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Chetan KK, Kishore Varma P, Chandrasekhar V, Anil Kumar P, Vasanthi V, Vamshi Krishna G. Unveiling the Biocontrol Potential of Rhizoplane Bacillus Species against Sugarcane Fusarium Wilt through Biochemical and Molecular Analysis. Braz J Microbiol 2024; 55:1883-1896. [PMID: 38609692 PMCID: PMC11153384 DOI: 10.1007/s42770-024-01307-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/10/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Biocontrol is regarded as a viable alternate technique for managing sugarcane wilt disease caused by Fusarium sacchari. Many fungal antagonists against F. sacchari, have been reported, but the potential of bacterial antagonists was explored to a limited extent, so the present study evaluated the antagonistic potential of rhizoplane Bacillus species and their mode of action. RESULTS A total of twenty Bacillus isolates from the rhizoplane of commercially grown sugarcane varieties were isolated. The potential isolate SRB2 had shown inhibition of 52.30, 33.33, & 44.44% and SRB20 of 35.00, 33.15, & 36.85% in direct, indirect, and remote confrontation respectively against F. sacchari. The effective strains were identified as Bacillus inaquosorum strain SRB2 and B. vallismortis strain SRB20, by PCR amplification of 16S-23S intergenic region. The biochemical studies on various direct and indirect biocontrol mechanisms revealed the production of IAA, Protease, Cellulase, Siderophores, and P solubilization. The molecular analysis revealed the presence of antimicrobial peptides biosynthetic genes like fenD (Fengycin), bmyB (Bacyllomicin) ituC (Iturin) and spaS (Subtilin) which provided a competitive edge to these isolates compared to other Bacillus strains. Under greenhouse experiments, the sett bacterization with SRB2, significantly (P < 0.001) reduced the seedling mortality by > 70% followed by SRB20 in F. sacchari inoculated pots. CONCLUSION The study revealed that the isolates B. inaquosorum SRB2 and B. vallismortis SRB20 can be used as potential bioagents against sugarcane Fusarium wilt.
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Affiliation(s)
- K K Chetan
- Division of Plant Pathology, ICAR-IARI, New Delhi, India.
| | | | - V Chandrasekhar
- Department of Plant Pathology, RARS, Anakapalle, Visakapatnam, India
| | - P Anil Kumar
- Department of Plant Pathology, Acharya NG Ranga Agricultural University, Guntur, India
| | - V Vasanthi
- Department of Plant Pathology, Agricultural College, Bapatla, India
| | - G Vamshi Krishna
- Department of Plant Pathology, Agricultural College, Bapatla, India
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Murugaiyan V, Utreja S, Hovey KM, Sun Y, LaMonte MJ, Wactawski-Wende J, Diaz PI, Buck MJ. Defining Porphyromonas gingivalis strains associated with periodontal disease. Sci Rep 2024; 14:6222. [PMID: 38485747 PMCID: PMC10940620 DOI: 10.1038/s41598-024-56849-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/12/2024] [Indexed: 03/18/2024] Open
Abstract
Porphyromonas gingivalis, a Gram-negative anaerobic bacterium commonly found in human subgingival plaque, is a major etiologic agent for periodontitis and has been associated with multiple systemic pathologies. Many P. gingivalis strains have been identified and different strains possess different virulence factors. Current oral microbiome approaches (16S or shotgun) have been unable to differentiate P. gingivalis strains. This study presents a new approach that aims to improve the accuracy of strain identification, using a detection method based on sequencing of the intergenic spacer region (ISR) which is variable between P. gingivalis strains. Our approach uses two-step PCR to amplify only the P. gingivalis ISR region. Samples are then sequenced with an Illumina sequencer and mapped to specific strains. Our approach was validated by examining subgingival plaque from 153 participants with and without periodontal disease. We identified the avirulent strain ATCC33277/381 as the most abundant strain across all sample types. The W83/W50 strain was significantly enriched in periodontitis, with 13% of participants harboring that strain. Overall, this approach can have significant implications not only for the diagnosis and treatment of periodontal disease but also for other diseases where P. gingivalis or its toxins have been implicated, such as Alzheimer's disease.
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Affiliation(s)
- Vijaya Murugaiyan
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Simran Utreja
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Kathleen M Hovey
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Michael J LaMonte
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Jean Wactawski-Wende
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Patricia I Diaz
- UB Microbiome Center, University at Buffalo, Buffalo, NY, USA
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY, USA
| | - Michael J Buck
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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Development and evaluation of a rapid, specific, and sensitive loop-mediated isothermal amplification assay to detect Tenacibaculum sp. strain pbs-1 associated with black-spot shell disease in Akoya pearl oysters. Arch Microbiol 2022; 205:43. [PMID: 36575332 DOI: 10.1007/s00203-022-03384-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022]
Abstract
Black-spot shell disease decreases pearl quality and threatens pearl oyster survival. Establishment of a rapid, specific, and sensitive assay to detect Tenacibaculum sp. strain Pbs-1 associated with black-spot shell disease is of commercial importance. We developed a rapid, specific, and highly sensitive loop-mediated isothermal amplification (LAMP) assay to detect Tenacibaculum sp. Pbs-1 in Akoya pearl oysters Pinctada fucata. A set of five specific primers (two inner, two outer, and a loop) were designed based on the 16S-23S internal spacer region of strain Pbs-1. The optimum reaction temperature was 63 °C, and concentrations of the inner and loop primers were 1.4 and 1.0 µM, respectively. The LAMP product can be detected using agarose gel electrophoresis, and the color change in the reaction tube can be detected visually (by the naked eye) following the addition of malachite green. Our assay proved to be specific for strain Pbs-1, with no cross-reactivity with five other species of Tenacibaculum. The detection limit of the LAMP assay at 35 min is 50 pg, and at 60 min it is 5 fg. We evaluated the LAMP assay using diseased and healthy pearl oysters. The results demonstrate the suitability and simplicity of this test for rapid field diagnosis of strain Pbs-1.
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Mohamed HMA, Abd-Elhafeez HH, Al-Jabr OA, El-Zamkan MA. Characterization of Acinetobacter baumannii Isolated from Raw Milk. BIOLOGY 2022; 11:biology11121845. [PMID: 36552354 PMCID: PMC9775129 DOI: 10.3390/biology11121845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Acinetobacter baumannii (A. baumannii) is an opportunistic pathogen associated with nosocomial infections. In this study, 100 raw milk samples were collected from Qena, Egypt, and subjected to conventional and molecular assays to determine the presence of A. baumannii and investigate their antimicrobial resistance and biofilm formation. Our findings revealed that, among the 100 samples, Acinetobacter spp. were found in 13 samples based on CHROM agar results. We further characterized them using rpoB and 16S-23SrRNA sequencing and gyrB multiplex PCR analysis and confirmed that 9 out of the 13 Acinetobacter spp. isolates were A. baumannii and 4 were other species. The A. baumannii isolates were resistant to β-lactam drugs, including cefotaxime (44%), ampicillin-sulbactam and levofloxacin (33.3% for each), imipenem, meropenem and aztreonam (22.2% for each). We observed different antimicrobial resistance patterns, with a multi-antibiotic resistant (MAR) index ranging from 0.2 to 0.3. According to the PCR results, blaOXA-51 and blaOXA-23 genes were amplified in 100% and 55.5% of the A. baumannii isolates, respectively, while the blaOXA-58 gene was not amplified. Furthermore, the metallo-β-lactamases (MBL) genes blaIMP and blaNDM were found in 11.1% and 22.2% of isolates, respectively, while blaVIM was not amplified. Additionally, eight A. baumannii isolates (88.8%) produced black-colored colonies on Congo red agar, demonstrating their biofilm production capacity. These results showed that, besides other foodborne pathogens, raw milk should also be examined for A. baumannii, which could be a public health concern.
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Affiliation(s)
- Hams M. A. Mohamed
- Department of Microbiology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Hanan H. Abd-Elhafeez
- Department of Cells and Tissues, Faculty of Veterinary Medicine, Assiut University, Assiut 71526, Egypt
- Correspondence:
| | - Omar A. Al-Jabr
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Mona A. El-Zamkan
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
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Es-sbata I, Castro R, Durán-Guerrero E, Zouhair R, Astola A. Production of prickly pear (Opuntia ficus-indica) vinegar in submerged culture using Acetobacter malorum and Gluconobacter oxydans: Study of volatile and polyphenolic composition. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104699] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ferreira EM, Romero LC, Cunha MDLRDSD, Malagó Junior W, Camargo CH, Barioni Júnior W, Zafalon LF. Persistence of Staphylococcus spp. in milk from cows undergoing homeopathy to control subclinical mastitis. BMC Vet Res 2022; 18:273. [PMID: 35831890 PMCID: PMC9277819 DOI: 10.1186/s12917-022-03364-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/15/2022] [Indexed: 11/25/2022] Open
Abstract
Background Mastitis is one of the major diseases in dairy cattle, as it causes great economic losses to producers due to the reduction of milk production and changes in the quality of the product. The disease is mainly caused by bacteria of the genus Staphylococcus spp., these microorganisms can express various virulence factors, such as biofilms for example. In herds with organic management, producers and technicians use unconventional ways to treat and control the disease, such as homeopathy. However, it is not known if this type of treatment is able to control pathogenic bacteria such as those of the genus Staphylococcus, of relevance to animal and human health. Thus, the objective of this study was to investigate the production of biofilm in vitro and its genes by Staphylococcus spp. isolated in the milk of cows treated with homeopathy, as well as the persistence of microorganisms in animals. Methods Ninety-nine isolates of Staphylococcus spp. from cows treated and not treated with homeopathy were identified by internal transcribed space-polymerase chain reaction and investigated for the presence of the icaABCD, bap, aap, atlE, and bhp genes and in vitro biofilm production using the adhesion method on polystyrene plates. The enzyme restriction profile was determined by Pulsed-Field Gel Electrophoresis. Clusters of S. aureus and S. epidermidis with three or more isolates had an isolate selected for Multilocus Sequence Typing. Results The frequency of S. aureus isolations was similar in treated and untreated cows, while 71.4% of the coagulase-negative identified were isolated in cows treated with homeopathy. The distribution of the operon ica genes was similar in animals with and without treatment, except for the icaD gene, more frequent in treated cows. Production of biofilm was associated with presence of one or more genes from the icaADBC operon. S. aureus revealed a greater diversity and greater dissemination in cows treated and not treated with homeopathy. Sequence Types ST1, ST5, and ST126 were identified in S. aureus. Conclusions The presence of biofilm-associated genes and the in vitro production of biofilms, combined with the persistence of clonal profiles of Staphylococcus spp. demonstrate other forms of control for bovine mastitis should be researched for organic production herds.
