scholarly journals Partial Sequencing of 16S rRNA Gene of Selected Staphylococcus aureus Isolates and its Antibiotic Resistance

2016 ◽  
Vol 39 (2) ◽  
pp. 67-74
Author(s):  
H. D. Kusumaningrum ◽  
L. Handayani ◽  
R. Novrianti
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Partial Sequencing

scholarly journals Effects of Antibiotics on the Bacterial Community, Metabolic Functions and Antibiotic Resistance Genes in Mariculture Sediments during Enrichment Culturing

2020 ◽  
Vol 8 (8) ◽  
pp. 604
Author(s):  
Meng-Qi Ye ◽  
Guan-Jun Chen ◽  
Zong-Jun Du
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Antibiotic Resistance Genes ◽  
Control Group ◽  
Rrna Gene ◽  
Metabolic Functions ◽  
Culture Dependent

The effect of antibiotics on the diversity and functioning of indigenous microorganisms in the environment has attracted much attention. In this study, effects of exposure to six different antibiotics on the bacterial community, metabolic functions and antibiotic resistance genes (ARGs) in marine sediments during enrichment culturing were investigated. Classical culture-dependent method and high-throughput 16S rRNA gene sequencing method were both applied. In the culture-dependent analysis, the obtained 1549 isolates belonged to four phyla (Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria) and 155 genera. Proteobacteria and Firmicutes were the dominant phyla. The diversity and abundance of obtained bacteria after antibiotic processing exhibited different degrees of decrease. Enrichment culturing for different time could also affect the bacterial community composition. Some genera of bacteria were not isolated in the control group, but they could be isolated in the antibiotic-treated groups. In high-throughput 16S rRNA gene amplicon sequencing analyses, all the effective reads were clustered into 2822 OTUs at 97% similarity cutoff; they were annotated to 49 phyla, 103 class, 220 orders, 347 families, 624 genera and 1122 species. An alpha diversity analysis indicated that the community diversity and richness decreased under antibiotic exposure. The changes at the genus level were much more obvious. Only 48 genera of 129 genera were shared by all the samples. A total of 29 genera which were not detected in the initial control sample could be detected in at least one antibiotic-treated group. SIMPER analysis showed that OTU2543 and OTU1450 were the most common taxa to the dissimilarity of bacterial community between antibiotic-treated groups and the control group. OTU2034 and OUT2543 were the most contributive taxa to dissimilarity of groups incubating for different time. Metabolism was the predominant bacterial function. A total of 30 ARGs were detected in the samples. This study mainly focused on the changes of microbiota under the selective pressure of antibiotics for different time and the results demonstrated that the antibiotic could affect the bacterial diversity and richness in the marine ecosystem.

scholarly journals Manure-based amendments influence surface-associated bacteria and markers of antibiotic resistance on radishes grown in different soil textures

2021 ◽  
Author(s):  
Giselle K. P. Guron ◽  
Chaoqi Chen ◽  
Pang Du ◽  
Amy Pruden ◽  
Monica A. Ponder
Keyword(s):  
Antibiotic Resistance ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dairy Cattle ◽  
Soil Texture ◽  
Antibiotic Use ◽  
Chemical Fertilizer ◽  
Plate Count ◽  
Rrna Gene ◽  
Greenhouse Study

A controlled greenhouse study was performed to determine the effect of manure or compost amendments, derived during or in absence of antibiotic treatment of beef and dairy cattle, on radish taproot-associated microbiota and indicators of antibiotic resistance when grown in different soil textures. Bacterial beta-diversity, determined by 16S rRNA gene amplicon sequencing, bifurcated according to soil texture (p<0.001, R=0.501). There was a striking cross-effect in which raw manure from antibiotic-treated and antibiotic-free beef and dairy cattle added to loamy sand (LS) elevated relative (16S rRNA gene-normalized) (by 0.9-1.9 log10) and absolute (per radish) (by 1.1-3.0 log10) abundances of intI1 (an integrase gene and indicator of mobile multi-antibiotic resistance) on radishes at harvest compared to chemical fertilizer only control conditions (p<0.001). Radishes tended to carry fewer copies of intI1 and sul1 when grown in silty clay loam than LS. Composting reduced relative abundance of intI1 on LS-grown radishes (0.6-2.4 log10 decrease vs corresponding raw manure; p<0.001). Effects of antibiotic use were rarely discernable. Heterotrophic plate count bacteria capable of growth on media containing tetracycline, vancomycin, sulfamethazine, or erythromycin tended to increase on radishes grown in turned composted antibiotic-treated dairy or beef control (no antibiotics) manures relative to the corresponding raw manure in LS (0.8-2.3 log10 increase; p<0.001), suggesting that composting sometimes enriches cultivable bacteria with phenotypic resistance. This study demonstrates that combined effects of soil texture and manure-based amendments influence the microbiota of radish surfaces and markers of antibiotic resistance illuminating future research directions for reducing agricultural sources of antibiotic resistance. Importance In working towards a comprehensive strategy to combat the spread of antibiotic resistance, potential farm-to-fork routes of dissemination are gaining attention. The effects of pre-harvest factors on the microbiota and corresponding antibiotic resistance indicators on the surfaces of produce commonly eaten raw is of special interest. Here we conducted a controlled greenhouse study, using radishes as a root vegetable grown in direct contact with soil, and compared the effects of manure-based soil amendments, antibiotic use in the cattle from which the manure was sourced, composting of the manure, and soil texture, with chemical fertilizer only as a control. We noted significant effects of amendment type and soil texture on the composition of the microbiota and genes used as indicators of antibiotic resistance on radish surfaces. The findings take a step towards identifying agricultural practices that aid in reducing carriage of antibiotic resistance and corresponding risks to consumers.

