Phylogenetic analyses suggested that a plasmid similar to the S. negevensis plasmid was originally acquired by the last common ancestor of all four families and that it was subsequently reduced, integrated into the chromosome, or lost during diversification, ultimately giving rise to the extant virulence-associated plasmid of pathogenic chlamydiae. Other virulence factors, including a type III secretion system, are conserved among the Chlamydiae to variable degrees and together with differences in the composition of the cell wall reflect adaptation to different host cells including convergent evolution among the four chlamydial families. Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote.
Grinblat-Huse, V., Drabek, E.F., Creasy, H.H., Daugherty, S.C., Jones, K.M., Santana-Cruz, I., Tallon, L.J., Read, T.D., Hatch, T.P., Bavoil, P. & Myers, G.S.A. 2011, 'Genome Sequences of the Zoonotic Pathogens Chlamydia psittaci 6BC and Cal10', JOURNAL OF BACTERIOLOGY, vol. 193, no. 15, pp. 4039-4040.View/Download from: UTS OPUS or Publisher's site
Mojica, S., Huot Creasy, H., Daugherty, S., Read, T.D., Kim, T., Kaltenboeck, B., Bavoil, P. & Myers, G.S.A. 2011, 'Genome sequence of the obligate intracellular animal pathogen Chlamydia pecorum E58.', Journal of bacteriology, vol. 193, no. 14, p. 3690.View/Download from: UTS OPUS or Publisher's site
Chlamydia pecorum is an obligate intracellular bacterial pathogen that causes diverse disease in a wide variety of economically important mammals. We report the finished complete genome sequence of C. pecorum E58, the type strain for the species.
Mitchell, C.M., Hovis, K.M., Bavoil, P.M., Myers, G.S.A., Carrasco, J.A. & Timms, P. 2010, 'Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species.', BMC genomics, vol. 11, p. 442.View/Download from: UTS OPUS or Publisher's site
Chlamydia pneumoniae is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on four essentially clonal (> 99% identity) C. pneumoniae human genomes (AR39, CWL029, J138 and TW183), providing relatively little insight into strain diversity and evolution of this species.We performed individual gene-by-gene comparisons of the recently sequenced C. pneumoniae koala genome and four C. pneumoniae human genomes to identify species-specific genes, and more importantly, to gain an insight into the genetic diversity and evolution of the species. We selected genes dispersed throughout the chromosome, representing genes that were specific to C. pneumoniae, genes with a demonstrated role in chlamydial biology and/or pathogenicity (n = 49), genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6), and extrachromosomal elements (9 plasmid and 2 bacteriophage genes).We have identified strain-specific differences and targets for detection of C. pneumoniae isolates from both human and animal origin. Such characterisation is necessary for an improved understanding of disease transmission and intervention.
Mitchell, C.M., Hutton, S., Myers, G.S.A., Brunham, R. & Timms, P. 2010, 'Chlamydia pneumoniae is genetically diverse in animals and appears to have crossed the host barrier to humans on (at least) two occasions.', PLoS pathogens, vol. 6, no. 5, p. e1000903.View/Download from: UTS OPUS or Publisher's site
Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of diseases. Since the first isolation of C. pneumoniae TWAR in 1965, all human isolates have been essentially clonal, providing little evolutionary insight. To address this gap, we investigated the genetic diversity of 30 isolates from diverse geographical locations, from both human and animal origin (amphibian, reptilian, equine and marsupial). Based on the level of variation that we observed at 23 discreet gene loci, it was clearly evident that the animal isolates were more diverse than the isolates of human origin. Furthermore, we show that C. pneumoniae isolates could be grouped into five major genotypes, A-E, with A, B, D and E genotypes linked by geographical location, whereas genotype C was found across multiple continents. Our evidence strongly supports two separate animal-to-human cross species transfer events in the evolutionary history of this pathogen. The C. pneumoniae human genotype identified in the USA, Canada, Taiwan, Iran, Japan, Korea and Australia (non-Indigenous) most likely originated from a single amphibian or reptilian lineage, which appears to have been previously geographically widespread. We identified a separate human lineage present in two Australian Indigenous isolates (independent geographical locations). This lineage is distinct and is present in Australian amphibians as well as a range of Australian marsupials.
Burall, L.S., Rodolakis, A., Rekiki, A., Myers, G.S.A. & Bavoil, P.M. 2009, 'Genomic analysis of an attenuated Chlamydia abortus live vaccine strain reveals defects in central metabolism and surface proteins.', Infection and immunity, vol. 77, no. 9, pp. 4161-4167.View/Download from: UTS OPUS or Publisher's site
Comparative genomic analysis of a wild-type strain of the ovine pathogen Chlamydia abortus and its nitrosoguanidine-induced, temperature-sensitive, virulence-attenuated live vaccine derivative identified 22 single nucleotide polymorphisms unique to the mutant, including nine nonsynonymous mutations, one leading to a truncation of pmpG, which encodes a polymorphic membrane protein, and two intergenic mutations potentially affecting promoter sequences. Other nonsynonymous mutations mapped to a pmpG pseudogene and to predicted coding sequences encoding a putative lipoprotein, a sigma-54-dependent response regulator, a PhoH-like protein, a putative export protein, two tRNA synthetases, and a putative serine hydroxymethyltransferase. One of the intergenic mutations putatively affects transcription of two divergent genes encoding pyruvate kinase and a putative SOS response nuclease, respectively. These observations suggest that the temperature-sensitive phenotype and associated virulence attenuation of the vaccine strain result from disrupted metabolic activity due to altered pyruvate kinase expression and/or alteration in the function of one or more membrane proteins, most notably PmpG and a putative lipoprotein.
