scholarly journals Antibiotic Resistance Genes in the Bacteriophage DNA Fraction of Human Fecal Samples

2013 ◽  
Vol 58 (1) ◽  
pp. 606-609 ◽  
Author(s):  
Pablo Quirós ◽  
Marta Colomer-Lluch ◽  
Alexandre Martínez-Castillo ◽  
Elisenda Miró ◽  
Marc Argente ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Real Time ◽  
Quantitative Pcr ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Fecal Samples ◽  
Real Time Quantitative Pcr ◽  
Healthy Humans ◽  
Phage Dna

ABSTRACTA group of antibiotic resistance genes (ARGs) (blaTEM,blaCTX-M-1,mecA,armA,qnrA, andqnrS) were analyzed by real-time quantitative PCR (qPCR) in bacteriophage DNA isolated from feces from 80 healthy humans. Seventy-seven percent of the samples were positive in phage DNA for one or more ARGs.blaTEM,qnrA, and,blaCTX-M-1were the most abundant, andarmA,qnrS, andmecAwere less prevalent. Free bacteriophages carrying ARGs may contribute to the mobilization of ARGs in intra- and extraintestinal environments.

scholarly journals Bacteriophages Carrying Antibiotic Resistance Genes in Fecal Waste from Cattle, Pigs, and Poultry

2011 ◽  
Vol 55 (10) ◽  
pp. 4908-4911 ◽  
Author(s):  
Marta Colomer-Lluch ◽  
Lejla Imamovic ◽  
Juan Jofre ◽  
Maite Muniesa
Keyword(s):  
Antibiotic Resistance ◽  
Quantitative Pcr ◽  
Resistance Genes ◽  
Horizontal Transfer ◽  
Antibiotic Resistance Genes ◽  
Gene Copies ◽  
Phage Dna ◽  
Fecal Waste

ABSTRACTThis study evaluates the occurrence of bacteriophages carrying antibiotic resistance genes in animal environments.blaTEM,blaCTX-M(clusters 1 and 9), andmecAwere quantified by quantitative PCR in 71 phage DNA samples from pigs, poultry, and cattle fecal wastes. Densities of 3 to 4 log10gene copies (GC) ofblaTEM, 2 to 3 log10GC ofblaCTX-M, and 1 to 3 log10GC ofmecAper milliliter or gram of sample were detected, suggesting that bacteriophages can be environmental vectors for the horizontal transfer of antibiotic resistance genes.

scholarly journals Identification, Detection, and Enumeration of Human Bifidobacterium Species by PCR Targeting the Transaldolase Gene

2002 ◽  
Vol 68 (5) ◽  
pp. 2420-2427 ◽  
Author(s):  
Teresa Requena ◽  
Jeremy Burton ◽  
Takahiro Matsuki ◽  
Karen Munro ◽  
Mary Alice Simon ◽  
...  
Keyword(s):  
Real Time ◽  
16S Rdna ◽  
Quantitative Pcr ◽  
Gene Sequence ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bifidobacterium Longum ◽  
Bifidobacterium Adolescentis ◽  
Fecal Samples ◽  
Real Time Quantitative Pcr ◽  
Pcr Targeting

ABSTRACT Methods that enabled the identification, detection, and enumeration of Bifidobacterium species by PCR targeting the transaldolase gene were tested. Bifidobacterial species isolated from the feces of human adults and babies were identified by PCR amplification of a 301-bp transaldolase gene sequence and comparison of the relative migrations of the DNA fragments in denaturing gradient gel electrophoresis (DGGE). Two subtypes of Bifidobacterium longum, five subtypes of Bifidobacterium adolescentis, and two subtypes of Bifidobacterium pseudocatenulatum could be differentiated using PCR-DGGE. Bifidobacterium angulatum and B. catenulatum type cultures could not be differentiated from each other. Bifidobacterial species were also detected directly in fecal samples by this combination of PCR and DGGE. The number of species detected was less than that detected by PCR using species-specific primers targeting 16S ribosomal DNA (rDNA). Real-time quantitative PCR targeting a 110-bp transaldolase gene sequence was used to enumerate bifidobacteria in fecal samples. Real-time quantitative PCR measurements of bifidobacteria in fecal samples from adults correlated well with results obtained by culture when either a 16S rDNA sequence or the transaldolase gene sequence was targeted. In the case of samples from infants, 16S rDNA-targeted PCR was superior to PCR targeting the transaldolase gene for the quantification of bifidobacterial populations.

