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. He is now the Director of the Institute, and leads the "Biology of Intracellular Bacteria" research group.
- Fellow, Australian Society of Microbiology
Can supervise: YES
My research program is focused upon intracellular microbial biology; intracellular bacteria are often recalcitrant to axenic culture and most genetic manipulation, which makes them difficult to study. I instead develop and/or apply genome-scale approaches to decipher their biology. This began with whole genome shotgun sequencing (WGSS) and phylogenomic/comparative genome analyses at TIGR, where WGSS was pioneered. Now my interests in intracellular biology span environmental, commensal, and pathogenic (agricultural, veterinary and human) bacteria, incorporating WGSS, transcriptomics, and the development and use of dual RNA-Seq, to super-resolution microscopy of intracellular bacteria, investigating the epigenomic impacts of intracellular bacteria on their host cells, and the application of single cell transcriptomics to bacteria-infected cells and tissues. My group has particular emphasis on the obligate intracellular bacteria within the Order Chlamydiales, including increasingly discovered non-pathogenic Chlamydia-like bacteria that reside within protozoans and other “simple” multi-cellular organisms in many environments, as well as the more familiar agents of animal, human and zoonotic disease. This body of work has led to publications in high impact journals, including Science, Nature Biotechnology, Proceedings of the National Academy of Sciences USA, Nucleic Acids Research, Journal of Bacteriology, and Genome Research.
- Program Director, Bachelor of Advanced Science (Infection and Immunity)
- Program Director, Masters of Biotechnology (BIoinformatics, in development)
Aili, SR, Touchard, A, Hayward, R, Robinson, SD, Pineda, SS, Lalague, H, Mrinalini, Vetter, I, Undheim, EAB, Kini, RM, Escoubas, P, Padula, MP, Myers, GSA & Nicholson, GM 2020, 'An Integrated Proteomic and Transcriptomic Analysis Reveals the Venom Complexity of the Bullet AntParaponera clavata', TOXINS, vol. 12, no. 5.View/Download from: Publisher's site
Hastak, P, Fourment, M, Darling, AE, Gottlieb, T, Cheong, E, Merlino, J, Myers, GSA, Djordjevic, SP & Chowdhury, PR 2020, 'Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex', Emerging Microbes and Infections, pp. 1-35.View/Download from: Publisher's site
© 2020, © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Shanghai Shangyixun Cultural Communication Co., Ltd. The H30Rx subclade of Escherichia coli ST131 is a clinically important, globally dispersed extra-pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum ß-lactams. Here we describe isolates EC233 and EC234, both variants of ST131-H30Rx with a novel sequence type (ST) 8196, from unrelated patients presenting with bacteraemia at Concord Repatriation Hospital in Sydney in 2014. EC233 and EC234 are phylogroup B2, serotype O25:H4A, resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both isolates carry an IncFII_2 plasmid similar to pSPRC_Ec234-FII (85,199 bp characterised in EC234), two small plasmids and a novel IncI1 plasmid similar to pSPRC_Ec234-I (92,955 bp characterised in EC234). Apart from a chromosomally located bla CTX-M-15 module, the resistance genes are flanked by IS26 and form a complex resistance locus (CRL) on pSPRC_Ec234-FII. SNP-based phylogenetic analysis of the core genome of all ST representatives within the ST131 clonal complex places both isolates in a small subclade with 3 other clinical Australian ST131-H30Rx clade C isolates. MrBayes phylogeny analysis of ST8196 using a global collection of ST131 genomes indicated EC233 and EC234 share a most recent common ancestor with EC70, a MDR ST131-H30Rx clone, isolated from the same Sydney hospital in 2013. Our study identified genomic hallmarks that define the ST131-H30Rx subclade in both the ST8196 isolates and highlights the requirement for unbiased genomic surveillance approaches to identify and track novel high-risk MDR E. coli pathogens that impact healthcare facilities.