Dean, D., Bruno, W.J., Wan, R., Gomes, J.P., Devignot, S., Mehari, T., de Vries, H.J.C., Morré, S.A., Myers, G., Read, T.D. & Spratt, B.G. 2009, 'Predicting phenotype and emerging strains among Chlamydia trachomatis infections.', Emerging infectious diseases, vol. 15, no. 9, pp. 1385-1394.View/Download from: UTS OPUS or Publisher's site
Chlamydia trachomatis is a global cause of blinding trachoma and sexually transmitted infections (STIs). We used comparative genomics of the family Chlamydiaceae to select conserved housekeeping genes for C. trachomatis multilocus sequencing, characterizing 19 reference and 68 clinical isolates from 6 continental/subcontinental regions. There were 44 sequence types (ST). Identical STs for STI isolates were recovered from different regions, whereas STs for trachoma isolates were restricted by continent. Twenty-nine of 52 alleles had nonuniform distributions of frequencies across regions (p<0.001). Phylogenetic analysis showed 3 disease clusters: invasive lymphogranuloma venereum strains, globally prevalent noninvasive STI strains (ompA genotypes D/Da, E, and F), and nonprevalent STI strains with a trachoma subcluster. Recombinant strains were observed among STI clusters. Single nucleotide polymorphisms (SNPs) were predictive of disease specificity. Multilocus and SNP typing can now be used to detect diverse and emerging C. trachomatis strains for epidemiologic and evolutionary studies of trachoma and STI populations worldwide.
Heinz, E., Tischler, P., Rattei, T., Myers, G., Wagner, M. & Horn, M. 2009, 'Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae.', BMC genomics, vol. 10, p. 634.View/Download from: UTS OPUS or Publisher's site
BACKGROUND: Chlamydiae are obligate intracellular bacteria comprising some of the most important bacterial pathogens of animals and humans. Although chlamydial outer membrane proteins play a key role for attachment to and entry into host cells, only few have been described so far. We developed a comprehensive, multiphasic in silico approach, including the calculation of clusters of orthologues, to predict outer membrane proteins using conservative criteria. We tested this approach using Escherichia coli (positive control) and Bacillus subtilis (negative control), and applied it to five chlamydial species; Chlamydia trachomatis, Chlamydia muridarum, Chlamydia (a.k.a. Chlamydophila) pneumoniae, Chlamydia (a.k.a. Chlamydophila) caviae, and Protochlamydia amoebophila. RESULTS: In total, 312 chlamydial outer membrane proteins and lipoproteins in 88 orthologous clusters were identified, including 238 proteins not previously recognized to be located in the outer membrane. Analysis of their taxonomic distribution revealed an evolutionary conservation among Chlamydiae, Verrucomicrobia, Lentisphaerae and Planctomycetes as well as lifestyle-dependent conservation of the chlamydial outer membrane protein composition. CONCLUSION: This analysis suggested a correlation between the outer membrane protein composition and the host range of chlamydiae and revealed a common set of outer membrane proteins shared by these intracellular bacteria. The collection of predicted chlamydial outer membrane proteins is available at the online database pCOMP http://www.microbial-ecology.net/pcomp and might provide future guidance in the quest for anti-chlamydial vaccines.
Myers, G.S.A., Mathews, S.A., Eppinger, M., Mitchell, C., O'Brien, K.K., White, O.R., Benahmed, F., Brunham, R.C., Read, T.D., Ravel, J., Bavoil, P.M. & Timms, P. 2009, 'Evidence that human Chlamydia pneumoniae was zoonotically acquired.', Journal of bacteriology, vol. 191, no. 23, pp. 7225-7233.View/Download from: UTS OPUS or Publisher's site
Zoonotic infections are a growing threat to global health. Chlamydia pneumoniae is a major human pathogen that is widespread in human populations, causing acute respiratory disease, and has been associated with chronic disease. C. pneumoniae was first identified solely in human populations; however, its host range now includes other mammals, marsupials, amphibians, and reptiles. Australian koalas (Phascolarctos cinereus) are widely infected with two species of Chlamydia, C. pecorum and C. pneumoniae. Transmission of C. pneumoniae between animals and humans has not been reported; however, two other chlamydial species, C. psittaci and C. abortus, are known zoonotic pathogens. We have sequenced the 1,241,024-bp chromosome and a 7.5-kb cryptic chlamydial plasmid of the koala strain of C. pneumoniae (LPCoLN) using the whole-genome shotgun method. Comparative genomic analysis, including pseudogene and single-nucleotide polymorphism (SNP) distribution, and phylogenetic analysis of conserved genes and SNPs against the human isolates of C. pneumoniae show that the LPCoLN isolate is basal to human isolates. Thus, we propose based on compelling genomic and phylogenetic evidence that humans were originally infected zoonotically by an animal isolate(s) of C. pneumoniae which adapted to humans primarily through the processes of gene decay and plasmid loss, to the point where the animal reservoir is no longer required for transmission.
