scholarly journals Metagenomic 16S rRNA gene sequencing survey of Borrelia species in Irish samples of Ixodes ricinus ticks

2018 ◽  
Author(s):  
John S Lambert ◽  
Michael John Cook ◽  
John Eoin Healy ◽  
Ross Murtagh ◽  
Gordana Avramovic ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ixodes Ricinus ◽  
Sanger Sequencing ◽  
Reference Sequence ◽  
Borrelia Burgdorferi Sensu Lato ◽  
Tick Population ◽  
Rrna Gene ◽  
Ixodes Ricinus Ticks ◽  
The 16S Rrna Gene

Lyme borreliosis is a systemic infection caused by tick-borne pathogenic borreliae of the Borrelia burgdorferi sensu lato complex or of the more heterogeneous relapsing fever borrelia group. Clinical distinction of the infections due to different borrelia species is difficult. Accurate knowledge of the prevalence and the species of borreliae in the infected ticks in the endemic areas is valuable for formulating appropriate guidelines for proper management of this infectious disease. The purpose of this research was to design a readily implementable protocol to detect the divergent species of borreliae known to exist in Europe, using Irish samples of Ixodes ricinus ticks as the subject for study. Questing I. ricinus nymph samples were taken at six localities within Ireland. The crude DNA of each dried tick was extracted by hot NH4OH and used to initiate a same-nested PCR with a pair of borrelial genus-specific primers to amplify a highly conserved 357/358 bp segment of the 16S rRNA gene for detection and as the template for Sanger sequencing. To distinguish B. garinii from B. burgdorferi and to discriminate the various strains of B. garinii, a second 282 bp segment of the 16S rRNA gene was amplified for Sanger sequencing. A signature segment of the DNA sequence excised from the computer-generated electropherogram was submitted to the GenBank for BLAST alignment analysis. A 100% ID match with the unique reference sequence in the GenBank was required for the molecular diagnosis of the borrelial species or strain. We found the overall rate of borrelial infection in the Irish tick population to be 5%, with a range from 2% to 12% depending on the locations of tick collection. At least 3 species, namely B. garinii, B. valaisiana and B. miyamotoi, are infecting the ticks collected in Ireland. The isolates of B. garinii were confirmed to be strain BgVir, strain Bernie or strain T25. Since antigens for diagnostic serology tests may be species- or even strain-specific, expanded surveillance of the species and strains of the borreliae among human-biting ticks in Ireland is needed to ensure that the antigens used for the serology tests do contain the epitopes matching the antibodies elicited by the borrelial species and strains in the ticks cohabitating in the same environment.

scholarly journals Quantitative Real-Time PCR for Detection of Members of the Ehrlichia phagocytophila Genogroup in Host Animals and Ixodes ricinus Ticks

1999 ◽  
Vol 37 (5) ◽  
pp. 1329-1331 ◽  
Author(s):  
Nicola Pusterla ◽  
Jon B. Huder ◽  
Christian M. Leutenegger ◽  
Ueli Braun ◽  
John E. Madigan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ixodes Ricinus ◽  
Nested Pcr ◽  
Rrna Gene ◽  
Granulocytic Ehrlichiosis ◽  
Ehrlichia Phagocytophila ◽  
Ixodes Ricinus Ticks ◽  
Taqman Pcr ◽  
The 16S Rrna Gene

A TaqMan PCR was established for identification and quantitation of members of the Ehrlichia phagocytophila group in experimentally infected cows and in Ixodes ricinus ticks. The TaqMan PCR identified a 106-bp section of the 16S rRNA gene by use of a specific fluorogenic probe and two primers. This technique was specific for members of the E. phagocytophila group, which include E. phagocytophila, Ehrlichia equi, and the agent of human granulocytic ehrlichiosis. The TaqMan system identified 10 copies of a cloned section of the 16S rRNA gene ofE. phagocytophila. The sensitivity and specificity of the TaqMan PCR were similar to those of conventional nested PCR. The numbers of ehrlichiae in leukocytes of the two cows experimentally infected with E. phagocytophila were measured daily by TaqMan PCR and had a course similar to that of the percentages of infected leukocytes determined daily by light microscopy. The prevalence of infected free-living ticks, which were collected from areas where bovine ehrlichiosis is endemic and from regions with sporadic occurrences of granulocytic ehrlichiosis in dogs and horses, was identical as determined by nested PCR and TaqMan PCR.

scholarly journals Cutibacterium modestum and “Propionibacterium humerusii” represent the same species that is commonly misidentified as Cutibacterium acnes

2021 ◽  
Author(s):  
Daniel Goldenberger ◽  
Kirstine K. Søgaard ◽  
Aline Cuénod ◽  
Helena Seth-Smith ◽  
Daniel de Menezes ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Reference Sequence ◽  
Rrna Gene ◽  
Correct Identification ◽  
Skin Microbiome ◽  
Isolation And Identification ◽  
Important Species ◽  
Cutibacterium Acnes ◽  
The 16S Rrna Gene

