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Roy Chowdhury P, Hastak P, DeMaere M, Wyrsch E, Li D, Elankumaran P, Dolejska M, Browning GF, Marenda MS, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP. Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission? mSystems 2023; 8:e0123622. [PMID: 37675998 PMCID: PMC10654095 DOI: 10.1128/msystems.01236-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/11/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Extraintestinal pathogenic Escherichia coli (ExPEC) sequence type (ST) 38 is one of the top 10 human pandemic lineages. Although a major cause of urinary tract and blood stream infections, ST38 has been poorly characterized from a global phylogenomic perspective. A comprehensive genome-scale analysis of 925 ST38 isolate genomes identified two broad ancestral clades and linkage of discrete ST38 clusters with specific bla CTX-M variants. In addition, the clades and clusters carry important virulence genes, with diverse but poorly characterized plasmids. Numerous putative interhost and environment transmission events were identified here by the presence of ST38 clones (defined as isolates with ≤35 SNPs) within humans, companion animals, food sources, urban birds, wildlife, and the environment. A small cluster of international ST38 clones from diverse sources, likely representing progenitors of a hospital outbreak that occurred in Brisbane, Australia, in 2017, was also identified. Our study emphasizes the importance of characterizing isolate genomes derived from nonhuman sources and geographical locations, without any selection bias.
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Affiliation(s)
- Piklu Roy Chowdhury
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Priyanka Hastak
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Matthew DeMaere
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Ethan Wyrsch
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Dmitriy Li
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Paarthiphan Elankumaran
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Monika Dolejska
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
- Central European Institute of Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
- Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
- Biomedical Center, Charles University, Brno, Czech Republic
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital, Brno, Czech Republic
| | - Glenn F. Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Mark S. Marenda
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Garry S. A. Myers
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Steven P. Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
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Luu LDW, Kasimov V, Phillips S, Myers GSA, Jelocnik M. Genome organization and genomics in Chlamydia: whole genome sequencing increases understanding of chlamydial virulence, evolution, and phylogeny. Front Cell Infect Microbiol 2023; 13:1178736. [PMID: 37287464 PMCID: PMC10242142 DOI: 10.3389/fcimb.2023.1178736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/10/2023] [Indexed: 06/09/2023] Open
Abstract
The genus Chlamydia contains important obligate intracellular bacterial pathogens to humans and animals, including C. trachomatis and C. pneumoniae. Since 1998, when the first Chlamydia genome was published, our understanding of how these microbes interact, evolved and adapted to different intracellular host environments has been transformed due to the expansion of chlamydial genomes. This review explores the current state of knowledge in Chlamydia genomics and how whole genome sequencing has revolutionised our understanding of Chlamydia virulence, evolution, and phylogeny over the past two and a half decades. This review will also highlight developments in multi-omics and other approaches that have complemented whole genome sequencing to advance knowledge of Chlamydia pathogenesis and future directions for chlamydial genomics.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Vasilli Kasimov
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Samuel Phillips
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Garry S. A. Myers
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Martina Jelocnik
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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Koong J, Johnson C, Rafei R, Hamze M, Myers GSA, Kenyon JJ, Lopatkin AJ, Hamidian M. Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1. Microb Genom 2021; 7. [PMID: 34874246 PMCID: PMC8767349 DOI: 10.1099/mgen.0.000705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geographical regions are needed to draw a more accurate population structure of this globally distributed clone.