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Affiliation(s)
- Elka Machado Ferreira
- Department of Pathology, Reproduction, and One Health, Paulista State University "Júlio de Mesquita Filho" - FCAV, Jaboticabal, São Paulo, Brazil.
| | - Letícia Castilho Romero
- Department of Microbiology and Immunology, Paulista State University "Júlio de Mesquita Filho" - IB, Botucatu, São Paulo, Brazil
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Sultana Y, Kong F, Mukutmoni M, Fahria L, Begum A, Lee R. Internal transcribed spacer region 1 as a promising target for detection of intra-specific polymorphisms for Strongyloides stercoralis. Trop Parasitol 2022; 12:48-53. [PMID: 35923272 PMCID: PMC9341138 DOI: 10.4103/tp.tp_13_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/18/2021] [Accepted: 09/13/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Strongyloides stercoralis, the causative agent of strongyloidiasis, is a parasitic worm that has larvae capable of reinfecting the same host. This nematode infection is therefore difficult to treat and to achieve total cure. Information about genetic variation and differences in drug susceptibility between strains is needed to improve treatment outcomes. Aim: To develop a polymerase chain reaction (PCR) to identify the intra-species variation among 13 S. stercoralis isolates collected from Bangladesh, USA and Australia. Material & Methods: PCR assays were designed by using primers targeting S. stercoralis internal transcribed spacer (ITS) regions 1 and 2. Sequence data generated by these PCR products were compared to the existing ITS1/2, 18S and 28S rRNA gene sequences in GenBank for phylogenetic analysis. Results: Intra-species single nucleotide polymorphisms (SNPs) were identified in ITS1 and in the 5.8S rRNA gene. The generated phylogram grouped the 13 isolates into dog, Orangutan and human clusters. Conclusion: This method could be used as an epidemiological tool to study strain differences in larger collections of S. stercoralis isolates. The study forms the basis for further development of an ITS-based assay for S. stercoralis molecular epidemiological studies
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Mijatović J, Severns PM, Kemerait RC, Walcott RR, Kvitko BH. Patterns of Seed-to-Seedling Transmission of Xanthomonas citri pv. malvacearum, the Causal Agent of Cotton Bacterial Blight. PHYTOPATHOLOGY 2021; 111:2176-2184. [PMID: 34032522 DOI: 10.1094/phyto-02-21-0057-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cotton bacterial blight (CBB), caused by Xanthomonas citri pv. malvacearum, was a major disease of cotton in the United States in the early part of the twentieth century. The reemergence of CBB revealed many gaps in our understanding of this important disease. In this study, we employed a wild-type (WT) field isolate of X. citri pv. malvacearum from Georgia (U.S.A.) to generate a nonpathogenic hrcV mutant lacking a functional type-III secretion system (T3SS-). We tagged the WT and T3SS- strains with an auto-bioluminescent Tn7 reporter and compared colonization patterns of CBB-susceptible and CBB-resistant cotton seedlings using macroscopic image analysis and bacterial load enumeration. WT and T3SS- X. citri pv. malvacearum strains colonized cotton cotyledons of CBB-resistant and CBB-susceptible cotton cultivars. However, X. citri pv. malvacearum populations were significantly higher in CBB-susceptible seedlings inoculated with the WT strain. Additionally, WT and T3SS- X. citri pv. malvacearum strains systemically colonized true leaves, although at different rates. Finally, we observed that seed-to-seedling transmission of X. citri pv. malvacearum may involve systemic spread through the vascular tissue of cotton plants. These findings yield novel insights into potential X. citri pv. malvacearum reservoirs for CBB outbreaks.
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Affiliation(s)
- Jovana Mijatović
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Paul M Severns
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Robert C Kemerait
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793
| | - Ron R Walcott
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
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Strain-Level Profiling of Oral Microbiota with Targeted Sequencing. Methods Mol Biol 2021. [PMID: 34410649 DOI: 10.1007/978-1-0716-1518-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Targeted sequencing of one or more regions of the bacterial 16S rRNA gene fragment has emerged as a gold standard for investigating taxonomic diversity in complex microbial communities, such as those found in the oral cavity. While this approach is useful for identifying bacteria up to genus level, its ability to distinguish between many closely related oral species, or explore strain-level variations within each species, is very limited. Here we present an approach based on targeted sequencing the 16S-23S Intergenic Spacer Region (ISR) in the bacterial ribosomal operon for taxonomic characterization of microbial communities at a subspecies or strain level. This approach retains the advantages of 16S-based methods, such as easy library preparation, high throughput, short amplicon sizes, and low cost of sequencing, while providing subspecies-level resolution as a result of naturally higher genetic diversity present in the ISR compared to the 16S hypervariable regions. These advantages make it an excellent tool for high-resolution oral microbiota characterization.
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Cyanobiont genetic diversity and host specificity of cyanobiont-bearing dinoflagellate Ornithocercus in temperate coastal waters. Sci Rep 2021; 11:9458. [PMID: 33947914 PMCID: PMC8097063 DOI: 10.1038/s41598-021-89072-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/23/2021] [Indexed: 11/17/2022] Open
Abstract
Cyanobacteria are ubiquitous in marine environments and play an important role as primary producers. Some cyanobacteria, the so-called cyanobionts (cyanobacterial symbionts), have a symbiotic relationship with unicellular organisms. Among these relationships, in particular, the nature (e.g., genetic diversity, host or cyanobiont specificity, and cyanobiont seasonality) of the cyanobiont-dinoflagellate host consortia remains poorly understood. In this study, 16S rDNA of cyanobionts in 138 single host cells isolated over four seasons from temperate waters were sequenced using the MiSeq platform. Genetic analysis of cyanobionts from the dinoflagellate host Ornithocercus revealed that three genetic types of Synechococcales cyanobionts occurred in a wide range of water temperatures (11–24 °C), and their distribution seemed to be closely associated with variations in salinity. Furthermore, a certain degree of host (or cyanobiont) specificity in cyanobionts (or the host) among Ornithocercus species as well as among other dinophysoid species (i.e. Amphisolenia, Citharistes, and Histioneis), was observed. In addition to the Synechococcales cyanobionts, this study identified OTU sequences affiliated with Vampirovibrionales and Chroococcidiopsidales in some Ornithocercus cells, suggesting that Ornithocercus species are an additional habitat for these bacterial groups.
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Cataneli Pereira V, Pinheiro-Hubinger L, de Oliveira A, Moraes Riboli DF, Benini Martins K, Calixto Romero L, Ribeiro de Souza da Cunha MDL. Detection of the agr System and Resistance to Antimicrobials in Biofilm-Producing S. epidermidis. Molecules 2020; 25:molecules25235715. [PMID: 33287389 PMCID: PMC7729762 DOI: 10.3390/molecules25235715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
The ability of Staphylococcus epidermidis to produce virulence factors, such as biofilm, added to its increased resistance to antimicrobials can cause infections that are difficult to treat. Many staphylococcal virulence factors are under the control of the accessory gene regulator (agr). The objective of this study was to establish the agr locus and susceptibility of biofilm-producing S. epidermidis specimens to antimicrobial agents, through PCR reactions, reverse transcription polymerase chain reaction (RT-PCR), and the determination of minimum inhibitory concentration (MIC), and to analyze the clonal profile of 300 strains isolated from blood culture specimens from inpatients at a University Hospital in Brazil, over a 20-year period by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) techniques. The ica operon expression was shown in 83.6% strains, bhp gene in 11.5%, and aap gene in 32.8%. Oxacillin resistance was detected in 90.1%, while 4.9% showed tigecycline resistance, and intermediate resistance to quinupristin/dalfopristin was identified in 0.4%. Clonal profile determination showed 11 clusters, with the ST2 type determined as the major cluster. The S. epidermidis biofilm producer demonstrated a predominance of agr I locus, oxacillin resistance, and SCCmec III as well as the potential dissemination of pathogenic clones in hospital settings over long periods.
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Affiliation(s)
- Valéria Cataneli Pereira
- Sector of Microbiology and Immunology, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP—University Estadual Paulista, Botucatu CEP 18618-689, São Paulo, Brazil; (V.C.P.); (L.P.-H.); (A.d.O.); (D.F.M.R.); (K.B.M.); (L.C.R.)
