Broad‐Range PCR for Detection and Identification of Bacteria

Maiwald, Matthias

doi:10.1128/9781555816834.ch31

Cited by 20 publications

(18 citation statements)

References 164 publications

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“…However, data from clone library analysis revealed that the species was not the most prevalent. The differences may have been due to the fact that species-specific PCR assays arguably display higher sensitivity than group-specific or broad-range primers (19,28). Nonetheless, because the cases for clone library analysis were selected on the basis of strong amplicon signal, the possibility exists that most cases positive for T. denticola were left out of the analysis.…”

Section: Discussionmentioning

confidence: 99%

Diversity of Spirochetes in Endodontic Infections

et al. 2009

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The diversity of spirochetes in primary endodontic infections of teeth with chronic apical periodontitis or acute apical abscesses was investigated using 16S rRNA gene clone library analysis. The prevalences of three common cultivable oral Treponema species were also determined using species-specific nested PCR. All detected spirochetes belonged to the genus Treponema. Overall, 28 different taxa were identified from the 431 clones sequenced: 9 cultivable and validly named species, 1 cultivable as-yet-uncharacterized strain, and 18 as-yet-uncultivated phylotypes, 17 of which were novel. The large majority of clones (94%) were from cultivable named species. The numbers of Treponema species/phylotypes per selected positive sample ranged from 2 to 12. Species-specific nested PCR detected T. denticola, T. socranskii, and T. maltophilum in 59 (66%), 33 (37%), and 26 (29%) of the 90 cases of primary endodontic infections, respectively. Clone library analysis revealed diverse Treponema species/phylotypes as part of the microbiota associated with asymptomatic and symptomatic (abscess) endodontic infections. Although several as-yet-uncultivated Treponema phylotypes were disclosed, including novel taxa, cultivable named species were more abundant and frequently detected.In his milestone study published in 1894, Willoughby Dayton Miller first suggested that spirochetes could play a role in the pathogenesis of apical periodontitis, particularly in cases of acute apical abscesses (21). However, despite several studies revealing their occurrence in endodontic infections by microscopy (49, 50), it was not until approximately 100 years after Miller's study that spirochetes were consistently detected and identified by culture-independent molecular techniques in association with diverse forms of apical periodontitis and pathogenetic involvement was supported (30,43,46). Phylogenetic analyses of 16S rRNA gene clone libraries suggest that all oral spirochetes belong to the genus Treponema (7), and so far, 10 oral species have been cultivated and validly named. They include four asaccharolytic species (Treponema denticola, T. medium, T. putidum, and "T. vincentii") and six saccharolytic species (T. socranskii, T. pectinovorum, T. maltophilum, T. amylovorum, T. lecithinolyticum, and T. parvum) (36). All these species have been recently targeted and disclosed in primary endodontic infections by studies using molecular methods (4, 11, 12, 15, 27, 38-40, 42-44, 51). The most predominant treponemes in these infections are usually T. denticola and T. socranskii (4, 27, 40, 43), while T. parvum, T. maltophilum, and T. lecithinolyticum have been moderately prevalent (4,15,25,38,40). Among several other taxa, a recent study targeted all 10 cultivable and 4 as-yet-uncharacterized oral treponemes (26). Of the nine treponemes detected, T. denticola and T. socranskii were the most prevalent species, which is consistent with other studies (4,27,40,43). The other most frequently found Treponema species/phylotypes included Treponema sp. oral taxon ...

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Section: Discussionmentioning

confidence: 99%

Diversity of Spirochetes in Endodontic Infections

et al. 2009

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“…Multiplex PCRs for the bla NDM , bla , bla KPC , bla IMP , bla VIM , and bla SPM genes were performed as previously described (29), except that primers 27F (AGAGTTTGATYMTGGCTCAG) and 1492R (GGTTACC TTGTTACGACTT) were included in order to amplify the 16S rRNA gene as an internal control (30). For full-length amplification of the bla NDM-1 gene, primers NDM-L-bleo-FW (5=-TGGGTCGAGGTCAGGATAGG) and NDM-R-Aba-125-RV (5=-GCTTTTGAAACTGTCGCACCT) were designed using Primer-BLAST.…”

