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Roh H, Kannimuthu D. Genomic and Transcriptomic Diversification of Flagellin Genes Provides Insight into Environmental Adaptation and Phylogeographic Characteristics in Aeromonas hydrophila. MICROBIAL ECOLOGY 2024; 87:65. [PMID: 38695873 PMCID: PMC11065939 DOI: 10.1007/s00248-024-02373-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/01/2024] [Indexed: 05/05/2024]
Abstract
Aeromonas hydrophila is an opportunistic motile pathogen with a broad host range, infecting both terrestrial and aquatic animals. Environmental and geographical conditions exert selective pressure on both geno- and phenotypes of pathogens. Flagellin, directly exposed to external environments and containing important immunogenic epitopes, may display significant variability in response to external conditions. In this study, we conducted a comparative analysis of ~ 150 A. hydrophila genomes, leading to the identification of six subunits of the flagellin gene (fla-1 to fla-4, flaA, and flaB). Individual strains harbored different composition of flagellin subunits and copies. The composition of subunits showed distinct patterns depending on environmental sources. Strains from aquatic environments were mainly comprised of fla-1 to fla-4 subunits, while terrestrial strains predominated in groups harboring flaA and flaB subunits. Each flagellin showed varying levels of expression, with flaA and flaB demonstrating significantly higher expression compared to others. One of the chemotaxis pathways that control flagellin movement through a two-component system was significantly upregulated in flaA(+ 1)/flaB(+ 1) group, whereas flaA and flaB showed different transcriptomic expressions. The genes positively correlated with flaA expression were relevant to biofilm formation and bacterial chemotaxis, but flaB showed a negative correlation with the genes in ABC transporters and quorum sensing pathway. However, the expression patterns of fla-2 to fla-4 were identical. This suggests various types of flagellin subunits may have different biological functions. The composition and expression levels of flagellin subunits could provide valuable insights into the adaptation of A. hydrophila and the differences among strains in response to various external environments.
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Affiliation(s)
- HyeongJin Roh
- Pathogen Transmission and Disease Research Group, Institute of Marine Research, PO Box 1870 Nordnes 5870, Bergen, Norway.
| | - Dhamotharan Kannimuthu
- Pathogen Transmission and Disease Research Group, Institute of Marine Research, PO Box 1870 Nordnes 5870, Bergen, Norway
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Yadav SK, Dash P, Sahoo PK, Garg LC, Dixit A. Recombinant outer membrane protein OmpC induces protective immunity against Aeromonashydrophila infection in Labeorohita. Microb Pathog 2021; 150:104727. [PMID: 33429054 DOI: 10.1016/j.micpath.2020.104727] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/26/2020] [Accepted: 12/27/2020] [Indexed: 01/06/2023]
Abstract
Aeromonashydrophila is an opportunistic pathogen that causes enormous loss to aquaculture industry. The outer membrane proteins of Aeromonas help in bacterium-host interaction, and are considered to be potential vaccine candidates. In the present study, we evaluated immunogenicity and protective efficacy of recombinant OmpC (rOmpC) of A. hydrophila in Indian major carp, Labeorohita. The rOmpC-vaccinated fish produced specific anti-rOmpC antibodies with a significant antibody titer, and the antisera could specifically detect the rOmpC in the cell lysates of Escherichia coli expressing rOmpC and cross-react with different Aeromonas lysates, indicating the suitability of the anti-rOmpC antisera to detect Aeromonas infection. A significant increase was noted in ceruloplasmin level, myeloperoxidase and anti-protease activities in transient and temporal manner the sera of the rOmpC-immunized fish as compared to PBS-control fish. Higher agglutination- and hemolytic activity titers in the anti-rOmpC antisera indicate stimulation of innate immunity. Expression of immune-related genes comprising various acute phase proteins, cytokines and inflammatory response molecules were modulated in the head kidney of rOmpC-immunized L. rohita. While IgM, IL1β, and TLR-22 were significantly up-regulated at early time points (3 h-72 h), the others showed a transient augmentation at both early and later time points (SOD, lysozymes C and G, NKEF-B, C3, CXCa and TNF-α) in the rOmpC-immunized L. rohita in comparison to PBS-injected controls. These data suggest that the rOmpC-induced immune response is temporally regulated to confer immunity. In vivo challenge of the rOmpC-immunized fish with A. hydrophila showed significantly greater survival when compared to PBS-injected control fish. Thus, our results highlight the immunomodulatory role of rOmpC and demonstrate its protective efficacy in L. rohita, along with the use of anti-rOmpC antisera in detecting Aeromonas infections.
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Affiliation(s)
- Sunita Kumari Yadav
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Pujarini Dash
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Pramoda Kumar Sahoo
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Lalit C Garg
- Gene Regulation Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Aparna Dixit
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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An ancestral genomic locus in Mycobacterium tuberculosis clinical isolates from India hints the genetic link with Mycobacterium canettii. Int Microbiol 2020; 23:397-404. [PMID: 31898033 DOI: 10.1007/s10123-019-00113-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/06/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Tuberculosis remains a worldwide public health emergency. To better understand M. tuberculosis and to identify genomic variations characteristic to the Indian clinical isolates by a low-cost method, a genomic subtractive hybridization between M. tuberculosis H37Rv and a clinical isolate from South India was performed. RESULTS This revealed a novel 0.4-kb subtractive fragment which was used as a handle to pull out a 4.5-kb genomic region characteristic to the clinical isolate and was absent in H37Rv. On further studies, this 4.5-kb region was found to be present in 91% of the M. tuberculosis clinical isolates screened from Kerala, a state in South India. Interestingly, this novel region has 99% identity (with 100% query coverage) with genomic regions of M. canettii. DISCUSSION The present study hypothesizes that this locus was present in the recent common environmental ancestor of mycobacteria, retained to the maximum extent in M. canettii and ancestral isolates of M. tuberculosis, and later deleted in other modern lineages of M. tuberculosis. Thus, this region may serve as one of the links between the pathogenic mycobacteria and the environmental species. We also propose that the Indian isolates of M. tuberculosis might be closely related to the putative progenitor M. prototuberculosis with respect to this locus. More studies on other genomic loci from different strains of M. tuberculosis are required to establish more links in this direction.
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Foysal MJ, Momtaz F, Ali MH, Siddik MAB, Chaklader MR, Rahman MM, Prodhan MSH, Cole A. Molecular characterization and interactome analysis of aerolysin (aer) gene from fish pathogen Aeromonas veronii: The pathogenicity inferred from sequence divergence and linked to histidine kinase (cheA). JOURNAL OF FISH DISEASES 2019; 42:465-475. [PMID: 30734315 DOI: 10.1111/jfd.12954] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 06/09/2023]
Abstract
Aerolysin (aer) is one of the most important and abundant virulence factors in the infection of fish by Aeromonas veronii. A comprehensive study on the molecular characterization and pathogenicity of the aer gene from 34 A. veronii isolates from diseased carp and catfish was carried out and its interactome was analysed to observe the functional correlations between aer and other proteins within the A. veronii network. The PCR-based amplification of aer from the 34 isolates of A. veronii showed more aer-positive isolates from catfish with a high pathogenic potential in the in vivo challenge test than the carp fish. The analysis of aer gene sequence from challenged fish revealed significant sequence divergence according to the types and geographical distribution of the fish. The networking analysis of aer from the model A. veronii B565 revealed histidine kinase (cheA) as the most functional interacting partner. The study of the interaction between aer from the experimental A. veronii and cheA demonstrated that the A chain of cheA plays a more important role than the corresponding B chain during contact, and a linker sequence of 15 residues controlled the entire interaction process. Therefore, cheA could be an excellent drug target for controlling A. veronii infection of fish.
