The Absence of Intervening Sequences in 23S rRNA Genes of Campylobacter coli Isolates from Turkeys Is a Unique Attribute of a Cluster of Related Strains Which Also Lack Resistance to Erythromycin

ABSTRACT Certain Campylobacter strains harbor a transcribed intervening sequence (IVS) in their 23S rRNA genes. Following transcription, the IVS is excised, leading to fragmentation of the 23S rRNA. The origin and possible functions of the IVS are unknown. Furthermore, the distribution of IVS-harboring strains within Campylobacter populations is poorly understood. In this study, 104 strains of Campylobacter coli from turkeys, representing 27 different multilocus sequence typing-based sequence types (STs), were characterized in terms of IVS content and erythromycin susceptibility. Sixty-nine strains harbored IVSs in all three 23S rRNA genes, whereas the other 35 strains lacked IVSs from at least one of the genes. The STs of the latter strains belonged to an unusual cluster of C. coli STs (cluster II), earlier found primarily in turkey strains and characterized by the presence of the C. jejuni aspA103 allele. The majority (66/69) of strains harboring IVSs in all three 23S rRNA genes were resistant to erythromycin, whereas none of the 35 strains with at least one IVS-free 23S rRNA gene were resistant. Cluster II strains could be transformed to erythromycin resistance with genomic DNA from C. coli that harbored IVS and the A2075G transition in the 23S rRNA gene, associated with resistance to erythromycin in Campylobacter. Erythromycin-resistant transformants harbored both the A2075 transition and IVS. The findings suggest that the absence of IVS in C. coli from turkeys is characteristic of a unique clonal group of erythromycin-susceptible strains and that IVS can be acquired by these strains via natural transformation to erythromycin resistance.

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Natural Transformation-Mediated Transfer of Erythromycin Resistance in Campylobacter coli Strains from Turkeys and Swine

Applied and Environmental Microbiology ◽

10.1128/aem.72.2.1316-1321.2006 ◽

2006 ◽

Vol 72 (2) ◽

pp. 1316-1321 ◽

Cited By ~ 31

Author(s):

Joo-Sung Kim ◽

Donna K. Carver ◽

Sophia Kathariou

Keyword(s):

Point Mutation ◽

Natural Transformation ◽

23S Rrna ◽

Rrna Gene ◽

Campylobacter Coli ◽

Erythromycin Resistance ◽

23S Rrna Gene ◽

High Level ◽

Human Infections ◽

Spontaneous Mutants

ABSTRACT Erythromycin resistance in Campylobacter coli from meat animals is frequently encountered and could represent a substantial barrier to antibiotic treatment of human infections. Erythromycin resistance in this organism has been associated with a point mutation (A2075G) in the 23S rRNA gene. However, the mechanisms responsible for possible dissemination of erythromycin resistance in C. coli remain poorly understood. In this study, we investigated transformation-mediated acquisition of erythromycin resistance by genotypically diverse C. coli strains from turkeys and swine, with total genomic DNA from erythromycin-resistant C. coli of either turkey or swine origin used as a donor. Overall, transformation to erythromycin resistance was significantly more frequent in C. coli strains from turkeys than in swine-derived strains (P < 0.01). The frequency of transformation to erythromycin resistance was 10−5 to 10−6 for turkey-derived strains but 10−7 or less for C. coli from swine. Transformants harbored the point mutation A2075G in the 23S rRNA gene, as did the erythromycin-resistant strains used as DNA donors. Erythromycin resistance was stable in transformants following serial transfers in the absence of the antibiotic, and most transformants had high MICs (>256 μg/ml), as did the C. coli donor strains. In contrast to the results obtained with transformation, spontaneous mutants had relatively low erythromycin MICs (32 to 64 μg/ml) and lacked the A2075G mutation in the 23S rRNA gene. These findings suggest that natural transformation has the potential to contribute to the dissemination of high-level resistance to erythromycin among C. coli strains colonizing meat animals.

