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Kenarkoohi A, Abdoli A, Rostamzad A, Rashnavadi M, Naserifar R, Abdi J, Shams M, Bozorgomid A, Saeb S, Al-Fahad D, Khezri K, Falahi S. Presence of CRISPR CAS-Like Sequences as a Proposed Mechanism for Horizontal Genetic Exchanges between Trichomonas vaginalis and Its Associated Virus: A Comparative Genomic Analysis with the First Report of a Putative CRISPR CAS Structures in Eukaryotic Cells. BIOMED RESEARCH INTERNATIONAL 2023; 2023:8069559. [PMID: 38058394 PMCID: PMC10696477 DOI: 10.1155/2023/8069559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/04/2023] [Accepted: 09/07/2023] [Indexed: 12/08/2023]
Abstract
Introduction Trichomonas vaginalis genome is among the largest genome size and coding capacities. Combinations of gene duplications, transposon, repeated sequences, and lateral gene transfers (LGTs) have contributed to the unexpected large genomic size and diversity. This study is aimed at investigating genomic exchange and seeking for presence of the CRISPR CAS system as one of the possible mechanisms for some level of genetic exchange. Material and Methods. In this comparative analysis, 398 publicly available Trichomonas vaginalis complete genomes were investigated for the presence of CRISPR CAS. Spacer sequences were also analyzed for their origin using BLAST. Results We identified a CRISPR CAS (Cas3). CRISPR spacers are highly similar to transposable genetic elements such as viruses of protozoan parasites, especially megavirals, some transposons, and, interestingly, papillomavirus and HIV-1 in a few cases. Discussion. There is a striking similarity between the prokaryotes/Archaean CRISPR and what we find as eukaryotic CRISPR. About 5-10% of the 398 T. vaginalis possess a CRISPR structure. Conclusion According to sequences and their organization, we assume that these repeated sequences and spacer, along with their mentioned features, could be the eukaryotic homolog of prokaryotes and Archaean CRISPR systems and may involve in a process similar to the CRISPR function.
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Affiliation(s)
- Azra Kenarkoohi
- Department of Laboratory Sciences, School of Allied Medical Sciences, Iran
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Amir Abdoli
- Zoonoses Research Centre, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Arman Rostamzad
- Department of Biology, Faculty of Sciences, Ilam University, Ilam, Iran
| | | | - Razi Naserifar
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Jahangir Abdi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Morteza Shams
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Arezoo Bozorgomid
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sepideh Saeb
- Qaen School of Nursing and Midwifery, Birjand University of Medical Sciences, Birjand, Iran
| | - Dhurgham Al-Fahad
- Pharmaceutical Department, College of Pharmacy, University of Thi-Qar, Iraq
| | - Kosar Khezri
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Shahab Falahi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
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Ramadan AA. Bacterial typing methods from past to present: A comprehensive overview. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Movahedi M, Zarei O, Hazhirkamal M, Karami P, Shokoohizadeh L, Taheri M. Molecular typing of Escherichia coli strains isolated from urinary tract infection by ERIC-PCR. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Fu H, Yu P, Liang W, Kan B, Peng X, Chen L. Virulence, Resistance, and Genomic Fingerprint Traits of Vibrio cholerae Isolated from 12 Species of Aquatic Products in Shanghai, China. Microb Drug Resist 2020; 26:1526-1539. [PMID: 33156741 PMCID: PMC7757592 DOI: 10.1089/mdr.2020.0269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Vibrio cholerae is a waterborne bacterium and can cause epidemic cholera disease worldwide. Continuous monitoring of V. cholerae contamination in aquatic products is imperative for assuring food safety. In this study, we determined virulence, antimicrobial susceptibility, heavy metal tolerance, and genomic fingerprints of 370 V. cholerae isolates recovered from 12 species of commonly consumed aquatic products collected from July to September of 2018 in Shanghai, China. Among the species, Leiocassis longirostris, Ictalurus punetaus, Ophiocephalus argus Cantor, and Pelteobagrus fulvidraco were for the first time detected for V. cholerae. Toxin genes ctxAB, tcpA, ace, and zot were absent from all the V. cholerae isolates. However, high occurrence of virulence-associated genes was detected, such as hapA (82.7%), hlyA (81.4%), rtxCABD (81.4%, 24.3%, 80.3%, and 80.8%, respectively), and tlh (80.5%). Approximately 62.2% of the 370 V. cholerae isolates exhibited resistance to streptomycin, followed by ampicillin (60.3%), rifampicin (53.8%), trimethoprim (38.4%), and sulfamethoxazole-trimethoprim (37.0%). Moreover, ∼57.6% of the isolates showed multidrug resistant phenotypes with 57 resistance profiles, which was significantly different among the 12 species (multiple antimicrobial resistance index, p < 0.001). Meanwhile, high incidence of tolerance to heavy metals Hg2+ (69.5%), Ni2+ (32.4%), and Cd2+ (30.8%) was observed among the isolates. The enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR)-based fingerprinting profiles classified the 370 V. cholerae isolates into 239 different ERIC-genotypes, which demonstrated diverse genomic variation among the isolates. Overall, the results in this study meet the increasing need of food safety risk assessment of aquatic products.
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Affiliation(s)
- Huiyu Fu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Pan Yu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Weili Liang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Biao Kan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
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Oliveira ÉMD, Beltrão EMB, Scavuzzi AML, Barros JF, Lopes ACS. High plasmid variability, and the presence of IncFIB, IncQ, IncA/C, IncHI1B, and IncL/M in clinical isolates of Klebsiella pneumoniae with bla KPC and bla NDM from patients at a public hospital in Brazil. Rev Soc Bras Med Trop 2020; 53:e20200397. [PMID: 33111914 PMCID: PMC7580274 DOI: 10.1590/0037-8682-0397-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Antibiotic resistance in carbapenemase-producing Klebsiella
pneumoniae is acquired and disseminated mainly by plasmids.
Therefore, we aimed to investigate the occurrence of carbapenemase genes,
analyze the genetic diversity by ERIC-PCR, and examine the most common
plasmid incompatibility groups (Incs) in clinical isolates of K.
pneumoniae from colonization and infection in patients from a
hospital in Brazil. METHODS Twenty-seven isolates of carbapenem-resistant K. pneumoniae
were selected and screened for the presence of carbapenemase genes and Incs
by PCR, followed by amplicon sequencing. RESULTS The blaKPC and blaNDM genes were detected in 24 (88.8 %) and 16 (59.2 %) of the
isolates, respectively. Thirteen isolates (48.1 %) were positive for both
genes. The IncFIB (92.6 %) and IncQ (88.8 %) were the most frequent
plasmids, followed by IncA/C, IncHI1B, and IncL/M, indicating that plasmid
variability existed in these isolates. To our knowledge, this is the first
report of IncHI1B in Brazil. We found eight isolates with clonal
relationship distributed in different sectors of the hospital. CONCLUSIONS The accumulation of resistance determinants, the variability of plasmid
Incs, and the clonal dissemination detected in K.
pneumoniae isolates demonstrate their potential for infection,
colonization, and the dissemination of different resistance genes and
plasmids.
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Affiliation(s)
- Érica Maria de Oliveira
- Universidade Federal de Pernambuco, Centro de Ciências Médicas, Área de Medicina Tropical, Recife, PE, Brasil
| | | | | | | | - Ana Catarina Souza Lopes
- Universidade Federal de Pernambuco, Centro de Ciências Médicas, Área de Medicina Tropical, Recife, PE, Brasil
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Liu W, Zhao H, Qiu Z, Jin M, Yang D, Xu Q, Feng H, Li J, Shen Z. Identifying geographic origins of the Escherichia coli isolates from food by a method based on single-nucleotide polymorphisms. J Microbiol Methods 2019; 168:105807. [PMID: 31837351 DOI: 10.1016/j.mimet.2019.105807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND E.coli is an important foodborne pathogen. Rapid and robust tracking of the source of E. coli is the key step to control foodborne infections. RESULTS In this study, a genotyping and tracing method based on highly discriminatory single nucleotide polymorphisms (SNPs) was developed to investigate the geographical origin of E. coli in food. A highly informative set of 12 SNPs was derived from 4 housekeeping genes in E. coli multilocus sequence typing (MLST) database. A collection of 253 E. coli isolates from food in 12 countries and regions were screened, resulting in a total of 61 profiles, 35 geographically specific SNP profiles were revealed and further verified by blind sample test. Also, the evolutionary relationship of 61 SNP profiles with different geographical origins was established by the enhanced analysis Based Upon Related Sequence Types (eBURST) analysis, which provided evidence that strains of different geographical origins owned the same ancestor strain. CONCLUSIONS Our study established a powerful method based on a set of 12 SNPs for identifying geographical origins. The blind sample analysis proved that this SNPs panel had a high traceability of E. coli in food. Furthermore, this method based on SNPs combined with eBURST analysis revealed the potential evolutionary relationship between E.coli strains of different geographical origins.