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Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Farhana Momtaz
- Department of Microbiology, Chittagong University, Chittagong, Bangladesh
| | - Md Hazrat Ali
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Muhammad A B Siddik
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Md Reaz Chaklader
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Md Mahbubur Rahman
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Md Shamsul Haque Prodhan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Anthony Cole
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
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Cai W, Willmon E, Burgos FA, Ray CL, Hanson T, Arias CR. Biofilm and Sediment are Major Reservoirs of Virulent Aeromonas hydrophila (vAh) in Catfish Production Ponds. JOURNAL OF AQUATIC ANIMAL HEALTH 2019; 31:112-120. [PMID: 30549304 DOI: 10.1002/aah.10056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
The genus Aeromonas comprises more than 60 recognized species that include many important fish pathogens such as the causative agents of furunculosis and motile Aeromonas septicemia (MAS). Although MAS is typically considered a secondary infection, a new virulent A. hydrophila (vAh) strain has been causing devastating losses to the catfish industry in Alabama since 2009. The objective of this study was to characterize the spatiotemporal distribution of Aeromonas sp. and, specifically, vAh in a commercial catfish farm in western Alabama. We sampled biofilm, sediment, and water from three ponds during four consecutive months during the growing season. Total aerobic counts were between 8.8 × 105 and 1.5 × 106 CFU/mL but were significantly higher in biofilm and sediment than in water throughout the sampling period. Total Aeromonas counts in water samples significantly increased in all three ponds after the month of August and ranged from 7.8 × 103 to 4.9 × 104 CFU/mL. A similar trend was observed in biofilm and sediment samples for which total Aeromonas counts increased in samples taken in late summer to early fall. Over time, the concentration of Aeromonas in water samples decreased by one order of magnitude, while there was a significant increase in sediments as temperature dropped. The virulent vAh was detected in 35.4% of biofilm samples and 22.9% of sediment samples, suggesting that both environments serve as the major reservoir for this pathogen. Future monitoring efforts should focus on targeting sediment and biofilms since samples of these appear to naturally enrich for the presence of vAh and other Aeromonas species.
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Affiliation(s)
- Wenlong Cai
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USA
| | - Evelyn Willmon
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USA
- Department of Poultry Sciences, Auburn University, 260 Lem Morrison Drive, Auburn, Alabama, 36849, USA
| | - Francisca A Burgos
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USA
| | - Candis L Ray
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USA
- U.S. Department of Agriculture, Agricultural Research Service, Harry K. Dupree Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas, 72160, USA
| | - Terry Hanson
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USA
| | - C R Arias
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USA
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Zhou Y, Fan Y, Jiang N, Liu W, Shi Y, Zhao J, Zeng L. Molecular characteristics and virulence analysis of eight Aeromonas hydrophila isolates obtained from diseased Amur sturgeon Acipenser schrenckii Brandt, 1869. J Vet Med Sci 2018; 80:421-426. [PMID: 29367518 PMCID: PMC5880820 DOI: 10.1292/jvms.17-0529] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Aeromonas hydrophila is an opportunistic pathogen of a variety of aquatic animals that displays extreme diversity in drug resistance, phenotypes, virulence genes, and virulence. In this study, eight
pathogenic A. hydrophila strains were isolated from diseased Amur sturgeons and investigated for their sensitivity to select antibiotics, their phenotype, virulence genes, and virulence. According to the
phylogenetic analysis of the DNA gyrase subunit B protein, the eight isolates formed a single branch in the A. hydrophila group. The antibiotics ceftazidime, cefuroxime, cefoperazone, cefotaxime,
ceftriaxone, aztreonam, and cefepime appeared effective against them. All of the isolates possessed the virulence genes for aerolysin, flagellin, heat-stable cytotonic enterotoxin, heat-labile cytotonic enterotoxin,
hemolysin, and elastase, while only one isolate, HZ8, possessed the gene for lateral flagella. The cytolytic enterotoxin and lipase genes were present in all isolates, except in ZJ10 and ZJ12. Enterobacterial repetitive
intergenic consensus sequence PCR indicated that the eight A. hydrophila isolates could be divided into four types. Isolates YW2, TR3, HZ8 and ZJ10, each representing a different type, were selected for
challenge experiments. The challenge tests revealed that isolate HZ8 had the lowest lethal dose, causing 50% mortality at 2.30 × 104 colony forming units (cfu)/ml. The isolate ZJ10 had the
highest LD50, 1.25 × 106 cfu/ml. Knowledge of the characteristics of the A. hydrophila isolates obtained from Amur sturgeon will be beneficial in developing
potential disease control strategies.
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Affiliation(s)
- Yong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
| | - Yuding Fan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
| | - Nan Jiang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
| | - Wenzhi Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
| | - Yuheng Shi
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
| | - Jianqing Zhao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
| | - Lingbing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
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Wang ST, Meng XZ, Li LS, Dang YF, Fang Y, Shen Y, Xu XY, Wang RQ, Li JL. Biological parameters, immune enzymes, and histological alterations in the livers of grass carp infected with Aeromonas hydrophila. FISH & SHELLFISH IMMUNOLOGY 2017; 70:121-128. [PMID: 28866274 DOI: 10.1016/j.fsi.2017.08.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/11/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Aeromonas hydrophila is the causative agent of bacterial septicemia that is frequently observed in grass carp, Ctenopharyngodon idellus. In this study, we evaluated the biological parameters and immune enzymes in the liver of grass carp following A. hydrophila infection and quantified the alterations in liver histology using a semi-quantitative system. For the biological parameters, we found that the liver somatic index (LSI) was more sensitive than Fulton's condition factor (CF) and was significantly decreased at three days post-injection (DPI). At the immune enzyme level, the level of peroxidase (POD) in the liver significantly increased at 1 and 3 DPI. The activity of alkaline phosphatase (ALP) significantly increased at 3 DPI. Similarly, acid phosphatase (ACP) activity significantly increased at 1, 3, and 5 DPI. Histologically, the results indicated that the liver index at 3, 5, and 7 DPI was significantly higher than that of control groups. The regressive alterations as the highly variable reactions patterns and its index at 5 DPI was significantly higher than that of 1, 21 DPI, and the control groups. Based on our results, we suggest that grass carp resist A. hydrophila infection via an innate immune mechanism in the liver. The findings of this study will help elucidate the underlying mechanisms of resistance to A. hydrophila infection.
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Affiliation(s)
- Shen-Tong Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Xin-Zhan Meng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Li-Sen Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Yun-Fei Dang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Yuan Fang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Xiao-Yan Xu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China
| | - Rong-Quan Wang
- Key Laboratory of Conventional Freshwater Fish Breeding and Health Culture Technology Germplasm Resources, Ministry of Agriculture, Suzhou Shenhang Eco-technology Development Limited Company, Suzhou 215221, China
| | - Jia-Le Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, PR China.
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Yadav SK, Meena JK, Sharma M, Dixit A. Recombinant outer membrane protein C of Aeromonas hydrophila elicits mixed immune response and generates agglutinating antibodies. Immunol Res 2016; 64:1087-99. [DOI: 10.1007/s12026-016-8807-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Abu-Elala N, Abdelsalam M, Marouf S, Setta A. Comparative analysis of virulence genes, antibiotic resistance and gyrB
-based phylogeny of motile Aeromonas
species isolates from Nile tilapia and domestic fowl. Lett Appl Microbiol 2015; 61:429-36. [DOI: 10.1111/lam.12484] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/04/2015] [Accepted: 08/04/2015] [Indexed: 11/25/2022]
Affiliation(s)
- N. Abu-Elala
- Department of Fish Diseases and Management; Faculty of Veterinary Medicine; Cairo University; Giza Egypt
| | - M. Abdelsalam
- Department of Fish Diseases and Management; Faculty of Veterinary Medicine; Cairo University; Giza Egypt
| | - Sh. Marouf
- Department of Microbiology; Faculty of Veterinary Medicine; Cairo University; Giza Egypt
| | - A. Setta
- Department of Poultry Diseases; Faculty of Veterinary Medicine; Cairo University; Giza Egypt
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Aeromonas hydrophila produces conductive nanowires. Res Microbiol 2014; 165:794-802. [DOI: 10.1016/j.resmic.2014.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 09/01/2014] [Accepted: 09/07/2014] [Indexed: 01/28/2023]
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Noor R, Hasan MF, Rahman MM. Molecular characterization of the virulent microorganisms along with their drug-resistance traits associated with the export quality frozen shrimps in Bangladesh. SPRINGERPLUS 2014; 3:469. [PMID: 25197622 PMCID: PMC4155057 DOI: 10.1186/2193-1801-3-469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/15/2014] [Indexed: 11/10/2022]
Abstract
Current investigation characterized export quality shrimp samples in terms of pathogenic load along with the drug-resistance traits of the isolates, and detected the major virulent genes present in those isolates. Among the 30 such shrimp samples (15 each of Macrobrachium rosenbergi or Golda and Penaeus monodon or Bagda) studied, almost all were found to be contaminated with a huge load of bacteria (106–108 cfu/g) and fungi (104–105 cfu/g). Among the specific pathogens, presence of Escherichia coli, Vibrio spp., Aeromonas spp., Klebsiella spp., Shigella spp., Staphylococcus spp. and Listeria spp. were detected, of which most were likely to be resistant against commonly used antibiotics. Gene specific polymerase chain reaction (PCR) study revealed the presence of eae gene in E. coli, aero specific gene in Aeromonas spp., and sodB gene in Vibrio spp. Together with the huge extent of microbial contamination with a drug-resistance attribute, presence of such virulent genes further projects the probable public health risk upon consumption of the export quality shrimps.