Hastak, P, Cummins, ML, Gottlieb, T, Cheong, E, Merlino, J, Myers, GSA, Djordjevic, SP & Chowdhury, PR 2020, 'Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital', MICROBIAL GENOMICS, vol. 6, no. 5.View/Download from: Publisher's site
Hayward, RJ, Marsh, JW, Humphrys, MS, Huston, WM & Myers, GSA 2019, 'Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution.', Frontiers in cellular and infection microbiology, vol. 9.View/Download from: Publisher's site
Chlamydia are Gram-negative obligate intracellular bacterial pathogens responsible for a variety of disease in humans and animals worldwide. Chlamydia trachomatis causes trachoma in disadvantaged populations, and is the most common bacterial sexually transmitted infection in humans, causing reproductive tract disease. Antibiotic therapy successfully treats diagnosed chlamydial infections, however asymptomatic infections are common. High-throughput transcriptomic approaches have explored chlamydial gene expression and infected host cell gene expression. However, these were performed on large cell populations, averaging gene expression profiles across all cells sampled and potentially obscuring biologically relevant subsets of cells. We generated a pilot dataset, applying single cell RNA-Seq (scRNA-Seq) to C. trachomatis infected and mock-infected epithelial cells to assess the utility, pitfalls and challenges of single cell approaches applied to chlamydial biology, and to potentially identify early host cell biomarkers of chlamydial infection. Two hundred sixty-four time-matched C. trachomatis-infected and mock-infected HEp-2 cells were collected and subjected to scRNA-Seq. After quality control, 200 cells were retained for analysis. Two distinct clusters distinguished 3-h cells from 6- and 12-h. Pseudotime analysis identified a possible infection-specific cellular trajectory for Chlamydia-infected cells, while differential expression analyses found temporal expression of metallothioneins and genes involved with cell cycle regulation, innate immune responses, cytoskeletal components, lipid biosynthesis and cellular stress. We find that changes to the host cell transcriptome at early times of C. trachomatis infection are readily discernible by scRNA-Seq, supporting the utility of single cell approaches to identify host cell biomarkers of chlamydial infection, and to further deconvolute the complex host response to infection.
Marsh, JW, Hayward, RJ, Shetty, A, Mahurkar, A, Humphrys, MS & Myers, GSA 2019, 'Dual RNA-Seq of Chlamydia and Host Cells.', Methods in Molecular Biology, vol. 2042, pp. 123-135.View/Download from: Publisher's site
During the infection of a host cell by a bacterial pathogen, a cascading series of gene expression changes occurs as each organism manipulates or responds to the other via defense or survival strategies. Unraveling this complex interplay is key for our understanding of bacterial virulence and host response pathways for the development of novel therapeutics. Dual RNA sequencing (dual RNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. Leveraging the sensitivity and resolution allowed by RNA-seq, dual RNA-Seq can be applied to any bacteria-eukaryotic host interaction. We pioneered dual RNA-Seq to simultaneously capture Chlamydia and host expression profiles during an in vitro infection as proof of principle. Here we provide a detailed laboratory protocol and bioinformatics analysis guidelines for dual RNA-seq experiments focusing on Chlamydia as the organism of interest.
De Puysseleyr, K, Kieckens, E, De Puysseleyr, L, Van den Wyngaert, H, Ahmed, B, Van Lent, S, Creasy, HH, Myers, GSA & 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: 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.