Ramsey, K.H., Sigar, I.M., Schripsema, J.H., Denman, C.J., Bowlin, A.K., Myers, G.A.S. & Rank, R.G. 2009, 'Strain and virulence diversity in the mouse pathogen Chlamydia muridarum.', Infection and immunity, vol. 77, no. 8, pp. 3284-3293.View/Download from: UTS OPUS or Publisher's site
The mouse chlamydial pathogen Chlamydia muridarum has been used as a model organism for the study of human Chlamydia trachomatis urogenital and respiratory tract infections. To date, two commonly used C. muridarum isolates have been used interchangeably and are essentially taken to be identical. Herein, we present data that indicate that this is not the case. The C. muridarum Weiss isolate and C. muridarum Nigg isolate varied significantly in their virulences in vivo and possessed different growth characteristics in vitro. Distinct differences were observed in intravaginal 50% infectious doses and in challenge infections, with the Weiss isolate displaying greater virulence. Respiratory infection by the intranasal route also indicated a greater virulence of the Weiss isolate. In vitro, morphometric analysis revealed that the Weiss isolate produced consistently smaller inclusions in human cervical adenocarcinoma cells (HeLa 229) and smaller plaques in monolayers of mouse fibroblasts (L929) than did the Nigg isolate. In addition, the Weiss isolate possessed significantly higher replicative yields in vitro than did the Nigg isolate. In plaque-purified isolates derived from our stocks of these two strains, total genomic sequencing identified several unique nonsynonymous single nucleotide polymorphisms and insertion/deletion mutations when our Weiss (n = 4) and Nigg (n = 5) isolates were compared with the published Nigg sequence. In addition, the two isolates shared 11 mutations compared to the published Nigg sequence. These results prove that there is genotypic and virulence diversity among C. muridarum isolates. These findings can be exploited to determine factors related to chlamydial virulence and immunity.
Stephens, R.S., Myers, G., Eppinger, M. & Bavoil, P.M. 2009, 'Divergence without difference: phylogenetics and taxonomy of Chlamydia resolved.', FEMS immunology and medical microbiology, vol. 55, no. 2, pp. 115-119.View/Download from: UTS OPUS or Publisher's site
Members of Chlamydiaceae have been extensively characterized by complete genome sequencing. This information provides new understanding concerning their natural evolutionary history. Comparative genome analysis is consistent with the conclusion that host-divergent strains of Chlamydiae are closely related biologically and ecologically. The previous taxonomic separation of the genus based on ribosomal sequences is neither consistent with the natural history of the organism revealed by genome comparisons, nor widely used by the Chlamydia research community 8 years after its introduction; thus, it is proposed to reunite the Chlamydiaceae into a single genus, Chlamydia.
Tsolis, R.M., Seshadri, R., Santos, R.L., Sangari, F.J., Lobo, J.M.G., de Jong, M.F., Ren, Q., Myers, G., Brinkac, L.M., Nelson, W.C., Deboy, R.T., Angiuoli, S., Khouri, H., Dimitrov, G., Robinson, J.R., Mulligan, S., Walker, R.L., Elzer, P.E., Hassan, K.A. & Paulsen, I.T. 2009, 'Genome degradation in Brucella ovis corresponds with narrowing of its host range and tissue tropism.', PloS one, vol. 4, no. 5, p. e5519.View/Download from: Publisher's site
Brucella ovis is a veterinary pathogen associated with epididymitis in sheep. Despite its genetic similarity to the zoonotic pathogens B. abortus, B. melitensis and B. suis, B. ovis does not cause zoonotic disease. Genomic analysis of the type strain ATCC25840 revealed a high percentage of pseudogenes and increased numbers of transposable elements compared to the zoonotic Brucella species, suggesting that genome degradation has occurred concomitant with narrowing of the host range of B. ovis. The absence of genomic island 2, encoding functions required for lipopolysaccharide biosynthesis, as well as inactivation of genes encoding urease, nutrient uptake and utilization, and outer membrane proteins may be factors contributing to the avirulence of B. ovis for humans. A 26.5 kb region of B. ovis ATCC25840 Chromosome II was absent from all the sequenced human pathogenic Brucella genomes, but was present in all of 17 B. ovis isolates tested and in three B. ceti isolates, suggesting that this DNA region may be of use for differentiating B. ovis from other Brucella spp. This is the first genomic analysis of a non-zoonotic Brucella species. The results suggest that inactivation of genes involved in nutrient acquisition and utilization, cell envelope structure and urease may have played a role in narrowing of the tissue tropism and host range of B. ovis.