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Affiliation(s)
- Weili Liu
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China
| | - Hong Zhao
- Animals, plants and food testing center of Tianjin Exit-Entry Inspection & Quarantine Bureau, Tianjin 300461, China
| | - Zhigang Qiu
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China
| | - Min Jin
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China
| | - Dong Yang
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China
| | - Qunying Xu
- School of Public Health, Nanchang University, Jiangxi 330006, China
| | - Hua Feng
- School of Public Health, Nanchang University, Jiangxi 330006, China
| | - Junwen Li
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China.
| | - Zhiqiang Shen
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China.
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Rokni N, Akbar Sadati SA, Safaie N, Ebrahimi MA, Samimifar M. Assessment of genetic relatedness among commercial and wild strains of Agaricus bisporus using repetitive extragenic palindromic sequences and polymerase chain reaction. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2019.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
In infectious disease epidemiology, the laboratory plays a critical role in diagnosis, outbreak investigations, surveillance, and characterizing biologic properties of microbes associated with their transmissibility, resistance to anti-infectives, and pathogenesis. The laboratory can inform and refine epidemiologic study design and data analyses. In public health, the laboratory functions to assess effect of an intervention. In addition to research laboratories, the new-generation molecular microbiology technology has been adapted into clinical and public health laboratories to simplify, accelerate, and make precise detection and identification of infectious disease pathogens. This technology is also being applied to subtype microbes to conduct investigations that advance our knowledge of epidemiology of old and emerging infectious diseases. Because of the recent explosive progress in molecular microbiology technology and the vast amount of data generated from the applications of this technology, this Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases describes these methods separately for bacteria, viruses, and parasites. This review discusses past and current advancements made in laboratory methods used to conduct epidemiologic studies of bacterial infections. It describes methods used to subtype bacterial organisms based on molecular microbiology techniques, following a discussion on what is meant by bacterial "species" and "clones." Discussions on past and new genotyping tests applied to epidemiologic investigations focus on tests that compare electrophoretic band patterns, hybridization matrices, and nucleic acid sequences. Applications of these genotyping tests to address epidemiologic issues are detailed elsewhere in other reviews of this series. *This article is part of a curated collection.
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Delihas N. Enterobacterial Small Mobile Sequences Carry Open Reading Frames and are Found Intragenically–-Evolutionary Implications for Formation of New Peptides. GENE REGULATION AND SYSTEMS BIOLOGY 2017. [DOI: 10.1177/117762500700100017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Intergenic repeat units of 127-bp (RU-1) and 168-bp (RU-2), as well as a newly-found class of 103-bp (RU-3), represent small mobile sequences in enterobacterial genomes present in multiple intergenic regions. These repeat sequences display similarities to eukaryotic miniature inverted-repeat transposable elements (MITE). The RU mobile elements have not been reported to encode amino acid sequences. An in silico approach was used to scan genomes for location of repeat units. RU sequences are found to have open reading frames, which are present in annotated gene loci whereby the RU amino acid sequence is maintained. Gene loci that display repeat units include those that encode large proteins which are part of super families that carry conserved domains and those that carry predicted motifs such as signal peptide sequences and transmembrane domains. A putative exported protein in Y. pestis and a phylogenetically conserved putative inner membrane protein in Salmonella species represent some of the more interesting constructs. We hypothesize that a major outcome of RU open reading frame fusions is the evolutionary emergence of new proteins.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, SUNY, Stony Brook, NY 11794-5222, U.S.A
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Zhu X, Sun Y, Zhang C, Liu H. Effects of berberine on a rat model of chronic stress and depression via gastrointestinal tract pathology and gastrointestinal flora profile assays. Mol Med Rep 2017; 15:3161-3171. [DOI: 10.3892/mmr.2017.6353] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/10/2016] [Indexed: 11/05/2022] Open
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Hellmuth JE, Hitzeroth AC, Bragg RR, Boucher CE. Evaluation of the ERIC-PCR as a probable method to differentiate Avibacterium paragallinarum serovars. Avian Pathol 2017; 46:272-277. [PMID: 27866411 DOI: 10.1080/03079457.2016.1259610] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Infectious coryza, an upper respiratory tract disease in chickens, caused by Avibacterium paragallinarum, leads to huge economic losses. The disease is controlled through vaccination; but vaccination efficacy is dependent on correct identification of the infecting serovar, as limited cross-protection is reported amongst some serovars. Current identification methods include the heamagglutination inhibition test, which is demanding and could be subjective. To overcome this, molecular typing methods proposed are the Multiplex polymerase chain reaction (PCR) and Restriction Fragment Length Polymorphism-PCR, but low reproducibility is reported. Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR has been suggested for molecular groupings of various bacterial species. This study focuses on evaluating the ERIC-PCR as a probable method to differentiate between different Av. paragallinarum serovars by grouping with reference isolates, based on clonal relations. The ERIC-PCR was performed on 12 reference isolates and 41 field isolates originating from South Africa and South America. The data indicate that the ERIC-PCR is not ideal for the differentiation or for molecular typing of Av. paragallinarum serovars, as no correlation is drawn upon comparison of banding patterns of field isolates and reference strains. However, the results do indicate isolates from the same origin sharing unique banding patterns, indicating potential clonal relationship; but when compared to the reference isolates dominant in the specific area, no correlation could be drawn. Furthermore, although the ERIC-PCR serves a purpose in epidemiological studies, it has proved to have little application in differentiating amongst serovars of Av. paragallinarum and to group untyped field strains with known reference strains.
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Affiliation(s)
- Julius Eduard Hellmuth
- a Department Microbial, Biochemical and Food Biotechnology, Faculty Natural and Agricultural Sciences , University of the Free State , Bloemfontein , South Africa
| | - Arina Corli Hitzeroth
- a Department Microbial, Biochemical and Food Biotechnology, Faculty Natural and Agricultural Sciences , University of the Free State , Bloemfontein , South Africa
| | - Robert Richard Bragg
- a Department Microbial, Biochemical and Food Biotechnology, Faculty Natural and Agricultural Sciences , University of the Free State , Bloemfontein , South Africa
| | - Charlotte Enastacia Boucher
- a Department Microbial, Biochemical and Food Biotechnology, Faculty Natural and Agricultural Sciences , University of the Free State , Bloemfontein , South Africa
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Ardakani MA, Ranjbar R. Molecular typing of uropathogenic E. coli strains by the ERIC-PCR method. Electron Physician 2016; 8:2291-6. [PMID: 27280007 PMCID: PMC4886573 DOI: 10.19082/2291] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 01/28/2016] [Indexed: 12/18/2022] Open
Abstract
Introduction Escherichia coli (E. coli) is the most common cause of urinary infections in hospitals. The aim of this study was to evaluate the ERIC-PCR method for molecular typing of uropathogenic E. coli strains isolated from hospitalized patients. Methods In a cross sectional study, 98 E. coli samples were collected from urine samples taken from patients admitted to Baqiyatallah Hospital from June 2014 to January 2015. The disk agar diffusion method was used to determine antibiotic sensitivity. DNA proliferation based on repetitive intergenic consensus was used to classify the E. coli strains. The products of proliferation were electrophoresed on 1.5% agarose gel, and their dendrograms were drawn. The data were analyzed by online Insillico software. Results The method used in this research proliferated numerous bands (4–17 bands), ranging from 100 to 3000 base pairs. The detected strains were classified into six clusters (E1–E6) with 70% similarity between them. Conclusion In this study, uropathogenic E. coli strains belonged to different genotypic clusters. It was found that ERIC-PCR had good differentiation power for molecular typing of uropathogenic E. coli strains isolated from the patients in the study.
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Affiliation(s)
- Maryam Afkhami Ardakani
- M.Sc. of Microbiology, Department of Microbiology, Faculty of Advanced Science & Technology, pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Reza Ranjbar
- Ph.D. of Medical Bacteriology, Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Ramees TP, Rathore RS, Bagalkot PS, Sailo B, Mohan HV, Kumar A, Dhama K, Singh RK. Genotyping and genetic diversity of Arcobacter butzleri and Arcobacter cryaerophilus isolated from different sources by using ERIC-PCR from India. Vet Q 2014; 34:211-7. [PMID: 25333916 DOI: 10.1080/01652176.2014.979511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
BACKGROUND Arcobacters are important zoonotic pathogens and are transmitted through food and water. They are implicated in causing enteritis in animals and humans. Among the Arcobacter species, a wide genetic diversity has been documented, which reflects continuous evolving nature of these pathogens. OBJECTIVES To genotype and to know the genetic diversity of Arcobacter spp. (Arcobacter butzleri and Arcobacter cryaerophilus) isolated from different sources in India. METHODS Enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) was performed using genomic DNA of 49 Arcobacter isolates (27 A. butzleri and 22 A. cryaerophilus), recovered from a total of 506 samples of chicken meat, poultry skin, dairy cow milk and human stool as template and employing published primers. RESULTS ERIC sequence was found to be present in all the 27 A. butzleri isolates which were grouped into 18 subtypes, while it was present in 20 out of 22 A. cryaerophilus isolates which were grouped into 14 subtypes. Less variation was observed within sequences of both the Arcobacter species as revealed in dendrogram analysis. The genotyping of A. butzleri isolates showed the presence of 2-8 distinct bands (∼150 to ∼1600 bp), while A. cryaerophilus showed 1-10 distinct bands (∼120 to ∼2900 bp). CONCLUSION This study is the first report regarding genetic diversity of Indian Arcobacter isolates using ERIC-PCR. Close clustering between arcobacters of human and animal origin are indicative of probable zoonotic significance. So for these purposes, further explorative studies are suggested which would also help revealing the possibility of epidemiological relationships of different Arcobacter spp. as well as their public health concerns.