Marsh, JW, Hayward, R, Shetty, A, Mahurkar, A, Humphreys, M & Myers, G 2018, 'Dual RNA sequencing (dRNA-Seq) of bacteria and their host cells', Briefings in Bioinformatics, vol. 19, no. 6, pp. 1115-1129.View/Download from: Publisher's site
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, JW, Hayward, RJ, Shetty, AC, Mahurkar, A, Humphrys, MS & Myers, GSA 2018, 'Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments', Briefings in Bioinformatics, vol. 19, no. 6, pp. 1115-1129.View/Download from: Publisher's site
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 sequencing technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. Several laboratory protocols have been presented that outline the collection, extraction and sequencing of total RNA for dRNA-Seq experiments, but there is relatively little guidance available for the detailed bioinformatic analyses required. This protocol outlines a typical dRNA-Seq experiment, based on a Chlamydia trachomatis-infected host cell, with a detailed description of the necessary bioinformatic analyses with currently available software tools
Wee, BA, Thomas, M, Sweeney, EL, Frentiu, FD, Samios, M, Ravel, J, Gajer, P, Myers, G, Timms, P, Allan, JA & Huston, WM 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), vol. 58.View/Download from: 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, JW, Humphrys, MS & Myers, GSA 2017, 'A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro', Frontiers in Microbiology, vol. 8.View/Download from: Publisher's site
Branley, J, Bachmann, NL, Jelocnik, M, Myers, GSA & 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.View/Download from: Publisher's site
Van Lent, S, Creasy, HH, Myers, GSA & 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: 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, NL, Sullivan, MJ, Jelocnik, M, Myers, GSA, 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: Publisher's site
Jelocnik, M, Bachmann, NL, Kaltenboeck, B, Waugh, C, Woolford, L, Speight, KN, Gillett, A, Higgins, DP, Flanagan, C, Myers, GSA, 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.View/Download from: Publisher's site
Neuendorf, E, Gajer, P, Bowlin, AK, Marques, PX, Ma, B, Yang, H, Fu, L, Humphrys, MS, Forney, LJ, Myers, GS, Bavoil, PM, Rank, RG & 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: 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: 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, NL, Myers, GSA, 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: Publisher's site
Bachmann, NL, Fraser, TA, Bertelli, C, Jelocnik, M, Gillett, A, Funnell, O, Flanagan, C, Myers, GSA, 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: 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, GS, Rasko, DA & White, O 2014, 'Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG', BIOINFORMATICS, vol. 30, no. 21, pp. 3125-3127.View/Download from: Publisher's site
Donati, M, Huot-Creasy, H, Humphrys, M, Di Paolo, M, Di Francesco, A & Myers, GSA 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: 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, VG, Emrich, SJ, Giraldo-Calderón, GI, Harb, OS, Newman, RM, Pickett, BE, Schriml, LM, Stockwell, TB, Stoeckert, CJ, Sullivan, DE, Singh, I, Ward, DV, Yao, A, Zheng, J, Barrett, T, Birren, B, Brinkac, L, Bruno, VM, Caler, E, Chapman, S, Collins, FH, Cuomo, CA, Di Francesco, V, Durkin, S, Eppinger, M, Feldgarden, M, Fraser, C, Fricke, WF, Giovanni, M, Henn, MR, Hine, E, Hotopp, JD, Karsch-Mizrachi, I, Kissinger, JC, Lee, EM, Mathur, P, Mongodin, EF, Murphy, CI, Myers, G, Neafsey, DE, Nelson, KE, Nierman, WC, Puzak, J, Rasko, D, Roos, DS, Sadzewicz, L, Silva, JC, Sobral, B, Squires, RB, Stevens, RL, Tallon, L, Tettelin, H, Wentworth, D, White, O, Will, R, Wortman, J, Zhang, Y & Scheuermann, RH 2014, 'Standardized metadata for human pathogen/vector genomic sequences.', PLoS ONE, vol. 9, no. 6, pp. 1-11.View/Download from: 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, HH, Weidmann, M, Myers, G, Vorimore, F, Vicari, N, Magnino, S, Liebler-Tenorio, E, Ruettger, A, Bavoil, PM, Hufert, FT, Rossello-Mora, 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: Publisher's site