- Sector of Microbiology and Immunology, UNOESTE—University of West Paulista, Presidente Prudente CEP 19050-920, São Paulo, Brazil
| | - Luiza Pinheiro-Hubinger
- Sector of Microbiology and Immunology, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP—University Estadual Paulista, Botucatu CEP 18618-689, São Paulo, Brazil; (V.C.P.); (L.P.-H.); (A.d.O.); (D.F.M.R.); (K.B.M.); (L.C.R.)
| | - Adilson de Oliveira
- Sector of Microbiology and Immunology, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP—University Estadual Paulista, Botucatu CEP 18618-689, São Paulo, Brazil; (V.C.P.); (L.P.-H.); (A.d.O.); (D.F.M.R.); (K.B.M.); (L.C.R.)
| | - Danilo Flávio Moraes Riboli
- Sector of Microbiology and Immunology, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP—University Estadual Paulista, Botucatu CEP 18618-689, São Paulo, Brazil; (V.C.P.); (L.P.-H.); (A.d.O.); (D.F.M.R.); (K.B.M.); (L.C.R.)
| | - Katheryne Benini Martins
- Sector of Microbiology and Immunology, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP—University Estadual Paulista, Botucatu CEP 18618-689, São Paulo, Brazil; (V.C.P.); (L.P.-H.); (A.d.O.); (D.F.M.R.); (K.B.M.); (L.C.R.)
| | - Letícia Calixto Romero
- Sector of Microbiology and Immunology, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP—University Estadual Paulista, Botucatu CEP 18618-689, São Paulo, Brazil; (V.C.P.); (L.P.-H.); (A.d.O.); (D.F.M.R.); (K.B.M.); (L.C.R.)
| | - Maria de Lourdes Ribeiro de Souza da Cunha
- Sector of Microbiology and Immunology, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP—University Estadual Paulista, Botucatu CEP 18618-689, São Paulo, Brazil; (V.C.P.); (L.P.-H.); (A.d.O.); (D.F.M.R.); (K.B.M.); (L.C.R.)
- Correspondence: ; Tel.: +55-14-3880-0428
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Lynch KM, Zannini E, Wilkinson S, Daenen L, Arendt EK. Physiology of Acetic Acid Bacteria and Their Role in Vinegar and Fermented Beverages. Compr Rev Food Sci Food Saf 2019; 18:587-625. [DOI: 10.1111/1541-4337.12440] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 02/06/2019] [Accepted: 02/18/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Kieran M. Lynch
- School of Food and Nutritional SciencesUniv. College Cork Cork T12 K8AF Ireland
| | - Emanuele Zannini
- School of Food and Nutritional SciencesUniv. College Cork Cork T12 K8AF Ireland
| | - Stuart Wilkinson
- Global Innovation & Technology CentreAnheuser‐Busch InBev nv/sa Leuven 3000 Belgium
| | - Luk Daenen
- Global Innovation & Technology CentreAnheuser‐Busch InBev nv/sa Leuven 3000 Belgium
| | - Elke K. Arendt
- School of Food and Nutritional SciencesUniv. College Cork Cork T12 K8AF Ireland
- APC Microbiome IrelandUniv. College Cork Cork T12 K8AF Ireland
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Li H, Zhang X, Long H, Hu C, Zhou Y, Wang S, Ke S, Xie Z. Vibrio alginolyticus 16S-23S intergenic spacer region analysis, and PCR assay for identification of coral pathogenic strain XSBZ03. DISEASES OF AQUATIC ORGANISMS 2018; 129:71-83. [PMID: 29916394 DOI: 10.3354/dao03233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Porites andrewsi white syndrome (PAWS), caused by Vibrio alginolyticus strains XSBZ03 and XSBZ14, poses a serious threat to corals in the South China Sea. To obtain a specific target against which to develop a rapid PCR detection method for the coral pathogenic strain XSBZ03, the 16S-23S rRNA gene intergenic spacer (IGS) region of 4 strains of V. alginolyticus, including the XSBZ03 and XSBZ14 strains, was amplified, sequenced and analyzed. Six types of IGS were found: IGS0, IGSG, IGSIA, IGSAG, IGSGLV, and IGSGLAV. IGS0, IGSG, IGSIA, IGSAG and IGSGLV appeared to be the most prevalent forms in the 4 strains and the percentage identity range within each type was 91.4-100%, 89.3-98.5%, 83.0-99.8%, 91.5-95.6%, and 88.7-99.3%, respectively. IGSGLAV was found only in the HN08155 strain, a causative agent of fish disease. IGSGLAV, IGSGLV and IGSAG are reported here for the first time in V. alginolyticus. An IGS sequence specific to the XSBZ03 strain was identified following alignment of the homologous IGSs, and used to design strain-specific primers for its rapid identification by PCR. The results from PCR analysis suggest that the method is a rapid, practical, and reliable tool for the identification of the XSBZ03 strain in samples of isolated bacteria, as well as seawater and coral samples spiked with the bacterial strain. This is the first report of a rapid diagnostic assay for a causative agent of PAWS, based on PCR detection of a coral pathogen at the strain level. After applying this assay in coral transplantation, the survival rates of transplanted corals were significantly increased. This diagnostic assay should aid with both the elucidation of the cause of the disease, and transplantation of PAWS-free P. andrewsi in the South China Sea.
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Affiliation(s)
- Hongyue Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, PR China
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14
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Tian H, Muhammad Z, Evivie SE, Gu CT, Huo GC. Exact identification of six starter-strain candidates of Streptococcus thermophilus
by analysing genotypic and industrial properties. INT J DAIRY TECHNOL 2018. [DOI: 10.1111/1471-0307.12398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui Tian
- Key Laboratory of Dairy Science; Ministry of Education; Northeast Agricultural University; Harbin 150030 China
| | - Zafarullah Muhammad
- Key Laboratory of Dairy Science; Ministry of Education; Northeast Agricultural University; Harbin 150030 China
| | - Smith Etareri Evivie
- Key Laboratory of Dairy Science; Ministry of Education; Northeast Agricultural University; Harbin 150030 China
| | - Chun Tao Gu
- Key Laboratory of Dairy Science; Ministry of Education; Northeast Agricultural University; Harbin 150030 China
| | - Gui Cheng Huo
- Key Laboratory of Dairy Science; Ministry of Education; Northeast Agricultural University; Harbin 150030 China
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15
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DiMichele LJ, Lewis MJ. Rapid, Species-Specific Detection of Lactic Acid Bacteria from Beer Using the Polymerase Chain Reaction. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-51-0063] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Luke J. DiMichele
- Department of Food Science & Technology, University of California, Davis, CA 95616 and Baxter Microscan, West Sacramento, CA 95691
| | - Michael J. Lewis
- Department of Food Science and Technology, University of California, Davis, CA 95616
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16
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Roberts JA, Ma B, Tredway LP, Ritchie DF, Kerns JP. Identification and Pathogenicity of Bacteria Associated with Etiolation and Decline of Creeping Bentgrass Golf Course Putting Greens. PHYTOPATHOLOGY 2018; 108:23-30. [PMID: 28846056 DOI: 10.1094/phyto-01-17-0015-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial etiolation and decline has developed into a widespread issue with creeping bentgrass (CBG) (Agrostis stolonifera) putting green turf. The condition is characterized by an abnormal elongation of turfgrass stems and leaves that in rare cases progresses into a rapid and widespread necrosis and decline. Recent reports have cited bacteria, Acidovorax avenae and Xanthomonas translucens, as causal agents; however, few cases exist where either bacterium were isolated in conjunction with turf exhibiting bacterial disease symptoms. From 2010 to 2014, turfgrass from 62 locations submitted to the NC State Turf Diagnostic Clinic exhibiting bacterial etiolation and/or decline symptoms were sampled for the presence of bacterial pathogens. Isolated bacteria were identified using rRNA sequencing of the 16S subunit and internal transcribed spacer region (16S-23S or ITS). Results showed diverse bacteria isolated from symptomatic turf and A. avenae and X. translucens were only isolated in 26% of samples. Frequently isolated bacterial species were examined for pathogenicity to 4-week-old 'G2' CBG seedlings and 8-week-old 'A-1' CBG turfgrass stands in the greenhouse. While results confirmed pathogenicity of A. avenae and X. translucens, Pantoea ananatis was also shown to infect CBG turf; although pathogenicity varied among isolated strains. These results illustrate that multiple bacteria are associated with bacterial disease and shed new light on culturable bacteria living in CBG turfgrass putting greens. Future research to evaluate additional microorganisms (i.e., bacteria and fungi) could provide new information on host-microbe interactions and possibly develop ideas for management tactics to reduce turfgrass pests.