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Affiliation(s)
- Thadiyam Puram Ramees
- a Division of Veterinary Public Health , Indian Veterinary Research Institute , Izatnagar, Bareilly , India
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Ye Y, Li H, Wu Q, Zhang J, Lu Y. TheCronobactersp. in milk and dairy products: Detection and typing. INT J DAIRY TECHNOL 2014. [DOI: 10.1111/1471-0307.12111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yingwang Ye
- School of Biotechnology and Food Engineering; Hefei University of Technology; Hefei 230009 China
- Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application; Guangdong Institute of Microbiology; Guangzhou 510070 China
| | - Hui Li
- School of Biotechnology and Food Engineering; Hefei University of Technology; Hefei 230009 China
- Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application; Guangdong Institute of Microbiology; Guangzhou 510070 China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application; Guangdong Institute of Microbiology; Guangzhou 510070 China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application; Guangdong Institute of Microbiology; Guangzhou 510070 China
| | - Yudong Lu
- School of Biotechnology and Food Engineering; Hefei University of Technology; Hefei 230009 China
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da Silva RB, Valicente FH. Molecular characterization of Bacillus thuringiensis using rep-PCR. SPRINGERPLUS 2013; 2:641. [PMID: 24363981 PMCID: PMC3867629 DOI: 10.1186/2193-1801-2-641] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/30/2013] [Indexed: 12/04/2022]
Abstract
The genetic divergence of 65 strains of Bacillus thuringiensis (Bt) was determined using Rep-PCR. Based on the repetitive sequences the BOX primer was the most informative with 26 fragments, followed by ERIC (19) and REP (10), generating a total of 55 fragments. The dendogram shows that ten groups were formed when 45% was the average distance of the population: group 1 with 41,5% of the isolates, 33,8% of the isolates were distributed in other groups and 24,6% did not formed distinct group. 53,2% of the isolates from Embrapa are in the group 1, and 29,8% of the isolates are distributed in other groups. Bt strains from USDA and Institute Pasteur showed more variability.
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Affiliation(s)
- Rosane Bezerra da Silva
- Department of Plant Biotechnology, Federal University of Lavras, Lavras, Minas Gerais Brazil
| | - Fernando Hercos Valicente
- Department of Biological control, Embrapa Maize and Sorghum research, Sete Lagoas, Minas Gerais Brazil
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Ramazanzadeh R, Zamani S, Zamani S. Genetic diversity in clinical isolates of Escherichia coli by enterobacterial repetitive intergenic consensus (ERIC)-PCR technique in Sanandaj hospitals. IRANIAN JOURNAL OF MICROBIOLOGY 2013; 5:126-31. [PMID: 23825729 PMCID: PMC3696847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND AND OBJECTIVES The Escherichia coli strains are greatly important in nosocomial and community acquired infections. The aim of this study was to determine the transmission of bacterial infections using genetic analysis. MATERIALS AND METHODS Two hundred and thirty Escherichia coli strains, isolated from different clinical samples, were characterized by enterobacterial repetitive intergenic consensus (ERIC)-PCR technique. The results and the similarity between the strains were determined on the basis of Jaccard similarity coefficient in the SAHN program of the NTSYS-pc software. RESULTS The ERIC-PCR profiles allowed typing of the 230 isolates into 205 ERIC-types which were grouped into twenty main clusters (C01-C20).The first group makes up 4.34% of the total isolates. Out of the 230 isolates, 34.2% belonged to D phylogenic group which were associated with extra-intestinal samples. CONCLUSION Our results showed high diversity in E. coli isolates indicating low rate of hospital infection in our university hospitals. The majority of the isolates belonged to the D phylogenic group.
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Affiliation(s)
- Rashid Ramazanzadeh
- Cellular & Molecular Research Center and Microbiology Department, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran, Corresponding author: Dr. Rashid Ramezanzadeh, Adress: Cellular & Molecular Research Center and Microbiology Department, Faculty of Medicine, Kurdistan University of Medical Sciences, Pasdaran Street, Sanandaj, Iran. Tel: +98-914-3104424. Fax: +98-871-6664674. E-mail:
| | - Serveh Zamani
- Student Research Committee of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Saman Zamani
- Student Research Committee of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
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Bokhari H, Shah MA, Asad S, Akhtar S, Akram M, Wren BW. Escherichia coli pathotypes in Pakistan from consecutive floods in 2010 and 2011. Am J Trop Med Hyg 2013; 88:519-25. [PMID: 23358642 DOI: 10.4269/ajtmh.12-0365] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
This study compares Escherichia coli pathotypes circulating among children in Pakistan during the floods of 2010 and 2011 and from sporadic cases outside flood affected areas. Using multiplex polymerase chain reaction 115 of 205 stool samples (56.29%) were positive for diarrheagenic E. coli from specimens taken during the floods compared with 50 of 400 (12.5%) stool samples being positive for sporadic cases. The E. coli pathotypes were categorized as Enteropathogenic E. coli 33 (28.69%) and 13 (26%), Enterotoxigenic E. coli 29 (25.21%) and 15 (30%), Enteroaggregative E. coli 21 (18.2%) and 18 (36%), Enterohemorrhagic E. coli 5 (4.34%) and 1 (2%) from flood and sporadic cases, respectively. Furthermore, patients co-infected with more than one pathotype were 26 (22.60%) and 3 (6%) from flood and sporadic cases, respectively. The study shows an unexpectedly high rate of isolation of E. coli pathotypes suggesting Pakistan as an endemic region that requires active surveillance particularly during flood periods.
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Affiliation(s)
- Habib Bokhari
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Islamabad, Pakistan.
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Taneja N, Sangar G, Chowdhury G, Ramamurthy T, Mishra A, Singh M, Sharma M. Molecular epidemiology of Vibrio cholerae causing outbreaks & sporadic cholera in northern India. Indian J Med Res 2012; 136:656-63. [PMID: 23168707 PMCID: PMC3516034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND & OBJECTIVES Several outbreaks of cholera have been reported in Chandigarh region during a span of seven years from 2002-2008. The genetic characteristics of Vibrio cholerae isolates obtained during these outbreaks have not been adequately studied. The aim of this study was to do molecular typing of V. cholerae isolated from the sporadic and outbreak cases by pulsed-field gel electrophoresis (PFGE), Rep-PCR and ribotyping. METHODS Fifty representative isolates of V. cholerae from outbreak as well as sporadic cases were subjected to molecular typing by PFGE, 173 isolates (163 clinical and 10 environmental) were typed by rep-PCR and ribotyping. Ribotyping was done by determination of rRNA restriction pattern of BglI restriction digestion and hybridization with 7.2 kb rRNA probe of pKK3535 plasmid using DIG DNA labelling and detection kit. Universal VC1 primer was used for rep-PCR. RESULTS PFGE generated 15 pulsotypes, of which four matched the published pulsotypes and there were 11 new pulsotypes. PFGE was the most discriminatory method that could differentiate between isolates belonging to single ribotype. Pulsotype P1 corresponding to known pulsotype H1 was the major pulsotype till 2003. Pulsotype P3 corresponding to known pulsotype L emerged in 2004. The 2007 outbreaks in Punjab and Haryana were caused by P5 though P1 and P3 were isolated from the sporadic cases from the same region. The 2008 outbreak was caused by pulsotypes P6 and P7. Ribotype IV was the most predominant followed by RIII. This ribotype was not isolated after 2003 and ribotype IV became the most predominant 2004 onwards. Of the two unknown ribotypes (UNI and UN2), UNI was more common (27 isolates). Rep-PCR was the least discriminatory and divided all clinical isolates into four major profiles. The dendrogram analysis of PFGE revealed similarity of some clinical isolates with environmental isolates indicating the genetic relatedness. INTERPRETATION & CONCLUSION Our findings showed that Rep-PCR was least discriminatory method. Ribotyping was a reliable and reproducible method. Ribotype IV was predominant ribotype followed by RIII. A total of 15 pulsotypes were generated and 11 of these were not reported earlier. Genetic relatedness was shown by clinical and environmental isolates which needs to be confirmed in future studies.