scholarly journals Methanotroph Diversity in Landfill Soil: Isolation of Novel Type I and Type II Methanotrophs Whose Presence Was Suggested by Culture-Independent 16S Ribosomal DNA Analysis

1999 ◽  
Vol 65 (11) ◽  
pp. 4887-4897 ◽  
Author(s):  
Mark G. Wise ◽  
J Vaun McArthur ◽  
Lawrence J. Shimkets
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ribosomal Dna ◽  
Rrna Gene ◽  
Type I ◽  
Type Ii ◽  
Partial Sequencing ◽  
16S Ribosomal Dna ◽  
Culture Independent ◽  
The 16S Rrna Gene

ABSTRACT The diversity of the methanotrophic community in mildly acidic landfill cover soil was assessed by three methods: two culture-independent molecular approaches and a traditional culture-based approach. For the first of the molecular studies, two primer pairs specific for the 16S rRNA gene of validly published type I (including the former type X) and type II methanotrophs were identified and tested. These primers were used to amplify directly extracted soil DNA, and the products were used to construct type I and type II clone libraries. The second molecular approach, based on denaturing gradient gel electrophoresis (DGGE), provided profiles of the methanotrophic community members as distinguished by sequence differences in variable region 3 of the 16S ribosomal DNA. For the culturing studies, an extinction-dilution technique was employed to isolate slow-growing but numerically dominant strains. The key variables of the series of enrichment conditions were initial pH (4.8 versus 6.8), air/CH4/CO2 headspace ratio (50:45:5 versus 90:9:1), and concentration of the medium (1× nitrate minimal salts [NMS] versus 0.2× NMS). Screening of the isolates showed that the nutrient-rich 1× NMS selected for type I methanotrophs, while the nutrient-poor 0.2× NMS tended to enrich for type II methanotrophs. Partial sequencing of the 16S rRNA gene from selected clones and isolates revealed some of the same novel sequence types. Phylogenetic analysis of the type I clone library suggested the presence of a new phylotype related to the Methylobacter-Methylomicrobiumgroup, and this was confirmed by isolating two members of this cluster. The type II clone library also suggested the existence of a novel group of related species distinct from the validly publishedMethylosinus and Methylocystis genera, and two members of this cluster were also successfully cultured. Partial sequencing of the pmoA gene, which codes for the 27-kDa polypeptide of the particulate methane monooxygenase, reaffirmed the phylogenetic placement of the four isolates. Finally, not all of the bands separated by DGGE could be accounted for by the clones and isolates. This polyphasic assessment of community structure demonstrates that much diversity among the obligate methane oxidizers has yet to be formally described.

Liver abscess due to Neisseria sicca after repeated transcatheter arterial embolization

2007 ◽  
Vol 56 (11) ◽  
pp. 1561-1562 ◽  
Author(s):  
Hsing-Chun Chung ◽  
Lee-Jene Teng ◽  
Po-Ren Hsueh
Keyword(s):  
Hepatocellular Carcinoma ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Liver Abscess ◽  
Transcatheter Arterial Embolization ◽  
Arterial Embolization ◽  
Rrna Gene ◽  
Biochemical Profile ◽  
Partial Sequencing ◽  
Neisseria Sicca

Neisseria sicca is rarely associated with clinical infections and to the authors' knowledge this organism has not been reported as a causative agent of infected biloma (liver abscess). A case of a diabetic man with infected biloma due to N. sicca after repeated transcatheter arterial embolization for hepatocellular carcinoma is reported. The patient was successfully treated with intravenous cefotaxime and metronidazole. The biochemical profile and 16S rRNA gene partial sequencing results of the isolate were in agreement with those of N. sicca.