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Affiliation(s)
- Jonathan Koong
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Claire Johnson
- Department of Biology, Barnard College Affiliated Faculty Data Science Institute, Columbia University Affiliated Faculty, Columbia University, Columbia, USA
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Garry S A Myers
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Johanna J Kenyon
- Centre for Immunology and Infection Control, School of Biomedical Sciences. Faculty of Health, Queensland University of Technology, Brisbane, Australia
| | - Allison J Lopatkin
- Department of Biology, Barnard College Affiliated Faculty Data Science Institute, Columbia University Affiliated Faculty, Columbia University, Columbia, USA
| | - Mohammad Hamidian
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
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Douraghi M, Aris P, To J, Myers GSA, Hamidian M. Two carbapenem-resistant ST1:ST231:KL1:OCL1 Acinetobacter baumannii strains recovered in Tehran, Iran, carry AbaR31 in the chromosome and AbaR4 and Tn aphA6 in a RepAci6 plasmid. JAC Antimicrob Resist 2021; 3:dlab112. [PMID: 34377981 PMCID: PMC8346695 DOI: 10.1093/jacamr/dlab112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
Objectives To analyse the context of genes conferring antibiotic resistance in two carbapenem-resistant Acinetobacter baumannii isolates recovered in Tehran, Iran. Methods The antibiotic resistance phenotype for 28 antibiotics was determined using disc diffusion. The whole genome sequences of ABH008 and ABS200 were determined using the Illumina HiSeq X Ten platform. Resistance genes were identified using ResFinder and multilocus sequence types were determined using the Oxford and Institut Pasteur schemes. Results Isolates ABH008 and ABS200, recovered in 2012 and 2013, respectively, in two different Tehran hospitals, belong to the common global clone 1 lineage, ST1IP and ST231OX. They are resistant to sulfamethoxazole, tetracycline, gentamicin, amikacin, third-generation cephalosporins and carbapenems. Despite being isolated in different hospitals, phylogenetic analysis indicated they are closely related. Consistent with this, both isolates carry catA1, sul1, aacC1 and aadA1 in a novel variant of the AbaR3-type resistance island, named AbaR31. Both isolates are resistant to amikacin and carbapenems owing to aphA6 and oxa23, respectively. The oxa23 gene is located in the AbaR4 resistance island, and aphA6 in TnaphA6, and both mobile elements are in an ∼90 kbp plasmid encoding the putative RepAci6 replication initiation protein. Resistance to third-generation cephalosporins is due to the acquisition by homologous recombination of a 5 kb DNA segment that contains ISAba1-ampC from a ST623 strain. Conclusions The resistance gene complements of ABH008 and ABS200 were found in AbaR31 and a plasmid that encodes RepAci6. The close genetic relationship of ABH008 and ABS200, despite each being recovered from different hospitals, indicates transmission between the two hospitals.
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Affiliation(s)
- Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Aris
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Joyce To
- The iThree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Garry S A Myers
- The iThree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mohammad Hamidian
- The iThree institute, University of Technology Sydney, Ultimo, NSW, Australia
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Hastak P, Fourment M, Darling AE, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP, Roy Chowdhury P. Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex. Emerg Microbes Infect 2020; 9:1780-1792. [PMID: 32686595 PMCID: PMC7473005 DOI: 10.1080/22221751.2020.1797541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/14/2020] [Indexed: 11/25/2022]
Abstract
The H30Rx subclade of Escherichia coli ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum β-lactams. Isolates EC233 and EC234, variants of ST131-H30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:H4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both harbour an IncFII_2 plasmid (pSPRC_Ec234-FII) that carries most of the resistance genes on an IS26 associated translocatable unit, two small plasmids and a novel IncI1 plasmid (pSPRC_Ec234-I). SNP-based phylogenetic analysis of the core genome of representatives within the ST131 clonal complex places both isolates in a subclade with three clinical Australian ST131-H30Rx clade-C isolates. A MrBayes phylogeny analysis of EC233 and EC234 indicates ST8196 share a most recent common ancestor with ST131-H30Rx strain EC70 isolated from the same hospital in 2013. Our study identified genomic hallmarks that define the ST131-H30Rx subclade in the ST8196 isolates and highlights a need for unbiased genomic surveillance approaches to identify novel high-risk MDR E. coli pathogens that impact healthcare facilities.
