Diversity of Domain V of 23S rRNA Gene Sequence in Different Enterococcus Species

The highly conserved central loop of domain V of 23S RNA (nucleotides 2042 to 2628; Escherichia coli numbering) is implicated in peptidyltransferase activity and represents one of the target sites for macrolide, lincosamide, and streptogramin B antibiotics. DNA encoding domain V (590 bp) of several species ofEnterococcus was amplified by PCR. Twenty enterococcal isolates were tested, including Enterococcus faecium (six isolates), Enterococcus faecalis, Enterococcus avium, Enterococcus durans, Enterococcus gallinarum, Enterococcus casseliflavus (two isolates of each), and Enterococcus raffinosus, Enterococcus mundtii, Enterococcus malodoratus, andEnterococcus hirae (one isolate of each). For all isolates, species identification by biochemical testing was corroborated by 16S rRNA gene sequencing. The sequence of domain V of the 23S rRNA gene from E. faecium and E. faecalis differed from those of all other enterococci. The domain V sequences of E. durans and E. hirae were identical. This was also true for E. gallinarum and E. casseliflavus. E. avium differed from E. casseliflavus by 23 bases, from E. durans by 16 bases, and from E. malodoratus by 2 bases. E. avium differed fromE. raffinosus by one base. Despite the fact that domain V is considered to be highly conserved, substantial differences were identified between several enterococcal species.

Download Full-text

Characterization of Lactic Bacteria Isolated from Raw Milk and Their Antibacterial Activity against Bacteria as the Cause of Clinical Bovine Mastitis

Journal of Food Quality ◽

10.1155/2021/6466645 ◽

2021 ◽

Vol 2021 ◽

pp. 1-8

Author(s):

Nada K. Alharbi ◽

Albandary Nasser Alsaloom

Keyword(s):

Bovine Mastitis ◽

16S Rrna Gene Sequencing ◽

Raw Milk ◽

Antibacterial Activities ◽

Antagonistic Activity ◽

23S Rrna ◽

Rrna Gene ◽

Technological Properties ◽

23S Rrna Gene ◽

Rrna Gene Sequencing

The objectives of this study were the selection of lactic acid bacteria (LAB) isolated from raw milk and studying their technological properties and antibacterial activities against bacteria as the cause of cattle mastitis. Biochemical and molecular identification using 16S–23S rRNA gene spacer analysis and 16S rRNA gene sequencing highlighted the presence of three species: Lactiplantibacillus plantarum, Lactococcus lactis, and Levilactobacillus brevis. The enzymatic characterization followed by the determination of technofunctional properties showed that LAB strains did not exhibit any hemolytic effect and were able to produce protease and lipase enzymes. Isolates showed very high antagonistic activity against Gram-positive and Gram-negative bacteria by producing H2O2, bacteriocin(s), and organic acid(s). APIZYM micromethod demonstrated that all selected strains are capable of producing valine arylamidase, cystine arylamidase, N-acetyl-β-glucosaminidase, and ᾳ-mannosidase. The antibiotic susceptibility assay showed that all selected strains were sensible to the majority of tested antibiotics. Based on these results, it can be concluded that the technological properties of the selected LAB allow considering their industrial use in order to formulate bioactive functional foods or drug(s).

Download Full-text

Drug Resistance Mechanisms ofMycoplasma pneumoniaeto Macrolide Antibiotics

BioMed Research International ◽

10.1155/2014/320801 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

Xijie Liu ◽

Yue Jiang ◽

Xiaogeng Chen ◽

Jing Li ◽

Dawei Shi ◽

...

Keyword(s):

Drug Resistance ◽

Resistance Mechanisms ◽

23S Rrna ◽

Macrolide Antibiotics ◽

Rrna Gene ◽

Site Mutation ◽

23S Rrna Gene ◽

Resistant Strains ◽

Domain V ◽

The 16S Rrna Gene

Throat swabs from children with suspectedMycoplasma pneumoniae(M. pneumoniae) infection were cultured for the presence ofM. pneumoniaeand its species specificity using the 16S rRNA gene. Seventy-sixM. pneumoniaestrains isolated from 580 swabs showed that 70 were erythromycin resistant with minimum inhibitory concentrations (MIC) around 32–512 mg/L. FiftyM. pneumoniaestrains (46 resistant, 4 sensitive) were tested for sensitivity to tetracycline, ciprofloxacin, and gentamicin. Tetracycline and ciprofloxacin had some effect, and gentamicin had an effect on the majority ofM. pneumoniaestrains. Domains II and V of the 23S rRNA gene and the ribosomal protein L4 and L22 genes, both of which are considered to be associated with macrolide resistance, were sequenced and the sequences were compared with the corresponding sequences in M129 registered with NCBI and the FH strain. The 70 resistant strains all showed a 2063 or 2064 site mutation in domain V of the 23S rRNA but no mutations in domain II. Site mutations of L4 or L22 can be observed in either resistant or sensitive strains, although it is not known whether this is associated with drug resistance.