AbstractCutibacterium spp. play an increasing role in soft tissue and implant-associated infections. We isolated a novel Cutibacterium spp. from an implant and investigated this isolate using multiple identification approaches. Correct identification was hampered by inconsistent reference data. The isolate was characterised using conventional methods such as Gram stain, MALDI-TOF MS, and antimicrobial susceptibility testing against multiple antimicrobials. Partial 16S rRNA gene sequencing and whole genome sequencing were also performed. In addition, we summarised the available published sequence data and compared prior data to our strain. Conventional phenotypic identification of our isolate resulted in Cutibacterium spp. After analysis of 16S rRNA gene and genome sequences, our isolate was identified as C. modestum, a very recently described species. The 16S rRNA gene analysis was hampered by three incorrect nucleotides within the 16S rRNA gene reference sequence of C. modestum M12T (accession no. LC466959). We also clearly demonstrate that this novel species is identical to tentatively named “Propionibacterium humerusii”. Retrospective data analysis indicates that C. modestum is a clinically important Cutibacterium species often misidentified as C. acnes. The isolation and identification of Cutibacterium spp. is still a challenge. The correct description of very recently named C. modestum and the availability of a correct 16S rRNA sequence of the type strain may help to clarify the taxonomical uncertainty concerning “P. humerusii”. The novel C. modestum is an additional, clinically important species within the genus Cutibacterium and may represent a new member of the human skin microbiome.

scholarly journals Rapid Sanger Sequencing of the 16S rRNA Gene for Identification of Some Common Pathogens

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e88886 ◽  
Author(s):  
Linxiang Chen ◽  
Ying Cai ◽  
Guangbiao Zhou ◽  
Xiaojun Shi ◽  
Jianhui Su ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sanger Sequencing ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals Metagenomic 16S rRNA gene sequencing survey of Borrelia species in Irish samples of Ixodes ricinus ticks

PLoS ONE ◽  
2019 ◽  
Vol 14 (4) ◽  
pp. e0209881 ◽  
Author(s):  
John S. Lambert ◽  
Michael John Cook ◽  
John Eoin Healy ◽  
Ross Murtagh ◽  
Gordana Avramovic ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ixodes Ricinus ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Ixodes Ricinus Ticks ◽  
Rrna Gene Sequencing

scholarly journals Identity of Ehrlichial DNA Sequences Derived from Ixodes ricinus Ticks with Those Obtained from Patients with Human Granulocytic Ehrlichiosis in Slovenia

1999 ◽  
Vol 37 (1) ◽  
pp. 209-210 ◽  
Author(s):  
M. Petrovec ◽  
J. W. Sumner ◽  
W. L. Nicholson ◽  
J. E. Childs ◽  
F. Strle ◽  
...  
Keyword(s):  
Heat Shock ◽  
16S Rrna ◽  
Ixodes Ricinus ◽  
Dna Sequences ◽  
Rrna Gene ◽  
Granulocytic Ehrlichiosis ◽  
Human Granulocytic Ehrlichiosis ◽  
Ixodes Ricinus Ticks ◽  
Pcr Assays ◽  
The 16S Rrna Gene

Adult Ixodes ricinus (Acari: Ixodidae) ticks collected near Ljubljana, Slovenia, were tested for the agent of human granulocytic ehrlichiosis (HGE) by using PCR assays based on the 16S rRNA gene. Three (3.2%) of 93 ticks were found to contain granulocytic ehrlichiae. Nucleotide sequences of portions of the bacterialgroESL heat shock operon amplified from these ticks were identical or nearly (99.8%) identical to those previously determined for human patients with HGE from Slovenia, providing additional evidence that the ticks were infected with the HGE agent. This study identified I. ricinus as the likely vector for these ehrlichial pathogens of humans in this part of Europe.

scholarly journals Anaplasma phagocytophilum in Questing Ixodes ricinus Ticks: Comparison of Prevalences and Partial 16S rRNA Gene Variants in Urban, Pasture, and Natural Habitats

2012 ◽  
Vol 79 (5) ◽  
pp. 1730-1734 ◽  
Author(s):  
Evelyn Overzier ◽  
Kurt Pfister ◽  
Claudia Thiel ◽  
Ingrid Herb ◽  
Monia Mahling ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ixodes Ricinus ◽  
Anaplasma Phagocytophilum ◽  
Rrna Gene ◽  
Gene Variants ◽  
Habitat Types ◽  
Natural Habitats ◽  
Content Type ◽  
Ixodes Ricinus Ticks

ABSTRACTUrban, natural, and pasture areas were investigated for prevalences and 16S rRNA gene variants ofAnaplasma phagocytophilumin questingIxodes ricinusticks. The prevalences differed significantly between habitat types, and year-to-year variations in prevalence and habitat-dependent occurrence of 16S rRNA gene variants were detected.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

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