A comparison of two DNA barcode markers for species discrimination in the red algal family Kallymeniaceae (Gigartinales, Florideophyceae), with a description of Euthora timburtonii sp. nov.

Botany ◽  
2010 ◽  
Vol 88 (2) ◽  
pp. 119-131 ◽  
Author(s):  
Bridgette E. Clarkston ◽  
Gary W. Saunders
Keyword(s):  
Dna Barcode ◽  
Morphological Characters ◽  
Universal Primers ◽  
23S Rrna ◽  
Species Discrimination ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Red Algal ◽  
23S Rrna Gene ◽  
Gene Coi

Accurate identification of many red algae to the species level using only morphological characters can be difficult. The emerging field of “molecular-assisted alpha taxonomy” can greatly alleviate this issue. In this approach, a large number of specimens are sequenced for a standard DNA marker as a first step to genetic species assignment, followed by detailed morphological observations. Regions of both the mitochondrial cytochrome c oxidase I gene (COI-5P) and the plastid 23S rRNA gene (UPA) have been proposed as DNA barcode markers to accomplish this task. We compared the utility of each marker as a species identification tool using members of the marine red algal family Kallymeniaceae from British Columbia, Canada. Our results indicate that COI-5P is a more sensitive marker for delimiting species, but that it can be difficult to acquire clean amplification products for many isolates of Kallymeniaceae, owing to biological contamination. This problem can be overcome by using specific primers. UPA, on the other hand, has universal primers that work in diverse lineages (e.g., red, brown, and green algae), but lower interspecific sequence variation, which has the potential to underestimate species diversity, although this was not observed in our study. During our survey, we uncovered a new species of the Kallymeniaceae, Euthora timburtonii Clarkston et G.W. Saunders sp. nov., which we describe here.

scholarly journals Establishment of the family Zarkiaceae (Oscillatoriales, Cyanobacteria) and description of the new marine genera Zarkia (Zarkiaceae, Oscillatoriales) and Romeriopsis (Leptolyngbyaceae, Synechococcales), from northern Portugal

2021 ◽  
Author(s):  
Guilherme S. Hentschke ◽  
Angela Pinheiro ◽  
Vitor Ramos ◽  
Aldo Barreiro ◽  
M. Sofia Costa ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Secondary Structures ◽  
Morphological Characters ◽  
23S Rrna ◽  
Rrna Gene ◽  
New Family ◽  
The Family ◽  
23S Rrna Gene ◽  
Taxonomical Revision

The morphology, 16S rRNA gene phylogeny and the 16S-23S rRNA gene ITS secondary structures of three strains of marine Cyanobacteria, isolated from inter- and subtidal environments from north Portugal were studied, resulting in the description of Zarkia subtidalensis gen. et. sp. nov. (Zarkiaceae fam. nov.) and Romeriopsis marina gen. et. sp. nov (Leptolyngbyaceae). No diacritical morphological characters were found either for the new family or for the new genera. The 16S rRNA gene Maximum Likelihood and Bayesian phylogenies supported that Zarkia and Zarkiaceae are members of the Oscillatoriales, positioned close to Microcoleaceae genera, but distant from Microcoleus. Romeriopsis is positioned within the Leptolyngbyaceae and is closely related to Alkalinema. The secondary structures of the D1-D1′, Box B, V2 and V3 helices corroborate with the phylogenetic results. Furthermore, our study supports previous observations of polyphyletic Oscillatoriales families and reinforces the need for their taxonomical revision.

scholarly journals Identification of Lactobacillus Isolates from the Gastrointestinal Tract, Silage, and Yoghurt by 16S-23S rRNA Gene Intergenic Spacer Region Sequence Comparisons

1999 ◽  
Vol 65 (9) ◽  
pp. 4264-4267 ◽  
Author(s):  
G. W. Tannock ◽  
A. Tilsala-Timisjarvi ◽  
S. Rodtong ◽  
J. Ng ◽  
K. Munro ◽  
...  
Keyword(s):  
Lactobacillus Rhamnosus ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Sequence Comparisons ◽  
Intergenic Spacer Region ◽  
23S Rrna Gene

Lactobacillus isolates were identified by PCR amplification and sequencing of the region between the 16S and 23S rRNA genes (spacer region). The sequences obtained from the isolates were compared to those of reference strains held in GenBank. A similarity of 97.5% or greater was considered to provide identification. To check the reliability of the method, the V2-V3 region of the 16S rRNA gene was amplified and sequenced in the case of isolates whose spacer region sequences were less than 99% similar to that of a reference strain. Confirmation of identity was obtained in all instances. Spacer region sequencing provided rapid and accurate identification ofLactobacillus isolates obtained from gastrointestinal, yoghurt, and silage samples. It had an advantage over 16S V2-V3 sequence comparisons because it distinguished between isolates ofLactobacillus casei and Lactobacillus rhamnosus.