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Affiliation(s)
- Priyanka Hastak
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Mathieu Fourment
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Aaron E. Darling
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Garry S. A. Myers
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Steven P. Djordjevic
- The ithree institute, University of Technology Sydney, Ultimo, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Broadway, Australia
| | - Piklu Roy Chowdhury
- The ithree institute, University of Technology Sydney, Ultimo, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Broadway, Australia
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6
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Hamidian M, Blasco L, Tillman LN, To J, Tomas M, Myers GSA. Analysis of Complete Genome Sequence of Acinetobacter baumannii Strain ATCC 19606 Reveals Novel Mobile Genetic Elements and Novel Prophage. Microorganisms 2020; 8:E1851. [PMID: 33255319 PMCID: PMC7760358 DOI: 10.3390/microorganisms8121851] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 11/16/2022] Open
Abstract
Acinetobacter baumannii isolate ATCC 19606 was recovered in the US prior to 1948. It has been used as a reference and model organism in many studies involving antibiotic resistance and pathogenesis of A. baumannii, while, until recently, a complete genome of this strain was not available. Here, we present an analysis of the complete 3.91-Mbp genome sequence, generated via a combination of short-read sequencing (Illumina) and long-read sequencing (MinION), and show it contains two small cryptic plasmids and a novel complete prophage of size 41.2 kb. We also characterised several regions of the ATCC 19606 genome, leading to the identification of a novel cadmium/mercury transposon, which was named Tn6551. ATCC 19606 is an antibiotic-sensitive strain, but a comparative analysis of all publicly available ST52 strains predicts a resistance to modern antibiotics by the accumulation of antibiotic-resistance genes via plasmids in recent isolates that belong to this sequence type.
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Affiliation(s)
- Mohammad Hamidian
- The iThree Institute, University of Technology Sydney, Ultimo 2007, NSW, Australia; (L.N.T.); (J.T.); (G.S.A.M.)
| | - Lucia Blasco
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15495 A Coruña, Spain; (L.B.); (M.T.)
| | - Lauren N. Tillman
- The iThree Institute, University of Technology Sydney, Ultimo 2007, NSW, Australia; (L.N.T.); (J.T.); (G.S.A.M.)
| | - Joyce To
- The iThree Institute, University of Technology Sydney, Ultimo 2007, NSW, Australia; (L.N.T.); (J.T.); (G.S.A.M.)
| | - María Tomas
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15495 A Coruña, Spain; (L.B.); (M.T.)
| | - Garry S. A. Myers
- The iThree Institute, University of Technology Sydney, Ultimo 2007, NSW, Australia; (L.N.T.); (J.T.); (G.S.A.M.)
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Hayward RJ, Marsh JW, Humphrys MS, Huston WM, Myers GSA. Chromatin accessibility dynamics of Chlamydia-infected epithelial cells. Epigenetics Chromatin 2020; 13:45. [PMID: 33109274 PMCID: PMC7590614 DOI: 10.1186/s13072-020-00368-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/15/2020] [Indexed: 01/08/2023] Open
Abstract
Chlamydia are Gram-negative, obligate intracellular bacterial pathogens responsible for a broad spectrum of human and animal diseases. In humans, Chlamydia trachomatis is the most prevalent bacterial sexually transmitted infection worldwide and is the causative agent of trachoma (infectious blindness) in disadvantaged populations. Over the course of its developmental cycle, Chlamydia extensively remodels its intracellular niche and parasitises the host cell for nutrients, with substantial resulting changes to the host cell transcriptome and proteome. However, little information is available on the impact of chlamydial infection on the host cell epigenome and global gene regulation. Regions of open eukaryotic chromatin correspond to nucleosome-depleted regions, which in turn are associated with regulatory functions and transcription factor binding. We applied formaldehyde-assisted isolation of regulatory elements enrichment followed by sequencing (FAIRE-Seq) to generate temporal chromatin maps of C. trachomatis-infected human epithelial cells in vitro over the chlamydial developmental cycle. We detected both conserved and distinct temporal changes to genome-wide chromatin accessibility associated with C. trachomatis infection. The observed differentially accessible chromatin regions include temporally-enriched sets of transcription factors, which may help shape the host cell response to infection. These regions and motifs were linked to genomic features and genes associated with immune responses, re-direction of host cell nutrients, intracellular signalling, cell-cell adhesion, extracellular matrix, metabolism and apoptosis. This work provides another perspective to the complex response to chlamydial infection, and will inform further studies of transcriptional regulation and the epigenome in Chlamydia-infected human cells and tissues.
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Affiliation(s)
- Regan J Hayward
- The ithree Institute, University of Technology Sydney, Sydney, NSW, Australia
| | - James W Marsh
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Wilhelmina M Huston
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Garry S A Myers
- The ithree Institute, University of Technology Sydney, Sydney, NSW, Australia. .,School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.