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Affiliation(s)
- Joseph A Roberts
- First, third, fourth, and fifth authors: Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7616, 2510 Thomas Hall, Raleigh 27695; and second author: SePRO Corporation, 16013 Watson Seed Farm Rd., Whitakers, NC 27891
| | - Bangya Ma
- First, third, fourth, and fifth authors: Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7616, 2510 Thomas Hall, Raleigh 27695; and second author: SePRO Corporation, 16013 Watson Seed Farm Rd., Whitakers, NC 27891
| | - Lane P Tredway
- First, third, fourth, and fifth authors: Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7616, 2510 Thomas Hall, Raleigh 27695; and second author: SePRO Corporation, 16013 Watson Seed Farm Rd., Whitakers, NC 27891
| | - David F Ritchie
- First, third, fourth, and fifth authors: Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7616, 2510 Thomas Hall, Raleigh 27695; and second author: SePRO Corporation, 16013 Watson Seed Farm Rd., Whitakers, NC 27891
| | - James P Kerns
- First, third, fourth, and fifth authors: Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7616, 2510 Thomas Hall, Raleigh 27695; and second author: SePRO Corporation, 16013 Watson Seed Farm Rd., Whitakers, NC 27891
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17
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Jaiswal SK, Msimbira LA, Dakora FD. Phylogenetically diverse group of native bacterial symbionts isolated from root nodules of groundnut (Arachis hypogaea L.) in South Africa. Syst Appl Microbiol 2017; 40:215-226. [PMID: 28372899 PMCID: PMC5460907 DOI: 10.1016/j.syapm.2017.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/05/2017] [Accepted: 02/12/2017] [Indexed: 11/30/2022]
Abstract
Groundnut is an economically important N2-fixing legume that can contribute about 100–190 kg N ha−1 to cropping systems. In this study, groundnut-nodulating native rhizobia in South African soils were isolated from root nodules. Genetic analysis of isolates was done using restriction fragment length polymorphism (RFLP)-PCR of the intergenic spacer (IGS) region of 16S-23S rDNA. A total of 26 IGS types were detected with band sizes ranging from 471 to 1415 bp. The rhizobial isolates were grouped into five main clusters with Jaccard's similarity coefficient of 0.00–1.00, and 35 restriction types in a UPGMA dendrogram. Partial sequence analysis of the 16S rDNA, IGS of 16S rDNA-23S rDNA, atpD, gyrB, gltA, glnII and symbiotic nifH and nodC genes obtained for representative isolates of each RFLP-cluster showed that these native groundnut-nodulating rhizobia were phylogenetically diverse, thus confirming the extent of promiscuity of this legume. Concatenated gene sequence analysis showed that most isolates did not align with known type strains, and may represent new species from South Africa. This underscored the high genetic variability associated with groundnut Rhizobium and Bradyrhizobium in South African soils, and the possible presence of a reservoir of novel groundnut-nodulating Bradyrhizobium and Rhizobium in the country.
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Affiliation(s)
- Sanjay K Jaiswal
- Department of Chemistry, Tshwane University of Technology, Pretoria, South Africa.
| | - Levini A Msimbira
- Department of Crop Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - Felix D Dakora
- Department of Chemistry, Tshwane University of Technology, Pretoria, South Africa.
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Ferreira AM, Martins KB, Silva VRD, Mondelli AL, Cunha MDLRDSD. Correlation of phenotypic tests with the presence of the blaZ gene for detection of beta-lactamase. Braz J Microbiol 2017; 48:159-166. [PMID: 27889420 PMCID: PMC5221353 DOI: 10.1016/j.bjm.2016.10.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 06/20/2016] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus and Staphylococcus saprophyticus are the most common and most important staphylococcal species associated with urinary tract infections. The objective of the present study was to compare and to evaluate the accuracy of four phenotypic methods for the detection of beta-lactamase production in Staphylococcus spp. Seventy-three strains produced a halo with a diameter ≤28mm (penicillin resistant) and all of them were positive for the blaZ gene. Among the 28 susceptible strain (halo ≥29mm), 23 carried the blaZ gene and five did not. The zone edge test was the most sensitive (90.3%), followed by MIC determination (85.5%), but the specificity of the former was low (40.0%). The nitrocefin test was the least sensitive (28.9%). However, the nitrocefin test together with the disk diffusion method showed the highest specificity (100%). The present results demonstrated that the zone edge test was the most sensitive phenotypic test for detection of beta-lactamase, although it is still not an ideal test to detect this type of resistance since its specificity was low. However, the inhibition halo diameter of the penicillin disk can be used together with the zone edge test since the same disk is employed in the two tests. Combined analysis of the two tests shows a sensitivity of 90.3% and specificity of 100%, proving better sensitivity, especially for S. saprophyticus. This is a low-cost test of easy application and interpretation that can be used in small and medium-sized laboratories where susceptibility testing is usually performed by the disk diffusion method.
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Affiliation(s)
- Adriano Martison Ferreira
- Universidade Estadual Paulista (UNESP), Botucatu Biosciences Institute, Department of Microbiology and Immunology, Botucatu, SP, Brazil; Universidade Estadual Paulista (UNESP), Botucatu School of Medicine University Hospital, Department of Tropical Diseases, Botucatu, SP, Brazil
| | - Katheryne Benini Martins
- Universidade Estadual Paulista (UNESP), Botucatu Biosciences Institute, Department of Microbiology and Immunology, Botucatu, SP, Brazil
| | - Vanessa Rocha da Silva
- Universidade Estadual Paulista (UNESP), Botucatu Biosciences Institute, Department of Microbiology and Immunology, Botucatu, SP, Brazil
| | - Alessandro Lia Mondelli
- Universidade Estadual Paulista (UNESP), Botucatu School of Medicine University Hospital, Department of Internal Medicine, Botucatu, SP, Brazil
| | - Maria de Lourdes Ribeiro de Souza da Cunha
- Universidade Estadual Paulista (UNESP), Botucatu Biosciences Institute, Department of Microbiology and Immunology, Botucatu, SP, Brazil; Universidade Estadual Paulista (UNESP), Botucatu School of Medicine University Hospital, Department of Tropical Diseases, Botucatu, SP, Brazil.
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19
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Ortega C, Mancera G, Enríquez R, Vargas A, Martínez S, Fajardo R, Avendaño-Herrera R, Navarrete MJ, Romero A. First identification of Francisella noatunensis subsp. orientalis causing mortality in Mexican tilapia Oreochromis spp. DISEASES OF AQUATIC ORGANISMS 2016; 120:205-215. [PMID: 27503916 DOI: 10.3354/dao02999] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Francisellosis, an emerging disease in tilapia Oreochromis spp., is caused by the facultative, intracellular bacterium Francisella noatunensis subsp. orientalis, which is present in various countries where tilapia farming is commercially important. We confirmed the presence of francisellosis in Mexican tilapia cultures in association with an outbreak during the second semester of 2012. Broodstock fish presented a mortality rate of approximately 40%, and disease was characterized by histologically classified granulomas, or whitish nodules, in different organs, mainly the spleen and kidney. Through DNA obtained from infected tissue and pure cultures in a cysteine heart medium supplemented with hemoglobin, F. noatunensis subsp. orientalis was initially confirmed through the amplification and analysis of the 16S rRNA gene and the internal transcribed spacer region. Phylogenetic analysis of these genes demonstrated close similarity with previously reported F. noatunensis subsp. orientalis sequences obtained from infected tilapia from various countries. The identification of this subspecies as the causative agent of the outbreak was confirmed using the iglC gene as a target sequence, which showed 99.5% identity to 2 F. noatunensis subsp. orientalis strains (Ethime-1 and Toba04). These findings represent the first documented occurrence of francisellosis in Mexican tilapia cultures, which highlights the importance of establishing preventative measures to minimize the spread of this disease within the Mexican aquaculture industry.
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Affiliation(s)
- Cesar Ortega
- Centro de Investigación y Estudios Avanzados en Salud Animal (CIESA), Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco Km. 15.5, Toluca 50200, Mexico
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20
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Monteiro ACM, Fortaleza CMCB, Ferreira AM, Cavalcante RDS, Mondelli AL, Bagagli E, da Cunha MDLRDS. Comparison of methods for the identification of microorganisms isolated from blood cultures. Ann Clin Microbiol Antimicrob 2016; 15:45. [PMID: 27496125 PMCID: PMC4974807 DOI: 10.1186/s12941-016-0158-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/14/2016] [Indexed: 11/12/2022] Open
Abstract
Background Bloodstream infections are responsible for thousands of deaths each year. The rapid identification of the microorganisms causing these infections permits correct therapeutic management that will improve the prognosis of the patient. In an attempt to reduce the time spent on this step, microorganism identification devices have been developed, including the VITEK® 2 system, which is currently used in routine clinical microbiology laboratories. Methods This study evaluated the accuracy of the VITEK® 2 system in the identification of 400 microorganisms isolated from blood cultures and compared the results to those obtained with conventional phenotypic and genotypic methods. In parallel to the phenotypic identification methods, the DNA of these microorganisms was extracted directly from the blood culture bottles for genotypic identification by the polymerase chain reaction (PCR) and DNA sequencing. Results The automated VITEK® 2 system correctly identified 94.7 % (379/400) of the isolates. The YST and GN cards resulted in 100 % correct identifications of yeasts (15/15) and Gram-negative bacilli (165/165), respectively. The GP card correctly identified 92.6 % (199/215) of Gram-positive cocci, while the ANC card was unable to correctly identify any Gram-positive bacilli (0/5). Conclusions The performance of the VITEK® 2 system was considered acceptable and statistical analysis showed that the system is a suitable option for routine clinical microbiology laboratories to identify different microorganisms.
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Affiliation(s)
- Aydir Cecília Marinho Monteiro
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Carlos Magno Castelo Branco Fortaleza
- Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Adriano Martison Ferreira
- Laboratório de Análises Clínicas do Hospital das Clínicas de Botucatu, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Ricardo de Souza Cavalcante
- Comissão de Controle de Infecção Relacionada à Assistência à Saúde, Hospital das Clínicas, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Alessandro Lia Mondelli
- Departamento de Clínica Médica, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Eduardo Bagagli
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Maria de Lourdes Ribeiro de Souza da Cunha
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil. .,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil.