scholarly journals Identification and Characterization of Staphylococcus aureus 16S rRNA gene isolated from different Food Specimens from South Indian Region

2020 ◽  
Vol 10 (5) ◽  
pp. 24-32
Author(s):  
Mondeddu Kiran Kumar ◽  
Charu Tyagi ◽  
Arjun Sahu ◽  
Nalini Desai ◽  
Jayanand Manjhi ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Infection Rate ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Food Borne

Staphylococcus aureus (S. aureus) associated food-borne diseases have global impact on human health. Genome wide analyses have shown that S. aureus contains specific endotoxin expressing gene and produce toxic proteins which is responsible for food contamination. Appropriate detection of pathogens is one of the major tool to avoid infection rate and reduce the health and socio-economic burden to human being. In addition, inappropriate handing the specimens, misdiagnosis and limited standard medical support could directly influence the infection rate. The objective of this study was to identify S. aureus from different food specimens from Hyderabad, India. A total of 70 random bacterial nutrient agar medium pure plates were made based on different morphological appearance of bacterial colonies. Preliminary identification of S. aureus based on standardized morphological method showed specific golden yellow colonies. Biochemical assay also verified bacterial specimens. Furthermore, molecular characterization was performed on the basis of polymerase chain reaction (PCR) and sequencing of 16S rRNA gene of S. aureus. Newly sequenced 16S rRNA gene sequences showed 100% homology to S. aureus, analyzed using NCBI-BLAST tool. The phylogenetic analysis and nucleotide base composition studies performed using 39 sequences of 16S rRNA gene from different isolates of Staphylococcus, including Staphylococcus aureus. For the purpose, 16S rRNA gene sequences were retrieved from the NCBI in FASTA format. The phylogenetic analysis was performed using Maximum Likelihood method and revealed the relationships and percent similarity of Staphylococcus aureus 16S rRNA gene. Keywords: Food-borne diseases; 16S rRNA gene; Maximum Likelihood; Phylogenetic analysis; Staphylococcus aureus.

scholarly journals The Role of Biofilm Formation in Antibiotic Resistance of Bacteria Isolated from Saliva of Patients with Dental Caries

2021 ◽  
pp. 40-49
Author(s):  
Merriam Ghadhanfar Alwan ◽  
Hadeel Adil Al Rubaye ◽  
Noor Adil Abood ◽  
Hind Tahseen Ibrahem ◽  
Hamiza Bt Hamidon ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Antibiotic Resistance ◽  
Dental Caries ◽  
Antimicrobial Resistance ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Enterococcus Faecalis ◽  
Biofilm Formation ◽  
Rrna Gene ◽  
Tissue Culture Plate

Objectives: This study aim to determine the bacterial diversity, biofilm forming ability and the antimicrobial resistance of bacteria isolated from saliva of patients with dental caries conditions with the using of 16S rRNA gene sequencing technique for identification of the most virulent isolates. Methods: Isolation and identification of microorganisms were done employing standard bacteriologic techniques, followed by biofilm detection using tissue culture plate method. The strong biofilm forming isolates were selected for antibiotic susceptibility test against selected antibiotics using disk diffusion technique. In order to identify the selected isolates. The genomic DNA obtained following the extraction process were used for the amplification of the bacterial 16S rRNA gene. Results: A total of 137 bacterial isolates were obtained and identified as belonging to 21 genera. Tissue culture plate (TCP) method were employed for screening the isolates according to its biofilm forming ability, its showed that 55 (40.1%) of the total isolates were strong, 57 (41.6%) were moderate and 25 (18.3%) were weak biofilm producers. The antimicrobial susceptibility test showed the multi antibiotics resistance of the strong biofilm former isolates to the conventional antibiotics. Enterococcus faecalis isolates showed the highest biofilm formation and antibiotic resistance. The 16S rRNA gene for two of these isolates have been amplified using PCR and the product sequenced, analyzed and registered in the National Center for Biotechnology Information (NCBI) as UKMS1 and UKMS2 and the accession numbers KX960104.1 and KX960105.1 respectively. Conclusion: The study has revealed that antimicrobial resistance of bacteria isolates from saliva of patients with dental caries conditions is associated with biofilm formation. Other uncommon pathogenic bacteria were also isolated in this study as a result of the use of non-selective enrichment medium for culturing. Enterococcus faecalis isolates indicated the highest biofilm formation and antibiotic resistance.

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