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Spontaneous Erythromycin Resistance Mutation in a 23S rRNA Gene, rrlA, of the Extreme Thermophile Thermus thermophilus IB-21

Journal of Bacteriology ◽

10.1128/jb.183.14.4382-4385.2001 ◽

2001 ◽

Vol 183 (14) ◽

pp. 4382-4385 ◽

Cited By ~ 9

Author(s):

Steven T. Gregory ◽

Jamie H. D. Cate ◽

Albert E. Dahlberg

Keyword(s):

Genetic Manipulation ◽

Thermus Thermophilus ◽

Resistance Mutation ◽

Rrna Genes ◽

23S Rrna ◽

Rrna Gene ◽

Erythromycin Resistance ◽

23S Rrna Gene ◽

Resistant Mutants ◽

23S Rrna Genes

ABSTRACT Spontaneous, erythromycin-resistant mutants of Thermus thermophilus IB-21 were isolated and found to carry the mutation A2058G in one of two 23S rRNA operons. The heterozygosity of these mutants indicates that A2058G confers a dominant or codominant phenotype in this organism. This mutation provides a valuable tool for the genetic manipulation of the 23S rRNA genes ofThermus.

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Cloning and sequence analysis of two copies of a 23S rRNA gene from Helicobacter pylori and association of clarithromycin resistance with 23S rRNA mutations.

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.41.12.2621 ◽

1997 ◽

Vol 41 (12) ◽

pp. 2621-2628 ◽

Cited By ~ 141

Author(s):

D E Taylor ◽

Z Ge ◽

D Purych ◽

T Lo ◽

K Hiratsuka

Keyword(s):

Helicobacter Pylori ◽

Natural Transformation ◽

Rrna Genes ◽

23S Rrna ◽

Rrna Gene ◽

Donor Strain ◽

Clarithromycin Resistance ◽

23S Rrna Gene ◽

23S Rrna Genes ◽

H Pylori

In this study, two identical copies of a 23S-5S gene cluster, which are separately situated within the Helicobacter pylori UA802 chromosome, were cloned and sequenced. Comparison of the DNA sequence of the H. pylori 23S rRNA gene with known sequences of other bacterial 23S rRNA genes indicated that the H. pylori UA802 23S rRNA genes are closely related to those of Campylobacter spp. and therefore belong in the proposed Proteobacteria subdivision. The 5'-terminal nucleotide T or A of the 23S rRNA is close to a Pribnow box which could be a -10 region of the transcription promoter for the 23S rRNA gene, suggesting that a posttranscriptional process is likely not involved in the maturation of the H. pylori 23S rRNA. Clinical isolates of H. pylori resistant to clarithromycin were examined by using natural transformation and pulsed-field gel electrophoresis. Cross-resistance to clarithromycin and erythromycin, which was transferred by natural transformation from the Cla(r) Ery(r) donor strain H. pylori E to the Cla(s) Ery(s) recipient strain H. pylori UA802, was associated with an single A-to-G transition mutation at position 2142 of both copies of the 23S rRNA in UA802 Cla(r) Ery(r) mutants. The transformation frequency for Cla(r) and Ery(r) was found to be approximately 2 x 10(-6) transformants per viable cell, and the MICs of both clarithromycin and erythromycin for the Cla(r) Ery(r) mutants were equal to those for the donor isolate. Our results confirmed the previous findings that mutations at positions 2142 and 2143 of the H. pylori 23S rRNA gene are responsible for clarithromycin resistance and suggest that acquisition of clarithromycin resistance in H. pylori could also result from horizontal transfer.

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

BioMed Research International ◽

10.1155/2018/4526576 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 3

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.

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Genotypes and antibiotic resistance of bovineCampylobacterand their contribution to human campylobacteriosis

Epidemiology and Infection ◽

10.1017/s0950268814003410 ◽

2014 ◽

Vol 143 (11) ◽

pp. 2373-2380 ◽

Cited By ~ 15

Author(s):

R. JONAS ◽

S. KITTL ◽

G. OVERESCH ◽

P. KUHNERT

Keyword(s):