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Detection of Enterotoxigenic Potential and Determination of Clonal Profile in Staphylococcus aureus and Coagulase-Negative Staphylococci Isolated from Bovine Subclinical Mastitis in Different Brazilian States. Toxins (Basel) 2016; 8:104. [PMID: 27092525 PMCID: PMC4848630 DOI: 10.3390/toxins8040104] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/15/2016] [Accepted: 01/20/2016] [Indexed: 11/16/2022] Open
Abstract
Epidemiological studies have identified Staphylococcus aureus as the most common agent involved in food poisoning. However, current research highlights the importance of toxigenic coagulase-negative staphylococci (CoNS) isolated from food. The aim of this study was to characterize Staphylococcus spp. isolated from cows with bovine subclinical mastitis regarding the presence of genes responsible for the production of staphylococcal enterotoxins and of the tst-1 gene encoding toxic shock syndrome toxin 1, and to determine the clonal profile of the isolates carrying any of the genes studied. A total of 181 strains isolated in different Brazilian states, including the South, Southeast, and Northeast regions, were analyzed. The sea gene was the most frequent, which was detected in 18.2% of the isolates, followed by seb in 7.7%, sec in 14.9%, sed in 0.5%, see in 8.2%, seg in 1.6%, seh in 25.4%, sei in 6.6%, and ser in 1.6%. The sej, ses, set, and tst-1 genes were not detected in any of the isolates. The typing of the isolates by pulsed-field gel electrophoresis revealed important S. aureus and S. epidermidis clusters in different areas and the presence of enterotoxin genes in lineages isolated from animals that belong to herds located geographically close to each other.
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22
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Mangal M, Bansal S, Sharma SK, Gupta RK. Molecular Detection of Foodborne Pathogens: A Rapid and Accurate Answer to Food Safety. Crit Rev Food Sci Nutr 2015; 56:1568-84. [DOI: 10.1080/10408398.2013.782483] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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23
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Minogue E, Tuite NL, Smith CJ, Reddington K, Barry T. A rapid culture independent methodology to quantitatively detect and identify common human bacterial pathogens associated with contaminated high purity water. BMC Biotechnol 2015; 15:6. [PMID: 25888294 PMCID: PMC4342816 DOI: 10.1186/s12896-015-0124-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/06/2015] [Indexed: 02/06/2023] Open
Abstract
Background Water and High Purity Water (HPW) distribution systems can be contaminated with human pathogenic microorganisms. This biocontamination may pose a risk to human health as HPW is commonly used in the industrial, pharmaceutical and clinical sectors. Currently, routine microbiological testing of HPW is performed using slow and labour intensive traditional microbiological based techniques. There is a need to develop a rapid culture independent methodology to quantitatively detect and identify biocontamination associated with HPW. Results A novel internally controlled 5-plex real-time PCR Nucleic Acid Diagnostics assay (NAD), was designed and optimised in accordance with Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines, to rapidly detect, identify and quantify the human pathogenic bacteria Stenotrophomonas maltophilia, Burkholderia species, Pseudomonas aeruginosa and Serratia marcescens which are commonly associated with the biocontamination of water and water distribution systems. The specificity of the 5-plex assay was tested against genomic DNA isolated from a panel of 95 microorganisms with no cross reactivity observed. The analytical sensitivities of the S. maltophilia, B. cepacia, P. aeruginosa and the S. marcescens assays are 8.5, 5.7, 3.2 and 7.4 genome equivalents respectively. Subsequently, an analysis of HPW supplied by a Millipore Elix 35 water purification unit performed using standard microbiological methods revealed high levels of naturally occurring microbiological contamination. Five litre water samples from this HPW delivery system were also filtered and genomic DNA was purified directly from these filters. These DNA samples were then tested using the developed multiplex real-time PCR NAD assay and despite the high background microbiological contamination observed, both S. maltophilia and Burkholderia species were quantitatively detected and identified. At both sampling points the levels of both S. maltophilia and Burkholderia species present was above the threshold of 10 cfu/100 ml recommended by both EU and US guidelines. Conclusions The novel culture independent methodology described in this study allows for rapid (<5 h), quantitative detection and identification of these four human pathogens from biocontaminated water and HPW distribution systems. We propose that the described NAD assay and associated methodology could be applied to routine testing of water and HPW distribution systems to assure microbiological safety and high water quality standards. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0124-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth Minogue
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
| | - Nina L Tuite
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
| | - Cindy J Smith
- Marine Microbial Ecology Laboratory, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
| | - Kate Reddington
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
| | - Thomas Barry
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
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Trček J, Barja F. Updates on quick identification of acetic acid bacteria with a focus on the 16S-23S rRNA gene internal transcribed spacer and the analysis of cell proteins by MALDI-TOF mass spectrometry. Int J Food Microbiol 2014; 196:137-44. [PMID: 25589227 DOI: 10.1016/j.ijfoodmicro.2014.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 11/13/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
Acetic acid bacteria have attracted much attention over the past few years, due mainly to their metabolic traits that are of interest to the biotechnology industry. In addition, it turns out that their ecological habitats are almost unlimited since they have been found as symbionts in different insects and also as emerging opportunistic human pathogens. Very surprising is the finding that they colonize niches considered anaerobic, disproving the generalized statement that they are strict aerobes. Since they have taken on different biological roles in our environment, more and more people are charged with the task of identifying them. However, this turns out to be not always easy, especially if we are using phenotypic approaches for identification. A substantial step forward in making the identification of acetic acid bacteria easier was made possible using molecular biological methods, which have been extensively tested since 2000. However, some molecular methods require expensive machines and experienced staff, and moreover the level of their discrimination varies. All these factors must be considered when selecting the most appropriate approach for identifying acetic acid bacteria. With this objective in mind, this review article discusses the benefits and drawbacks of molecular biological methods for identification of acetic acid bacteria, with a focus on the 16S-23S rRNA gene ITS regions and the recently described alternative method for identification of acetic acid bacteria, MALDI-TOF MS.
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Affiliation(s)
- Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia; Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia.
| | - François Barja
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Jussy-Geneva, Switzerland
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Pinheiro L, Brito CI, Pereira VC, Oliveira AD, Camargo CH, Cunha MDLRDSD. Reduced susceptibility to vancomycin and biofilm formation in methicillin-resistant Staphylococcus epidermidis isolated from blood cultures. Mem Inst Oswaldo Cruz 2014; 109:871-8. [PMID: 25410990 PMCID: PMC4296491 DOI: 10.1590/0074-0276140120] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 09/10/2014] [Indexed: 11/21/2022] Open
Abstract
This study aimed to correlate the presence of ica genes, biofilm
formation and antimicrobial resistance in 107 strains of Staphylococcus
epidermidis isolated from blood cultures. The isolates were analysed to
determine their methicillin resistance, staphylococcal cassette chromosome
mec (SCCmec) type, ica genes
and biofilm formation and the vancomycin minimum inhibitory concentration (MIC) was
measured for isolates and subpopulations growing on vancomycin screen agar. The
mecA gene was detected in 81.3% of the S.
epidermidis isolated and 48.2% carried SCCmec type III.
The complete icaADBC operon was observed in 38.3% of the isolates;
of these, 58.5% produced a biofilm. Furthermore, 47.7% of the isolates grew on
vancomycin screen agar, with an increase in the MIC in 75.9% of the isolates.
Determination of the MIC of subpopulations revealed that 64.7% had an MIC ≥ 4 μg
mL-1, including 15.7% with an MIC of 8 μg mL-1 and 2% with
an MIC of 16 μg mL-1. The presence of the icaADBC operon,
biofilm production and reduced susceptibility to vancomycin were associated with
methicillin resistance. This study reveals a high level of methicillin resistance,
biofilm formation and reduced susceptibility to vancomycin in subpopulations of
S. epidermidis. These findings may explain the selection of
multidrug-resistant isolates in hospital settings and the consequent failure of
antimicrobial treatment.
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Affiliation(s)
- Luiza Pinheiro
- Laboratório de Microbiologia, Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, SP, Brasil
| | - Carla Ivo Brito
- Laboratório de Microbiologia, Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, SP, Brasil
| | - Valéria Cataneli Pereira
- Laboratório de Microbiologia, Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, SP, Brasil
| | - Adilson de Oliveira
- Laboratório de Microbiologia, Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, SP, Brasil
| | - Carlos Henrique Camargo
- Laboratório de Microbiologia, Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, SP, Brasil
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Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members. PLoS One 2014; 9:e105390. [PMID: 25141005 PMCID: PMC4139376 DOI: 10.1371/journal.pone.0105390] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 07/17/2014] [Indexed: 11/19/2022] Open
Abstract
To determine whether ITS sequences in the rrn operon are suitable for identifying individual Acinetobacter Acb complex members, we analysed length and sequence differences between multiple ITS copies within the genomes of individual strains. Length differences in ITS reported previously between A. nosocomialis BCRC15417T (615 bp) and other strains (607 bp) can be explained by presence of an insertion (indel 13i/1) in the longer ITS variant. The same Indel 13i/1 was also found in ITS sequences of ten strains of A. calcoaceticus, all 639 bp long, and the 628 bp ITS of Acinetobacter strain BENAB127. Four additional indels (13i/2–13i/5) were detected in Acinetobacter strain c/t13TU 10090 ITS length variants (608, 609, 620, 621 and 630 bp). These ITS variants appear to have resulted from horizontal gene transfer involving other Acinetobacter species or in some cases unrelated bacteria. Although some ITS copies in strain c/t13TU 10090 are of the same length (620 bp) as those in Acinetobacter strains b/n1&3, A. pittii (10 strains), A. calcoaceticus and A. oleivorans (not currently acknowledged as an Acb member), their individual ITS sequences differ. Thus ITS length by itself can not by itself be used to identify Acb complex strains. A shared indel in ITS copies in two separate Acinetobacter species compromises the specificity of ITS targeted probes, as shown with the Aun-3 probe designed to target the ITS in A. pitti. The presence of indel 13i/5 in the ITS of Acinetobacter strain c/t13TU means it too responded positively to this probe. Thus, neither ITS sequencing nor the currently available ITS targeted probes can distinguish reliably between Acb member species.