Laroucau, K., Thierry, S., Vorimore, F., Blanco, K., Kaleta, E., Hoop, R., Magnino, S., Vanrompay, D., Sachse, K., Myers, G.S.A., Bavoil, P.M., Vergnaud, G. & Pourcel, C. 2008, 'High resolution typing of Chlamydophila psittaci by multilocus VNTR analysis (MLVA).', Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, vol. 8, no. 2, pp. 171-181.View/Download from: UTS OPUS or Publisher's site
A multilocus VNTR analysis (MLVA) system for detection of tandem repeats across the whole genome of Chlamydophila psittaci has been developed. Twenty selected genetic loci were initially tested on 9 avian reference strains including representatives of all major serotypes (A to F). Thereafter, 8 loci were retained for a more complete study performed on over 150 C. psittaci isolates from different bird species and geographical origins. Comparative analysis of the MLVA results and those obtained from currently available methods including serotyping and/or ompA sequencing indicate that the MLVA system provides an additional level of discrimination, with 20 distinct patterns identified to date. The newly developed MLVA system therefore provides a highly sensitive, high resolution test for the differentiation of C. psittaci isolates from different origins that is suitable for molecular epidemiological studies.
Mohamad, K.Y., Rekiki, A., Myers, G., Bavoil, P.M. & Rodolakis, A. 2008, 'Identification and characterisation of coding tandem repeat variants in incA gene of Chlamydophila pecorum', Veterinary Research, vol. 39, no. 6.View/Download from: UTS OPUS or Publisher's site
Bacteria of the family Chlamydiaceae are obligate intracellular pathogens of human and animals. Chlamydophila pecorum is associated with different pathological conditions in ruminants, swine and koala. To characterize a coding tandem repeat (CTR) identified at the 3' end of incA gene of C. pecorum, 51 strains of different chlamydial species were examined. The CTR were observed in 18 of 18 tested C. pecorum isolates including symptomatic and asymptomatic animals from diverse geographical origins. The CTR were also found in two strains of C. abortus respectively isolated from faeces from a healthy ewe and from a goat belonging to asymptomatic herds, but were absent in C. abortus strains isolated from clinical disease specimens, and in tested strains of C. psittaci, C. caviae, C. felis and C. trachomatis. The number of CTR repeats is variable and encode several motifs that are rich in alanine and proline. The CTR-derived variable structure of incA, which encode the Chlamydiaceae-specific type III secreted inclusion membrane protein, IncA, may be involved in the adaptation of C. pecorum to its environment by allowing it to persist in the host cell. © 2008 INRA EDP Sciences.
Rasko, D.A., Rosovitz, M.J., Myers, G.S.A., Mongodin, E.F., Fricke, W.F., Gajer, P., Crabtree, J., Sebaihia, M., Thomson, N.R., Chaudhuri, R., Henderson, I.R., Sperandio, V. & Ravel, J. 2008, 'The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates.', Journal of bacteriology, vol. 190, no. 20, pp. 6881-6893.View/Download from: UTS OPUS or Publisher's site
Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of approximately 2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.
Yousef Mohamad, K., Rekiki, A., Myers, G., Bavoil, P.M. & Rodolakis, A. 2008, 'Identification and characterisation of coding tandem repeat variants in incA gene of Chlamydophila pecorum.', Veterinary research, vol. 39, no. 6, p. 56.View/Download from: Publisher's site
Bacteria of the family Chlamydiaceae are obligate intracellular pathogens of human and animals. Chlamydophila pecorum is associated with different pathological conditions in ruminants, swine and koala. To characterize a coding tandem repeat (CTR) identified at the 3' end of incA gene of C. pecorum, 51 strains of different chlamydial species were examined. The CTR were observed in 18 of 18 tested C. pecorum isolates including symptomatic and asymptomatic animals from diverse geographical origins. The CTR were also found in two strains of C. abortus respectively isolated from faeces from a healthy ewe and from a goat belonging to asymptomatic herds, but were absent in C. abortus strains isolated from clinical disease specimens, and in tested strains of C. psittaci, C. caviae, C. felis and C. trachomatis. The number of CTR repeats is variable and encode several motifs that are rich in alanine and proline. The CTR-derived variable structure of incA, which encode the Chlamydiaceae-specific type III secreted inclusion membrane protein, IncA, may be involved in the adaptation of C. pecorum to its environment by allowing it to persist in the host cell.