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Hastak P, Cummins ML, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP, Roy Chowdhury P. Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital. Microb Genom 2020; 6:e000371. [PMID: 32374251 PMCID: PMC7371115 DOI: 10.1099/mgen.0.000371] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 04/03/2020] [Indexed: 11/29/2022] Open
Abstract
This study sought to assess the genetic variability of Escherichia coli isolated from bloodstream infections (BSIs) presenting at Concord Hospital, Sydney during 2013-2016. Whole-genome sequencing was used to characterize 81 E. coli isolates sourced from community-onset (CO) and hospital-onset (HO) BSIs. The cohort comprised 64 CO and 17 HO isolates, including 35 multidrug-resistant (MDR) isolates exhibiting phenotypic resistance to three or more antibiotic classes. Phylogenetic analysis identified two major ancestral clades. One was genetically diverse with 25 isolates distributed in 16 different sequence types (STs) representing phylogroups A, B1, B2, C and F, while the other comprised phylogroup B2 isolates in subclades representing the ST131, ST73 and ST95 lineages. Forty-seven isolates contained a class 1 integron, of which 14 carried blaCTX -M-gene. Isolates with a class 1 integron carried more antibiotic resistance genes than isolates without an integron and, in most instances, resistance genes were localized within complex resistance loci (CRL). Resistance to fluoroquinolones could be attributed to point mutations in chromosomal parC and gyrB genes and, in addition, two isolates carried a plasmid-associated qnrB4 gene. Co-resistance to fluoroquinolone and broad-spectrum beta-lactam antibiotics was associated with ST131 (HO and CO), ST38 (HO), ST393 (CO), ST2003 (CO) and ST8196 (CO and HO), a novel ST identified in this study. Notably, 10/81 (12.3 %) isolates with ST95 (5 isolates), ST131 (2 isolates), ST88 (2 isolates) and a ST540 likely carry IncFII-IncFIB plasmid replicons with a full spectrum of virulence genes consistent with the carriage of ColV-like plasmids. Our data indicate that IncF plasmids play an important role in shaping virulence and resistance gene carriage in BSI E. coli in Australia.
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Affiliation(s)
- Priyanka Hastak
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Max L. Cummins
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
- Faculty of Medicine, University of Sydney, NSW Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia
- Faculty of Medicine, University of Sydney, NSW Australia
| | - Garry S. A. Myers
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Steven P. Djordjevic
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Piklu Roy Chowdhury
- The ithree institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
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9
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Hayward RJ, Marsh JW, Humphrys MS, Huston WM, Myers GSA. Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution. Front Cell Infect Microbiol 2019; 9:392. [PMID: 31803632 PMCID: PMC6877545 DOI: 10.3389/fcimb.2019.00392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/01/2019] [Indexed: 12/22/2022] Open
Abstract
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.
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Affiliation(s)
- Regan J. Hayward
- Faculty of Science, School of Life Sciences, The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - James W. Marsh
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael S. Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Wilhelmina M. Huston
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Garry S. A. Myers
- Faculty of Science, School of Life Sciences, The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
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10
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Marsh JW, Hayward RJ, Shetty AC, Mahurkar A, Humphrys MS, Myers GSA. Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments. Brief Bioinform 2019; 19:1115-1129. [PMID: 28535295 DOI: 10.1093/bib/bbx043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Indexed: 12/18/2022] Open
Abstract
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.
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Affiliation(s)
- James W Marsh
- The ithree institute, University of Technology Sydney
| | | | - Amol C Shetty
- Institute for Genome Sciences at the University of Maryland, Baltimore
| | - Anup Mahurkar
- Institute for Genome Sciences at the University of Maryland, Baltimore
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Abstract
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.
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Affiliation(s)
- James W Marsh
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Regan J Hayward
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Amol Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Garry S A Myers
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia.
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De Puysseleyr K, Kieckens E, De Puysseleyr L, Van den Wyngaert H, Ahmed B, Van Lent S, Creasy HH, Myers GSA, Vanrompay D. 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. Transbound Emerg Dis 2018; 65:e457-e469. [PMID: 29314736 DOI: 10.1111/tbed.12783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Indexed: 12/21/2022]
Abstract
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.