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Affiliation(s)
- Rashed Noor
- Department of Microbiology, Stamford University Bangladesh, 51 Siddeswari Road, Dhaka, 1217 Bangladesh
| | - Md Faqrul Hasan
- Department of Microbiology, University of Dhaka, Fullar Road, Dhaka, 1000 Bangladesh
| | - M Majibur Rahman
- Department of Microbiology, University of Dhaka, Fullar Road, Dhaka, 1000 Bangladesh
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12
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Phenotypic and molecular characteristics of an Aeromonas hydrophila strain isolated from the River Nile. Microbiol Res 2014; 169:547-52. [DOI: 10.1016/j.micres.2013.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/28/2013] [Accepted: 11/05/2013] [Indexed: 11/22/2022]
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13
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Yadav SK, Sahoo PK, Dixit A. Characterization of immune response elicited by the recombinant outer membrane protein OmpF of Aeromonas hydrophila, a potential vaccine candidate in murine model. Mol Biol Rep 2014; 41:1837-48. [DOI: 10.1007/s11033-014-3033-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 01/03/2014] [Indexed: 11/28/2022]
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14
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Kumar P, Virdi JS. Identification and distribution of putative virulence genes in clinical strains of Yersinia enterocolitica biovar 1A by suppression subtractive hybridization. J Appl Microbiol 2012; 113:1263-72. [PMID: 22897337 DOI: 10.1111/j.1365-2672.2012.05427.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/29/2012] [Accepted: 08/02/2012] [Indexed: 01/13/2023]
Abstract
AIMS To detect putative virulence genes in clinical strains of Yersinia enterocolitica biovar 1A by suppression subtractive hybridization between two closely related strains of clinical and nonclinical origin having the same serotype (O:6,30-6,31). METHODS AND RESULTS Suppression Subtractive Hybridization (SSH) was used to identify genomic differences between clinical (serotype O:6,30-6,31, from diarrhoeic human stools) and nonclinical (serotype O:6,30-6,31, from wastewater) strains of Y. enterocolitica biovar 1A. Following genomic subtraction and DNA sequencing, nine DNA sequences that were present only in clinical biovar 1A strains were identified. The sequences identified using SSH showed similarity to conserved hypothetical proteins, proteins related to iron acquisition and haemin storage, type 1 secretion proteins, flagellar hook proteins, exported protein and ABC transport system. All these sequences showed high similarity with Y. enterocolitica 8081 (biovar 1B). The distribution of these genes was further analysed using PCR in 26 clinical strains of Y. enterocolitica biovar 1A. The results revealed that the distribution of these genes was not uniform. CONCLUSIONS Genes related to iron acquisition and storage, and flagellar proteins might be responsible for virulence of some of the clinical strains of Y. enterocolitica biovar 1A. SIGNIFICANCE AND IMPACT OF THE STUDY Genes identified in this study might be useful in understanding the pathogenic potential of clinical strains of Y. enterocolitica biovar 1A.
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Affiliation(s)
- P Kumar
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, New Delhi, India
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Banerjee C, Goswami R, Verma G, Datta M, Mazumder S. Aeromonas hydrophila induced head kidney macrophage apoptosis in Clarias batrachus involves the activation of calpain and is caspase-3 mediated. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 37:323-333. [PMID: 22366184 DOI: 10.1016/j.dci.2012.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 02/13/2012] [Accepted: 02/15/2012] [Indexed: 05/31/2023]
Abstract
The mechanism of macrophage cytotoxicity induced by Aeromonas hydrophila is yet unresolved. We observed A. hydrophila induces Head Kidney Macrophage (HKM) apoptosis in Clarias batrachus, as evident from Hoechst 33342 and AnnexinV-Propidium Iodide staining and presence of oligonucleosomal DNA ladder. Initiation of apoptosis required the bacteria to be alive, be actively phagocytosed into HKM and was dependent on host proteins. Elevated cytosolic calcium and consequent calpain activity that declined following pre-incubation with EGTA, verapamil and nifedipine implicates the role of calcium influx through voltage gated calcium channels and calpain in A. hydrophila-induced HKM apoptosis. Though, calpain-1 and -2 were involved, calpain-2 appeared to be more important in the process. EGTA, verapamil, nifedipine and calpain-2 inhibitor reduced caspase-3 activity and apoptosis. We conclude that A. hydrophila alters cytosolic calcium homeostasis initiating the activation of calpains, more specifically calpain-2, which leads to caspase-3 mediated HKM apoptosis in C. batrachus.
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Affiliation(s)
- Chaitali Banerjee
- Immunobiology Laboratory, Department of Zoology, University of Delhi, Delhi 110 007, India
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Zhao Y, Liu Q, Wang X, Zhou L, Wang Q, Zhang Y. Surface display of Aeromonas hydrophila GAPDH in attenuated Vibrio anguillarum to develop a Noval multivalent vector vaccine. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:963-970. [PMID: 21246232 DOI: 10.1007/s10126-010-9359-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 12/23/2010] [Indexed: 05/30/2023]
Abstract
Displaying foreign antigens on the surface of attenuated or avirulent bacteria is an important strategy to develop live multivalent vector vaccines. In our previous work, several efficient surface display systems have been established based on outer membrane anchoring elements, which could successfully display heterologous proteins in attenuated Vibrio anguillarum. In this work, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from pathogenic Aeromonas hydrophila LSA34 was fused to seven display systems and introduced into attenuated V. anguillarum strain MVAV6203 (AV) to get seven GAPDH-display strains. The strain AV/pN-gapA showed the best display efficacy of GAPDH and was tested as the multivalent vaccine candidate. Further immune protection evaluation of AV/pN-gapA in turbot (Scophtalmus maximus) demonstrated that the attenuated V. anguillarum with surface-displayed GAPDH of A. hydrophila LSA34 effectively protected turbot from the infections of A. hydrophila and V. anguillarum and showed potential value for further multivalent vaccine development.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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17
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Pridgeon JW, Klesius PH, Mu X, Carter D, Fleming K, Xu D, Srivastava K, Reddy G. Identification of unique DNA sequences present in highly virulent 2009 Alabama isolates of Aeromonas hydrophila. Vet Microbiol 2011; 152:117-25. [DOI: 10.1016/j.vetmic.2011.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 04/07/2011] [Accepted: 04/08/2011] [Indexed: 10/18/2022]
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18
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Reimundo P, Rivas AJ, Osorio CR, Méndez J, Pérez-Pascual D, Navais R, Gómez E, Sotelo M, Lemos ML, Guijarro JA. Application of suppressive subtractive hybridization to the identification of genetic differences between two Lactococcus garvieae strains showing distinct differences in virulence for rainbow trout and mouse. MICROBIOLOGY-SGM 2011; 157:2106-2119. [PMID: 21546587 DOI: 10.1099/mic.0.047969-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lactococcus garvieae is the causative microbial agent of lactococcosis, an important and damaging fish disease in aquaculture. This bacterium has also been isolated from vegetables, milk, cheese, meat and sausages, from cow and buffalo as a mastitis agent, and even from humans, as an opportunistic infectious agent. In this work pathogenicity experiments were performed in rainbow trout and mouse models with strains isolated from human (L. garvieae HF) and rainbow trout (L. garvieae UNIUDO74; henceforth referred to as 074). The mean LD(50) value in rainbow trout obtained for strain 074 was 2.1 × 10(2) ± 84 per fish. High doses of the bacteria caused specific signs of disease as well as histological alterations in mice. In contrast, strain HF did not prove to be pathogenic either for rainbow trout or for mice. Based on these virulence differences, two suppressive subtractive hybridizations were carried out to identify unique genetic sequences present in L. garvieae HF (SSHI) and L. garvieae 074 (SSHII). Differential dot-blot screening of the subtracted libraries allowed the identification of 26 and 13 putative ORFs specific for L. garvieae HF and L. garvieae 074, respectively. Additionally, a PCR-based screening of 12 of the 26 HF-specific putative ORFs and the 13 074-specific ones was conducted to identify their presence/absence in 25 L. garvieae strains isolated from different origins and geographical areas. This study demonstrates the existence of genetic heterogeneity within L. garvieae isolates and provides a more complete picture of the genetic background of this bacterium.