Yousef Mohamad, K., Roche, S.M., Myers, G., Bavoil, P.M., Laroucau, K., Magnino, S., Laurent, S., Rasschaert, D. & Rodolakis, A. 2008, 'Preliminary phylogenetic identification of virulent Chlamydophila pecorum strains.', Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, vol. 8, no. 6, pp. 764-771.View/Download from: UTS OPUS or Publisher's site
Chlamydophila pecorum is an obligate intracellular bacterium associated with different pathological conditions in ruminants, swine and koala, which is also found in the intestine of asymptomatic animals. A multi-virulence locus sequence typing (MVLST) system was developed using 19 C. pecorum strains (8 pathogenic and 11 non-pathogenic intestinal strains) isolated from ruminants of different geographical origins. To evaluate the ability of MVLST to distinguish the pathogenic from the non-pathogenic strains of C. pecorum, the sequences of 12 genes were analysed: 6 potential virulence genes (ompA, incA, incB, incC, mip and copN), 5 housekeeping genes (recA, hemD, aroC, efp, gap), and the ORF663 gene encoding a hypothetical protein (HP) that includes a variant 15-nucleotides coding tandem repeat (CTR). MVLST provided high discriminatory power (100%) in allowing to distinguish 6 of 8 pathogenic strains in a single group, and overall more discriminatory than MLST targeting housekeeping genes. ompA was the most polymorphic gene and the phylogenetic tree based only on its sequence differentiated 4 groups with high bootstrap values. The number of CTRs (rich in serine, proline and lysine) in ORF663 detected in the pathogenic strains was generally lower than that found in the intestinal strains. MVLST appears to be a promising method for the differential identification of virulent C. pecorum strains, and the ompA, incA and ORF663 genes appear to be good molecular markers for further epidemiological investigation of C. pecorum.
Liu, Z., Rank, R., Kaltenboeck, B., Magnino, S., Dean, D., Burall, L., Plaut, R.D., Read, T.D., Myers, G. & Bavoil, P.M. 2007, 'Genomic plasticity of the rrn-nqrF intergenic segment in the Chlamydiaceae.', Journal of bacteriology, vol. 189, no. 5, pp. 2128-2132.View/Download from: UTS OPUS or Publisher's site
In Chlamydiaceae, the nucleotide sequence between the 5S rRNA gene and the gene for subunit F of the Na(+)-translocating NADH-quinone reductase (nqrF or dmpP) has varied lengths and gene contents. We analyzed this site in 45 Chlamydiaceae strains having diverse geographical and pathological origins and including members of all nine species.
Myers, G.S.A., Parker, D., Al-Hasani, K., Kennan, R.M., Seemann, T., Ren, Q., Badger, J.H., Selengut, J.D., Deboy, R.T., Tettelin, H., Boyce, J.D., McCarl, V.P., Han, X., Nelson, W.C., Madupu, R., Mohamoud, Y., Holley, T., Fedorova, N., Khouri, H., Bottomley, S.P., Whittington, R.J., Adler, B., Songer, J.G., Rood, J.I. & Paulsen, I.T. 2007, 'Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.', Nature biotechnology, vol. 25, no. 5, pp. 569-575.View/Download from: UTS OPUS or Publisher's site
Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine.
Peters, J., Wilson, D.P., Myers, G., Timms, P. & Bavoil, P.M. 2007, 'Type III secretion à la Chlamydia.', Trends in microbiology, vol. 15, no. 6, pp. 241-251.View/Download from: UTS OPUS or Publisher's site
Type III secretion (T3S) is a mechanism that is central to the biology of the Chlamydiaceae and many other pathogens whose virulence depends on the translocation of toxic effector proteins to cytosolic targets within infected eukaryotic cells. Biomathematical simulations, using a previously described model of contact-dependent, T3S-mediated chlamydial growth and late differentiation, suggest that chlamydiae contained in small non-fusogenic inclusions will persist. Here, we further discuss the model in the context of in vitro-persistent, stress-induced aberrantly enlarged forms and of recent studies using small molecule inhibitors of T3S. A general mechanism is emerging whereby both early- and mid-cycle T3S-mediated activities and late T3S inactivation upon detachment of chlamydiae from the inclusion membrane are crucial for chlamydial intracellular development.
Ding, X.Z., Paulsen, I.T., Bhattacharjee, A.K., Nikolich, M.P., Myers, G. & Hoover, D.L. 2006, 'A high efficiency cloning and expression system for proteomic analysis.', Proteomics, vol. 6, no. 14, pp. 4038-4046.View/Download from: Publisher's site
The recent description of the complete genomes of the two most pathogenic species of Brucella opens the way for genome-based analysis of the antigenicity of their proteins. In the present report, we describe a bench-level high-efficiency cloning and expression system (HECES) that allow expression of large numbers of Brucella proteins based on genomic sequence information. Purified proteins are produced with high efficiency in a microarray format conducive to analysis of their sero-reactivity against serum from immunized animals. This method is applicable at either small or large scale of protein processing. While it does not require robotics, the format is amenable to robotic implementation for all aspects of the process and subsequent analysis of protein characteristics. This method will allow selection of new reagents for diagnosis of brucellosis and development of vaccine against Brucella, an important zoonotic disease and biothreat agent.