Antibiotic Resistance ◽

Point Mutations ◽

Human Infection ◽

Rrna Genes ◽

23S Rrna ◽

Campylobacter Coli ◽

Source Attribution ◽

23S Rrna Genes ◽

Sequence Types ◽

Human Campylobacteriosis

SUMMARYCampylobacter jejuniandCampylobacter coliare the most important bacterial causes of human gastroenteritis. Chicken has been recognized as a major source for human infection, whereas cattle might also contribute to a lesser extent. However, there is a paucity of information available regardingCampylobacterin Swiss cattle and their role for human campylobacteriosis. To gain more information on genotypes and antibiotic resistance of bovineC. jejuniandC. coliand on their contribution to human disease, 97 cattle isolates were analysed. Multilocus sequence typing (MLST) andflaBtyping were applied and thegyrAand 23S rRNA genes were screened for point mutations responsible for quinolone and macrolide resistance, respectively. A total of 37 sequence types (STs) and 44flaBtypes were identified, including two sequence types and fiveflaBtypes not previously described. Most common sequence types were ST21 (21%), ST61 (12%) and ST48 (11%). Only one isolate was macrolide resistant while 31% (n= 30) were quinolone resistant. Source attribution indicated chicken as the main source of human infection with cattle being second. In conclusion, cattle should not be underestimated as a potential source of human campylobacteriosis.

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Rapid Detection and Estimation by Pyrosequencing of 23S rRNA Genes with a Single Nucleotide Polymorphism Conferring Linezolid Resistance in Enterococci

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.47.11.3620-3622.2003 ◽

2003 ◽

Vol 47 (11) ◽

pp. 3620-3622 ◽

Cited By ~ 68

Author(s):

Alistair Sinclair ◽

Catherine Arnold ◽

Neil Woodford

Keyword(s):

Fragment Length Polymorphism ◽

Rrna Genes ◽

23S Rrna ◽

Rrna Gene ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Linezolid Resistance ◽

Gene Copies ◽

23S Rrna Gene ◽

23S Rrna Genes

ABSTRACT Pyrosequencing was used to detect rapidly and estimate the number of 23S rRNA genes with a G2576T mutation in 43 linezolid-resistant and -susceptible clinical isolates of enterococci. The method showed 100% concordance with PCR-restriction fragment length polymorphism for detecting isolates homozygous for either G2576 or T2576 or heterozygous for this mutation. A good correlation was found between linezolid MICs and the number of 23S rRNA gene copies carrying the mutation.

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Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter: Implications for Phylogenetic Inference and Systematics

Journal of Bacteriology ◽

10.1128/jb.187.17.6106-6118.2005 ◽

2005 ◽

Vol 187 (17) ◽

pp. 6106-6118 ◽

Cited By ~ 91

Author(s):

Floyd E. Dewhirst ◽

Zeli Shen ◽

Michael S. Scimeca ◽

Lauren N. Stokes ◽

Tahani Boumenna ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Sequence Data ◽

Rrna Genes ◽

23S Rrna ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

23S Rrna Gene ◽

23S Rrna Genes

ABSTRACT Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31′ and 27′. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.

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The Internal Transcribed Spacer Region, a New Tool for Use in Species Differentiation and Delineation of Systematic Relationships within the Campylobacter Genus

Applied and Environmental Microbiology ◽

10.1128/aem.02551-09 ◽

2010 ◽

Vol 76 (10) ◽

pp. 3071-3081 ◽

Cited By ~ 27

Author(s):

Si Ming Man ◽

Nadeem O. Kaakoush ◽

Sophie Octavia ◽

Hazel Mitchell

Keyword(s):