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Affiliation(s)
- Pilar Reimundo
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Amable J Rivas
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carlos R Osorio
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jéssica Méndez
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - David Pérez-Pascual
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Roberto Navais
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Esther Gómez
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Miguel Sotelo
- Biomar Iberia, Apdo 16, 34210 Dueñas, Palencia, Spain
| | - Manuel L Lemos
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José A Guijarro
- Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
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19
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Turska-Szewczuk A, Guz L, Lindner B, Pietras H, Russa R, Holst O. Structural characterization of the O-specific polysaccharide from the lipopolysaccharide of the fish pathogen Aeromonas bestiarum strain P1S. Carbohydr Res 2011; 346:815-21. [PMID: 21377659 DOI: 10.1016/j.carres.2011.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/31/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
The O-specific polysaccharide obtained by mild-acid degradation of lipopolysaccharide of Aeromonas bestiarum P1S was studied by sugar and methylation analyses along with (1)H and (13)C NMR spectroscopy. The sequence of the sugar residues was determined using (1)H,(1)H NOESY and (1)H,(13)C HMBC experiments. The O-specific polysaccharide was found to be a high-molecular-mass polysaccharide composed of tetrasaccharide repeating units of the structure [formula in text]. Since small amounts of a terminal Quip3N residue were identified in methylation analysis, it was assumed that the elucidated structure also represented the biological repeating unit of the O-specific polysaccharide.
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Affiliation(s)
- Anna Turska-Szewczuk
- Department of Genetics and Microbiology, M. Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland.
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20
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Stevens P, van Elsas JD. A putative genomic island, PGI-1, in Ralstonia solanacearum biovar 2 revealed by subtractive hybridization. Antonie van Leeuwenhoek 2010; 98:359-77. [PMID: 20467813 PMCID: PMC2935973 DOI: 10.1007/s10482-010-9450-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/20/2010] [Indexed: 01/14/2023]
Abstract
Ralstonia solanacearum biovar 2, a key bacterial pathogen of potato, has recently established in temperate climate waters. On the basis of isolates obtained from diseased (potato) plants, its genome has been assumed to be virtually clonal, but information on environmental isolates has been lacking. Based on differences in pulsed-field gel electrophoresis patterns, we compared the genomes of two biovar 2 strains with different life histories. Thus, genomic DNA of the novel environmental strain KZR-5 (The Netherlands) was compared to that of reference potato strain 715 (Bangladesh) by suppressive subtractive hybridization. Various strain-specific sequences were found, all being homologous to those found in the genome of reference potato strain 1609. Approximately 20% of these were related to genes involved in recombinational processes. We found a deletion of a 17.6-Kb region, denoted as a putative genomic island PGI-1, in environmental strain KZR-5. The deleted region was, at both extremes, flanked by a composite of two insertion sequence (IS) elements, identified as ISRso2 and ISRso3. The PGI-1 region contained open reading frames that putatively encoded a (p)ppGpp synthetase, a transporter protein, a transcriptional regulator, a cellobiohydrolase, a site-specific integrase/recombinase, a phage-related protein and seven hypothetical proteins. As yet, no phenotype could be assigned to the loss of PGI-1. The ecological behavior of strain KZR-5 was compared to that of reference strain 715. Strain KZR-5 showed enhanced tolerance to 4°C as compared to the reference strain, but was not affected in its virulence on tomato.
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Affiliation(s)
- Patricia Stevens
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen, 9759 AA Haren, The Netherlands
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21
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Poobalane S, Thompson KD, Ardó L, Verjan N, Han HJ, Jeney G, Hirono I, Aoki T, Adams A. Production and efficacy of an Aeromonas hydrophila recombinant S-layer protein vaccine for fish. Vaccine 2010; 28:3540-7. [DOI: 10.1016/j.vaccine.2010.03.011] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 03/06/2010] [Accepted: 03/08/2010] [Indexed: 11/25/2022]
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22
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Turska-Szewczuk A, Kozinska A, Russa R, Holst O. The structure of the O-specific polysaccharide from the lipopolysaccharide of Aeromonas bestiarum strain 207. Carbohydr Res 2010; 345:680-4. [PMID: 20080230 DOI: 10.1016/j.carres.2009.12.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 12/16/2009] [Accepted: 12/29/2009] [Indexed: 11/19/2022]
Abstract
The O-specific polysaccharide obtained by mild-acid degradation of Aeromonas bestiarum 207 lipopolysaccharide was studied by sugar and methylation analyses along with (1)H and (13)C NMR spectroscopy. The sequence of the sugar residues was determined by ROESY and HMBC experiments. It is concluded that the O-polysaccharide is composed of branched pentasaccharide repeating units of the following structure: [structure: see the text]
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Affiliation(s)
- Anna Turska-Szewczuk
- Department of Genetics and Microbiology, M. Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland.
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23
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Fünfhaus A, Ashiralieva A, Borriss R, Genersch E. Use of suppression subtractive hybridization to identify genetic differences between differentially virulent genotypes of Paenibacillus larvae, the etiological agent of American Foulbrood of honeybees. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:240-250. [PMID: 23765853 DOI: 10.1111/j.1758-2229.2009.00039.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Paenibacillus larvae is the causative agent of American Foulbrood of honeybees, a fatal brood disease not only killing infected larvae but also lethal to infected colonies. Recently four different genotypes of P. larvae (enterobacterial repetitive intergenic consensus I-IV) have been described and it was shown that these genotypes also differ in phenotype, especially in virulence. To unravel the genetic differences between these four genotypes, suppression subtractive hybridization was used. From 106 analysed clones, 92 represented genotype-specific sequences, whereas 14 sequences turned out to be specific only for the particular strain used as tester in the subtraction. Nearly half of the sequences (46%) could only be annotated based on poorly characterized sequences. The remaining sequences corresponded to categories related to metabolism, especially secondary metabolite biosynthesis, transport and catabolism, to information storage and processing, and to cellular processes. In particular, we could show that the P. larvae genome contains genes and/or giant gene clusters coding for antibiotics, and we identified the first P. larvae toxin, a member of the family of adenosine diphosphate-ribosyltransferases.
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Affiliation(s)
- Anne Fünfhaus
- Institute for Bee Research, Friedrich-Engels-Str. 32, 16540 Hohen Neuendorf, Germany. Institute for Biology/Bacterial Genetics, Humboldt University Berlin, Chausseestr. 117, 10115 Berlin, Germany
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24
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Khushiramani R, Girisha SK, Karunasagar I, Karunasagar I. Evaluation of a digoxigenin-labelled probe for detection of Aeromonas spp. Lett Appl Microbiol 2009; 48:383-5. [PMID: 19187505 DOI: 10.1111/j.1472-765x.2008.02491.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An outer membrane protein-based Digoxigenin (DIG)-labelled DNA probe was developed for the specific detection of Aeromonas sp. from food/environmental/clinical samples. Dot blot reaction answered for all the Aeromonas isolates and was negative for Escherichia coli, Pseudomonas sp., Klebsiella sp., Vibrio parahaemolyticus, V. harveyi, V. alginolyticus, V. vulnificus. Edwardsiella tarda and Staphylococcus sp. As this protein is highly conserved in various Aeromonas species, the probe has the potential for use as a rapid and reliable diagnostic tool.