Myers, G.S.A., Rasko, D.A., Cheung, J.K., Ravel, J., Seshadri, R., DeBoy, R.T., Ren, Q., Varga, J., Awad, M.M., Brinkac, L.M., Daugherty, S.C., Haft, D.H., Dodson, R.J., Madupu, R., Nelson, W.C., Rosovitz, M.J., Sullivan, S.A., Khouri, H., Dimitrov, G.I., Watkins, K.L., Mulligan, S., Benton, J., Radune, D., Fisher, D.J., Atkins, H.S., Hiscox, T., Jost, B.H., Billington, S.J., Songer, J.G., McClane, B.A., Titball, R.W., Rood, J.I., Melville, S.B. & Paulsen, I.T. 2006, 'Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens.', Genome research, vol. 16, no. 8, pp. 1031-1040.View/Download from: UTS OPUS or Publisher's site
Clostridium perfringens is a Gram-positive, anaerobic spore-forming bacterium commonly found in soil, sediments, and the human gastrointestinal tract. C. perfringens is responsible for a wide spectrum of disease, including food poisoning, gas gangrene (clostridial myonecrosis), enteritis necroticans, and non-foodborne gastrointestinal infections. The complete genome sequences of Clostridium perfringens strain ATCC 13124, a gas gangrene isolate and the species type strain, and the enterotoxin-producing food poisoning strain SM101, were determined and compared with the published C. perfringens strain 13 genome. Comparison of the three genomes revealed considerable genomic diversity with >300 unique "genomic islands" identified, with the majority of these islands unusually clustered on one replichore. PCR-based analysis indicated that the large genomic islands are widely variable across a large collection of C. perfringens strains. These islands encode genes that correlate to differences in virulence and phenotypic characteristics of these strains. Significant differences between the strains include numerous novel mobile elements and genes encoding metabolic capabilities, strain-specific extracellular polysaccharide capsule, sporulation factors, toxins, and other secreted enzymes, providing substantial insight into this medically important bacterial pathogen.
Palenik, B., Ren, Q., Dupont, C.L., Myers, G.S., Heidelberg, J.F., Badger, J.H., Madupu, R., Nelson, W.C., Brinkac, L.M., Dodson, R.J., Durkin, A.S., Daugherty, S.C., Sullivan, S.A., Khouri, H., Mohamoud, Y., Halpin, R. & Paulsen, I.T. 2006, 'Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 103, no. 36, pp. 13555-13559.View/Download from: UTS OPUS or Publisher's site
Parker, D., Kennan, R.M., Myers, G.S., Paulsen, I.T., Songer, J.G. & Rood, J.I. 2006, 'Regulation of type IV fimbrial biogenesis in Dichelobacter nodosus', JOURNAL OF BACTERIOLOGY, vol. 188, no. 13, pp. 4801-4811.View/Download from: UTS OPUS or Publisher's site
Paulsen, I.T., Press, C.M., Ravel, J., Kobayashi, D.Y., Myers, G.S.A., Mavrodi, D.V., DeBoy, R.T., Seshadri, R., Ren, Q., Madupu, R., Dodson, R.J., Durkin, A.S., Brinkac, L.M., Daugherty, S.C., Sullivan, S.A., Rosovitz, M.J., Gwinn, M.L., Zhou, L., Schneider, D.J., Cartinhour, S.W., Nelson, W.C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E.A., Pierson, L.S., Thomashow, L.S. & Loper, J.E. 2006, 'Erratum: Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5 (Nature Biotechnology (2005) 23 (873-878))', Nature Biotechnology, vol. 24, no. 4, p. 466.View/Download from: Publisher's site
Ding, X.Z., Bhattacharjee, A., Nikolich, M.P., Paulsen, I.T., Myers, G., Seshadri, R. & L Hoover, D. 2005, 'Cloning, expression, and purification of Brucella suis outer membrane proteins.', Protein expression and purification, vol. 40, no. 1, pp. 134-141.View/Download from: UTS OPUS or Publisher's site
Brucella, an aerobic, nonsporeforming, nonmotile Gram-negative coccobacillus, is a NIH/CDC category B bioterror threat agent that causes incapacitating human illness. Medical defense against the bioterror threat posed by Brucella would be strengthened by development of a human vaccine and improved diagnostic tests. Central to advancement of these goals is discovery of bacterial constituents that are immunogenic or antigenic for humans. Outer membrane proteins (OMPs) are particularly attractive for this purpose. In this study, we cloned, expressed, and purified seven predicted OMPs of Brucella suis. The recombinant proteins were fused with 6-His and V5 epitope tags at their C termini to facilitate detection and purification. The B. suis surface genes were PCR synthesized based on their ORF sequences and directly cloned into an entry vector. The recombinant entry constructs were propagated in TOP 10 cells, recombined into a destination vector, pET-DEST42, then transformed into Escherichia coli BL21 cells for IPTG-induced protein expression. The expressed recombinant proteins were confirmed with Western blot analysis using anti-6-His antibody conjugated with alkaline phosphatase. These B. suis OMPs were captured and purified using a HisGrab plate. The purified recombinant proteins were examined for their binding activity with antiserum. Serum derived from a rabbit immunized intramuscularly with dialyzed cell lysate of Brucella rough mutant WRR51. The OMPs were screened using the rabbit antiserum and purified IgG. The results suggested that recombinant B. suis OMPs were successfully cloned, expressed and purified. Some of the expressed OMPs showed high binding activity with immunized rabbit antiserum.