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Affiliation(s)
- Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India,Reprint requests: Dr Neelam Taneja, Associate Professor, Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh 160 012, India e-mail:
| | - Garima Sangar
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Goutam Chowdhury
- Department of Medical Microbiology, National Institute of Cholera & Enteric Diseases (ICMR), Kolkata, India
| | - T. Ramamurthy
- Department of Medical Microbiology, National Institute of Cholera & Enteric Diseases (ICMR), Kolkata, India
| | - Arti Mishra
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Meenakshi Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Meera Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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Purves J, Blades M, Arafat Y, Malik SA, Bayliss CD, Morrissey JA. Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution. BMC Genomics 2012; 13:515. [PMID: 23020678 PMCID: PMC3532100 DOI: 10.1186/1471-2164-13-515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 09/24/2012] [Indexed: 01/05/2023] Open
Abstract
Background Staphylococcus aureus Repeat (STAR) elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published staphylococcal genome sequences and through sequencing of specific STAR element loci from a large set of S. aureus isolates. Results Using bioinformatic analyses, we found that the STAR elements were located in different genomic loci within each staphylococcal species. There was no correlation between the number of STAR elements in each genome and the evolutionary relatedness of staphylococcal species, however higher levels of repeats were observed in both S. aureus and S. lugdunensis compared to other staphylococcal species. Unexpectedly, sequencing of the internal spacer sequences of individual repeat elements from multiple isolates showed conservation at the sequence level within deep evolutionary lineages of S. aureus. Whilst individual STAR element loci were demonstrated to expand and contract, the sequences associated with each locus were stable and distinct from one another. Conclusions The high degree of lineage and locus-specific conservation of these intergenic repeat regions suggests that STAR elements are maintained due to selective or molecular forces with some of these elements having an important role in cell physiology. The high prevalence in two of the more virulent staphylococcal species is indicative of a potential role for STAR elements in pathogenesis.
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Xiao L, Liu C, Xie CC, Cai J, Chen YH. The direct repeat sequence upstream of Bacillus chitinase genes is cis-acting elements that negatively regulate heterologous expression in E. coli. Enzyme Microb Technol 2012; 50:280-6. [PMID: 22500893 DOI: 10.1016/j.enzmictec.2012.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 01/06/2012] [Accepted: 02/08/2012] [Indexed: 11/17/2022]
Abstract
To explore the influence of the direct repeat sequence (DRS) in Bacillus chitinase genes on heterogonous expression in Escherichia coli, we cloned and sequenced the entire open reading frame (ORF) and upstream sequences of the chitinase B (chiB) and chitinase MY75 (chiMY75) from Bacillus thuringiensis and Bacillus licheniformis. A pair of 8-bp DRS was found upstream of each chi gene. Chi ORFs with a series of truncated DRS were cloned and transformed into E. coli XL-Blue. The activity of the transformants without the DRS were significantly higher in chitinase assays than transformants containing the DRS. SDS-PAGE showed that part and full deletion of the DRS increased chi gene expression by approximately 1.7 and 3.8-fold, respectively. Northern blotting revealed deletion of the DRS regions increased chiB and chiMY75 mRNA expression. Specific binding of DNA-binding factors in the E. coli cell lyaste was observed to both the chiB and chiMY75 promoter regions and DRS elements. This is the first investigation to demonstrate that heterologous expression of Bacillus chi genes in E. coli is negatively regulated by their upstream DRS regions, which act as cis-acting elements.
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Affiliation(s)
- Liang Xiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, PR China
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Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population. J Bacteriol 2012; 194:3636-42. [PMID: 22563047 DOI: 10.1128/jb.00333-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The genomes of the two closely related freshwater thermophilic cyanobacteria Synechococcus sp. strain JA-3-3Ab and Synechococcus sp. strain JA-2-3B'a(2-13) each host several families of insertion sequences (ISSoc families) at various copy numbers, resulting in an overall high abundance of insertion sequences in the genomes. In addition to full-length copies, a large number of internal deletion variants have been identified. ISSoc2 has two variants (ISSoc2∂-1 and ISSoc2∂-2) that are observed to have multiple near-exact copies. Comparison of environmental metagenomic sequences to the Synechococcus genomes reveals novel placement of copies of ISSoc2, ISSoc2∂-1, and ISSoc2∂-2. Thus, ISSoc2∂-1 and ISSoc2∂-2 appear to be active nonautonomous mobile elements derived by internal deletion from ISSoc2. Insertion sites interrupting genes that are likely critical for cell viability were detected; however, most insertions either were intergenic or were within genes of unknown function. Most novel insertions detected in the metagenome were rare, suggesting a stringent selective environment. Evidence for mobility of internal deletion variants of other insertion sequences in these isolates suggests that this is a general mechanism for the formation of miniature insertion sequences.
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Sridhar J, Sabarinathan R, Balan SS, Rafi ZA, Gunasekaran P, Sekar K. Junker: an intergenic explorer for bacterial genomes. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 9:179-82. [PMID: 22196361 PMCID: PMC5054447 DOI: 10.1016/s1672-0229(11)60021-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 06/21/2011] [Indexed: 11/28/2022]
Abstract
In the past few decades, scientists from all over the world have taken a keen interest in novel functional units such as small regulatory RNAs, small open reading frames, pseudogenes, transposons, integrase binding attB/attP sites, repeat elements within the bacterial intergenic regions (IGRs) and in the analysis of those “junk” regions for genomic complexity. Here we have developed a web server, named Junker, to facilitate the in-depth analysis of IGRs for examining their length distribution, four-quadrant plots, GC percentage and repeat details. Upon selection of a particular bacterial genome, the physical genome map is displayed as a multiple loci with options to view any loci of interest in detail. In addition, an IGR statistics module has been created and implemented in the web server to analyze the length distribution of the IGRs and to understand the disordered grouping of IGRs across the genome by generating the four-quadrant plots. The proposed web server is freely available at the URL http://pranag.physics.iisc.ernet.in/junker/.
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Affiliation(s)
- Jayavel Sridhar
- Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamilnadu, India
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Castellanos E, Juan LD, Domínguez L, Aranaz A. Progress in molecular typing of Mycobacterium avium subspecies paratuberculosis. Res Vet Sci 2012; 92:169-79. [DOI: 10.1016/j.rvsc.2011.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/08/2011] [Accepted: 05/21/2011] [Indexed: 10/18/2022]
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Waturangi DE, Joanito I, Yogi Y, Thomas S. Use of REP- and ERIC-PCR to reveal genetic heterogeneity of Vibrio cholerae from edible ice in Jakarta, Indonesia. Gut Pathog 2012; 4:2. [PMID: 24576322 PMCID: PMC3359277 DOI: 10.1186/1757-4749-4-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 03/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vibrio cholerae is the causative organism of waterborne disease, cholera. V. cholerae has caused many epidemics and pandemics of cholera for many years. In this study, V. cholerae recovered from edible ice were investigated for their genetic diversity using Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR and Repetitive Extragenic Palindromic (REP) PCR. Isolation was done using selective medium and the presumptive isolates were confirmed through biochemical and serological assays. RESULTS Seventy-five isolates of V. cholerae were recovered from ice samples collected from different locations of Jakarta. Specifically, 19 of them were identified as O1 serotype, 16 were Ogawa, 3 isolates were Inaba and the remaining isolates were non-O1. The fingerprinting profiles of V.cholerae isolated from ice samples were very diverse. CONCLUSION This result showed that the ERIC sequence is more informative and discriminative than REP sequence for analysis of V. cholerae diversity.
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Affiliation(s)
- Diana E Waturangi
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jalan Jenderal Sudirman 51, Jakarta 12930, Indonesia.
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Abstract
Prokaryotes are in general believed to possess small, compactly organized genomes, with repetitive sequences forming only a small part of them. Nonetheless, many prokaryotic genomes in fact contain species-specific repeats (>85 bp long genomic sequences with less than 60% identity to other species) as we have previously demonstrated. However, it is not known at present how frequent such species-specific repeats are and what their functional roles in bacterial genomes may be. Therefore, we have conducted a comprehensive survey of prokaryotic species-specific repeats and characterized them to examine as to whether there are functional classes among different repeats or not and how they are mutually related to each other. Of the 613 distinct prokaryotic species analyzed, 97% were found to contain at least one species-specific repeats. It seems interesting to note that the species-specific repeats thus identified appear to be functionally variable in different genomes: in some genomes, they are mostly associated with duplicated protein-coding genes, whereas in some other genomes with rRNA and tRNA genes. Contrary to what may be expected, only one-fourth of the species-specific repeats were found to be associated with mobile genetic elements.