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Affiliation(s)
- R Khushiramani
- Department of Fishery Microbiology, Karnataka Veterinary, Animal and Fisheries Sciences University, College of Fisheries, Mangalore, India
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25
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Vidal M, Prado V, Whitlock GC, Solari A, Torres AG, Vidal RM. Subtractive hybridization and identification of putative adhesins in a Shiga toxin-producing eae-negative Escherichia coli. Microbiology (Reading) 2008; 154:3639-3648. [DOI: 10.1099/mic.0.2008/021212-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Maricel Vidal
- Programa de Microbiología y Micologia, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Valeria Prado
- Programa de Microbiología y Micologia, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gregory C. Whitlock
- Department of Clinical Laboratory Sciences, University of Texas Medical Branch, Galveston, TX 77555-1070, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1070, USA
| | - Aldo Solari
- Programa de Biologia Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Alfredo G. Torres
- Department of Pathology and Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX 77555-1070, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1070, USA
| | - Roberto M. Vidal
- Programa de Microbiología y Micologia, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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26
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Identification of differentially expressed immune-relevant genes in Chinese soft-shelled turtle (Trionyx sinensis) infected with Aeromonas hydrophila. Vet Immunol Immunopathol 2008; 125:82-91. [DOI: 10.1016/j.vetimm.2008.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 05/08/2008] [Accepted: 05/08/2008] [Indexed: 12/18/2022]
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27
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Correlation between detection of a plasmid and high-level virulence of Vibrio nigripulchritudo, a pathogen of the shrimp Litopenaeus stylirostris. Appl Environ Microbiol 2008; 74:3038-47. [PMID: 18359828 DOI: 10.1128/aem.02680-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio nigripulchritudo, the etiological agent of Litopenaeus stylirostris summer syndrome, is responsible for mass mortalities of shrimp in New Caledonia. Epidemiological studies led to the suggestion that this disease is caused by an emergent group of pathogenic strains. Genomic subtractive hybridization was carried out between two isolates exhibiting low and high virulence. Our subtraction library was constituted of 521 specific fragments; 55 of these were detected in all virulent isolates from our collection (n = 32), and 13 were detected only in the isolates demonstrating the highest pathogenicity (n = 19), suggesting that they could be used as genetic markers for high virulence capacity. Interestingly, 10 of these markers are carried by a replicon of 11.2 kbp that contains sequences highly similar to those of a plasmid detected in Vibrio shilonii, a coral pathogen. The detection of this plasmid was correlated with the highest pathogenicity status of the isolates from our collection. The origin and consequence of this plasmid acquisition are discussed.
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28
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Mena J, Chen C. Identification of strain-specific DNA of Actinobacillus actinomycetemcomitans by representational difference analysis. ACTA ACUST UNITED AC 2007; 22:429-32. [PMID: 17949347 DOI: 10.1111/j.1399-302x.2007.00371.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A genomic subtraction method, the representational difference analysis (RDA), was tested for its use in identifying strain-specific DNA in Actinobacillus actinomycetemcomitans. Subtraction of strain D7S with strain HK1651 yielded D7S-specific 2.3-kilobase (kb) islet-A and 5.3-kb islet-B. Islet-A contains a 1.5-kb region that is homologous to a region found in the A. actinomycetemcomitans plasmid pVT745. Islet-B contains a 2.1-kb homolog of vgr, a component of a DNA repeat element rhs. The distribution of these islets among A. actinomycetemcomitans strains was further examined by polymerase chain reaction. Islet-A was found in nine serotype a and two serotype b strains but was missing from 34 strains. Islet-B was found in one serotype a strain, four serotype d strains and two serotype e strains, but was missing from 34 strains.
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Affiliation(s)
- J Mena
- Division of Primary Oral Health Care, School of Dentistry, University of Southern California, Los Angeles, CA 90089, USA
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29
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Li AQ, Dai N, Yan J, Zhu YL. Screening for metronidazole-resistance associated gene fragments of H pylori by suppression subtractive hybridization. World J Gastroenterol 2007; 13:1847-50. [PMID: 17465479 PMCID: PMC4149965 DOI: 10.3748/wjg.v13.i12.1847] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To screen for metronidazole (MTZ)-resistance associated gene fragments of H pylori by suppression subtractive hybridization (SSH).
METHODS: Five MTZ-resistant (tester, T) and 1 MTZ-susceptible (driver, D) clinical H pylori isolates were selected. Genomic DNAs were prepared and submitted to RsaIdigestion. Then two different adaptors were ligated respectively to the 5’-end of two aliquots of the tester DNA fragments and SSH was made between the tester and driver DNAs. The specific inserts of tester strains were screened and MTZ-resistance related gene fragments were identified by dot blotting.
RESULTS: Among the randomly selected 120 subtractive colonies, 37 DNA fragments had a different number of DNA copies (≥ 2 times) in resistant and susceptible strains and 17 of them had a significantly different number of DNA copies (≥ 3 times). Among the sequences obtained from the 17 DNA fragments, new sequences were found in 10 DNA fragments and duplicated sequences in 7 DNA fragments, representing respectively the sequences of depeptide ABC transporter periplasmic dipeptide-binding protein (dppA), permease protein (dppB), ribosomal protein S4 (rps4), ribonuclease III (rnc), protease (pqqE), diaminopimelate epimerase (dapF), acetatekinase (ackA), H pylori plasmid pHP51 and H pylori 1334.
CONCLUSION: Gene fragments specific to MTZ-resistant H pylori strains can be screened by SSH and may be associated with MTZ-resistant H pylori.
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Affiliation(s)
- Ai-Qing Li
- Department of Gastroenterology, Sir Run Run Shaw Affiliated Hospital, College of Medcine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.
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30
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Guo LH, Shi JN, Zhang Y, Liu XD, Duan J, Wei S. Identification of genetic differences between two clinical isolates of Streptococcus mutans by suppression subtractive hybridization. ACTA ACUST UNITED AC 2006; 21:372-80. [PMID: 17064395 DOI: 10.1111/j.1399-302x.2006.00306.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptococcus mutans is generally considered to be the principal aetiological agent for dental caries. Phenotypic variation in strains is often associated with differences in gene content, so the isolation of DNA fragments from these genes or associated regions is illuminating. The S. mutans strains 9-1 and 9-2, which both colonized the same oral cavity, were selected after screening for the possession of suspected virulence traits. Genomic DNA of strain 9-1 was used as the tester, and that of 9-2 was used as the driver. Suppression subtractive hybridization (SSH) was applied between the tester and the driver DNAs. The subtractive products were cloned into a pCR2.1 vector. Clone libraries representing sequence differences were obtained. The subtractive fragments that were found specifically in strain 9-1 but not in strain 9-2 were identified by dot blotting and then sequenced. BLASTn and BLASTx sequence homology analyses were subsequently performed. Twenty-seven sequences were found in the genome of strain 9-1 that were not in 9-2. Among them, three revealed no homology to published nucleotide sequences while the remaining sequences showed 81-100% homology to known genes of S. mutans strain UA159. These sequences are involved in competence development, signal transduction and transcriptional regulation, repairing stress damage, transport, carbohydrate catabolism, biochemical synthesis, or unknown functions. Differences exist in the genomes of different S. mutans isolates. SSH is effective in screening for S. mutans strain specific DNA sequences.
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Affiliation(s)
- L H Guo
- Department of Oral Biology, Peking University School and Hospital of Stomatology, Beijing, China.
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31
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Jones H, Ostrowski M, Scanlan DJ. A suppression subtractive hybridization approach reveals niche-specific genes that may be involved in predator avoidance in marine Synechococcus isolates. Appl Environ Microbiol 2006; 72:2730-7. [PMID: 16597977 PMCID: PMC1449036 DOI: 10.1128/aem.72.4.2730-2737.2006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Picocyanobacteria of the genus Synechococcus are important contributors to marine primary production and are ubiquitous in the world's oceans. This genus is genetically diverse, and at least 10 discrete lineages or clades have been identified phylogenetically. However, little if anything is known about the genetic attributes which characterize particular lineages or are unique to specific strains. Here, we used a suppression subtractive hybridization (SSH) approach to identify strain- and clade-specific genes in two well-characterized laboratory strains, Synechococcus sp. strain WH8103 (clade III) and Synechococcus sp. strain WH7803 (clade V). Among the genes that were identified as potentially unique to each strain were genes encoding proteins that may be involved in specific predator avoidance, including a glycosyltransferase in strain WH8103 and a permease component of an ABC-type polysaccharide/polyol phosphate export system in WH7803. During this work the genome of one of these strains, WH7803, became available. This allowed assessment of the number of false-positive sequences (i.e., sequences present in the tester genome) present among the SSH-enriched sequences. We found that approximately 9% of the WH8103 sequences were potential false-positive sequences, which demonstrated that caution should be used when this technology is used to assess genomic differences in genetically similar bacterial strains.
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Affiliation(s)
- H Jones
- Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
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32
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Lee CT, Amaro C, Sanjuán E, Hor LI. Identification of DNA sequences specific for Vibrio vulnificus biotype 2 strains by suppression subtractive hybridization. Appl Environ Microbiol 2005; 71:5593-7. [PMID: 16151155 PMCID: PMC1214656 DOI: 10.1128/aem.71.9.5593-5597.2005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio vulnificus can be divided into three biotypes, and only biotype 2, which is further divided into serovars, contains eel-virulent strains. We compared the genomic DNA of a biotype 2 serovar E isolate (tester) with the genomic DNAs of three biotype 1 strains by suppression subtractive hybridization and then tested the distribution of the tester-specific DNA sequences in a wide collection of bacterial strains. In this way we identified three plasmid-borne DNA sequences that were specific for biotype 2 strains irrespective of the serovar and three chromosomal DNA sequences that were specific for serovar E biotype 2 strains. These sequences have potential for use in the diagnosis of eel vibriosis caused by V. vulnificus and in the detection of biotype 2 serovar E strains.