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Affiliation(s)
- K De Puysseleyr
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - E Kieckens
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - L De Puysseleyr
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - H Van den Wyngaert
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - B Ahmed
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - S Van Lent
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - H H Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - G S A Myers
- i3 Institute, University of Technology, Sydney, NSW, Australia
| | - D Vanrompay
- Department of Animal Production, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
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Marsh JW, Humphrys MS, Myers GSA. A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro. Front Microbiol 2017; 8:1830. [PMID: 28983295 PMCID: PMC5613115 DOI: 10.3389/fmicb.2017.01830] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022] Open
Abstract
Dual RNA-Sequencing leverages established next-generation sequencing (NGS)-enabled RNA-Seq approaches to measure genome-wide transcriptional changes of both an infecting bacteria and host cells. By simultaneously investigating both organisms from the same biological sample, dual RNA-Seq can provide unique insight into bacterial infection processes and reciprocal host responses at once. However, the difficulties involved in handling both prokaryotic and eukaryotic material require distinct, optimized procedures. We previously developed and applied dual RNA-Seq to measure prokaryotic and eukaryotic expression profiles of human cells infected with bacteria, using in vitro Chlamydia-infected epithelial cells as proof of principle. Here we provide a detailed laboratory protocol for in vitro dual RNA-Seq that is readily adaptable to any host-bacteria system of interest.
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Affiliation(s)
- James W Marsh
- School of Life Sciences, The ithree institute, University of Technology SydneyUltimo, NSW, Australia
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimore, MD, United States
| | - Garry S A Myers
- School of Life Sciences, The ithree institute, University of Technology SydneyUltimo, NSW, Australia
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Jelocnik M, Bachmann NL, Kaltenboeck B, Waugh C, Woolford L, Speight KN, Gillett A, Higgins DP, Flanagan C, Myers GSA, Timms P, Polkinghorne A. 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 2015; 16:893. [PMID: 26531162 PMCID: PMC4632680 DOI: 10.1186/s12864-015-2053-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/08/2015] [Indexed: 12/22/2022] Open
Abstract
Background 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. Methods 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. Results 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 clustered porcine isolates into a distinct clade, highlighting the polyphyletic origin of C. pecorum in livestock. Most surprising, we also discovered a plasmid in the porcine C. pecorum genome. Using this novel C. pecorum plasmid (pCpec) sequence, a) we developed a pCpec screening assay to evaluate the plasmid distribution in C. pecorum from different hosts; and b) to characterise the pCpec sequences from available previously sequenced C. pecorum genome data. pCpec screening showed that the pCpec is common in all hosts of C. pecorum, however not all C. pecorum strains carry pCpec. Conclusions This study provides further insight into the complexity of C. pecorum epidemiology and novel genomic regions that may be linked to host specificity. C. pecorum plasmid characterisation may aid in improving our understanding of C. pecorum pathogenesis across the variety of host species this animal pathogen infects. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2053-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martina Jelocnik
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia
| | - Nathan L Bachmann
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia
| | | | - Courtney Waugh
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia
| | - Lucy Woolford
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - K Natasha Speight
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, 5371, Australia
| | - Amber Gillett
- Australia Zoo Wildlife Hospital, Beerwah, QLD, 4519, Australia
| | - Damien P Higgins
- Faculty of Veterinary Science, The University of Sydney, New South Wales, 2006, Australia
| | - Cheyne Flanagan
- Port Macquarie Koala Hospital, Port Macquarie, NSW, 2444, Australia
| | - Garry S A Myers
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Peter Timms
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia
| | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4558, Australia.
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Neuendorf E, Gajer P, Bowlin AK, Marques PX, Ma B, Yang H, Fu L, Humphrys MS, Forney LJ, Myers GSA, Bavoil PM, Rank RG, Ravel J. Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota. Pathog Dis 2015; 73:ftv019. [PMID: 25761873 PMCID: PMC4445005 DOI: 10.1093/femspd/ftv019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2015] [Indexed: 01/09/2023] Open
Abstract
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. The vaginal microbiota of the guinea pig differs from that of humans and cannot prevent chlamydial infections efficiently.