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Affiliation(s)
- Triinu Koressaar
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
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Terta M, Azelmat S, M’hand RA, Achbani EH, Barakate M, Bouteau F, Ennaji MM. Molecular typing of Pectobacterium carotovorum isolated from potato tuber soft rot in Morocco. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0391-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Abstract
Intergenic regions of prokaryotic genomes carry multiple copies of terminal inverted repeat (TIR) sequences, the nonautonomous miniature inverted-repeat transposable element (MITE). In addition, there are the repetitive extragenic palindromic (REP) sequences that fold into a small stem loop rich in G–C bonding. And the clustered regularly interspaced short palindromic repeats (CRISPRs) display similar small stem loops but are an integral part of a complex genetic element. Other classes of repeats such as the REP2 element do not have TIRs but show other signatures. With the current availability of a large number of whole-genome sequences, many new repeat elements have been discovered. These sequences display diverse properties. Some show an intimate linkage to integrons, and at least one encodes a small RNA. Many repeats are found fused with chromosomal open reading frames, and some are located within protein coding sequences. Small repeat units appear to work hand in hand with the transcriptional and/or post-transcriptional apparatus of the cell. Functionally, they are multifaceted, and this can range from the control of gene expression, the facilitation of host/pathogen interactions, or stimulation of the mammalian immune system. The CRISPR complex displays dramatic functions such as an acquired immune system that defends against invading viruses and plasmids. Evolutionarily, mobile repeat elements may have influenced a cycle of active versus inactive genes in ancestral organisms, and some repeats are concentrated in regions of the chromosome where there is significant genomic plasticity. Changes in the abundance of genomic repeats during the evolution of an organism may have resulted in a benefit to the cell or posed a disadvantage, and some present day species may reflect a purification process. The diverse structure, eclectic functions, and evolutionary aspects of repeat elements are described.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, State University of New York, Stony Brook, NY, USA.
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Hot D, Slupek S, Wulbrecht B, D'Hondt A, Hubans C, Antoine R, Locht C, Lemoine Y. Detection of small RNAs in Bordetella pertussis and identification of a novel repeated genetic element. BMC Genomics 2011; 12:207. [PMID: 21524285 PMCID: PMC3110155 DOI: 10.1186/1471-2164-12-207] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 04/27/2011] [Indexed: 11/16/2022] Open
Abstract
Background Small bacterial RNAs (sRNAs) have been shown to participate in the regulation of gene expression and have been identified in numerous prokaryotic species. Some of them are involved in the regulation of virulence in pathogenic bacteria. So far, little is known about sRNAs in Bordetella, and only very few sRNAs have been identified in the genome of Bordetella pertussis, the causative agent of whooping cough. Results An in silico approach was used to predict sRNAs genes in intergenic regions of the B. pertussis genome. The genome sequences of B. pertussis, Bordetella parapertussis, Bordetella bronchiseptica and Bordetella avium were compared using a Blast, and significant hits were analyzed using RNAz. Twenty-three candidate regions were obtained, including regions encoding the already documented 6S RNA, and the GCVT and FMN riboswitches. The existence of sRNAs was verified by Northern blot analyses, and transcripts were detected for 13 out of the 20 additional candidates. These new sRNAs were named Bordetella pertussis RNAs, bpr. The expression of 4 of them differed between the early, exponential and late growth phases, and one of them, bprJ2, was found to be under the control of BvgA/BvgS two-component regulatory system of Bordetella virulence. A phylogenetic study of the bprJ sequence revealed a novel, so far undocumented repeat of ~90 bp, found in numerous copies in the Bordetella genomes and in that of other Betaproteobacteria. This repeat exhibits certain features of mobile elements. Conclusion We shown here that B. pertussis, like other pathogens, expresses sRNAs, and that the expression of one of them is controlled by the BvgA/BvgS system, similarly to most virulence genes, suggesting that it is involved in virulence of B. pertussis.
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Affiliation(s)
- David Hot
- Center for Infection and Immunity of Lille, Institut Pasteur de Lille, France.
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Saito S, Kobayashi M, Kimoto-Nira H, Aoki R, Mizumachi K, Miyata S, Yamamoto K, Kitagawa Y, Suzuki C. Intraspecies discrimination of Lactobacillus paraplantarum by PCR. FEMS Microbiol Lett 2011; 316:70-6. [PMID: 21204929 DOI: 10.1111/j.1574-6968.2010.02193.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Lactobacillus paraplantarum is a species phenotypically close to Lactobacillus plantarum. Several PCR methods were evaluated to discriminate L. paraplantarum strains and among them, a PCR using an enterobacterial repetitive intergenic consensus (ERIC) sequence differentiated L. paraplantarum from other Lactobacillus species. In addition, a combination of ERIC and random amplified polymorphic DNA (RAPD) analysis distinguished among seven strains of L. paraplantarum tested. ERIC-PCR profiles showed several strain-specific DNA fragments in L. paraplantarum, among them, a 2.2-kb ERIC marker, termed LpF1, found to be specific to strain FBA1, which improved the skin integrity in an animal model. The LpF1 encodes three proteins similar to Lactobacillus fermentum AroA, TyrA, and AroK, which are involved in the shikimate pathway. A primer pair specific to FBA1 based on the internal sequence of LpF1 amplified a 950-bp FBA1-specific fragment LpF2. Southern blot analysis of Dra I-digested genomic DNA of L. paraplantarum strains using LpF2 as a probe showed that LpF2 is distinctive of strain FBA1 among 16 L. paraplantarum strains. Because both ERIC- and RAPD-PCR are fast and technically simple methods, they are useful for the rapid discrimination of L. paraplantarum strains and for the development of new strain-specific DNA markers for identifying industrially important strains.
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Affiliation(s)
- Shinichi Saito
- National Institute of Livestock and Grassland Science, Tsukuba, Ibaraki, Japan
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Kristoffersen SM, Tourasse NJ, Kolstø AB, Økstad OA. Interspersed DNA repeats bcr1-bcr18 of Bacillus cereus group bacteria form three distinct groups with different evolutionary and functional patterns. Mol Biol Evol 2010; 28:963-83. [PMID: 20961964 DOI: 10.1093/molbev/msq269] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many short (<400 bp) interspersed sequence repeats exist in bacteria, yet little is known about their origins, mode of generation, or possible function. Here, we present a comprehensive analysis of 18 different previously identified repeated DNA elements, bcr1-bcr18 (Økstad OA, Hegna I, Lindback T, Rishovd AL, Kolstø AB. 1999. Genome organization is not conserved between Bacillus cereus and Bacillus subtilis. Microbiology. 145:621-631.; Tourasse NJ, Helgason E, Økstad OA, Hegna IK, Kolstø AB. 2006. The Bacillus cereus group: novel aspects of population structure and genome dynamics. J Appl Microbiol. 101:579-593.), in 36 sequenced genomes from the Bacillus cereus group of bacteria. This group consists of genetically closely related species with variable pathogenic specificity toward different hosts and includes among others B. anthracis, B. cereus, and B. thuringiensis. The B. cereus group repeat elements could be classified into three categories with different properties: Group A elements (bcr1-bcr3) exhibited highly variable copy numbers ranging from 4 to 116 copies per strain, showed a nonconserved chromosomal distribution pattern between strains, and displayed several features characteristic of mobile elements. Group B repeats (bcr4-bcr6) were present in 0-10 copies per strain and were associated with strain-specific genes and disruptions of genome synteny, implying a possible contribution to genome rearrangements and/or horizontal gene transfer events. bcr5, in particular, was associated with large gene clusters showing resemblance to integrons. In agreement with their potentially mobile nature or involvement in horizontal transfers, the sequences of the repeats from Groups A and B (bcr1-bcr6) followed a phylogeny different from that of the host strains. Conversely, repeats from Group C (bcr7-bcr18) had a conserved chromosomal location and orthologous gene neighbors in the investigated B. cereus group genomes, and their phylogeny matched that of the host chromosome. Several of the group C repeats exhibited a conserved secondary structure or had parts of the structure conserved, possibly indicating functional RNAs. Accordingly, five of the repeats in group C overlapped regions encoding previously characterized riboswitches. Similarly, other group C repeats could represent novel riboswitches, encode small RNAs, and/or constitute other types of regulatory elements with specific biological functions. The current analysis suggests that the multitude of repeat elements identified in the B. cereus group promote genome dynamics and plasticity and could contribute to the flexible and adaptive life style of these bacteria.