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Ruegger PM, Clark RT, Weger JR, Braun J, Borneman J. Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer. J Microbiol Methods 2014; 105:82-7. [PMID: 25034229 DOI: 10.1016/j.mimet.2014.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/02/2014] [Indexed: 02/01/2023]
Abstract
Current high throughput sequencing (HTS) methods are limited in their ability to resolve bacteria at or below the genus level. While the impact of this limitation may be relatively minor in whole-community analyses, it constrains the use of HTS as a tool for identifying and examining individual bacteria of interest. The limited resolution is a consequence of both short read lengths and insufficient sequence variation within the commonly targeted variable regions of the small-subunit rRNA (SSU) gene. The goal of this work was to improve the resolving power of bacterial HTS. We developed an assay targeting the hypervariable rRNA internal transcribed spacer (ITS) region residing between the SSU and large-subunit (LSU) rRNA genes. Comparisons of the ITS region and two SSU regions using annotated bacterial genomes in GenBank showed much greater resolving power is possible with the ITS region. This report presents a new HTS method for analyzing bacterial composition with improved capabilities. The greater resolving power enabled by the ITS region arises from its high sequence variation across a wide range of bacterial taxa and an associated decrease in taxonomic heterogeneity within its OTUs. Although the method should be adaptable to any HTS platform, this report presents PCR primers, amplification parameters, and protocols for Illumina-based analyses.
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Affiliation(s)
- Paul M Ruegger
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Robin T Clark
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - John R Weger
- Department of Botany & Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Jonathan Braun
- Department of Pathology and Lab Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.
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Kryuchkova YV, Burygin GL, Gogoleva NE, Gogolev YV, Chernyshova MP, Makarov OE, Fedorov EE, Turkovskaya OV. Isolation and characterization of a glyphosate-degrading rhizosphere strain, Enterobacter cloacae K7. Microbiol Res 2014; 169:99-105. [PMID: 23545355 DOI: 10.1016/j.micres.2013.03.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 02/22/2013] [Accepted: 03/02/2013] [Indexed: 11/13/2022]
Abstract
Plant-growth-promoting rhizobacteria exert beneficial effects on plants through their capacity for nitrogen fixation, phytohormone production, phosphate solubilization, and improvement of the water and mineral status of plants. We suggested that these bacteria may also have the potential to express degradative activity toward glyphosate, a commonly used organophosphorus herbicide. In this study, 10 strains resistant to a 10 mM concentration of glyphosate were isolated from the rhizoplane of various plants. Five of these strains--Alcaligenes sp. K1, Comamonas sp. K4, Azomonas sp. K5, Pseudomonas sp. K3, and Enterobacter cloacae K7--possessed a number of associative traits, including fixation of atmospheric nitrogen, solubilization of phosphates, and synthesis of the phytohormone indole-3-acetic acid. One strain, E. cloacae K7, could utilize glyphosate as a source of P. Gas-liquid chromatography showed that E. cloacae growth correlated with a decline in herbicide content in the culture medium (40% of the initial 5mM content), with no glyphosate accumulating inside the cells. Thin-layer chromatography analysis of the intermediate metabolites of glyphosate degradation found that E. cloacae K7 had a C-P lyase activity and degraded glyphosate to give sarcosine, which was then oxidized to glycine. In addition, strain K7 colonized the roots of common sunflower (Helianthus annuus L.) and sugar sorghum (Sorghum saccharatum Pers.), promoting the growth and development of sunflower seedlings. Our findings extend current knowledge of glyphosate-degrading rhizosphere bacteria and may be useful for developing a biotechnology for the cleanup and restoration of glyphosate-polluted soils.
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Affiliation(s)
- Yelena V Kryuchkova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov 410049, Russia.
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AYU EVELINE, SUWANTO ANTONIUS, BARUS TATI. Klebsiella pneumoniae from Indonesian Tempeh were Genetically Different from that of Pathogenic Isolates. MICROBIOLOGY INDONESIA 2014. [DOI: 10.5454/mi.8.1.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Martins A, Riboli DFM, Camargo CH, Pereira VC, de Almeida Sampaio R, de Souza da Cunha MDLR. Antimicrobial resistance and persistence of Staphylococcus epidermidis clones in a Brazilian university hospital. Diagn Microbiol Infect Dis 2013; 77:164-8. [PMID: 23906562 DOI: 10.1016/j.diagmicrobio.2013.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 05/24/2013] [Accepted: 06/01/2013] [Indexed: 11/27/2022]
Abstract
Oxacillin is an alternative for the treatment of Staphylococcus spp. infections; however, resistance to this drug has become a major problem over recent decades. The main objective of this study was to epidemiologically characterize coagulase-negative staphylococci (CoNS) strains recovered from blood of patients hospitalized in a Brazilian teaching hospital. Oxacillin resistance was analyzed in 160 strains isolated from blood culture samples by phenotypic methods, detection of the mecA gene, and determination of intermediate sensitivity to vancomycin on brain heart infusion agar supplemented with 4 and 6 μg/mL vancomycin. In addition, characterization of the epidemiological profile by staphylococcal cassette chromosome mec (SCCmec) typing and clonal analysis by pulsed-field gel electrophoresis (PFGE) were performed. The mecA gene was detected in 72.5% of the isolates. Methicillin-resistant CoNS isolates exhibited the highest minimum inhibitory concentrations and multiresistance when compared to methicillin-susceptible CoNS strains. Typing classified 32.8% of the isolates as SCCmec I and 50% as SCCmec III. PFGE typing of the SCCmec III Staphylococcus epidermidis isolates identified 6 clones disseminated in different wards that persisted from 2002 to 2009. The high oxacillin resistance rates found in this study and clonal dissemination in different wards highlight the importance of good practices in nosocomial infection control and of the rational use of antibiotic therapy in order to prevent the dissemination of these clones.
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Affiliation(s)
- André Martins
- Department of Tropical Diseases and Diagnostic Imaging, Botucatu Medical School, UNESP - Univ Estadual Paulista, City of Botucatu, Brazil; Department of Microbiology and Immunology, Biosciences Institute, UNESP - Univ Estadual Paulista, City of Botucatu, Brazil
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López-Pérez M, Gonzaga A, Martin-Cuadrado AB, López-García P, Rodriguez-Valera F, Kimes NE. Intra- and intergenomic variation of ribosomal RNA operons in concurrent Alteromonas macleodii strains. MICROBIAL ECOLOGY 2013; 65:720-730. [PMID: 23269455 DOI: 10.1007/s00248-012-0153-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
Biodiversity estimates based on ribosomal operon sequence diversity rely on the premise that a sequence is characteristic of a single specific taxon or operational taxonomic unit (OTU). Here, we have studied the sequence diversity of 14 ribosomal RNA operons (rrn) contained in the genomes of two isolates (five operons in each genome) and four metagenomic fosmids, all from the same seawater sample. Complete sequencing of the isolate genomes and the fosmids establish that they represent strains of the same species, Alteromonas macleodii, with average nucleotide identity (ANI) values >97 %. Nonetheless, we observed high levels of intragenomic heterogeneity (i.e., variability between operons of a single genome) affecting multiple regions of the 16S and 23S rRNA genes as well as the internally transcribed spacer 1 (ITS-1) region. Furthermore, the ribosomal operons exhibited intergenomic heterogeneity (i.e., variability between operons located in separate genomes) in each of these regions, compounding the variability. Our data reveal the extensive heterogeneity observed in natural populations of A. macleodii at a single point in time and support the idea that distinct lineages of A. macleodii exist in the deep Mediterranean. These findings highlight the potential of rRNA fingerprinting methods to misrepresent species diversity while simultaneously failing to recognize the ecological significance of individual strains.
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Affiliation(s)
- Mario López-Pérez
- División de Microbiología, Universidad Miguel Hernández, San Juan, Alicante, Spain
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Gurung M, Nam H, Tamang M, Chae M, Jang G, Jung S, Lim S. Prevalence and antimicrobial susceptibility of Acinetobacter from raw bulk tank milk in Korea. J Dairy Sci 2013; 96:1997-2002. [DOI: 10.3168/jds.2012-5965] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 11/16/2012] [Indexed: 11/19/2022]
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Ferreira AM, Bonesso MF, Mondelli AL, Camargo CH, Cunha MDLRS. Oxacillin resistance and antimicrobial susceptibility profile of Staphylococcus saprophyticus and other staphylococci isolated from patients with urinary tract infection. Chemotherapy 2013; 58:482-91. [PMID: 23548376 DOI: 10.1159/000346529] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 12/18/2012] [Indexed: 11/19/2022]
Abstract
BACKGROUND Staphylococcus saprophyticus is the second most frequent community-acquired causative agent of urinary tract infection (UTI). The objective of this study was to evaluate the susceptibility profile and resistance detection in Staphylococcus species. isolated from patients with UTI. MATERIALS AND METHODS The isolates were investigated using the disk diffusion method, Vitek I system, E-test®, and detection of the mecA gene. RESULTS Most isolates (76.2%) were resistant to oxacillin by the disk diffusion method, followed by those resistant to penicillin (72.2%). The oxacillin disk diffusion method, E-test, and Vitek I method showed higher sensitivity (94.4%) and lower specificity (28.9, 26.5, and 24.0%, respectively) than the cefoxitin disk diffusion test (sensitivity: 83.5%, specificity: 85.5%) for the detection of oxacillin resistance. CONCLUSIONS The large number of oxacillin-resistant isolates indicates that the breakpoint value recommended by the Clinical and Laboratory Standards Institute may overestimate oxacillin resistance in S. saprophyticus. Thus, changes in these guidelines are necessary for the correct detection of this resistance.