Sait, M, Livingstone, M, Clark, EM, Wheelhouse, N, Spalding, L, Markey, B, Magnino, S, Lainson, FA, Myers, GSA & 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: 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, GSA, Spencer, N, Creasy, HH, Adams, NE, Maurelli, AT, McChesney, GR, Cleves, MA, Ravel, J, Bowlin, A & Rank, RG 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: 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-α), 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, JC, Goicochea, M, Nadai, Y, Eyzaguirre, LM, Carr, JK, Tallon, LJ, Sadzewicz, L, Myers, G, Fraser, CM, Su, Q, Djavani, M, Lukashevich, IS & Salvato, MS 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: Publisher's site
Hovis, KM, Mojica, S, McDermott, JE, Pedersen, L, Simhi, C, Rank, RG, Myers, GSA, Ravel, J, Hsia, R-C & Bavoil, PM 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: Publisher's site
Humphrys, MS, Creasy, T, Sun, Y, Shetty, AC, Chibucos, MC, Drabek, EF, Fraser, CM, Farooq, U, Sengamalay, N, Ott, S, Shou, H, Bavoil, PM, Mahurkar, A & Myers, GSA 2013, 'Simultaneous transcriptional profiling of bacteria and their host cells.', PLoS ONE, vol. 8, no. 12, pp. 1-13.View/Download from: 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.View/Download from: Publisher's site
Van Lent, S, Piet, JR, 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: Publisher's site
Collingro, A, Tischler, P, Weinmaier, T, Penz, T, Heinz, E, Brunham, RC, Read, TD, Bavoil, PM, Sachse, K, Kahane, S, Friedman, MG, Rattei, T, Myers, GSA & 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: Publisher's site
Grinblat-Huse, V, Drabek, EF, Creasy, HH, Daugherty, SC, Jones, KM, Santana-Cruz, I, Tallon, LJ, Read, TD, Hatch, TP, Bavoil, P & Myers, GSA 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: Publisher's site
Mojica, S, Creasy, HH, Daugherty, S, Read, TD, Kim, T, Kaltenboeck, B, Bavoil, P & Myers, GSA 2011, 'Genome Sequence of the Obligate Intracellular Animal Pathogen Chlamydia pecorum E58', JOURNAL OF BACTERIOLOGY, vol. 193, no. 14, pp. 3690-3690.View/Download from: Publisher's site
Mitchell, CM, Hovis, KM, Bavoil, PM, Myers, GSA, Carrasco, JA & Timms, P 2010, 'Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species', BMC GENOMICS, vol. 11.View/Download from: Publisher's site
Mitchell, CM, Hutton, S, Myers, GSA, 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.View/Download from: Publisher's site
Burall, LS, Rodolakis, A, Rekiki, A, Myers, GSA & Bavoil, PM 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: Publisher's site
Dean, D, Bruno, WJ, Wan, R, Gomes, JP, Devignot, S, Mehari, T, de Vries, HJC, Morre, SA, Myers, G, Read, TD & Spratt, BG 2009, 'Predicting Phenotype and Emerging Strains among Chlamydia trachomatis Infections', EMERGING INFECTIOUS DISEASES, vol. 15, no. 9, pp. 1385-1394.View/Download from: Publisher's site
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.View/Download from: 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. © 2009 Heinz et al; licensee BioMed Central Ltd.
Myers, GSA, Mathews, SA, Eppinger, M, Mitchell, C, O'Brien, KK, White, OR, Benahmed, F, Brunham, RC, Read, TD, Ravel, J, Bavoil, PM & Timms, P 2009, 'Evidence that Human Chlamydia pneumoniae Was Zoonotically Acquired', JOURNAL OF BACTERIOLOGY, vol. 191, no. 23, pp. 7225-7233.View/Download from: Publisher's site
Ramsey, KH, Sigar, IM, Schripsema, JH, Denman, CJ, Bowlin, AK, Myers, GAS & Rank, RG 2009, 'Strain and Virulence Diversity in the Mouse Pathogen Chlamydia muridarum', INFECTION AND IMMUNITY, vol. 77, no. 8, pp. 3284-3293.View/Download from: Publisher's site
Stephens, RS, Myers, G, Eppinger, M & Bavoil, PM 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: Publisher's site
Tsolis, RM, Seshadri, R, Santos, RL, Sangari, FJ, Garcia Lobo, JM, de Jong, MF, Ren, Q, Myers, G, Brinkac, LM, Nelson, WC, DeBoy, RT, Angiuoli, S, Khouri, H, Dimitrov, G, Robinson, JR, Mulligan, S, Walker, RL, Elzer, PE, Hassan, KA & Paulsen, IT 2009, 'Genome Degradation in Brucella ovis Corresponds with Narrowing of Its Host Range and Tissue Tropism', PLOS ONE, vol. 4, no. 5.View/Download from: Publisher's site
Laroucau, K, Thierry, S, Vorimore, F, Blanco, K, Kaleta, E, Hoop, R, Magnino, S, Vanrompay, D, Sachse, K, Myers, GSA, Bavoil, PM, Vergnaud, G & Pourcel, C 2008, 'High resolution typing of Chlamydophila psittaci by multilocus VNTR analysis (MLVA)', INFECTION GENETICS AND EVOLUTION, vol. 8, no. 2, pp. 171-181.View/Download from: Publisher's site
Mohamad, KY, Rekiki, A, Myers, G, Bavoil, PM & 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: 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.