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Affiliation(s)
- Chung-Te Lee
- Department of Microbiology and Immunology, College of Medicine, National Cheng-Kung University, Tainan 701, Taiwan, Republic of China
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33
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Yu HB, Zhang YL, Lau YL, Yao F, Vilches S, Merino S, Tomas JM, Howard SP, Leung KY. Identification and characterization of putative virulence genes and gene clusters in Aeromonas hydrophila PPD134/91. Appl Environ Microbiol 2005; 71:4469-77. [PMID: 16085838 PMCID: PMC1183340 DOI: 10.1128/aem.71.8.4469-4477.2005] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aeromonas hydrophila is a gram-negative opportunistic pathogen of animals and humans. The pathogenesis of A. hydrophila is multifactorial. Genomic subtraction and markers of genomic islands (GIs) were used to identify putative virulence genes in A. hydrophila PPD134/91. Two rounds of genomic subtraction led to the identification of 22 unique DNA fragments encoding 19 putative virulence factors and seven new open reading frames, which are commonly present in the eight virulence strains examined. In addition, four GIs were found, including O-antigen, capsule, phage-associated, and type III secretion system (TTSS) gene clusters. These putative virulence genes and gene clusters were positioned on a physical map of A. hydrophila PPD134/91 to determine their genetic organization in this bacterium. Further in vivo study of insertion and deletion mutants showed that the TTSS may be one of the important virulence factors in A. hydrophila pathogenesis. Furthermore, deletions of multiple virulence factors such as S-layer, serine protease, and metalloprotease also increased the 50% lethal dose to the same level as the TTSS mutation (about 1 log) in a blue gourami infection model. This observation sheds light on the multifactorial and concerted nature of pathogenicity in A. hydrophila. The large number of putative virulence genes identified in this study will form the basis for further investigation of this emerging pathogen and help to develop effective vaccines, diagnostics, and novel therapeutics.
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Affiliation(s)
- H B Yu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Science Drive 4, Singapore 117543, Republic of Singapore
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Juíz-Río S, Osorio CR, de Lorenzo V, Lemos ML. Subtractive hybridization reveals a high genetic diversity in the fish pathogen Photobacterium damselae subsp. piscicida: evidence of a SXT-like element. Microbiology (Reading) 2005; 151:2659-2669. [PMID: 16079344 DOI: 10.1099/mic.0.27891-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photobacterium damselae subsp. piscicida is the causative agent of fish pasteurellosis, a severe disease affecting cultured marine fish worldwide. In this study, suppression subtractive hybridization was used to identify DNA fragments present in the virulent strain PC554.2, but absent in the avirulent strain EPOY 8803-II. Twenty-one genomic regions of this type (that included twenty-six distinct putative ORFs) were analysed by DNA sequencing. Twenty ORFs encoded proteins with homology to proteins in other bacteria, including four homologues involved in siderophore biosynthesis, and four homologues related to mobile elements; three of these were putative transposases and one was a putative conjugative transposon related to the Vibrio cholerae SXT element. This sequence was shown to be integrated into a prfC gene homologue. Six ORFs showed no significant homology to known bacterial proteins. Among the 21 DNA fragments specific to strain PC554.2, 5 DNA fragments (representing 7 ORFs) were also absent in the avirulent strain ATCC 29690. The analysis of these differential regions, as well as the screening of their presence in a collection of strains, demonstrated the high genetic heterogeneity of this pathogen.
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Affiliation(s)
- Sandra Juíz-Río
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus de Cantoblanco, 28049 Madrid, Spain
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Carlos R Osorio
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Víctor de Lorenzo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Manuel L Lemos
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Williams ML, Lawrence ML. Identification and characterization of a two-component hemolysin from Edwardsiella ictaluri. Vet Microbiol 2005; 108:281-9. [PMID: 15923091 DOI: 10.1016/j.vetmic.2005.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2004] [Revised: 04/20/2005] [Accepted: 04/27/2005] [Indexed: 10/25/2022]
Abstract
The channel catfish pathogen Edwardsiella ictaluri possesses hemolysin activity, and strains that are adapted for growth in fish tend to have greater hemolysin activity than strains that are adapted for in vitro growth conditions. To investigate its potential role in virulence, an isogenic hemolysin mutant strain of E. ictaluri R4383 was constructed by transposon mutagenesis. Sequencing of the chromosomal insertion site identified two genes, designated eihA and eihB, that encode proteins with homology to the Serratia family of two-component hemolysins. EihB is similar to the secretion/activation proteins from this family, and EihA is similar to the cytolysin proteins from this family. Bacterial challenge in channel catfish fingerlings did not show a significant difference in virulence between the wild type E. ictaluri strain and the hemolysin deficient E. ictaluri mutant strain.
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Affiliation(s)
- M L Williams
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
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Purdy A, Rohwer F, Edwards R, Azam F, Bartlett DH. A glimpse into the expanded genome content of Vibrio cholerae through identification of genes present in environmental strains. J Bacteriol 2005; 187:2992-3001. [PMID: 15838025 PMCID: PMC1082809 DOI: 10.1128/jb.187.9.2992-3001.2005] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2004] [Accepted: 01/17/2005] [Indexed: 02/02/2023] Open
Abstract
Vibrio cholerae has multiple survival strategies which are reflected both in its broad distribution in many aquatic environments and its high genotypic diversity. To obtain additional information regarding the content of the V. cholerae genome, suppression subtractive hybridization (SSH) was used to prepare libraries of DNA sequences from two southern California coastal isolates which are divergent or absent in the clinical strain V. cholerae O1 El Tor N16961. More than 1,400 subtracted clones were sequenced. This revealed the presence of novel sequences encoding functions related to cell surface structures, transport, metabolism, signal transduction, luminescence, mobile elements, stress resistance, and virulence. Flanking sequence information was determined for loci of interest, and the distribution of these sequences was assessed for a collection of V. cholerae strains obtained from southern California and Mexican environments. This led to the surprising observation that sequences related to the toxin genes toxA, cnf1, and exoY are widespread and more common in these strains than those of the cholera toxin genes which are a hallmark of the pandemic strains of V. cholerae. Gene transfer among these strains could be facilitated by a 4.9-kbp plasmid discovered in one isolate, which possesses similarity to plasmids from other environmental vibrios. By investigating some of the nucleotide sequence basis for V. cholerae genotypic diversity, DNA fragments have been uncovered which could promote survival in coastal environments. Furthermore, a set of genes has been described which could be involved in as yet undiscovered interactions between V. cholerae and eukaryotic organisms.
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Affiliation(s)
- Alexandra Purdy
- Marine Biology Research Division, Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA
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Abstract
Extraintestinal pathogenic Escherichia coli strains (ExPEC) are the cause of a diverse spectrum of invasive infections in humans and animals, and these infections often lead to septicemia. Strains of serogroups O2 and O78 of E. coli are involved in human urinary tract infections and newborn meningitis and also constitute the major serotypes involved in avian colisepticemia. In the present study we compared the unique genomic sequences of two such septicemic strains, strains O2-1772 and O78-9, obtained by suppression subtractive hybridization. Evaluation of the degree of similarity between these two strains, which cause the same disease, revealed a high degree of diversity, with only a few shared genes. Subsequently, additional strains of each serogroup of human and animal origin were screened by PCR, and the results provided further evidence for the existence of a high degree of genome plasticity. These results were unexpected, in view of data showing that the two O157:H7 strains that have been sequenced are nearly identical in terms of virulence factors. Furthermore, the data obtained for the septicemic strains suggest that each step in the infection can be mediated by a number of alternative virulence factors, indicating the existence of a mix-and-match combinatorial system. Although whole-genome comparisons of E. coli strains causing different diseases have shown great differences in gene contents, we show that such differences exist even within strains that cause the same disease and that target the same host tissues. Moreover, in addition to the high level of genome plasticity, we show that the large pool of virulence genes in the septicemic strains is independent of the host, implying a high degree of zoonotic risk.
