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Bujold AR, Shure AE, Liu R, Kropinski AM, MacInnes JI. Investigation of putative invasion determinants of Actinobacillus species using comparative genomics. Genomics 2018; 111:59-66. [PMID: 29317305 DOI: 10.1016/j.ygeno.2018.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/13/2017] [Accepted: 01/02/2018] [Indexed: 11/24/2022]
Abstract
Actinobacillus spp. are Gram-negative bacteria associated with mucosal membranes. While some are commensals, others can cause important human and animal diseases. A. pleuropneumoniae causes severe fibrinous hemorrhagic pneumonia in swine but not systemic disease whereas other species invade resulting in septicemia and death. To understand the invasive phenotype of Actinobacillus spp., complete genomes of eight isolates were obtained and pseudogenomes of five isolates were assembled and annotated. Phylogenetically, A. suis isolates clustered by surface antigen type and were more closely related to the invasive A. ureae, A. equuli equuli, and A. capsulatus than to the other swine pathogen, A. pleuropneumoniae. Using the LS-BSR pipeline, 251 putative virulence genes associated with serum resistance and invasion were detected. To our knowledge, this is the first genome-wide study of the genus Actinobacillus and should contribute to a better understanding of host tropism and mechanisms of invasion of pathogenic Actinobacillus and related genera.
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Affiliation(s)
- Adina R Bujold
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph N1G 2W1, Ontario, Canada.
| | - Andrew E Shure
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph N1G 2W1, Ontario, Canada
| | - Rui Liu
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph N1G 2W1, Ontario, Canada
| | - Andrew M Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph N1G 2W1, Ontario, Canada
| | - Janet I MacInnes
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph N1G 2W1, Ontario, Canada.
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Califano G, Castanho S, Soares F, Ribeiro L, Cox CJ, Mata L, Costa R. Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream ( Sparus aurata) Hatchery. Front Microbiol 2017; 8:204. [PMID: 28261166 PMCID: PMC5306143 DOI: 10.3389/fmicb.2017.00204] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/27/2017] [Indexed: 12/20/2022] Open
Abstract
As wild fish stocks decline worldwide, land-based fish rearing is likely to be of increasing relevance to feeding future human generations. Little is known about the structure and role of microbial communities in fish aquaculture, particularly at larval developmental stages where the fish microbiome develops and host animals are most susceptible to disease. We employed next-generation sequencing (NGS) of 16S rRNA gene reads amplified from total community DNA to reveal the structure of bacterial communities in a gilthead seabream (Sparus aurata) larviculture system. Early- (2 days after hatching) and late-stage (34 days after hatching) fish larvae presented remarkably divergent bacterial consortia, with the genera Pseudoalteromonas, Marinomonas, Acinetobacter, and Acidocella (besides several unclassified Alphaproteobacteria) dominating the former, and Actinobacillus, Streptococcus, Massilia, Paracoccus, and Pseudomonas being prevalent in the latter. A significant reduction in rearing-water bacterial diversity was observed during the larviculture trial, characterized by higher abundance of the Cryomorphaceae family (Bacteroidetes), known to populate microniches with high organic load, in late-stage rearing water in comparison with early-stage rearing-water. Furthermore, we observed the recruitment, into host tissues, of several bacterial phylotypes-including putative pathogens as well as mutualists-that were detected at negligible densities in rearing-water or in the live feed (i.e., rotifers and artemia). These results suggest that, besides host-driven selective forces, both the live feed and the surrounding rearing environment contribute to shaping the microbiome of farmed gilthead sea-bream larvae, and that a differential establishment of host-associated bacteria takes place during larval development.