Section: Methodsmentioning

confidence: 99%

Characterization of Tn 3000 , a Transposon Responsible for bla _NDM-1 Dissemination among Enterobacteriaceae in Brazil, Nepal, Morocco, and India

Campos

Silva

Santos³

et al. 2015

Antimicrob Agents Chemother

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kIn Enterobacteriaceae, the bla NDM genes have been found in many different genetic contexts, and a wide diversity of plasmid scaffolds bearing those genes has been found. In August 2013, we identified NDM-1-producing Escherichia coli and Enterobacter hormaechei strains from a single rectal swab sample from a patient hospitalized in Rio de Janeiro, Brazil, who had no history of travel abroad. Complete DNA sequencing using the Illumina platform and annotation of the two plasmids harboring the bla NDM-1 gene, one from each strain, showed that they belonged to incompatibility groups IncFII K and IncX3 and harbored a novel transposon named Tn3000. Similar genetic structures have been identified among other isolates in Brazil but also on plasmids from other continents. Our findings suggest that the bla NDM-1 gene may be transmitted by Tn3000 in different parts of the world.

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“…Sequence analysis of the 16S rRNA gene was performed on a bird and a fish isolate (26). A search of the Microseq (ABI, Foster City, CA) and GenBank (http://www.ncbi.nlm.nih.gov/genbank/) databases yielded a strong (Ͼ99%) homology with C. botulinum group II; this group includes C. botulinum type E.…”

Section: Resultsmentioning

confidence: 99%

Biodiversity of Clostridium botulinum Type E Associated with a Large Outbreak of Botulism in Wildlife from Lake Erie and Lake Ontario

Hannett

Stone

Davis

et al. 2011

Appl Environ Microbiol

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The genetic relatedness of Clostridium botulinum type E isolates associated with an outbreak of wildlife botulism was studied using random amplification of polymorphic DNA (RAPD). Specimens were collected from November 2000 to December 2008 during a large outbreak of botulism affecting birds and fish living in and around Lake Erie and Lake Ontario. In our present study, a total of 355 wildlife samples were tested for the presence of botulinum toxin and/or organisms. Type E botulinum toxin was detected in 110 samples from birds, 12 samples from fish, and 2 samples from mammals. Sediment samples from Lake Erie were also examined for the presence of C. botulinum. Fifteen of 17 sediment samples were positive for the presence of C. botulinum type E. Eighty-one C. botulinum isolates were obtained from plants, animals, and sediments; of these isolates, 44 C. botulinum isolates produced type E toxin, as determined by mouse bioassay, while the remaining 37 isolates were not toxic for mice. All toxin-producing isolates were typed by RAPD; that analysis showed 12 different RAPD types and multiple subtypes. Our study thus demonstrates that multiple genetically distinct strains of C. botulinum were involved in the present outbreak of wildlife botulism. We found that C. botulinum type E is present in the sediments of Lake Erie and that a large range of bird and fish species is affected.

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Broad‐Range PCR for Detection and Identification of Bacteria

Cited by 20 publications

References 164 publications

Diversity of Spirochetes in Endodontic Infections

Diversity of Spirochetes in Endodontic Infections

Characterization of Tn 3000 , a Transposon Responsible for bla _NDM-1 Dissemination among Enterobacteriaceae in Brazil, Nepal, Morocco, and India

Biodiversity of Clostridium botulinum Type E Associated with a Large Outbreak of Botulism in Wildlife from Lake Erie and Lake Ontario

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Broad‐Range PCR for Detection and Identification of Bacteria

Cited by 20 publications

References 164 publications

Diversity of Spirochetes in Endodontic Infections

Diversity of Spirochetes in Endodontic Infections

Characterization of Tn 3000 , a Transposon Responsible for bla NDM-1 Dissemination among Enterobacteriaceae in Brazil, Nepal, Morocco, and India

Biodiversity of Clostridium botulinum Type E Associated with a Large Outbreak of Botulism in Wildlife from Lake Erie and Lake Ontario

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Characterization of Tn 3000 , a Transposon Responsible for bla _NDM-1 Dissemination among Enterobacteriaceae in Brazil, Nepal, Morocco, and India