Parker, D., Kennan, R.A., Myers, G.S., Paulsen, I.T. & Rood, J.I. 2005, 'Identification of a Dichelobacter nodosus ferric uptake regulator and determination of its regulatory targets', JOURNAL OF BACTERIOLOGY, vol. 187, no. 1, pp. 366-375.View/Download from: UTS OPUS or Publisher's site
Paulsen, I.T., Press, C.M., Ravel, J., Kobayashi, D.Y., Myers, G.S.A., Mavrodi, D.V., DeBoy, R.T., Seshadri, R., Ren, Q., Madupu, R., Dodson, R.J., Durkin, A.S., Brinkac, L.M., Daugherty, S.C., Sullivan, S.A., Rosovitz, M.J., Gwinn, M.L., Zhou, L., Schneider, D.J., Cartinhour, S.W., Nelson, W.C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E.A., Pierson, L.S., Thomashow, L.S. & Loper, J.E. 2005, 'Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5.', Nature biotechnology, vol. 23, no. 7, pp. 873-878.View/Download from: UTS OPUS or Publisher's site
Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.
The first microbial genome sequence, Haemophilus influenzae, was published in 1995. Since then, more than 400 microbial genome sequences have been completed or commenced. This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis.The BLAST Score Ratio (BSR) approach, implemented in a Perl script, classifies all putative peptides within three genomes using a measure of similarity based on the ratio of BLAST scores. The output of the BSR analysis enables global visualization of the degree of proteome similarity between all three genomes. Additional output enables the genomic synteny (conserved gene order) between each genome pair to be assessed. Furthermore, we extend this synteny analysis by overlaying BSR data as a color dimension, enabling visualization of the degree of similarity of the peptides being compared.Combining the degree of similarity, synteny and annotation will allow rapid identification of conserved genomic regions as well as a number of common genomic rearrangements such as insertions, deletions and inversions. The script and example visualizations are available at: http://www.microbialgenomics.org/BSR/.
Myers, G.S.A. & Fraser, C.M. 2004, 'Non-pathogenic bacteria take center stage: a lesson in contrasts.', Trends in microbiology, vol. 12, no. 7, pp. 303-305.View/Download from: UTS OPUS or Publisher's site
Seshadri, R., Myers, G.S.A., Tettelin, H., Eisen, J.A., Heidelberg, J.F., Dodson, R.J., Davidsen, T.M., DeBoy, R.T., Fouts, D.E., Haft, D.H., Selengut, J., Ren, Q., Brinkac, L.M., Madupu, R., Kolonay, J., Durkin, S.A., Daugherty, S.C., Shetty, J., Shvartsbeyn, A., Gebregeorgis, E., Geer, K., Tsegaye, G., Malek, J., Ayodeji, B., Shatsman, S., McLeod, M.P., Smajs, D., Howell, J.K., Pal, S., Amin, A., Vashisth, P., McNeill, T.Z., Xiang, Q., Sodergren, E., Baca, E., Weinstock, G.M., Norris, S.J., Fraser, C.M. & Paulsen, I.T. 2004, 'Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes.', Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 15, pp. 5646-5651.View/Download from: UTS OPUS or Publisher's site
We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function.
Paulsen, I.T., Banerjei, L., Myers, G.S., Nelson, K.E., Seshadri, R., Read, T.D., Fouts, D.E., Eisen, J.A., Gill, S.R., Heidelberg, J.F., Tettelin, H., Dodson, R.J., Umayam, L., Brinkac, L., Beanan, M., Daugherty, S., DeBoy, R.T., Durkin, S., Kolonay, J., Madupu, R., Nelson, W., Vamathevan, J., Tran, B., Upton, J., Hansen, T., Shetty, J., Khouri, H., Utterback, T., Radune, D., Ketchum, K.A., Dougherty, B.A. & Fraser, C.M. 2003, 'Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.', Science (New York, N.Y.), vol. 299, no. 5615, pp. 2071-2074.View/Download from: UTS OPUS or Publisher's site
The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.