16S Rrna ◽

Internal Transcribed Spacer ◽

Its Region ◽

Rrna Genes ◽

23S Rrna ◽

Species Differentiation ◽

Rrna Gene ◽

23S Rrna Gene ◽

Systematic Relationships ◽

23S Rrna Genes

ABSTRACT The Campylobacter genus consists of a number of important human and animal pathogens. Although the 16S rRNA gene has been used extensively for detection and identification of Campylobacter species, there is currently limited information on the 23S rRNA gene and the internal transcribed spacer (ITS) region that lies between the 16S and 23S rRNA genes. We examined the potential of the 23S rRNA gene and the ITS region to be used in species differentiation and delineation of systematic relationships for 30 taxa within the Campylobacter genus. The ITS region produced the highest mean pairwise percentage difference (35.94%) compared to the 16S (5.34%) and 23S (7.29%) rRNA genes. The discriminatory power for each region was further validated using Simpson's index of diversity (D value). The D values were 0.968, 0.995, and 0.766 for the ITS region and the 23S and 16S rRNA genes, respectively. A closer examination of the ITS region revealed that Campylobacter concisus, Campylobacter showae, and Campylobacter fetus subsp. fetus harbored tRNA configurations not previously reported for other members of the Campylobacter genus. We also observed the presence of strain-dependent intervening sequences in the 23S rRNA genes. Neighbor-joining trees using the ITS region revealed that Campylobacter jejuni and Campylobacter coli strains clustered in subgroups, which was not observed in trees derived from the 16S or 23S rRNA gene. Of the three regions examined, the ITS region is by far the most cost-effective region for the differentiation and delineation of systematic relationships within the Campylobacter genus.

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BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons

BMC Bioinformatics ◽

10.1186/s12859-020-03829-3 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Christophe Djemiel ◽

Samuel Dequiedt ◽

Battle Karimi ◽

Aurélien Cottin ◽

Thibault Girier ◽

...

Keyword(s):

High Throughput Sequencing ◽

Biological Database ◽

Rrna Genes ◽

23S Rrna ◽

Reference Database ◽

Rrna Gene ◽

Sequence Variant ◽

Sequencing Technologies ◽

23S Rrna Gene ◽

23S Rrna Genes

Abstract Background The ability to compare samples or studies easily using metabarcoding so as to better interpret microbial ecology results is an upcoming challenge. A growing number of metabarcoding pipelines are available, each with its own benefits and limitations. However, very few have been developed to offer the opportunity to characterize various microbial communities (e.g., archaea, bacteria, fungi, photosynthetic microeukaryotes) with the same tool. Results BIOCOM-PIPE is a flexible and independent suite of tools for processing data from high-throughput sequencing technologies, Roche 454 and Illumina platforms, and focused on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryote amplicons. Various original methods were implemented in BIOCOM-PIPE to (1) remove chimeras based on read abundance, (2) align sequences with structure-based alignments of RNA homologs using covariance models, and (3) a post-clustering tool (ReClustOR) to improve OTUs consistency based on a reference OTU database. The comparison with two other pipelines (FROGS and mothur) and Amplicon Sequence Variant definition highlighted that BIOCOM-PIPE was better at discriminating land use groups. Conclusions The BIOCOM-PIPE pipeline makes it possible to analyze 16S, 18S and 23S rRNA genes in the same packaged tool. The new post-clustering approach defines a biological database from previously analyzed samples and performs post-clustering of reads with this reference database by using open-reference clustering. This makes it easier to compare projects from various sequencing runs, and increased the congruence among results. For all users, the pipeline was developed to allow for adding or modifying the components, the databases and the bioinformatics tools easily, giving high modularity for each analysis.

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An unusual rRNA gene organization in Mycoplasma fermentans (incognitus strain)

Canadian Journal of Microbiology ◽

10.1139/m95-056 ◽

1995 ◽

Vol 41 (4-5) ◽

pp. 424-427 ◽

Cited By ~ 8

Author(s):

Y. Huang ◽

G. W. Stemke ◽

J. A. Robertson

Keyword(s):

Physical Map ◽

Gene Clusters ◽

Gene Organization ◽

Rrna Genes ◽

23S Rrna ◽

Rrna Gene ◽

Mycoplasma Fermentans ◽

23S Rrna Gene ◽

5S Rrna Genes ◽

23S Rrna Genes

The macro-restriction map of Mycoplasma fermentans (incognitus strain) was constructed and its rRNA genes were located on the map. It was found that this organism contains two sets of rRNA genes. The 16S and 23S rRNA genes were closely linked as two clusters. However, both 5S rRNA genes were separated from the 16S and 23S genes. The two 16S–23S rRNA gene clusters were arranged in an unusual tail to tail orientation.Key words: physical map, rRNA, Mycoplasma fermentans, genome, gene organization.

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