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Affiliation(s)
- Gianmaria Califano
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of AlgarveFaro, Portugal; Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität JenaJena, Germany
| | - Sara Castanho
- Portuguese Institute for the Ocean and Atmosphere, Aquaculture Research Station Olhão, Portugal
| | - Florbela Soares
- Portuguese Institute for the Ocean and Atmosphere, Aquaculture Research Station Olhão, Portugal
| | - Laura Ribeiro
- Portuguese Institute for the Ocean and Atmosphere, Aquaculture Research Station Olhão, Portugal
| | - Cymon J Cox
- Plant Systematics and Bioinformatics, Centre of Marine Sciences, University of Algarve Faro, Portugal
| | - Leonardo Mata
- MACRO-the Centre for Macroalgal Resources and Biotechnology, James Cook University Townsville, QLD, Australia
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, University of AlgarveFaro, Portugal; Department of Bioengineering, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal
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Differential expression of putative adhesin genes of Actinobacillus suis grown in in vivo-like conditions. Vet Microbiol 2016; 195:60-69. [PMID: 27771071 DOI: 10.1016/j.vetmic.2016.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/13/2016] [Accepted: 09/16/2016] [Indexed: 01/09/2023]
Abstract
Actinobacillus suis is an opportunistic pathogen that resides in the tonsils of the soft palate of swine. Unknown stimuli can cause this organism to invade the host, resulting in septicaemia and sequelae including death. To better understand its pathogenesis, the expression of several adhesin genes was evaluated by semi-quantitative real-time PCR in A. suis grown in conditions that mimic the host environment, including different nutrient and oxygen levels, exponential and stationary phases of growth, and in the presence of the stress hormone epinephrine. Fifty micromolar epinephrine did not affect the growth rate or expression of A. suis adhesin genes, but there was a significant growth phase effect for many genes. Most adhesin genes were also differentially expressed during anoxic static growth or aerobic growth, and in this study, all genes were differentially expressed in either exponential or stationary phase. Based on the time*treatment interactions observed in the anoxic study, a model of persistence of A. suis in the host environment in biofilm and planktonic states is proposed. Biofilm dynamics were further studied using wild type and isogenic mutants of the type IVb pilin (Δ flp1), the OmpA outer membrane protein (ΔompA), and the fibronectin-binding (ΔcomE1) genes. Disruption of these adhesin genes affected the early stages of biofilm formation, but in most cases, biofilm formation of the mutant strains was similar to that of the wild type by 24h of incubation. We postulate that other adhesins may have overlapping functions that can compensate for those of the missing adhesins.
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Rossi CC, Bossé JT, Li Y, Witney AA, Gould KA, Langford PR, Bazzolli DMS. A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae. RNA (NEW YORK, N.Y.) 2016; 22:1373-85. [PMID: 27402897 PMCID: PMC4986893 DOI: 10.1261/rna.055129.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 05/24/2016] [Indexed: 05/26/2023]
Abstract
Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies.
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Affiliation(s)
- Ciro C Rossi
- Laboratório de Genética Molecular de Micro-organismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| | - Janine T Bossé
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Yanwen Li
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Kate A Gould
- Institute for Infection and Immunity, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Imperial College London, St. Mary's Campus, London W2 1PG, United Kingdom
| | - Denise M S Bazzolli
- Laboratório de Genética Molecular de Micro-organismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária-BIOAGRO, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
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Attachment of Actinobacillus suis H91-0380 and Its Isogenic Adhesin Mutants to Extracellular Matrix Components of the Tonsils of the Soft Palate of Swine. Infect Immun 2016; 84:2944-52. [PMID: 27481253 DOI: 10.1128/iai.00456-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/22/2016] [Indexed: 11/20/2022] Open
Abstract
Tonsils conduct immune surveillance of antigens entering the upper respiratory tract. Despite their immunological function, they are also sites of persistence and invasion of bacterial pathogens. Actinobacillus suis is a common resident of the tonsils of the soft palate in pigs, but under certain circumstances it can invade, causing septicemia and related sequelae. Twenty-four putative adhesins are predicted in the A. suis genome, but to date, little is known about how they might participate in colonization or invasion. To better understand these processes, swine tonsil lysates were characterized by mass spectrometry. Fifty-nine extracellular matrix (ECM) proteins were identified, including small leucine-rich proteoglycans, integrins, and other cell surface receptors. Additionally, attachment of the wild type and 3 adhesin mutants to 5 ECM components was evaluated. Exponential cultures of wild-type A. suis adhered significantly more than stationary cultures to all ECM components studied except collagen I. During exponential growth, the A. suis Δflp1 mutant attached less to collagen IV while the ΔompA mutant attached less to all ECMs. The ΔcomE1 strain attached less to collagen IV, fibronectin, and vitronectin during exponential growth and exhibited differential attachment to collagen I over short adherence time points. These results suggest that Flp1, OmpA, and ComE1 are important during early stages of attachment to ECM components found in tonsils, which supports the notion that other adhesins have compensatory effects during later stages of attachment.