scholarly journals Evaluation of residual antibacterial potency in antibiotic production wastewater using a real-time quantitative method

2015 ◽  
Vol 17 (11) ◽  
pp. 1923-1929 ◽  
Author(s):  
Hong Zhang ◽  
Yu Zhang ◽  
Min Yang ◽  
Miaomiao Liu
Keyword(s):  
Antibiotic Resistance ◽  
Real Time ◽  
Environmental Impacts ◽  
Resistance Genes ◽  
Quantitative Method ◽  
Antibiotic Production ◽  
Antibiotic Resistance Genes ◽  
Antibiotic Activity ◽  
Wastewater Discharge ◽  
Related Substances

While antibiotic pollution has attracted considerable attention due to its potential in promoting the dissemination of antibiotic resistance genes in the environment, the antibiotic activity of their related substances has been neglected, which may underestimate the environmental impacts of antibiotic wastewater discharge.

scholarly journals The Transferable Resistome of Produce

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Khald Blau ◽  
Antje Bettermann ◽  
Sven Jechalke ◽  
Eva Fornefeld ◽  
Yann Vanrobaeys ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Real Time ◽  
Resistance Genes ◽  
Real Time Pcr ◽  
Direct Detection ◽  
Blot Hybridization ◽  
Antibiotic Resistance Genes ◽  
Human Pathogens ◽  
Content Type ◽  
E Coli

ABSTRACTProduce is increasingly recognized as a reservoir of human pathogens and transferable antibiotic resistance genes. This study aimed to explore methods to characterize the transferable resistome of bacteria associated with produce. Mixed salad, arugula, and cilantro purchased from supermarkets in Germany were analyzed by means of cultivation- and DNA-based methods. Before and after a nonselective enrichment step, tetracycline (TET)-resistantEscherichia coliwere isolated and plasmids conferring TET resistance were captured by exogenous plasmid isolation. TET-resistantE. coliisolates, transconjugants, and total community DNA (TC-DNA) from the microbial fraction detached from leaves or after enrichment were analyzed for the presence of resistance genes, class 1 integrons, and various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time PCR primers were developed for IncI and IncF plasmids. TET-resistantE. coliisolated from arugula and cilantro carried IncF, IncI1, IncN, IncHI1, IncU, and IncX1 plasmids. Three isolates from cilantro were positive for IncN plasmids andblaCTX-M-1. From mixed salad and cilantro, IncF, IncI1, and IncP-1β plasmids were captured exogenously. Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these plasmids became detectable in DNA extracted from enrichment cultures. This confirms that cultivation-independent DNA-based methods are not always sufficiently sensitive to detect the transferable resistome in the rare microbiome. In summary, this study showed that an impressive diversity of self-transmissible multiple resistance plasmids was detected in bacteria associated with produce that is consumed raw, and exogenous capturing intoE. colisuggests that they could transfer to gut bacteria as well.IMPORTANCEProduce is one of the most popular food commodities. Unfortunately, leafy greens can be a reservoir of transferable antibiotic resistance genes. We found that IncF and IncI plasmids were the most prevalent plasmid types inE. coliisolates from produce. This study highlights the importance of the rare microbiome associated with produce as a source of antibiotic resistance genes that might escape cultivation-independent detection, yet may be transferred to human pathogens or commensals.