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Affiliation(s)
- Elizabeth Neuendorf
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Anne K Bowlin
- Arkansas Children's Hospital Research Institute, Little Rock, AR 72202, USA
| | - Patricia X Marques
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hongqiu Yang
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Li Fu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Larry J Forney
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83843, USA
| | - Garry S A Myers
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Patrik M Bavoil
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83843, USA
| | - Roger G Rank
- Arkansas Children's Hospital Research Institute, Little Rock, AR 72202, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Bachmann NL, Fraser TA, Bertelli C, Jelocnik M, Gillett A, Funnell O, Flanagan C, Myers GSA, Timms P, Polkinghorne A. Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum. BMC Genomics 2014; 15:667. [PMID: 25106440 PMCID: PMC4137089 DOI: 10.1186/1471-2164-15-667] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/31/2014] [Indexed: 12/21/2022] Open
Abstract
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 origin of these point mutations. CONCLUSIONS The genomic data revealed that variation between C. pecorum strains were mainly due to the accumulation of SNPs, some of which cause gene inactivation. The identification of these genetic differences will provide the basis for further studies to understand the biology and evolution of this important animal pathogen.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Adam Polkinghorne
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs 4558, Queensland, Australia.
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Sait M, Livingstone M, Clark EM, Wheelhouse N, Spalding L, Markey B, Magnino S, Lainson FA, Myers GSA, Longbottom D. Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes. BMC Genomics 2014; 15:23. [PMID: 24417976 PMCID: PMC3932018 DOI: 10.1186/1471-2164-15-23] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/06/2014] [Indexed: 11/17/2022] Open
Abstract
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. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-23) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - David Longbottom
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian EH26 0PZ, UK.
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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. Simultaneous transcriptional profiling of bacteria and their host cells. PLoS One 2013; 8:e80597. [PMID: 24324615 PMCID: PMC3851178 DOI: 10.1371/journal.pone.0080597] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 10/14/2013] [Indexed: 02/06/2023] Open
Abstract
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.
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Affiliation(s)
- Michael S. Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Todd Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Yezhou Sun
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Amol C. Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Marcus C. Chibucos
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Elliott F. Drabek
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Umar Farooq
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Naomi Sengamalay
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Sandy Ott
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Huizhong Shou
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Patrik M. Bavoil
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland, United States of America
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Garry S. A. Myers
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland, United States of America
- * E-mail:
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Hovis KM, Mojica S, McDermott JE, Pedersen L, Simhi C, Rank RG, Myers GSA, Ravel J, Hsia RC, Bavoil PM. Genus-optimized strategy for the identification of chlamydial type III secretion substrates. Pathog Dis 2013; 69:213-22. [PMID: 23873765 DOI: 10.1111/2049-632x.12070] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 06/10/2013] [Accepted: 07/09/2013] [Indexed: 12/14/2022] Open
Abstract
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.
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Affiliation(s)
- Kelley M Hovis
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD, USA
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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. Unity in variety--the pan-genome of the Chlamydiae. Mol Biol Evol 2011; 28:3253-70. [PMID: 21690563 DOI: 10.1093/molbev/msr161] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
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.
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Affiliation(s)
- Astrid Collingro
- Department of Microbial Ecology, University of Vienna, Vienna, Austria
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21
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Mitchell CM, Hovis KM, Bavoil PM, Myers GSA, Carrasco JA, Timms P. Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species. BMC Genomics 2010; 11:442. [PMID: 20646324 PMCID: PMC3091639 DOI: 10.1186/1471-2164-11-442] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 07/21/2010] [Indexed: 11/28/2022] Open
Abstract
Background 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. Results 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). Conclusions 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.