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Bujold AR, MacInnes JI. Identification of putative adhesins of Actinobacillus suis and their homologues in other members of the family Pasteurellaceae. BMC Res Notes 2015; 8:675. [PMID: 26567540 PMCID: PMC4644294 DOI: 10.1186/s13104-015-1659-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/02/2015] [Indexed: 12/03/2022] Open
Abstract
Background Actinobacillus suis disease has been reported in a wide range of vertebrate species, but is most commonly found in swine. A. suis is a commensal of the tonsils of the soft palate of swine, but in the presence of unknown stimuli it can invade the bloodstream, causing septicaemia and sequelae such as meningitis, arthritis, and death. It is genotypically and phenotypically similar to A. pleuropneumoniae, the causative agent of pleuropneumonia, and to other members of the family Pasteurellaceae that colonise tonsils. At present, very little is known about the genes involved in attachment, colonisation, and invasion by A. suis (or related members of the tonsil microbiota). Results Bioinformatic analyses of the A. suis H91-0380 genome were done using BASys and blastx in GenBank. Forty-seven putative adhesin-associated genes predicted to encode 24 putative adhesins were discovered. Among these are 6 autotransporters, 25 fimbriae-associated genes (encoding 3 adhesins), 12 outer membrane proteins, and 4 additional genes (encoding 3 adhesins). With the exception of 2 autotransporter-encoding genes (aidA and ycgV), both with described roles in virulence in other species, all of the putative adhesin-associated genes had homologues in A. pleuropneumoniae. However, the majority of the closest homologues of the A. suis adhesins are found in A. ureae and A. capsulatus—species not known to infect swine, but both of which can cause systemic infections. Conclusions A. suis and A. pleuropneumoniae share many of the same putative adhesins, suggesting that the different diseases, tissue tropism, and host range of these pathogens are due to subtle genetic differences, or perhaps differential expression of virulence factors during infection. However, many of the putative adhesins of A. suis share even greater homology with those of other pathogens within the family Pasteurellaceae. Similar to A. suis, these pathogens (A. capsulatus and A. ureae) cause systemic infections and it is tempting to speculate that they employ similar strategies to invade the host, but more work is needed before that assertion can be made. This work begins to examine adhesin-associated factors that allow some members of the family Pasteurellaceae to invade the bloodstream while others cause a more localised infection. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1659-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adina R Bujold
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Ontario, N1G 2W1, Canada.
| | - Janet I MacInnes
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Ontario, N1G 2W1, Canada.
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First Human Case of Meningitis and Sepsis in a Child Caused by Actinobacillus suis or Actinobacillus equuli. J Clin Microbiol 2015; 53:1990-2. [PMID: 25878346 DOI: 10.1128/jcm.00339-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/08/2015] [Indexed: 11/20/2022] Open
Abstract
We report the first human case of meningitis and sepsis caused in a child by Actinobacillus suis or A. equuli, a common opportunistic pathogen of swine or horses, respectively. Identification was performed by matrix-assisted laser desorption ionization-time of flight mass spectrometry and real-time PCR assay. A previous visit to a farm was suspected as the source of infection.