Download Full-text

Identification of a Novel Mutation Affecting Domain V of the 23S rRNA Gene inHelicobacter pylori

Helicobacter ◽

10.1111/j.1083-4389.2004.00267.x ◽

2004 ◽

Vol 9 (5) ◽

pp. 396-399 ◽

Cited By ~ 23

Author(s):

Sonia Toracchio ◽

Gitana M. Aceto ◽

Renato Mariani-Costantini ◽

Pasquale Battista ◽

Leonardo Marzio

Keyword(s):

Novel Mutation ◽

23S Rrna ◽

Rrna Gene ◽

23S Rrna Gene ◽

Domain V

Download Full-text

Community structure of microbes in natural environments

10.1093/oso/9780198789406.003.0004 ◽

2018 ◽

Author(s):

David L. Kirchman

Keyword(s):

Community Structure ◽

16S Rrna ◽

Deep Ocean ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Natural Environments ◽

Viral Lysis ◽

Structure Information ◽

Rrna Gene Sequencing ◽

Biochemical Testing

Community structure refers to the taxonomic types of microbes and their relative abundance in an environment. This chapter focuses on bacteria with a few words about fungi; protists and viruses are discussed in Chapters 9 and 10. Traditional methods for identifying microbes rely on biochemical testing of phenotype observable in the laboratory. Even for cultivated microbes and larger organisms, the traditional, phenotype approach has been replaced by comparing sequences of specific genes, those for 16S rRNA (archaea and bacteria) or 18S rRNA (microbial eukaryotes). Cultivation-independent approaches based on 16S rRNA gene sequencing have revealed that natural microbial communities have a few abundant types and many rare ones. These organisms differ substantially from those that can be grown in the laboratory using cultivation-dependent approaches. The abundant types of microbes found in soils, freshwater lakes, and oceans all differ. Once thought to be confined to extreme habitats, Archaea are now known to occur everywhere, but are particularly abundant in the deep ocean, where they make up as much as 50% of the total microbial abundance. Dispersal of bacteria and other small microbes is thought to be easy, leading to the Bass Becking hypothesis that “everything is everywhere, but the environment selects.” Among several factors known to affect community structure, salinity and temperature are very important, as is pH especially in soils. In addition to bottom-up factors, both top-down factors, grazing and viral lysis, also shape community structure. According to the Kill the Winner hypothesis, viruses select for fast-growing types, allowing slower growing defensive specialists to survive. Cultivation-independent approaches indicate that fungi are more diverse than previously appreciated, but they are less diverse than bacteria, especially in aquatic habitats. The community structure of fungi is affected by many of the same factors shaping bacterial community structure, but the dispersal of fungi is more limited than that of bacteria. The chapter ends with a discussion about the relationship between community structure and biogeochemical processes. The value of community structure information varies with the process and the degree of metabolic redundancy among the community members for the process.

Download Full-text

Emergence of Macrolide-Resistant Mycoplasma pneumoniae with a 23S rRNA Gene Mutation

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.49.6.2302-2306.2005 ◽

2005 ◽

Vol 49 (6) ◽

pp. 2302-2306 ◽

Cited By ~ 90

Author(s):

Miyuki Morozumi ◽

Keiko Hasegawa ◽

Reiko Kobayashi ◽

Nagako Inoue ◽

Satoshi Iwata ◽

...

Keyword(s):

Mycoplasma Pneumoniae ◽

Acute Bronchitis ◽

23S Rrna ◽

Rrna Gene ◽

Microdilution Method ◽

23S Rrna Gene ◽

Pediatric Outpatients ◽

Tract Infections ◽

Domain V ◽

Epidemiol Infect

ABSTRACT A total of 195 Mycoplasma pneumoniae strains were isolated from 2,462 clinical specimens collected between April 2002 and March 2004 from pediatric outpatients with respiratory tract infections. Susceptibilities to six macrolide antibiotics (ML), telithromycin, minocycline, levofloxacin, and sitafloxacin were determined by the microdilution method using PPLO broth. A total of 183 M. pneumoniae isolates were susceptible to all agents and had excellent MIC90s in the following order: 0.00195 μg/ml for azithromycin and telithromycin, 0.0078 μg/ml for clarithromycin, 0.0156 μg/ml for erythromycin, 0.0625 μg/ml for sitafloxacin, 0.5 μg/ml for minocycline, and 1 μg/ml for levofloxacin. Notably, 12 ML-resistant M. pneumoniae strains were isolated from patients with pneumonia (10 strains) or acute bronchitis (2 strains). These strains showed resistance to ML with MICs of ≥1 μg/ml, except to rokitamycin. Transition mutations of A2063G or A2064G, which correspond to A2058 and A2059 in Escherichia coli, in domain V on the 23S rRNA gene in 11 ML-resistant strains were identified. By pulsed-field gel electrophoresis typing, these strains were classified into groups I and Vb, as described previously (A. Cousin-Allery, A. Charron, B. D. Barbeyrac, G. Fremy, J. S. Jensen, H. Renaudin, and C. Bebear, Epidemiol. Infect. 124:103-111, 2000). These findings suggest that excessive usage of MLs acts as a trigger to select mutations on the corresponding 23S rRNA gene with the resultant occurrence of ML-resistant M. pneumoniae. Monitoring ML susceptibilities for M. pneumoniae is necessary in the future.