scholarly journals Molecular pathways to high-level azithromycin resistance in Neisseria gonorrhoeae

2021 ◽  
Author(s):  
J G E Laumen ◽  
S S Manoharan-Basil ◽  
E Verhoeven ◽  
S Abdellati ◽  
I De Baetselier ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Ribosomal Proteins ◽  
Efflux Pump ◽  
23S Rrna ◽  
Rrna Gene ◽  
23S Rrna Gene ◽  
Evolution Of Resistance ◽  
High Level ◽  
Azithromycin Resistance ◽  
Level Resistance

Abstract Background The prevalence of azithromycin resistance in Neisseria gonorrhoeae is increasing in numerous populations worldwide. Objectives To characterize the genetic pathways leading to high-level azithromycin resistance. Methods A customized morbidostat was used to subject two N. gonorrhoeae reference strains (WHO-F and WHO-X) to dynamically sustained azithromycin pressure. We tracked stepwise evolution of resistance by whole genome sequencing. Results Within 26 days, all cultures evolved high-level azithromycin resistance. Typically, the first step towards resistance was found in transitory mutations in genes rplD, rplV and rpmH (encoding the ribosomal proteins L4, L22 and L34 respectively), followed by mutations in the MtrCDE-encoded efflux pump and the 23S rRNA gene. Low- to high-level resistance was associated with mutations in the ribosomal proteins and MtrCDE efflux pump. However, high-level resistance was consistently associated with mutations in the 23S ribosomal RNA, mainly the well-known A2059G and C2611T mutations, but also at position A2058G. Conclusions This study enabled us to track previously reported mutations and identify novel mutations in ribosomal proteins (L4, L22 and L34) that may play a role in the genesis of azithromycin resistance in N. gonorrhoeae.

scholarly journals Molecular characterization of a ceftriaxone-resistant Neisseria gonorrhoeae strain found in Switzerland: a case report

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Konrad Egli ◽  
Anna Roditscheff ◽  
Ursula Flückiger ◽  
Martin Risch ◽  
Lorenz Risch ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
23S Rrna ◽  
Rrna Gene ◽  
Limited Information ◽  
Specific Pcr ◽  
Appropriate Treatment ◽  
23S Rrna Gene ◽  
Allele Type ◽  
Ciprofloxacin Resistance

Abstract Background The resistance of Neisseria gonorrhoeae to ceftriaxone is unusual in Switzerland. The underlying genotype responsible for resistance is suspected to be novel. Generally, resistance in Neisseria gonorrhoeae (Ng) involves a comprehensive set of genes with many different mutations leading to resistance to different β-lactams and fluoroquinolones. Case presentation A patient had a positive result from specific PCR for Ng. We routinely culture all clinical specimens with a positive NG-PCR. In this particular case, we isolated a strain with resistance to ceftriaxone in Switzerland. A total of seven different genes (penA, ponA, porinB, mtr, gyrA, parC, 23S rRNA gene) in this strain were partially sequenced for comparison with phenotypic susceptibility testing. Interestingly, two different mutations in the porinB gene were observed, and data on this gene are limited. Information on the identified allele type of the penA gene is very limited as well. Three different mutations of parC and gyrA that correlate with ciprofloxacin resistance were found. The combination of ceftriaxone and ciprofloxacin resistance makes an appropriate treatment difficult to obtain due to multidrug resistance. Conclusion The combined results for all genes show the appearance of new mutations in central Europe either due to worldwide spread or the emergence of new genetic combinations of mutations.

scholarly journals Molecular Basis of Macrolide Resistance inCampylobacterStrains Isolated from Poultry in South Korea

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Bai Wei ◽  
Min Kang
Keyword(s):  
Molecular Mechanisms ◽  
Macrolide Resistance ◽  
23S Rrna ◽  
Rrna Gene ◽  
Campylobacter Coli ◽  
Erythromycin Resistance ◽  
23S Rrna Gene ◽  
Ribosomal Protein L22 ◽  
Resistant Strains ◽  
Azithromycin Resistance

We investigated the molecular mechanisms underlying macrolide resistance in 38 strains ofCampylobacterisolated from poultry. Twenty-seven strains were resistant to azithromycin and erythromycin, five showed intermediate azithromycin resistance and erythromycin susceptibility, and six showed azithromycin resistance and erythromycin susceptibility. FourCampylobacter jejuniand sixCampylobacter colistrains had azithromycin MICs which were 8–16 and 2–8-fold greater than those of erythromycin, respectively. The A2075G mutation in the 23S rRNA gene was detected in 11 resistant strains with MICs ranging from 64 to ≥ 512μg/mL. Mutations including V137A, V137S, and a six-amino acid insertion (114-VAKKAP-115) in ribosomal protein L22 were detected in theC. jejunistrains. Erythromycin ribosome methylase B-erm(B) was not detected in any strain. All strains except three showed increased susceptibility to erythromycin with twofold to 256-fold MIC change in the presence of phenylalanine arginine ß-naphthylamide (PAßN); the effects of PAßN on azithromycin MICs were limited in comparison to those on erythromycin MICs, and 13 strains showed no azithromycin MIC change in the presence of PAßN. Differences between azithromycin and erythromycin resistance and macrolide resistance phenotypes and genotypes were observed even in highly resistant strains. Further studies are required to better understand macrolide resistance inCampylobacter.