Mohamad, KY, Roche, SM, Myers, G, Bavoil, PM, Laroucau, K, Magnino, S, Laurent, S, Rasschaert, D & Rodolakis, A 2008, 'Preliminary phylogenetic identification of virulent Chlamydophila pecorum strains', INFECTION GENETICS AND EVOLUTION, vol. 8, no. 6, pp. 764-771.View/Download from: Publisher's site
Rasko, DA, Rosovitz, MJ, Myers, GSA, Mongodin, EF, Fricke, WF, Gajer, P, Crabtree, J, Sebaihia, M, Thomson, NR, Chaudhuri, R, Henderson, IR, 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: Publisher's site
Yousef Mohamad, K, Rekiki, A, Myers, G, Bavoil, PM & 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.
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.
Liu, Z, Rank, R, Kaltenboeck, B, Magnino, S, Dean, D, Burall, L, Plaut, RD, Read, TD, Myers, G & Bavoil, PM 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: Publisher's site
Myers, GSA, Parker, D, Al-Hasani, K, Kennan, RM, Seemann, T, Ren, Q, Badger, JH, Selengut, JD, DeBoy, RT, Tettelin, H, Boyce, JD, McCarl, VP, Han, X, Nelson, WC, Madupu, R, Mohamoud, Y, Holley, T, Fedorova, N, Khouri, H, Bottomley, SP, Whittington, RJ, Adler, B, Songer, JG, Rood, JI & Paulsen, IT 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: Publisher's site
Ding, XZ, Paulsen, IT, Bhattacharjee, AK, Nikolich, MP, Myers, G & Hoover, DL 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
Myers, GSA, Rasko, DA, Cheung, JK, Ravel, J, Seshadri, R, DeBoy, RT, Ren, Q, Varga, J, Awad, MM, Brinkac, LM, Daugherty, SC, Haft, DH, Dodson, RJ, Madupu, R, Nelson, WC, Rosovitz, MJ, Sullivan, SA, Khouri, H, Dimitrov, GI, Watkins, KL, Mulligan, S, Benton, J, Radune, D, Fisher, DJ, Atkins, HS, Hiscox, T, Jost, BH, Billington, SJ, Songer, JG, McClane, BA, Titball, RW, Rood, JI, Melville, SB & Paulsen, IT 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: Publisher's site
Palenik, B, Ren, Q, Dupont, CL, Myers, GS, Heidelberg, JF, Badger, JH, Madupu, R, Nelson, WC, Brinkac, LM, Dodson, RJ, Durkin, AS, Daugherty, SC, Sullivan, SA, Khouri, H, Mohamoud, Y, Halpin, R & Paulsen, IT 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: Publisher's site
Parker, D, Kennan, RM, Myers, GS, Paulsen, IT, Songer, JG & Rood, JI 2006, 'Regulation of type IV fimbrial biogenesis in Dichelobacter nodosus', JOURNAL OF BACTERIOLOGY, vol. 188, no. 13, pp. 4801-4811.View/Download from: Publisher's site
Paulsen, IT, Press, CM, Ravel, J, Kobayashi, DY, Myers, GSA, Mavrodi, DV, DeBoy, RT, Seshadri, R, Ren, Q, Madupu, R, Dodson, RJ, Durkin, AS, Brinkac, LM, Daugherty, SC, Sullivan, SA, Rosovitz, MJ, Gwinn, ML, Zhou, L, Schneider, DJ, Cartinhour, SW, Nelson, WC, Weidman, J, Watkins, K, Tran, K, Khouri, H, Pierson, EA, Pierson, LS, Thomashow, LS & Loper, JE 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, XZ, Bhattacharjee, A, Nikolich, MP, Paulsen, IT, Myers, G, Seshadri, R & Hoover, DL 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: Publisher's site