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Affiliation(s)
- Simen M Kristoffersen
- Laboratory for Microbial Dynamics (LaMDa), Department of Pharmaceutical Biosciences, University of Oslo, Blindern, Oslo, Norway
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Chu MK, Lin LF, Twu CS, Lin RH, Lin YC, Hsu ST, Tzeng KC, Huang HC. Unique features of Erwinia chrysanthemi (Dickeya dadantii) RA3B genes involved in the blue indigoidine production. Microbiol Res 2010; 165:483-95. [DOI: 10.1016/j.micres.2009.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 09/09/2009] [Accepted: 09/16/2009] [Indexed: 11/28/2022]
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Labes G, Ulrich A, Lentzsch P. Influence of Bovine Slurry Deposition on the Structure of Nodulating Rhizobium leguminosarum bv. viciae Soil Populations in a Natural Habitat. Appl Environ Microbiol 2010; 62:1717-22. [PMID: 16535318 PMCID: PMC1388856 DOI: 10.1128/aem.62.5.1717-1722.1996] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The population of nodulating R. leguminosarum bv. viciae in soil from a grass-covered valley area which had been used for bovine slurry deposition over a period of 5 years was analyzed. For these studies, a rapid and reproducible method based on enterobacterial repetitive intergenic consensus (ERIC)-PCR was applied to identify Rhizobium strains which had infected pea nodules. Soil samples were taken from different areas and further analyzed in plant tests to determine the impact of the application of slurry (polluted or nonpolluted), the slope position (summit or toe), and exposure (north or south). After comparison of all PCR fingerprint patterns, 24 strain groups were defined. Some strain groups from the nonpolluted soil were suppressed in the polluted samples, and new strain groups were detected in the slurry-polluted soil. After analyzing relationships between the strain groups, we determined the influences of local factors on the nodulating R. leguminosarum bv. viciae population. We show that one of those local parameters, slope position, had significantly greater impact on the composition of the Rhizobium population than the presence of slurry.
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Jensen BD, Vicente JG, Manandhar HK, Roberts SJ. Occurrence and Diversity of Xanthomonas campestris pv. campestris in Vegetable Brassica Fields in Nepal. PLANT DISEASE 2010; 94:298-305. [PMID: 30754254 DOI: 10.1094/pdis-94-3-0298] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Black rot caused by Xanthomonas campestris pv. campestris was found in 28 sampled cabbage fields in five major cabbage-growing districts in Nepal in 2001 and in four cauliflower fields in two districts and a leaf mustard seed bed in 2003. Pathogenic X. campestris pv. campestris strains were obtained from 39 cabbage plants, 4 cauliflower plants, and 1 leaf mustard plant with typical lesions. Repetitive DNA polymerase chain reaction-based fingerprinting (rep-PCR) using repetitive extragenic palindromic, enterobacterial repetitive intergenic consensus, and BOX primers was used to assess the genetic diversity. Strains were also race typed using a differential series of Brassica spp. Cabbage strains belonged to five races (races 1, 4, 5, 6, and 7), with races 4, 1, and 6 the most common. All cauliflower strains were race 4 and the leaf mustard strain was race 6. A dendrogram derived from the combined rep-PCR profiles showed that the Nepalese X. campestris pv. campestris strains clustered separately from other Xanthomonas spp. and pathovars. Race 1 strains clustered together and strains of races 4, 5, and 6 were each split into at least two clusters. The presence of different races and the genetic variability of the pathogen should be considered when resistant cultivars are bred and introduced into regions in Nepal to control black rot of brassicas.
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Affiliation(s)
- Brita Dahl Jensen
- Department of Plant Biology and Biotechnology and Department of Agriculture and Ecology, The Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Joana G Vicente
- Warwick HRI, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
| | - Hira K Manandhar
- Plant Pathology Division, Nepal Agricultural Research Council, Khumaltar, Lalitpur, Nepal
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Yuan W, Chai TJ, Miao ZM. ERIC-PCR identification of the spread of airborne Escherichia coli in pig houses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2010; 408:1446-50. [PMID: 20067850 DOI: 10.1016/j.scitotenv.2009.12.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 11/27/2009] [Accepted: 12/10/2009] [Indexed: 05/04/2023]
Abstract
To understand the spread of microbial aerosols in pig houses, with Escherichia coli (E. coli) as indicator, the airborne E. coli in 4 pig houses and their surroundings at different points 10, 50m upwind and 10, 50, 100, 200 and 400m downwind respectively from the pig houses were collected, and the concentrations were calculated at each sampling point. Furthermore, the feces of pigs were collected to separate E. coli. The ERIC-PCR (Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction) technology was used to amplify the isolated E. coli DNA samples, then the amplified results were analyzed by NTSYS-pc (Version 2.10) to identify the similarity of isolated E. coli. The results showed that the airborne E. coli concentrations in indoor air of the 4 pig houses (21-35CFUm(-)(3) air) were much higher than those in upwind and downwind air (P<0.05), but there were no significant differences (P>0.05) at downwind distances. The ERIC-PCR results also showed that 52.4% of the fecal E. coli (four houses being respectively 2/4, 50%; 2/4, 50%; 3/6, 50%; 4/7, 57.1%) were identical to the indoor airborne E. coli isolates, and there was more than 90% similarity between the majority of E. coli (50%, 21/42) isolated from downwind air at 10, 50, 100 and 200m and those from indoor air or feces. It could be concluded that the aerosols in pig houses can spread to the surroundings, and thus effective measures should be taken to control and minimize the spread of microbial aerosols.
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Affiliation(s)
- W Yuan
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai'an, China
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35
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American Foulbrood in honeybees and its causative agent, Paenibacillus larvae. J Invertebr Pathol 2009; 103 Suppl 1:S10-9. [PMID: 19909971 DOI: 10.1016/j.jip.2009.06.015] [Citation(s) in RCA: 285] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 06/22/2009] [Indexed: 11/20/2022]
Abstract
After more than a century of American Foulbrood (AFB) research, this fatal brood infection is still among the most deleterious bee diseases. Its etiological agent is the Gram-positive, spore-forming bacterium Paenibacillus larvae. Huge progress has been made, especially in the last 20 years, in the understanding of the disease and of the underlying host-pathogen interactions. This review will place these recent developments in the study of American Foulbrood and of P. larvae into the general context of AFB research.
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DNA profiling of complex bacterial populations: toxic cyanobacterial blooms. Appl Microbiol Biotechnol 2009; 85:237-52. [DOI: 10.1007/s00253-009-2180-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 08/03/2009] [Accepted: 08/03/2009] [Indexed: 11/25/2022]
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37
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Duan H, Chai T, Liu J, Zhang X, Qi C, Gao J, Wang Y, Cai Y, Miao Z, Yao M, Schlenker G. Source identification of airborne Escherichia coli of swine house surroundings using ERIC-PCR and REP-PCR. ENVIRONMENTAL RESEARCH 2009; 109:511-7. [PMID: 19349045 PMCID: PMC7126843 DOI: 10.1016/j.envres.2009.02.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 02/19/2009] [Accepted: 02/24/2009] [Indexed: 05/19/2023]
Abstract
Evidence is mounting that microorganisms originating from livestock impact the air quality of the animal houses themselves and the public in the surrounding neighborhoods. The aim of this study was to develop efficient bacterial source tracking capabilities to identify sources of Escherichia coli aerosol pollution caused by pigs. Airborne E. coli were isolated from indoor air, upwind air (10 and 50 m away) and downwind air samples (10, 50, 100, 200 and 400 m away) for five swine houses using six-stage Andersen microbial samplers and Reuter-Centrifugal samplers (RCS). E. coli strains from pig fecal samples were also collected simultaneously. The enterobacterial repetitive intergenic consensus polymerize chain reaction (ERIC-PCR) and the repetitive extragenic palindromic (REP-PCR) approaches were used to study the genetic variability and to determine the strain relationships among E. coli isolated from different sites in each swine house. Results showed that 35.1% (20/57) of the bacterial DNA fingerprints from the fecal isolates matched with the corresponding strains isolated from indoor and downwind air samples (similarity > or = 90%). E. coli strains from the indoor and downwind air samples were closely related to the E. coli strains isolated from feces, while those isolated from upwind air samples (swine house C) had low similarity (61-69%). Our results suggest that some strains isolated from downwind and indoor air originated in the swine feces. Effective hygienic measures should be taken in animal farms to prevent or minimize the downwind spread of microorganism aerosol.