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Affiliation(s)
- Daphna Mokady
- Department of Molecular Microbiology and Biotechnology, the George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
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Kimura Y, Ishida S, Matoba H, Okahisa N. RppA, a transducer homologue, and MmrA, a multidrug transporter homologue, are involved in the biogenesis and/or assembly of polysaccharide in Myxococcus xanthus. MICROBIOLOGY-SGM 2004; 150:631-639. [PMID: 14993312 DOI: 10.1099/mic.0.26786-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Myxococcus xanthus cells move by gliding, and form multicellular fruiting bodies under conditions of starvation. The authors cloned a gene, designated rppA (for receptor for polysaccharide production), which encodes a methyl-accepting protein homologous to the chemotaxis transducers in eubacteria. The rppA gene was co-transcribed with mmrA, a gene homologous to various multidrug transporter genes. The rppA or mmrA single mutants showed almost identical phenotypes to the wild-type strain; however, the rppA-mmrA double mutant exhibited reduced colony expansion, cell-cell agglutination and cellular reversal frequency. The double-mutant cells also showed less binding to Congo red, which mainly binds to fibril polysaccharide, than wild-type cells. Analysis of total polysaccharide in stationary-phase cells demonstrated that in the double mutant, polysaccharide levels were decreased by about 30 % as compared with the wild-type strain. These results indicated that RppA and MmrA play a role in the biogenesis and/or assembly of polysaccharide, and the phenotypes of the double mutant may be due to the reduction in fibril polysaccharide.
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Affiliation(s)
- Yoshio Kimura
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Miki-Cho, Kagawa 761-0795, Japan
| | - Saori Ishida
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Miki-Cho, Kagawa 761-0795, Japan
| | - Hideki Matoba
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Miki-Cho, Kagawa 761-0795, Japan
| | - Naoki Okahisa
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Miki-Cho, Kagawa 761-0795, Japan
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Abdullah AI, Hart CA, Winstanley C. Molecular characterization and distribution of virulence-associated genes amongst Aeromonas isolates from Libya. J Appl Microbiol 2004; 95:1001-7. [PMID: 14633028 DOI: 10.1046/j.1365-2672.2003.02092.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The aim of the study was to type 52 Aeromonas spp. isolates from chicken carcasses, children with diarrhoea and a hospital environment in Libya, and to determine the distribution of putative virulence genes amongst them. METHODS AND RESULTS Macrorestriction analysis using pulsed-field gel electrophoresis (PFGE) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of 16S rRNA and aroA genes were used to type the isolates. Whereas 30 of 32 chicken isolates were identified as Aeromonas veronii, eight of 12 environmental isolates were Aer. caviae. Three species were identified amongst the eight isolates from children. Aeromonas veronii and Aer. caviae isolates could be divided into eight and five PFGE types, respectively. All species could be further subtyped into one of 21 aroA PCR-RFLP groups. Aerolysin-like haemolysin or enterotoxin gene sequences were detected in all the isolates. Overall carriage rates for hlyA and alt were 77 and 75%, respectively. CONCLUSIONS Seven of eight isolates from children were of different subtypes, indicating a lack of any common source of acquisition. Isolates of common molecular type did not share identical distributions of putative virulence genes. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrates the effectiveness of using molecular typing to identify and study genetic variation amongst Aeromonas isolates.
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Affiliation(s)
- A I Abdullah
- Department Medical Microbiology and Genitourinary Medicine, University of Liverpool, Liverpool, UK
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Pomati F, Neilan BA. PCR-based positive hybridization to detect genomic diversity associated with bacterial secondary metabolism. Nucleic Acids Res 2004; 32:e7. [PMID: 14718552 PMCID: PMC373313 DOI: 10.1093/nar/gnh012] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A PCR-based positive hybridization (PPH) method was developed to explore toxic-specific genes in common between toxigenic strains of Anabaena circinalis, a cyanobacterium able to produce saxitoxin (STX). The PPH technique is based on the same principles of suppression subtractive hybridization (SSH), although with the former no driver DNA is required and two tester genomic DNAs are hybridized at high stringency. The aim was to obtain genes associated with cyanobacterial STX production. The genetic diversity within phylogenetically similar strains of A.circinalis was investigated by comparing the results of the standard SSH protocol to the PPH approach by DNA-microarray analysis. SSH allowed the recovery of DNA libraries that were mainly specific for each of the two STX-producing strains used. Several candidate sequences were found by PPH to be in common between both the STX-producing testers. The PPH technique performed using unsubtracted genomic libraries proved to be a powerful tool to identify DNA sequences possibly transferred laterally between two cyanobacterial strains that may be candidate(s) in STX biosynthesis. The approach presented in this study represents a novel and valid tool to study the genetic basis for secondary metabolite production in microorganisms.
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Affiliation(s)
- Francesco Pomati
- Cyanobacteria and Astrobiology Research Laboratory, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, NSW, Australia
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42
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Jenkin GA, Stinear TP, Johnson PDR, Davies JK. Subtractive hybridization reveals a type I polyketide synthase locus specific to Mycobacterium ulcerans. J Bacteriol 2004; 185:6870-82. [PMID: 14617651 PMCID: PMC262701 DOI: 10.1128/jb.185.23.6870-6882.2003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium ulcerans causes Buruli ulcer, the third most prevalent mycobacterial infection of immunocompetent humans after tuberculosis and leprosy. Recent work has shown that the production by M. ulcerans of mycolactone, a novel polyketide, may partly explain the pathogenesis of Buruli ulcer. To search for the genetic basis of virulence in M. ulcerans, we took advantage of the close genetic relationship between M. ulcerans and Mycobacterium marinum by performing genomic suppressive subtractive hybridization of M. ulcerans with M. marinum. We identified several DNA fragments specific to M. ulcerans, in particular, a type I polyketide synthase locus with a highly repetitive modular arrangement. We postulate that this locus is responsible for the synthesis of mycolactone in M. ulcerans.
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Affiliation(s)
- Grant A Jenkin
- Bacterial Pathogenesis Research Group, Department of Microbiology, Monash University, Clayton, Victoria, Australia
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Page WJ, Kwon E, Cornish AS, Tindale AE. ThecsbXgene ofAzotobacter vinelandiiencodes an MFS efflux pump required for catecholate siderophore export. FEMS Microbiol Lett 2003; 228:211-6. [PMID: 14638426 DOI: 10.1016/s0378-1097(03)00753-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The csbX gene of Azotobacter vinelandii was regulated in an iron-repressible manner from a divergent promoter upstream of the catecholate siderophore biosynthesis (csb) operon and was predicted to encode an efflux pump of the major facilitator superfamily. Other proteins that were most similar to CsbX were encoded by genes found in the catecholate siderophore biosynthesis operons of Aeromonas hydrophila and Stigmatella aurantiaca. Inactivation of csbX resulted in 57-100% decrease in the amount of catecholates released when compared to the wild-type in iron-limited medium. CsbX was most important for the export of the high affinity chelator protochelin with the majority of the catecholates released by csbX mutants being the protochelin intermediates azotochelin and aminochelin.
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Affiliation(s)
- William J Page
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9.
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Golubov A, Heesemann J, Rakin A. Uncovering genomic differences in human pathogenic Yersinia enterocolitica. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 2003; 38:107-11. [PMID: 13129644 DOI: 10.1016/s0928-8244(03)00182-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To map out genomic differences between highly pathogenic Yersinia enterocolitica WA-314C biogroup 1B, serotype O:8 strain and low-pathogenic Y. enterocolitica Y-108C biogroup 4, serotype O:3 strain we have applied a method of suppression subtractive hybridization (SSH). In total, 428 WA-314-specific and 83 Y-108-specific sequences were uncovered by SSH. Among them were DNA fragments with similarity to known genes from several groups: (1) genes involved in O-antigen biosynthesis, (2) host-specific restriction-modification systems, (3) systems of iron and heme acquisition and storage, (4) flagellar biogenesis genes, (5) putative virulence factors, (6) drug resistance genes, and (7) mobile elements. Mapped out genomic differences may be applied in identification and development of novel therapeutic strategies for the treatment of enteropathogenic Yersinia.
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Affiliation(s)
- Andrey Golubov
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Pettenkofer Str. 9a, 80336 Munich, Germany
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45
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Braschler TR, Merino S, Tomás JM, Graf J. Complement resistance is essential for colonization of the digestive tract of Hirudo medicinalis by Aeromonas strains. Appl Environ Microbiol 2003; 69:4268-71. [PMID: 12839811 PMCID: PMC165153 DOI: 10.1128/aem.69.7.4268-4271.2003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
From the crop of the medicinal leech, Hirudo medicinalis, only Aeromonas veronii bv. sobria can be cultured consistently. Serum-sensitive A. veronii mutants were unable to colonize H. medicinalis, indicating the importance of the mammalian complement system for this unusual simplicity. Complementation of one selected mutant restored its ability to colonize. Serum-sensitive mutants are the first mutant class with a colonization defect for this symbiosis.