Read, T.D., Myers, G.S.A., Brunham, R.C., Nelson, W.C., Paulsen, I.T., Heidelberg, J., Holtzapple, E., Khouri, H., Federova, N.B., Carty, H.A., Umayam, L.A., Haft, D.H., Peterson, J., Beanan, M.J., White, O., Salzberg, S.L., Hsia, R.-.C., McClarty, G., Rank, R.G., Bavoil, P.M. & Fraser, C.M. 2003, 'Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae.', Nucleic acids research, vol. 31, no. 8, pp. 2134-2147.View/Download from: UTS OPUS or Publisher's site
The genome of Chlamydophila caviae (formerly Chlamydia psittaci, GPIC isolate) (1 173 390 nt with a plasmid of 7966 nt) was determined, representing the fourth species with a complete genome sequence from the Chlamydiaceae family of obligate intracellular bacterial pathogens. Of 1009 annotated genes, 798 were conserved in all three other completed Chlamydiaceae genomes. The C.caviae genome contains 68 genes that lack orthologs in any other completed chlamydial genomes, including tryptophan and thiamine biosynthesis determinants and a ribose-phosphate pyrophosphokinase, the product of the prsA gene. Notable amongst these was a novel member of the virulence-associated invasin/intimin family (IIF) of Gram-negative bacteria. Intriguingly, two authentic frameshift mutations in the ORF indicate that this gene is not functional. Many of the unique genes are found in the replication termination region (RTR or plasticity zone), an area of frequent symmetrical inversion events around the replication terminus shown to be a hotspot for genome variation in previous genome sequencing studies. In C.caviae, the RTR includes several loci of particular interest including a large toxin gene and evidence of ancestral insertion(s) of a bacteriophage. This toxin gene, not present in Chlamydia pneumoniae, is a member of the YopT effector family of type III-secreted cysteine proteases. One gene cluster (guaBA-add) in the RTR is much more similar to orthologs in Chlamydia muridarum than those in the phylogenetically closest species C.pneumoniae, suggesting the possibility of horizontal transfer of genes between the rodent-associated Chlamydiae. With most genes observed in the other chlamydial genomes represented, C.caviae provides a good model for the Chlamydiaceae and a point of comparison against the human atherosclerosis-associated C.pneumoniae. This crucial addition to the set of completed Chlamydiaceae genome sequences is enabling dissection of the roles played by niche-specific gen...
Myers, G.S., Grinvalds, R., Booth, S., Hutton, S.I., Binks, M., Kemp, D.J. & Sriprakash, K.S. 2000, 'Expression of two novel proteins in Chlamydia trachomatis during natural infection.', Microbial pathogenesis, vol. 29, no. 2, pp. 63-72.View/Download from: UTS OPUS or Publisher's site
Genes for a putative membrane associated protein (mvi -homologue) and a 48 kDa protein (ctr48) in Chlamydia trachomatis were characterized. The mvi -homologue has 12 transmembrane domains and shows considerable homology to the members of this gene family in various organisms. The ctr48 has a leader sequence and the C-proximal half is tryptophan-rich. The latter region shares 65% identity with the N-proxima third of C. pneumoniae 76 kDa protein over an overlap of 231 amino acid residues. The genes for the mvi -homologue and the ctr48 are present in the B, Ba, D, E, J and L2 serotypes of C. trachomatis. Immediately downstream from the ctr48 gene are multiple stop codons which are followed by a functional rho-independent terminator. The mvi -homologue and ctr48 genes are independently transcribed, albeit poorly in serotype B. However, protein products corresponding to these genes could not be detected by western blotting in HEp2 cells infected with C. trachomatis. Nevertheless, antibodies to peptides corresponding to these proteins were detected in sera with high micro-immunofluorescence titre against C. trachoImatic, collected from a Chlamydia -endemic population. These results suggest that the mvi -homologue and ctr48 are expressed by C. trachomatis during natural infection.
Carter, J.S., Bowden, F.J., Bastian, I., Myers, G.M., Sriprakash, K.S. & Kemp, D.J. 1999, 'Phylogenetic evidence for reclassification of Calymmatobacterium granulomatis as Klebsiella granulomatis comb. nov.', International journal of systematic bacteriology, vol. 49 Pt 4, pp. 1695-1700.View/Download from: Publisher's site
By sequencing a total of 2089 bp of the 16S rRNA and phoE genes it was demonstrated that Calymmatobacterium granulomatis (the causative organism of donovanosis) shows a high level of identity with Klebsiella species pathogenic to humans (Klebsiella pneumoniae, Klebsiella rhinoscleromatis). It is proposed that C. granulomatis should be reclassified as Klebsiella granulomatis comb. nov. An emended description of the genus Klebsiella is given.
Holt, D.C., Gardiner, D.L., Thomas, E.A., Mayo, M., Bourke, P.F., Sutherland, C.J., Carter, R., Myers, G., Kemp, D.J. & Trenholme, K.R. 1999, 'The cytoadherence linked asexual gene family of Plasmodium falciparum: are there roles other than cytoadherence?', International journal for parasitology, pp. 939-944.View/Download from: Publisher's site
The binding of erythrocytes infected with Plasmodium falciparum to the endothelium lining the small blood vessels of the brain and other organs can mediate severe pathology. A region at the right end of chromosome 9 has been implicated in the binding of parasitised erythrocytes to the endothelial receptor CD36. A gene expressed in asexual erythrocytic stage parasites has been identified in this region and termed the cytoadherence linked asexual gene (clag). Antisense RNA production and targeted gene disruption of clag resulted in greatly reduced binding to CD36. Hybridisation to 3D7 chromosomes showed clag to be a part of a gene family of at least nine members. All members analysed so far have a conserved gene structure of at least nine exons, as well as putative transmembrane domains. The possible functions of the gene family are discussed.