Download Full-text

Novel Genotypes in Helicobacter pylori Involving Domain V of the 23S rRNA Gene

Helicobacter ◽

10.1111/j.1523-5378.2007.00506.x ◽

2007 ◽

Vol 12 (5) ◽

pp. 505-509 ◽

Cited By ~ 26

Author(s):

Leonardo Garrido ◽

Hector Toledo

Keyword(s):

Helicobacter Pylori ◽

23S Rrna ◽

Rrna Gene ◽

23S Rrna Gene ◽

Domain V

Download Full-text

Actinomyces dentalis sp. nov., from a human dental abscess

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63376-0 ◽

2005 ◽

Vol 55 (1) ◽

pp. 427-431 ◽

Cited By ~ 22

Author(s):

Val Hall ◽

Matthew D. Collins ◽

Paul A. Lawson ◽

Enevold Falsen ◽

Brian I. Duerden

Keyword(s):

Novel Species ◽

Sequence Divergence ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Dental Abscess ◽

Unknown Species ◽

Sequencing Studies ◽

Molecular Phylogenetic ◽

Rrna Gene Sequencing ◽

Biochemical Testing

A previously undescribed filamentous, beaded, Gram-positive, rod-shaped bacterium was isolated from pus of a human dental abscess. Based on its cellular morphology and the results of biochemical testing the organism was tentatively identified as a member of the genus Actinomyces, but it did not correspond to any currently recognized species of this genus. Comparative 16S rRNA gene sequencing studies showed the bacterium represents a distinct subline within the genus Actinomyces, clustering within a group of species that includes Actinomyces bovis, the type species of the genus. Sequence divergence values of >8 % with other recognized species within this phylogenetic group clearly demonstrated that the organism represents a hitherto unknown species. Based on biochemical and molecular phylogenetic evidence, it is proposed that the unidentified organism recovered from a dental abscess be classified as a novel species, Actinomyces dentalis sp. nov. The type strain is R18165T (=CCUG 48064T=CIP 108337T).

Download Full-text

Infective Arthritis: Bacterial 23S rRNA Gene Sequencing as a Supplementary Diagnostic Method

The Open Microbiology Journal ◽

10.2174/1874285800802010085 ◽

2008 ◽

Vol 2 (1) ◽

pp. 85-88 ◽

Cited By ~ 5

Author(s):

Claus Moser ◽

Keld Andresen ◽

Anne Kjerulf ◽

Suheil Salamon ◽

Michael Kemp ◽

...

Keyword(s):

Diagnostic Method ◽

Gene Sequencing ◽

23S Rrna ◽

Rrna Gene ◽

23S Rrna Gene ◽

Rrna Gene Sequencing ◽

Infective Arthritis

Download Full-text

Clinical-Use-Associated Decrease in Susceptibility of Vancomycin-Resistant Enterococcus faecium to Linezolid: a Comparison with Quinupristin-Dalfopristin

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.48.9.3583-3585.2004 ◽

2004 ◽

Vol 48 (9) ◽

pp. 3583-3585 ◽

Cited By ~ 39

Author(s):

Issam I. Raad ◽

Hend A. Hanna ◽

Ray Y. Hachem ◽

Tanya Dvorak ◽

Rebecca B. Arbuckle ◽

...

Keyword(s):

Gene Mutation ◽

Enterococcus Faecium ◽

23S Rrna ◽

Rrna Gene ◽

Clinical Use ◽

Vancomycin Resistant Enterococcus ◽

23S Rrna Gene ◽

Vancomycin Resistant ◽

Domain V

ABSTRACT The susceptibility of 135 vancomycin-resistant Enterococcus faecium bacteremic isolates to linezolid and quinupristin-dalfopristin was determined. All were susceptible to linezolid, while 88% were susceptible to quinupristin-dalfopristin prior to the clinical use of the drugs at our hospital. More than 6 months after their clinical use, a decrease in susceptibility was noted for only linezolid at 83%. This was related in part to a single G2576U gene mutation in domain V of the 23S rRNA gene.

Download Full-text