Parker, D, Kennan, RA, Myers, GS, Paulsen, IT & Rood, JI 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: Publisher's site
Paulsen, IT, Press, CM, Ravel, J, Kobayashi, DY, Myers, GSA, Mavrodi, DV, DeBoy, RT, Seshadri, R, Ren, QH, Madupu, R, Dodson, RJ, Durkin, AS, Brinkac, LM, Daugherty, SC, Sullivan, SA, Rosovitz, MJ, Gwinn, ML, Zhou, LW, Schneider, DJ, Cartinhour, SW, Nelson, WC, Weidman, J, Watkins, K, Tran, K, Khouri, H, Pierson, EA, Pierson, LS, Thomashow, LS & Loper, JE 2005, 'Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5', NATURE BIOTECHNOLOGY, vol. 23, no. 7, pp. 873-878.View/Download from: Publisher's site
Seshadri, R, Myers, GSA, Tettelin, H, Eisen, JA, Heidelberg, JF, Dodson, RJ, Davidsen, TM, DeBoy, RT, Fouts, DE, Haft, DH, Selengut, J, Ren, Q, Brinkac, LM, Madupu, R, Kolonay, J, Durkin, SA, Daugherty, SC, Shetty, J, Shvartsbeyn, A, Gebregeorgis, E, Geer, K, Tsegaye, G, Malek, J, Ayodeji, B, Shatsman, S, McLeod, MP, Šmajs, D, Howell, JK, Pal, S, Amin, A, Vashisth, P, McNeill, TZ, Xiang, Q, Sodergren, E, Baca, E, Weinstock, GM, Norris, SJ, Fraser, CM & Paulsen, IT 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: 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, IT, Banerjei, L, Myers, GSA, Nelson, KE, Seshadri, R, Read, TD, Fouts, DE, Eisen, JA, Gill, SR, Heidelberg, JF, Tettelin, H, Dodson, RJ, Umayam, L, Brinkac, L, Beanan, M, Daugherty, S, DeBoy, RT, 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, KA, Dougherty, BA & Fraser, CM 2003, 'Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis', SCIENCE, vol. 299, no. 5615, pp. 2071-2074.View/Download from: Publisher's site
Read, TD, Myers, GSA, Brunham, RC, Nelson, WC, Paulsen, IT, Heidelberg, J, Holtzapple, E, Khouri, H, Federova, NB, Carty, HA, Umayam, LA, Haft, DH, Peterson, J, Beanan, MJ, White, O, Salzberg, SL, Hsia, RC, McClarty, G, Rank, RG, Bavoil, PM & Fraser, CM 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: Publisher's site
Myers, GSA, Grinvalds, R, Booth, S, Hutton, SI, Binks, M, Kemp, DJ & Sriprakash, KS 2000, 'Expression of two novel proteins in Chlamydia trachomatis during natural infection', MICROBIAL PATHOGENESIS, vol. 29, no. 2, pp. 63-72.View/Download from: Publisher's site
Carter, JS, Bowden, FJ, Bastian, I, Myers, GM, Sriprakash, KS & Kemp, DJ 1999, 'Phylogenetic evidence for reclassification of Calymmatobacterium granulomatis as Klebsiella granulomatis comb. nov.', INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY, vol. 49, pp. 1695-1700.View/Download from: Publisher's site
Holt, DC, Gardiner, DL, Thomas, EA, Mayo, M, Bourke, PF, Sutherland, CJ, Carter, R, Myers, G, Kemp, DJ & Trenholme, KR 1999, 'The cytoadherence linked asexual gene family of Plasmodium falciparum: re 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. Copyright (C) 1999 Australian Society for Parasitology Inc.