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Bujold AR, MacInnes JI. Validation of reference genes for quantitative real-time PCR (qPCR) analysis of Actinobacillus suis. BMC Res Notes 2015; 8:86. [PMID: 25884823 PMCID: PMC4369107 DOI: 10.1186/s13104-015-1045-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/04/2015] [Indexed: 12/25/2022] Open
Abstract
Background Quantitative real-time PCR is a valuable tool for evaluating bacterial gene expression. However, in order to make best use of this method, endogenous reference genes for expression data normalisation must first be identified by carefully validating the stability of expression under experimental conditions. Therefore, the objective of this study was to validate eight reference genes of the opportunistic swine pathogen, Actinobacillus suis, grown in aerobic cultures with (Epinephrine) or without (Aerobic) epinephrine in the growth medium and in anoxic static cultures (Anoxic), and sampled during exponential and stationary phases. Results Using the RefFinder tool, expression data were analysed to determine whether comprehensive stability rankings of selected reference genes varied with experimental design. When comparing Aerobic and Epinephrine cultures by growth phase, pyk and rpoB were both among the most stably expressed genes, but when analysing both growth phases together, only pyk remained in the top three rankings. When comparing Aerobic and Anoxic samples, proS ranked among the most stable genes in exponential and stationary phase data sets as well as in combined rankings. When analysing the Aerobic, Epinephrine, and Anoxic samples together, only gyrA ranked consistently among the top three most stably expressed genes during exponential and stationary growth as well as in combined rankings; the rho gene ranked as least stably expressed gene in this data set. Conclusions Reference gene stability should be carefully assessed with the design of the experiment in mind. In this study, even the commonly used reference gene 16S rRNA demonstrated large variability in stability depending on the conditions studied and how the data were analysed. As previously suggested, the best approach may be to use a geometric mean of multiple genes to normalise qPCR results. As researchers continue to validate reference genes for various organisms in multiple growth conditions and sampling time points, it may be possible to make informed predictions as to which genes may be most suitable to validate for a given experimental design, but in the meantime, the reference genes used to normalise qPCR data should be selected with caution.
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Affiliation(s)
- Adina R Bujold
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, Ontario, Canada.
| | - Janet I MacInnes
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, Ontario, Canada.
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Ito H. The genetic organization of the capsular polysaccharide biosynthesis region of Actinobacillus pleuropneumoniae serotype 14. J Vet Med Sci 2015; 77:583-6. [PMID: 25648373 PMCID: PMC4478738 DOI: 10.1292/jvms.14-0174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The genetic organization of the gene involved in the capsular polysaccharide
(CPS) biosynthesis of Actinobacillus pleuropneumoniae serotype 14 has
been determined. The DNA region for the CPS biosynthesis of serotype 14
(cps14) comprised 9 open reading frames, designated as
cps14AB1B2B3CDEFG genes, encoding
Cps14A to Cps14G protein, respectively. Cps14A was similar to CpsA of A.
pleuropneumoniae serotypes 1, 4 and 12; the Cps14B1 and
Cps14B2 were similar to CpsB of A. pleuropneumoniae
serotypes 1, 4 and 12, suggesting that CPS structure of A.
pleuropneumoniae serotype 14 would belong to Group I including A.
pleuropneumoniae serotypes 1, 4, 12 and 15. Surprisingly, the overall
nucleotide sequence, deduced amino acid sequence, and the genetic organization of the
cps14 were nearly identical to those of Actinobacillus
suis. This study will provide the molecular basic knowledge for development of
diagnostics and vaccine of A. pleuropneumoniae serotype 14.
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Affiliation(s)
- Hiroya Ito
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, Japan
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Ito H, Sueyoshi M. The genetic organization of the capsular polysaccharide biosynthesis region of Actinobacillus pleuropneumoniae serotype 15. J Vet Med Sci 2014; 77:483-6. [PMID: 25502540 PMCID: PMC4427752 DOI: 10.1292/jvms.14-0203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Nucleotide sequence determination and analysis of the cps gene involved
in the capsular polysaccharide biosynthesis of Actinobacillus
pleuropneumoniae serotype 15 revealed the presence of three open reading
frames, designated as cps15ABC genes. At the protein level, Cps15A and
Cps15B showed considerably high homology to CpsA (67.0 to 68.7%) and CpsB (31.7 to 36.8%),
respectively, of A. pleuropneumoniae serotypes 1, 4 and 12, revealing the
common genetic organization of the cps among serotypes 1, 4, 12 and 15.
However, Cps15C showed no homology to any proteins of A. pleuropneumoniae
serotypes, indicating that cps15C may be specific to serotype 15. This
study will provide the basic molecular knowledge necessary for the development of
diagnostics and a vaccine for A. pleuropneumoniae serotype 15.
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Affiliation(s)
- Hiroya Ito
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
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Abstract
The assembled and annotated genome of Actinobacillus suis ATCC 33415T is reported here. The 2,501,598-bp genome encodes 2,246 open reading frames (ORFs) with strain variable incursion of an integrative conjugative element into a tRNA locus. Comparative analysis of the deduced gene set should inform our understanding of pathogenesis, genomic plasticity, and serotype variation.
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