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Affiliation(s)
- Adriano M Ferreira
- Department of Microbiology and Immunology, Botucatu Biosciences Institute, Universidade Estadual Paulista, Botucatu, SP 18618-970, Brazil
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Soo PC, Tseng CC, Ling SR, Liou ML, Liu CC, Chao HJ, Lin TY, Chang KC. Rapid and sensitive detection of Acinetobacter baumannii using loop-mediated isothermal amplification. J Microbiol Methods 2012; 92:197-200. [PMID: 23220188 DOI: 10.1016/j.mimet.2012.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 11/27/2012] [Accepted: 11/28/2012] [Indexed: 10/27/2022]
Abstract
Here we report the design and evaluation of a loop-mediated isothermal amplification (LAMP) assay for detecting Acinetobacter baumannii DNA based on the 16S-23S rRNA intergenic spacer (ITS) sequence. The results showed that target DNA was amplified and visualized within 30min and with a detection limit 100-fold greater than PCR.
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Affiliation(s)
- Po-Chi Soo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
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35
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Ramírez AS, Dare C, Yavari CA, Bradbury JM. A diagnostic polymerase chain reaction for Mycoplasma iowae using primers located in the intergenic spacer region and the 23S rRNA gene. Avian Pathol 2012; 41:317-22. [PMID: 22702460 DOI: 10.1080/03079457.2012.686660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Mycoplasma iowae is primarily a pathogen of turkeys and, although uncommon, it still persists in some areas of the world, where it may cause embryo mortality and leg lesions. A species-specific diagnostic polymerase chain reaction was developed using a forward primer based in the intergenic spacer region between the 16S rRNA and the 23S rRNA ribosomal genes and a reverse primer located within the 23S rRNA gene. The polymerase chain reaction proved to be both sensitive and specific. It detected M. iowae DNA in the six reference strains of serotypes I, J, K, N, Q and R and in 28 field isolates. With the six serotypes the test detected between 1 and 5 pg of M. iowae DNA. There were no non-specific reactions with the other avian Mycoplasma species. When the closest phylogenetically related species were checked, a weak reaction with Mycoplasma muris was observed that disappeared when the annealing temperature was increased by 2°C.
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Affiliation(s)
- Ana S Ramírez
- Institute of Infection and Global Health and School of Veterinary Science, University of Liverpool, Leahurst Campus, Neston, UK
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Jaiswal SK, Anand A, Dhar B, Vaishampayan A. Genotypic characterization of phage-typed indigenous soybean bradyrhizobia and their host range symbiotic effectiveness. MICROBIAL ECOLOGY 2012; 63:116-26. [PMID: 21984348 DOI: 10.1007/s00248-011-9950-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 09/20/2011] [Indexed: 05/31/2023]
Abstract
Analysis of genetic diversity among indigenous rhizobia and its symbiotic effectiveness with soybean cultivar is important for development of knowledge about rhizobial ecology. In India, little is known about the genetic resources and diversity of rhizobia nodulating soybean. Indigenous bradyrhizobia isolated from root nodules of soybean plants, collected from traditional cultivating regions of two states (Madhya Pradesh and Uttar Pradesh) of India, were screened for bacteriophage sensitivity to identify successful broad host range symbiotic effectivity. Of 172 rhizobial isolates, 91 showed sensitivities to eight lytic phages and form ten groups on the basis of sensitivity patterns. The genetic diversity of 23 isolates belonging to different phage groups was assessed along with that of strains USDA123 and USDA94 by the restriction fragment length polymorphism (RFLP) analysis of 16S rDNA, intergenic spacer (IGS) (16S-23S rDNA), and DnaK regions. RFLP analysis of 16S rDNA formed 5 groups, whereas 19 and 9 groups were revealed by IGS and the DnaK genes, respectively. The IGS regions showed many amplified polymorphic bands. Nine isolates which revealed high RFLP polymorphism in the abovementioned regions (16S rRNA, IGS, DnaK) were used for 16S rRNA sequence analyses. The results indicate that taxonomically, all isolates were related to Rhizobium etli, Bradyrhizobium spp., and Bradyrhizobium yuanmingense. The doubling time of isolates varied from 9 h (MPSR155) to 16.2 h (MPSR068) in YM broth. Five isolates which did not show cross infectivity with isolated phage strains were studied for symbiotic efficiency. All isolates showed broad host range symbiotic effectiveness forming effective nodules on Vigna mungo, Vigna radiata, Vigna unguiculata, and Cajanus cajan. The present study provides information on genetic diversity and host range symbiosis of indigenous soybean rhizobia typed by different phages.
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Affiliation(s)
- Sanjay Kumar Jaiswal
- Microbiology Laboratory, Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India.
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Differentiation of petroleum hydrocarbon-degrading Pseudomonas spp. based on PCR-RFLP of the 16S-23S rDNA intergenic spacer region. Folia Microbiol (Praha) 2011; 57:47-52. [DOI: 10.1007/s12223-011-0088-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Accepted: 11/16/2011] [Indexed: 11/27/2022]
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Ravindran A, Levy J, Pierson E, Gross DC. Development of Primers for Improved PCR Detection of the Potato Zebra Chip Pathogen, 'Candidatus Liberibacter solanacearum'. PLANT DISEASE 2011; 95:1542-1546. [PMID: 30731998 DOI: 10.1094/pdis-05-11-0386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Zebra chip disease poses a major economic threat to potato production. The causative agent is a phloem-limited bacterium identified as 'Candidatus Liberibacter solanacearum' that is transmitted by the potato/ tomato psyllid. Currently, there are no effective controls and existing control strategies depend largely on the early detection of the pathogen via polymerase chain reaction (PCR) assays. Most primer sets used for PCR detection target a region of the bacterial 16S rDNA gene, and detection of the pathogen in symptomatic potato tissue with existing primers has been variable depending on the specific primer sets used. This study describes the development of two new primer sets that target a conserved intergenic region between the 16S and 23S rDNA genes and a conserved bacterial housekeeping gene, adenylate kinase (adk). Results demonstrate that the new primer sets are more reliable in detecting 'Ca. L. solanacearum' in field and glasshouse samples than the currently used LsoF/OI2 primers. The newly developed primers differentiated between 'Ca. L. solanacearum' and a closely related 'Ca. Liberibacter' spp. and were more sensitive than the LsoF/OI2 primers. The low detection limit for the new primers was four times lower (0.65 ng) than the limit (2.5 ng) for the LsoF/OI2 primers.
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Affiliation(s)
| | | | | | - Dennis C Gross
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station 77843
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Saïdi S, Mnasri B, Mhamdi R. Diversity of nodule-endophytic agrobacteria-like strains associated with different grain legumes in Tunisia. Syst Appl Microbiol 2011; 34:524-30. [DOI: 10.1016/j.syapm.2011.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/03/2010] [Accepted: 01/03/2011] [Indexed: 11/30/2022]
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López JR, Hamman-Khalifa AM, Navas JI, de la Herran R. Characterization of ISR region and development of a PCR assay for rapid detection of the fish pathogen Tenacibaculum soleae. FEMS Microbiol Lett 2011; 324:181-8. [PMID: 22092820 DOI: 10.1111/j.1574-6968.2011.02404.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/21/2011] [Accepted: 08/26/2011] [Indexed: 11/29/2022] Open
Abstract
The aims of this work were to characterize the 16S-23S internal spacer region of the fish pathogen Tenacibaculum soleae and to develop a PCR assay for its identification and detection. All T. soleae strains tested displayed a single internal spacer region class, containing tRNA(I) (le) and tRNA(A) (la) genes; nevertheless, a considerable intraspecific heterogeneity was observed. However, this region proved to be useful for differentiation of T. soleae from related and non-related species. Species-specific primers were designed targeting the 16S rRNA gene and the internal spacer region region, yielding a 1555-bp fragment. Detection limit was of 1 pg DNA per reaction (< 30 bacterial cells) when using pure cultures. The detection level in the presence of DNA from fish or other bacteria was lower; however, 10 pg were detected at a target/background ratio of 1 : 10(5) . The PCR assay proved to be more sensitive than agar cultivation for the detection of T. soleae from naturally diseased fish, offering a useful tool for diagnosis and for understanding the epidemiology of this pathogen.
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Identification and targeted cultivation of abundant novel freshwater sphingomonads and analysis of their population substructure. Appl Environ Microbiol 2011; 77:7355-64. [PMID: 21873487 DOI: 10.1128/aem.05832-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Little is known with respect to bacterial population structures in freshwater environments. Using complementary culture-based, cloning, and high-throughput Illumina sequencing approaches, we investigated microdiverse clusters of bacteria that comprise members with identical or very similar 16S rRNA gene sequences. Two 16S rRNA phylotypes could be recovered by cultivation in low-nutrient-strength liquid media from two lakes of different trophic status. Both phylotypes were found to be physiologically active in situ throughout most of the year, as indicated by the presence of their rRNA sequences in the samples. Analyses of internal transcribed spacer (ITS1) sequences revealed the presence of seven different sequence types among cultured representatives and the cloned rrn fragments. Illumina sequencing yielded 8,576 ITS1 sequences that encompassed 15 major and numerous rare sequence types. The major ITS1 types exhibited distinct temporal patterns, suggesting that the corresponding Sphingomonadaceae lineages occupy different ecological niches. However, since strains of the same ITS1 type showed highly variable substrate utilization patterns, the potential mechanism of niche separation in Sphingomonadaceae cannot be explained by substrate utilization alone and may be related to other traits.