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Affiliation(s)
- Candice M Mitchell
- Faculty of Science and Technology, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia
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22
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Mitchell CM, Hutton S, Myers GSA, Brunham R, Timms P. Chlamydia pneumoniae is genetically diverse in animals and appears to have crossed the host barrier to humans on (at least) two occasions. PLoS Pathog 2010; 6:e1000903. [PMID: 20502684 PMCID: PMC2873915 DOI: 10.1371/journal.ppat.1000903] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 04/09/2010] [Indexed: 11/23/2022] Open
Abstract
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. Chlamydia pneumoniae is an intracellular bacterial pathogen with an extremely diverse host range (humans, amphibians, reptiles and marsupials). We selected 23 target genes in order to investigate genetic diversity: seven of these had been lost or gained by C. pneumoniae, a further six were conserved, four were polymorphic (defined by greater than 20 SNPs per 1 kbp; in this study), and six were truncated or length polymorphic in one strain or the other. Our research highlights that C. pneumoniae animal isolates are much more genetically diverse than C. pneumoniae human isolates, and have crossed the host barrier to humans on at least two occasions. Our study provides new insights into the evolution of this complex pathogen.
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Affiliation(s)
- Candice M. Mitchell
- Institute of Health and Biomedical Innovation, School of Life Sciences, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | - Susan Hutton
- Menzies School of Health Research, Royal Darwin Hospital Campus, Casuarina, Northern Territory, Australia
| | - Garry S. A. Myers
- Institute for Genome Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Robert Brunham
- British Columbia Centre for Disease Control, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Timms
- Institute of Health and Biomedical Innovation, School of Life Sciences, Queensland University of Technology, Kelvin Grove, Queensland, Australia
- * E-mail:
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23
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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. Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nat Biotechnol 2007; 25:569-75. [PMID: 17468768 DOI: 10.1038/nbt1302] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 04/04/2007] [Indexed: 11/09/2022]
Abstract
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.
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Affiliation(s)
- Garry S A Myers
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
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24
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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. Correction: Corrigendum: Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 2006. [DOI: 10.1038/nbt0406-466b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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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. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 2005; 23:873-8. [PMID: 15980861 PMCID: PMC7416659 DOI: 10.1038/nbt1110] [Citation(s) in RCA: 421] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Accepted: 05/04/2005] [Indexed: 12/11/2022]
Abstract
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.
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Affiliation(s)
- Ian T Paulsen
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Caroline M Press
- US Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, Oregon USA
| | - Jacques Ravel
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Donald Y Kobayashi
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey USA
| | | | - Dmitri V Mavrodi
- Department of Plant Pathology, Washington State University, Pullman, Washington USA
| | - Robert T DeBoy
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Rekha Seshadri
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Qinghu Ren
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Ramana Madupu
- The Institute for Genomic Research, Rockville, Maryland USA
| | | | - A Scott Durkin
- The Institute for Genomic Research, Rockville, Maryland USA
| | | | | | | | | | | | - Liwei Zhou
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Davd J Schneider
- US Department of Agriculture, Agricultural Research Service, Ithaca, New York USA
| | - Samuel W Cartinhour
- US Department of Agriculture, Agricultural Research Service, Ithaca, New York USA
| | | | - Janice Weidman
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Kisha Watkins
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Kevin Tran
- The Institute for Genomic Research, Rockville, Maryland USA
| | - Hoda Khouri
- The Institute for Genomic Research, Rockville, Maryland USA
| | | | - Leland S Pierson
- Department of Plant Sciences, University of Arizona, Tucson, Arizona USA
| | - Linda S Thomashow
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, Washington USA
| | - Joyce E Loper
- US Department of Agriculture, Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, Oregon USA
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Affiliation(s)
- Garry S A Myers
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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27
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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, Smajs 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. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci U S A 2004; 101:5646-51. [PMID: 15064399 PMCID: PMC397461 DOI: 10.1073/pnas.0307639101] [Citation(s) in RCA: 211] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Rekha Seshadri
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
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28
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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. Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic Acids Res 2003; 31:2134-47. [PMID: 12682364 PMCID: PMC153749 DOI: 10.1093/nar/gkg321] [Citation(s) in RCA: 237] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
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 genes in these important bacterial pathogens.
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Affiliation(s)
- T D Read
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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29
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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. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 2003; 299:2071-4. [PMID: 12663927 DOI: 10.1126/science.1080613] [Citation(s) in RCA: 686] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
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.
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Affiliation(s)
- I T Paulsen
- Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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