Prevalence and Antimicrobial Resistance of Campylobacter spp. Isolated from Poultry Carcasses in Poland

2013 ◽  
Vol 76 (8) ◽  
pp. 1451-1455 ◽  
Author(s):  
KINGA WIECZOREK ◽  
IWONA KANIA ◽  
JACEK OSEK
Keyword(s):  
Campylobacter Jejuni ◽  
23S Rrna ◽  
Rrna Gene ◽  
Campylobacter Coli ◽  
Genetic Determinants ◽  
Gyra Gene ◽  
23S Rrna Gene ◽  
Pcr Method ◽  
Almost All ◽  
Campylobacter Spp

The purpose of the present study was to determine the prevalence of Campylobacter in poultry carcasses at slaughter in Poland. For the isolated strains, resistance to selected antibiotics and the associated genetic determinants were identified. A total of 498 Campylobacter isolates were obtained from 802 poultry samples during the 2-year study period. Strains were identified to species with the PCR method; 53.6% of the strains were Campylobacter jejuni and 46.4% were Campylobacter coli. A high percentage of the tested Campylobacter strains were resistant to ciprofloxacin and nalidixic acid (74.1 and 73.5%, respectively) followed by tetracycline (47.4%) and streptomycin (20.5%). Only one C. jejuni and two C. coli isolates were resistant to gentamicin. Seventy-nine (15.9%) of the 498 strains were resistant to three or more classes of antibiotics examined. Higher levels of resistance, irrespective of the antimicrobial agent tested, were found within the C. coli group. Almost all strains resistant to quinolones (99.5%) and to tetracycline (99.6%) carried the Thr-86-to-Ile mutation in the gyrA gene and possessed the tet(O) marker, respectively. All isolates resistant to erythromycin had the A2075G mutation in the 23S rRNA gene. These results reveal that poultry carcasses in Poland are a reservoir of potentially pathogenic and antimicrobial-resistant Campylobacter strains for humans, which may pose a public health risk.

Identification of a 23S rRNA Gene Mutation in Clarithromycin-Resistant Helicobacter pylori

Helicobacter ◽  
1996 ◽  
Vol 1 (4) ◽  
pp. 227-228 ◽  
Author(s):  
Gregory G. Stone ◽  
Dee Shortridge ◽  
Robert K. Flamm ◽  
James Versalovic ◽  
Jill Beyer ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Gene Mutation ◽  
23S Rrna ◽  
Rrna Gene ◽  
23S Rrna Gene

scholarly journals Leptospira Survey in Wild Boar (Sus scrofa) Hunted in Tuscany, Central Italy

Pathogens ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 377 ◽  
Author(s):  
Giovanni Cilia ◽  
Fabrizio Bertelloni ◽  
Marta Angelini ◽  
Domenico Cerri ◽  
Filippo Fratini
Keyword(s):  
16S Rrna ◽  
Wild Boar ◽  
Sus Scrofa ◽  
Central Italy ◽  
23S Rrna ◽  
Rrna Gene ◽  
Pathogenic Leptospira ◽  
Molecular Assays ◽  
Realtime Pcr ◽  
23S Rrna Gene

Leptospirosis is a re-emerging, worldwide zoonosis, and wild boar (Sus scrofa) are involved in its epidemiology as the reservoir. The aim of this study was to investigate the prevalence of Leptospira with serological, bacteriological, and molecular assays in wild boar hunted in Tuscany (Italy) during two hunting seasons. In total, 287 specimens of sera, kidneys, and liver were collected to perform microscopic agglutination tests (MATs), isolation, and RealTime PCR to detect pathogenic (lipL32 gene), intermediate (16S rRNA gene), and saprophytic (23S rRNA gene) Leptospira. Within sera, 39 (13.59%) were positive to the MAT, and Australis was the most represented serogroup (4.88%), followed by Pomona (4.18%), and Tarassovi (3.14%). Moreover, four Leptospira cultures were positive, and once isolates were identified, one was identified as L. borgpetersenii serovar Tarassovi, and three as L. interrogans serovar Bratislava. Pathogenic Leptospira DNA were detected in 32 wild boar kidneys (11.15%). The characterization through the amplification of the rrs2 gene highlighted their belonging to L. interrogans (23 kidneys), L. borgpetersenii (four), and L. kirschneri (one), while nine kidneys (3.14%) were positive for intermediate Leptospira, all belonging to L. fainei. The results of this study confirmed the importance of wild boar in the epidemiology of leptospirosis among wildlife in Central Italy.

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