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Vasconcelos NG, Pereira VC, Araújo Júnior JP, da Cunha MDLRS. Molecular detection of enterotoxins E, G, H and I in Staphylococcus aureus and coagulase-negative staphylococci isolated from clinical samples of newborns in Brazil. J Appl Microbiol 2011; 111:749-62. [PMID: 21672099 DOI: 10.1111/j.1365-2672.2011.05076.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS The objective of this study was to investigate the detection of SEE, SEG, SEH and SEI in strains of Staphylococcus aureus and coagulase-negative staphylococci (CNS) using RT-PCR. METHODS AND RESULTS In this study, 90 Staph. aureus strains and 90 CNS strains were analysed by PCR for the detection of genes encoding staphylococcal enterotoxins (SE) E, G, H and I. One or more genes were detected in 54 (60%) Staph. aureus isolates and in 29 (32.2%) CNS isolates. Staphylococcus epidermidis was the most frequently isolated CNS species (n = 64, 71.1%), followed by Staphylococcus warneri (n = 8, 8.9%) and other species (Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus lugdunensis, Staphylococcus simulans, Staphylococcus saprophyticus and Staphylococcus xylosus: n = 18, 20%). The genes studied were detected in Staph. epidermidis, Staph. warneri, Staph. haemolyticus, Staph. hominis, Staph. simulans and Staph. lugdunensis. The highest frequency of genes was observed in Staph. epidermidis and Staph. warneri, a finding indicating differences in the pathogenic potential between CNS species and highlighting the importance of the correct identification of these micro-organisms. RT-PCR used for the detection of mRNA revealed the expression of SEG, SEH and/or SEI in 32 (59.3%) of the 90 Staph. aureus isolates, whereas expression of some of these genes was observed in 10 (34.5%) of the 90 CNS isolates. CONCLUSIONS Staphylococcus epidermidis was the most toxigenic CNS species. Among the other species, only Staph. warneri and Staph. lugdunensis presented a positive RT-PCR result. PCR was efficient in confirming the toxigenic capacity of Staph. aureus and CNS. SIGNIFICANCE AND IMPACT OF THE STUDY This study permitted to confirm the toxigenic capacity of CNS to better characterize the pathogenic potential of this group of micro-organisms. In addition, it permitted the detection of SEG, SEH and SEI, enterotoxins that cannot be detected by commercially available immunological methods.
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Affiliation(s)
- N G Vasconcelos
- Department of Microbiology and Immunology, Institute of Biosciences, UNESP-Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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Salman V, Amann R, Girnth AC, Polerecky L, Bailey JV, Høgslund S, Jessen G, Pantoja S, Schulz-Vogt HN. A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria. Syst Appl Microbiol 2011; 34:243-59. [PMID: 21498017 DOI: 10.1016/j.syapm.2011.02.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 02/20/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
Abstract
The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properties, leading to polyphyletic taxa. We performed sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, together with detailed morphological analysis of hand-picked individuals of novel non-filamentous as well as known filamentous large sulfur bacteria, including the hitherto only partially sequenced species Thiomargarita namibiensis, Thioploca araucae and Thioploca chileae. Based on 128 nearly full-length 16S rRNA-ITS sequences, we propose the retention of the family Beggiatoaceae for the genera closely related to Beggiatoa, as opposed to the recently suggested fusion of all colorless sulfur bacteria into one family, the Thiotrichaceae. Furthermore, we propose the addition of nine Candidatus species along with seven new Candidatus genera to the family Beggiatoaceae. The extended family Beggiatoaceae thus remains monophyletic and is phylogenetically clearly separated from other related families.
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Affiliation(s)
- Verena Salman
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Francois P, Tangomo M, Hibbs J, Bonetti EJ, Boehme CC, Notomi T, Perkins MD, Schrenzel J. Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications. ACTA ACUST UNITED AC 2011; 62:41-8. [PMID: 21276085 DOI: 10.1111/j.1574-695x.2011.00785.x] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We evaluated the robustness of loop-mediated isothermal amplification (LAMP) of DNA for bacterial diagnostic applications. Salmonella enterica serovar Typhi was used as the target organism and compared with a real-time quantitative PCR (qPCR) for testing assay performance and reproducibly, as well as the impact of pH and temperature stability. This isothermal amplification method appeared to be particularly robust across 2 pH units (7.3-9.3) and temperature values (57-67 °C). The detection limit was comparable to that observed using optimized home-brew qPCR assays. The specificity of the amplification reaction remained high even at temperatures markedly different from the optimal one. Exposing reagents to the ambient temperature during the preparation of the reaction mixture as well as prolonging times for preparing the amplification reaction did not yield false-positive results. LAMP remained sensitive and specific despite the addition of untreated biological fluids such as stool or urine that commonly inhibit PCR amplification. Whereas the detection of microorganisms from whole blood or a blood-culture medium typically requires extensive sample purification and removal of inhibitors, LAMP amplification remained more sensitive than conventional qPCR when omitting such preparatory steps. Our results demonstrate that LAMP is not only easy to use, but is also a very robust, innovative and powerful molecular diagnostic method for both industrialized and developing countries.
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Affiliation(s)
- Patrice Francois
- Genomic Research Laboratory, University Hospitals of Geneva, Service of Infectious Diseases, Geneva, Switzerland.
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Nikolić P, Mehle N, Gruden K, Ravnikar M, Dermastia M. A panel of real-time PCR assays for specific detection of three phytoplasmas from the apple proliferation group. Mol Cell Probes 2010; 24:303-9. [PMID: 20600822 DOI: 10.1016/j.mcp.2010.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 06/18/2010] [Indexed: 11/27/2022]
Abstract
We report here on the development of combination of assays for fast, reliable, specific and sensitive detection and discrimination of 'Candidatus Phytoplasma mali', 'Ca. P. prunorum' and 'Ca. P. pyri' from the 16Sr-X (apple proliferation - AP) group. These phytoplasmas are causal agents of diseases of fruit trees within the family Rosaceae, namely apple proliferation (AP), European stone fruit yellows (ESFY) and pear decline (PD). The designed panel of assays uses TaqMan minor groove binder probes (MGB). It comprises the same set of primers and specific probes for species-specific amplification within the 16S-23S rRNA intergenic spacer region, a set of primers and probes for amplification of the 16S ribosomal DNA region for the universal phytoplasma detection, and an additional set of primers and probe for 18S rRNA as an endogenous quality control of DNA extraction. The performance characteristics of the panel were evaluated. The advantages of new assays were shown in a comparative study with the conventional PCR, which proved their higher sensitivity combined with three-fold shorter time of testing process; and in comparison with two reported multiplex real-time PCR assays for detection of 'Ca. P. mali' or 'Ca. P. pyri'. New panel of assays were tested on the DNA samples of 'Ca. P. mali', 'Ca. P. prunorum', 'Ca. P. pyri', other phytoplasmas and other bacteria isolated from plant material. Additionally, 198 symptomatic and asymptomatic fruit tree field samples collecting during several growing seasons were tested with new assays as well. The results of this study indicate that the combination of three specific assays may be applied in routine phytoplasma surveys and in the certification programs.
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Affiliation(s)
- Petra Nikolić
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia.
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Baudoin E, Lerner A, Mirza MS, El Zemrany H, Prigent-Combaret C, Jurkevich E, Spaepen S, Vanderleyden J, Nazaret S, Okon Y, Moënne-Loccoz Y. Effects of Azospirillum brasilense with genetically modified auxin biosynthesis gene ipdC upon the diversity of the indigenous microbiota of the wheat rhizosphere. Res Microbiol 2010; 161:219-26. [PMID: 20138146 DOI: 10.1016/j.resmic.2010.01.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 01/05/2010] [Accepted: 01/07/2010] [Indexed: 10/19/2022]
Abstract
The phytostimulatory properties of Azospirillum inoculants, which entail production of the phytohormone indole-3-acetic acid (IAA), can be enhanced by genetic means. However, it is not known whether this could affect their interactions with indigenous soil microbes. Here, wheat seeds were inoculated with the wild-type strain Azospirillum brasilense Sp245 or one of three genetically modified (GM) derivatives and grown for one month. The GM derivatives contained a plasmid vector harboring the indole-3-pyruvate/phenylpyruvate decarboxylase gene ipdC (IAA production) controlled either by the constitutive promoter PnptII or the root exudate-responsive promoter PsbpA, or by an empty vector (GM control). All inoculants displayed equal rhizosphere population densities. Only inoculation with either ipdC construct increased shoot biomass compared with the non-inoculated control. At one month after inoculation, automated ribosomal intergenic spacer analysis (ARISA) revealed that the effect of the PsbpA construct on bacterial community structure differed from that of the GM control, which was confirmed by 16S rDNA-based denaturing gradient gel electrophoresis (DGGE). The fungal community was sensitive to inoculation with the PsbpA construct and especially the GM control, based on ARISA data. Overall, fungal and bacterial communities displayed distinct responses to inoculation of GM A. brasilense phytostimulators, whose effects could differ from those of the wild-type.
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Affiliation(s)
- Ezékiel Baudoin
- Université de Lyon, F-69622 Lyon, France; Université Lyon 1, Villeurbanne, France
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Berezina OV, Brandt A, Yarotsky S, Schwarz WH, Zverlov VV. Isolation of a new butanol-producing Clostridium strain: High level of hemicellulosic activity and structure of solventogenesis genes of a new Clostridium saccharobutylicum isolate. Syst Appl Microbiol 2009; 32:449-59. [DOI: 10.1016/j.syapm.2009.07.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/08/2009] [Accepted: 07/10/2009] [Indexed: 11/25/2022]
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Yamamoto S, Otsuka S, Murakami Y, Nishiyama M, Senoo K. Genetic diversity of gamma-hexachlorocyclohexane-degrading sphingomonads isolated from a single experimental field. Lett Appl Microbiol 2009; 49:472-7. [DOI: 10.1111/j.1472-765x.2009.02691.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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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