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Affiliation(s)
- Huiyong Duan
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
- College of Animal Husbandry and Veterinary Medicine, Jining Agricultural School, 272100 Jining, Shandong, China
| | - Tongjie Chai
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
- Corresponding author. Fax: +86 538 8241503.
| | - Jianzhu Liu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Xingxiao Zhang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Chunhua Qi
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Jing Gao
- Central Hospital of Taian City, Shandong, China
| | - Yaling Wang
- College of Life Science, Dalian Nationalities University, China
| | - Yumei Cai
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Zengmin Miao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Meiling Yao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Research Center for Animal Disease Control Engineering Shandong Province, Tai’an 271018, China
| | - Gerd Schlenker
- Institute of Animal and Environmental Hygiene, Free University Berlin, Germany
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Comparative analysis of the locus of enterocyte effacement and its flanking regions. Infect Immun 2009; 77:3501-13. [PMID: 19506015 DOI: 10.1128/iai.00090-09] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The attaching-and-effacing (A/E) phenotype mediated by factors derived from the locus of enterocyte effacement (LEE) is a hallmark of clinically important intestinal pathotypes of Escherichia coli, including enteropathogenic (EPEC), atypical EPEC (ATEC), and enterohemorrhagic E. coli strains. Epidemiological studies indicate that the frequency of diarrhea outbreaks caused by ATEC is increasing. Hence, it is of major importance to further characterize putative factors contributing to the pathogenicity of these strains and to gain additional insight into the plasticity and evolutionary aspects of this emerging pathotype. Here, we analyzed the two clinical ATEC isolates B6 (O26:K60) and 9812 (O128:H2) and compared the genetic organizations, flanking regions, and chromosomal insertion loci of their LEE with those of the LEE of other A/E pathogens. Our analysis shows that the core LEE is largely conserved-particularly among genes coding for the type 3 secretion system-whereas genes encoding effector proteins display a higher variability. Chromosomal insertion loci appear to be restricted to selC, pheU, and pheV. In contrast, striking differences were found between the 5'- and 3'-associated flanking regions reflecting the different histories of the various strains and also possibly indicating different lines in evolution.
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Treangen TJ, Abraham AL, Touchon M, Rocha EPC. Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev 2009; 33:539-71. [PMID: 19396957 DOI: 10.1111/j.1574-6976.2009.00169.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA repeats are causes and consequences of genome plasticity. Repeats are created by intrachromosomal recombination or horizontal transfer. They are targeted by recombination processes leading to amplifications, deletions and rearrangements of genetic material. The identification and analysis of repeats in nearly 700 genomes of bacteria and archaea is facilitated by the existence of sequence data and adequate bioinformatic tools. These have revealed the immense diversity of repeats in genomes, from those created by selfish elements to the ones used for protection against selfish elements, from those arising from transient gene amplifications to the ones leading to stable duplications. Experimental works have shown that some repeats do not carry any adaptive value, while others allow functional diversification and increased expression. All repeats carry some potential to disorganize and destabilize genomes. Because recombination and selection for repeats vary between genomes, the number and types of repeats are also quite diverse and in line with ecological variables, such as host-dependent associations or population sizes, and with genetic variables, such as the recombination machinery. From an evolutionary point of view, repeats represent both opportunities and problems. We describe how repeats are created and how they can be found in genomes. We then focus on the functional and genomic consequences of repeats that dictate their fate.
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Ishii S, Sadowsky MJ. Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution. Environ Microbiol 2009; 11:733-40. [PMID: 19207574 DOI: 10.1111/j.1462-2920.2008.01856.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.
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Affiliation(s)
- Satoshi Ishii
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
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41
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Molecular Epidemiology. BACTERIAL INFECTIONS OF HUMANS 2009. [PMCID: PMC7176198 DOI: 10.1007/978-0-387-09843-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Molecular epidemiology is now an established discipline in epidemiology.(1) It is the contemporary stage in the evolution of laboratory-based epidemiology that may have begun with the discovery in the late 1800s of ways to differentiate bacterial organisms by pure culture in artificial media.(2) Molecular epidemiology uses new molecular biology tools to address questions difficult or not possible to address by old laboratory tools. Just as statistical tools have become indispensable in epidemiological investigations and interpretations of epidemiologic data, molecular biology tools today have come to elucidate epidemiologic features of diseases that cannot be easily characterized by conventional techniques. Applied to infectious diseases, molecular biology methods have also come to challenge our traditional notions about the epidemiology of these diseases and have engendered novel opportunities for their prevention and control. This chapter will (1) review definitions commonly used in molecular epidemiology, (2) present an overview of molecular biology methods used to study infectious disease epidemiology, and (3) describe examples of the types of epidemiologic problems that can be addressed by molecular biology techniques, highlighting new concepts that emerged in the process of applying this approach to study bacterial infectious diseases.
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42
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Ye Y, Wu Q, Zhou Y, Dong X, Zhang J. Analysis of major band of Enterobacter sakazakii by ERIC-PCR and development of a species-specific PCR for detection of Ent. sakazakii in dry food samples. J Microbiol Methods 2008; 75:392-7. [PMID: 18718850 DOI: 10.1016/j.mimet.2008.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 07/11/2008] [Accepted: 07/17/2008] [Indexed: 11/16/2022]
Abstract
ERIC (Enterobacterial Repetitive Intergenic Consensus)-PCR was employed to generate stable and reproductive ERIC-PCR fingerprints of Ent. sakazakii ATCC51329. Moreover, this study also cloned and sequenced a major band of Ent. sakazakii (ATCC51329) ERIC-PCR fingerprints. The major band was amplified with primer ERIC2 and sequences extending primer ERIC 2 showed poor similarity with ERIC elements. A comparison of the nucleotide acid with other sequences available in the GenBank revealed 90% of identity with Ent. sakazakii ATCC BAA-894, and 73%-74% of identity with oligopeptiase gene or protease gene of some species from the Enterobacteriaceae family. Two primers were synthesized to develop and optimize an Enterobacter sakazakii-specific PCR based on regions of major band unique to Ent. sakazakii. The expected fragment was amplified from all of Ent. sakazkaii but not from the negative controls. As few as 10(2) CFU/ml of Ent. sakazakii of PCR were directly detected in the infant formulas. This was the case even in the presence of other bacteria. A comparison of traditional methods and new developed PCR in commercial foods suggested that without using API20-E test, the DFI chromogenic medium and FDA method showed 46.15% and 50% false positive respectively. Moreover, one false negative was observed with FDA method. In contrast, PCR was highly sensitive and specific to Ent. sakazakii. A high heterogeneity between Ent. sakazakii and the other microorganisms was found on expected fragment sequence. In addition, Ent. sakazakii ATCC51329 formed a separate branch with >5% divergence from the type strain ATCC BAA-894 and major strains.
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Affiliation(s)
- Yingwang Ye
- Guangdong Provincial Key Laboratory of Microbiol Culture Collection and Application, Guangdong Institute of Microbiology, No. 100 # Central Xianiie Road, Guangzhou, China.
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43
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Cozzuto L, Petrillo M, Silvestro G, Di Nocera PP, Paolella G. Systematic identification of stem-loop containing sequence families in bacterial genomes. BMC Genomics 2008; 9:20. [PMID: 18201379 PMCID: PMC2267715 DOI: 10.1186/1471-2164-9-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Accepted: 01/17/2008] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Analysis of non-coding sequences in several bacterial genomes brought to the identification of families of repeated sequences, able to fold as secondary structures. These sequences have often been claimed to be transcribed and fulfill a functional role. A previous systematic analysis of a representative set of 40 bacterial genomes produced a large collection of sequences, potentially able to fold as stem-loop structures (SLS). Computational analysis of these sequences was carried out by searching for families of repetitive nucleic acid elements sharing a common secondary structure. RESULTS The initial clustering procedure identified clusters of similar sequences in 29 genomes, corresponding to about 1% of the whole population. Sequences selected in this way have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Removal of redundancies and regrouping of the selected sequences resulted in a final set of 92 families, defined by HMM analysis. 25 of them include all well-known SLS containing repeats and others reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure and are located within intergenic regions. CONCLUSION Systematic analysis of 40 bacterial genomes revealed a large number of repeated sequence families, including known and novel ones. Their predicted structure and genomic location suggest that, even in compact bacterial genomes, a relatively large fraction of the genome consists of non-protein-coding sequences, possibly functioning at the RNA level.
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Affiliation(s)
- Luca Cozzuto
- CEINGE Biotecnologie Avanzate scarl, Via Comunale Margherita 482, 80145 Napoli, Italy.
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44
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Abstract
Small repeat sequences in bacterial genomes, which represent non-autonomous mobile elements, have close similarities to archaeon and eukaryotic miniature inverted repeat transposable elements. These repeat elements are found in both intergenic and intragenic chromosomal regions, and contain an array of diverse motifs. These can include DNA sequences containing an integration host factor binding site and a proposed DNA methyltransferase recognition site, transcribed RNA secondary structural motifs, which are involved in mRNA regulation, and translated open reading frames found fused to other open reading frames. Some bacterial mobile element fusions are in evolutionarily conserved protein and RNA genes. Others might represent or lead to creation of new protein genes. Here we review the remarkable properties of these small bacterial mobile elements in the context of possible beneficial roles resulting from random insertions into the genome.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, SUNY, Stony Brook, NY 11794-5222, USA.