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Affiliation(s)
- Thomas R Braschler
- Institute for Infectious Diseases, University of Berne, CH-3010 Berne, Switzerland
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Zhang YL, Lau YL, Arakawa E, Leung KY. Detection and genetic analysis of group II capsules in Aeromonas hydrophila. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1051-1060. [PMID: 12686647 DOI: 10.1099/mic.0.26144-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genetic organization and sequences of the group II capsule gene cluster of Aeromonas hydrophila PPD134/91 have been determined previously. The purified capsular polysaccharides can increase the ability of avirulent strain PPD35/85 to survive in naive tilapia serum but have no inhibitory effect on the adhesion of PPD134/91 to carp epithelial cells. In this study, the presence of group II capsules among 33 randomly chosen A. hydrophila strains was examined by electron microscopy and genetic analysis. Ten strains were found to produce group II capsules. A PCR detection system was developed to identify two types of group II capsules (IIA and IIB) based on their genetic organization in the region II gene clusters. Group IIA capsules in the authors' collection of A. hydrophila strains are mainly found in the O : 18 and O : 34 serogroups, while group IIB capsules are found in the O : 21 and O : 27 serogroups. The presence of group II capsules in A. hydrophila strongly correlates with the serum and phagocyte survival abilities (seven out of ten strains). The results indicate that the authors' PCR detection system can constitute a reliable assay for the classification of group II capsules in A. hydrophila.
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Affiliation(s)
- Y L Zhang
- Department of Biological Sciences, Faculty of Science, The National University of Singapore, Singapore 117543
| | - Y L Lau
- Department of Biological Sciences, Faculty of Science, The National University of Singapore, Singapore 117543
| | - E Arakawa
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, Japan 162-8640
| | - K Y Leung
- Tropical Marine Science Institute, The National University of Singapore, Singapore 117543
- Department of Biological Sciences, Faculty of Science, The National University of Singapore, Singapore 117543
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Harakava R, Gabriel DW. Genetic differences between two strains of Xylella fastidiosa revealed by suppression subtractive hybridization. Appl Environ Microbiol 2003; 69:1315-9. [PMID: 12571065 PMCID: PMC143624 DOI: 10.1128/aem.69.2.1315-1319.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Suppression subtractive hybridization was used to rapidly identify 18 gene differences between a citrus variegated chlorosis (CVC) strain and a Pierce's disease of grape (PD) strain of Xylella fastidiosa. The results were validated as being highly representative of actual differences by comparison of the completely sequenced genome of a CVC strain with that of a PD strain.
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Affiliation(s)
- Ricardo Harakava
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, USA
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Nilsson WB, Paranjype RN, DePaola A, Strom MS. Sequence polymorphism of the 16S rRNA gene of Vibrio vulnificus is a possible indicator of strain virulence. J Clin Microbiol 2003; 41:442-6. [PMID: 12517889 PMCID: PMC149629 DOI: 10.1128/jcm.41.1.442-446.2003] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio vulnificus exhibits considerable strain-to-strain variation in virulence. Attempts to associate phenotypic or genotypic characteristics with strain virulence have been largely unsuccessful. Based on a 17-nucleotide difference throughout the sequence of the small subunit 16S rRNA gene, there are two major groups of V. vulnificus designated types A and B. In a survey of the 16S rRNA genotype in 67 V. vulnificus human clinical and nonclinical strains, we determined that the majority of nonclinical isolates are type A (31 of 33) and that there is a statistically significant association between the type B genotype and human clinical strains (26 of 34).
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Affiliation(s)
- William B Nilsson
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, U.S. Department of Commerce, Seattle, Washington 98112, USA
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49
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Posteraro B, Sanguinetti M, Sanglard D, La Sorda M, Boccia S, Romano L, Morace G, Fadda G. Identification and characterization of a Cryptococcus neoformans ATP binding cassette (ABC) transporter-encoding gene, CnAFR1, involved in the resistance to fluconazole. Mol Microbiol 2003; 47:357-71. [PMID: 12519188 DOI: 10.1046/j.1365-2958.2003.03281.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Resistance to fluconazole is a possible event during prolonged suppressive drug therapy for cryptococ-cal meningitis, the most frequently encountered life-threatening manifestation of cryptococcosis. The knowledge of this resistance at the molecular level is important for management of cryptococcosis. In order to identify genes involved in azole resistance in Cryptococcus neoformans, a cDNA subtraction library technique was chosen as a strategy. First, a fluconazole-resistant mutant BPY22.17 was obtained from a susceptible clinical isolate BPY22 by in vitro exposure to the drug. Then, a subtractive hybridization procedure was used to compare gene expression between the obtained strains. We identified a cDNA overexpressed in the fluconazole-resistant strain BPY22.17 that was used as a probe to isolate the entire gene in a C. neoformans genomic library. Sequence analysis of this gene identified an ATP Binding Cassette (ABC) transporter-encoding gene called C. neoformans AntiFungal Resistance 1 (CnAFR1). Disruption of CnAFR1 gene in the resistant isolate (BPY22.17) resulted in an enhanced susceptibility of the knock-out mutant cnafr1 against fluconazole, whereas reintroduction of the gene in cnafr1 resulted in restoration of the resistance phenotype, thus confirming that CnAFR1 is involved in fluconazole resistance of C. neoformans. Our findings therefore reveal that an active drug efflux mechanism can be involved in the development of azole resistance in this important human pathogen.
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Affiliation(s)
- Brunella Posteraro
- Istituto Microbiologia, Università Cattolica del S. Cuore, L. go F. Vito, 1, 00168 Rome, Italy
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50
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Chanto G, Occhialini A, Gras N, Alm RA, Mégraud F, Marais A. Identification of strain-specific genes located outside the plasticity zone in nine clinical isolates of Helicobacter pylori. MICROBIOLOGY (READING, ENGLAND) 2002; 148:3671-3680. [PMID: 12427957 DOI: 10.1099/00221287-148-11-3671] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Helicobacter pylori is a Gram-negative bacterium that is associated with the development of peptic ulcers and gastric carcinoma in humans. This species appears to be one of the most genetically variable bacteria described to date. The overall level of heterogeneity within strains of this organism was determined by comparing the genome sequences of two reference strains, J99 and 26695. The aim of this study was to measure the genetic diversity within strains of H. pylori by looking for strain-specific genes in nine H. pylori strains isolated from patients suffering from chronic gastritis (n=3), duodenal ulcers (n=3) or gastric cancer (n=3). Seven loci that contained strain-specific genes in strains J99 and 26695 were studied. These regions were subsequently amplified from most of the clinical isolates studied and their sequences were determined. ORFs were predicted from the sequence data and were compared to sequences within the databases. The results showed that the genes flanking the ORFs specific to either strain J99 or strain 26695 were also present in a similar configuration in the genomes of the nine clinical isolates. Moreover, in most regions, ORFs homologous to those found in the corresponding loci in the two reference strains were detected. However, in 10 regions, genes similar to those located at another locus in the genome of J99 or 26695 were found. Finally, six strain-specific genes were identified in three regions of three of the H. pylori strains isolated from patients with duodenal ulcers (n=2) and gastric cancer (n=1). Of these six genes, five were putative genes and one was an orthologue of a gene encoding a transposase in Thermotoga maritima. However, no association with disease was found for these genes.
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Affiliation(s)
- Grettel Chanto
- Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2 and Hôpital Pellegrin, Place Amélie Raba-Léon, 33076 Bordeaux Cedex, France1
| | - Alessandra Occhialini
- Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2 and Hôpital Pellegrin, Place Amélie Raba-Léon, 33076 Bordeaux Cedex, France1
| | - Nathalie Gras
- Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2 and Hôpital Pellegrin, Place Amélie Raba-Léon, 33076 Bordeaux Cedex, France1
| | - Richard A Alm
- Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2 and Hôpital Pellegrin, Place Amélie Raba-Léon, 33076 Bordeaux Cedex, France1
| | - Francis Mégraud
- Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2 and Hôpital Pellegrin, Place Amélie Raba-Léon, 33076 Bordeaux Cedex, France1
| | - Armelle Marais
- Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2 and Hôpital Pellegrin, Place Amélie Raba-Léon, 33076 Bordeaux Cedex, France1
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