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45
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Ferrières L, Aslam SN, Cooper RM, Clarke DJ. The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production. MICROBIOLOGY-SGM 2007; 153:1070-1080. [PMID: 17379715 DOI: 10.1099/mic.0.2006/002907-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The RcsCDB phosphorelay was originally identified as the main regulator of colanic acid biosynthesis in Escherichia coli K-12. However, recent transcriptomic analyses have identified more than 150 genes belonging to the Rcs regulon, including yjbE, yjbF, yjbG and yjbH. These genes are clustered on the genome and oriented in the same direction but their function remains unknown. In this work it is shown that yjbE, yjbF, yjbG and yjbH are transcribed as a single operon and it is confirmed that the expression of this operon is controlled by the Rcs phosphorelay, in a manner that is dependent on the auxiliary regulatory protein RcsA. Interestingly, Northern blot analysis revealed that the amount of yjbE transcripts in the cell is higher than the amount of yjbEFGH transcripts and it is proposed that this differential expression is mediated by the presence of a strong stem-loop structure in the yjbE-yjbF intergenic region. Finally, evidence is provided that the overexpression of yjbEFGH affects colony morphology and leads to the production of an extracellular polysaccharide that binds Congo red and toluidine blue-O.
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Affiliation(s)
- Lionel Ferrières
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Shazia N Aslam
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Richard M Cooper
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - David J Clarke
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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46
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Jomantiene R, Zhao Y, Davis RE. Sequence-variable mosaics: composites of recurrent transposition characterizing the genomes of phylogenetically diverse phytoplasmas. DNA Cell Biol 2007; 26:557-64. [PMID: 17688407 DOI: 10.1089/dna.2007.0610] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phytoplasmas are cell wall-less prokaryotes characterized by small, AT-rich genomes that encode capabilities for obligate, transkingdom parasitism and pathogenicity in plants and insect vectors. Inability to isolate and characterize phytoplasmas in pure culture has led to adoption of the 'Candidatus species' convention to refer to distinct phytoplasma lineages. In this study, we provide evidence that multiple, sequence-variable mosaics (SVMs) of clustered genes and repetitive extragenic palindromes are characteristic features of phytoplasma genome architecture in phylogenetically diverse species. The findings suggest that the origin of SVMs was an ancient event in evolution of the phytoplasma clade, while current forms of SVMs are results of dramatic and more recent events. Sequence diversity of hypervariable regions indicated rapid evolution possibly involving capture of mobile elements recurrently targeted to SVMs. Multiple events of targeted mobile element attack, recombination, and rearrangement conceivably account for the composite structure of SVMs. Proteins encoded by the highly variable region included a lysophospholipase and other putatively secreted and/or transmembrane, cell surface-interacting proteins potentially significant in phytoplasma-host interactions.
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47
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Budowle B, Beaudry JA, Barnaby NG, Giusti AM, Bannan JD, Keim P. Role of law enforcement response and microbial forensics in investigation of bioterrorism. Croat Med J 2007; 48:437-49. [PMID: 17696298 PMCID: PMC2080552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
The risk and threat of bioterrorism and biocrime have become a large concern and challenge for governments and society to enhance biosecurity. Law enforcement plays an important role in assessing and investigating activities involved in an event of bioterrorism or biocrime. Key to a successful biosecurity program is increased awareness and early detection of threats facilitated by an integrated network of responsibilities and capabilities from government, academic, private, and public assets. To support an investigation, microbial forensic sciences are employed to analyze and characterize forensic evidence with the goal of attribution or crime scene reconstruction. Two different molecular biology-based assays--real time polymerase chain reaction (PCR) and repetitive element PCR--are described and demonstrate how molecular biology tools may be utilized to aid in the investigative process. Technologies relied on by microbial forensic scientists need to be properly validated so that the methods used are understood and so that interpretation of results is carried out within the limitations of the assays. The three types of validation are preliminary, developmental, and internal. The first is necessary for rapid response when a threat is imminent or an attack has recently occurred. The latter two apply to implementation of routinely used procedures.
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Affiliation(s)
- Bruce Budowle
- Scientific Analysis Section, Federal Bureau of Investigation, Quantico, Va, USA.
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48
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Wang XW, Zhang L, Jin LQ, Jin M, Shen ZQ, An S, Chao FH, Li JW. Development and application of an oligonucleotide microarray for the detection of food-borne bacterial pathogens. Appl Microbiol Biotechnol 2007; 76:225-33. [PMID: 17492283 DOI: 10.1007/s00253-007-0993-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2007] [Revised: 04/10/2007] [Accepted: 04/11/2007] [Indexed: 01/10/2023]
Abstract
The rapid and accurate detection and identification of food-borne pathogenic bacteria is critical for food safety. In this paper, we describe a rapid (<4 h) high-throughput detection and identification system that uses universal polymerase chain reaction (PCR) primers to amplify a variable region of bacterial the 16S rRNA gene, followed by reverse hybridization of the products to species-specific oligonucleotide probes on a chip. This procedure was successful in discriminating 204 strains of bacteria from pure culture belonging to 13 genera of bacteria. When this method was applied directly to 115 strains of bacteria isolated from foods, 112/115 (97.4%) were correctly identified; two strains were indistinguishable due to weak signal, while one failed to produce a PCR product. The array was used to detect and successfully identify two strains of bacteria from food poisoning outbreak samples, giving results through hybridization that were identical to those obtained by traditional methods. The sensitivity of the microarray assay was 10(2) CFU of bacteria. Thus, the oligonucleotide microarray is a powerful tool for the detection and identification of pathogens from foods.
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Affiliation(s)
- Xin-Wei Wang
- Institute of Environment and Health, No. 1, Dali Road, Tianjin, 300050, People's Republic of China
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Hiett KL, Seal BS, Siragusa GR. Campylobacter spp. subtype analysis using gel-based repetitive extragenic palindromic-PCR discriminates in parallel fashion to flaA short variable region DNA sequence analysis. J Appl Microbiol 2006; 101:1249-58. [PMID: 17105555 DOI: 10.1111/j.1365-2672.2006.03026.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The repetitive extragenic palindromic-PCR (rep-PCR) subtyping technique, which targets repetitive extragenic DNA sequences in a PCR, was optimized for Campylobacter spp. These data were then used for comparison with the established genotyping method of flaA short variable region (SVR) DNA sequence analysis as a tool for molecular epidemiology. METHODS AND RESULTS Uprime Dt, Uprime B1 or Uprime RI primers were utilized to generate gel-based fingerprints from a set of 50 Campylobacter spp. isolates recovered from a variety of epidemiological backgrounds and sources. Analysis and phenogram tree construction, using the unweighted pair group method with arithmetic mean, of the generated fingerprints demonstrated that the Uprime Dt primers were effective in providing reproducible patterns (100% typability, 99% reproducibility) and at placing isolates into epidemiological relevant groups. Genetic stability of the rep-PCR Uprime Dt patterns under nonselective, short-term transfer conditions revealed a Pearson's correlation approaching 99%. These same 50 Campylobacter spp. isolates were analysed by flaA SVR DNA sequence analysis to obtain phylogenetic relationships. CONCLUSIONS The Uprime Dt primer-generated rep-PCR phenogram was compared with a phenogram generated from flaA SVR DNA sequence analysis of the same isolates. Comparison of the two sets of resulting genomic relationships revealed that both methods segregated isolates into similar groups. SIGNIFICANCE AND IMPACT OF THE STUDY These results indicate that rep-PCR analysis performed using the Mo Bio Ultra Clean Microbial Genomic DNA Isolation Kit for DNA isolation and the Uprime DT primer set for amplification is a useful and effective tool for accurate differentiation of Campylobacter spp. for subtyping and epidemiological analyses.
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Affiliation(s)
- K L Hiett
- U.S. Department of Agriculture, Agricultural Research Service, Poultry Microbiological Safety Research Unit, Russell Research Center, Athens, GA 30604-5677, USA.
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50
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Jin LQ, Li JW, Wang SQ, Chao FH, Wang XW, Yuan ZQ. Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays. World J Gastroenterol 2006; 11:7615-9. [PMID: 16437687 PMCID: PMC4727218 DOI: 10.3748/wjg.v11.i48.7615] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To detect the common intestinal pathogenic bacteria quickly and accurately. METHODS A rapid (<3 h) experimental procedure was set up based upon the gene chip technology. Target genes were amplified and hybridized by oligonucleotide microarrays. RESULTS One hundred and seventy strains of bacteria in pure culture belonging to 11 genera were successfully discriminated under comparatively same conditions, and a series of specific hybridization maps corresponding to each kind of bacteria were obtained. When this method was applied to 26 divided cultures, 25 (96.2%) were identified. CONCLUSION Salmonella sp., Escherichia coli, Shigella sp., Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus, Proteus sp., Bacillus cereus, Vibrio cholerae, Enterococcus faecalis, Yersinia enterocolitica, and Campylobacter jejuni can be detected and identified by our microarrays. The accuracy, range, and discrimination power of this assay can be continually improved by adding further oligonucleotides to the arrays without any significant increase of complexity or cost.
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Affiliation(s)
- Lian-Qun Jin
- Tianjin Institute of Hygiene and Environmental Medicine 1, Da Li Road, Tianjin 300050, China.
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