Real time quantitative PCR of Bacteroides vulgatus and Escherichia coli in mucosal samples from healthy humans and patients with IBD

2000 ◽  
Vol 118 (4) ◽  
pp. A1347
Author(s):  
Xander W. Huijsdens ◽  
Ronald K. Linskens ◽  
Mariette Mak ◽  
Jeroen Stoof ◽  
Paul Hm Savelkoul ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Real Time ◽  
Quantitative Pcr ◽  
Real Time Quantitative Pcr ◽  
Healthy Humans

scholarly journals Development of cpn60-Based Real-Time Quantitative PCR Assays for the Detection of 14 Campylobacter Species and Application to Screening of Canine Fecal Samples

2009 ◽  
Vol 75 (10) ◽  
pp. 3055-3061 ◽  
Author(s):  
Bonnie Chaban ◽  
Kristyna M. Musil ◽  
Chelsea G. Himsworth ◽  
Janet E. Hill
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Animal Health ◽  
Independent Manner ◽  
Fecal Samples ◽  
Complex Samples ◽  
Real Time Quantitative Pcr ◽  
Culture Independent ◽  
Biochemical Identification ◽  
Species Specific

ABSTRACT Campylobacter species are important organisms in both human and animal health. The identification of Campylobacter currently requires the growth of organisms from complex samples and biochemical identification. In many cases, the condition of the sample being tested and/or the fastidious nature of many Campylobacter species has limited the detection of campylobacters in a laboratory setting. To address this, we have designed a set of real-time quantitative PCR (qPCR) assays to detect and quantify 14 Campylobacter species, C. coli, C. concisus, C. curvus, C. fetus, C. gracilis, C. helveticus, C. hyointestinalis, C. jejuni, C. lari, C. mucosalis, C. rectus, C. showae, C. sputorum, and C. upsaliensis, directly from DNA extracted from feces. By use of a region of the cpn60 (also known as hsp60 or groEL) gene, which encodes the universally conserved 60-kDa chaperonin, species-specific assays were designed and validated. These assays were then employed to determine the prevalence of Campylobacter species in fecal samples from dogs. Fecal samples were found to contain detectable and quantifiable levels of C. fetus, C. gracilis, C. helveticus, C. jejuni, C. showae, and C. upsaliensis, with the majority of samples containing multiple Campylobacter species. This study represents the first report of C. fetus, C. gracilis, C. mucosalis, and C. showae detection in dogs and implicates dogs as a reservoir for these species. The qPCR assays described offer investigators a new tool to study many Campylobacter species in a culture-independent manner.

scholarly journals Quantification of Shiga Toxin-Converting Bacteriophages in Wastewater and in Fecal Samples by Real-Time Quantitative PCR

2010 ◽  
Vol 76 (17) ◽  
pp. 5693-5701 ◽  
Author(s):  
Lejla Imamovic ◽  
Elisenda Ballesté ◽  
Juan Jofre ◽  
Maite Muniesa
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Shiga Toxin ◽  
Enteric Bacteria ◽  
Fecal Samples ◽  
Urban Sewage ◽  
Real Time Quantitative Pcr ◽  
Gene Copies ◽  
Animal Wastewater ◽  
Wastewater Samples

ABSTRACT Shiga toxin-converting bacteriophages (Stx phages) are involved in the pathogenicity of some enteric bacteria, such as Escherichia coli O157:H7. Stx phages are released from their bacterial hosts after lytic induction and remain free in the environment. Samples were analyzed for the presence of free Stx phages by an experimental approach based on the use of real-time quantitative PCR (qPCR), which enables stx to be detected in the DNA from the viral fraction of each sample. A total of 150 samples, including urban raw sewage samples, wastewater samples with fecal contamination from cattle, pigs, and poultry, and fecal samples from humans and diverse animals, were used in this study. Stx phages were detected in 70.0% of urban sewage samples (10 to 103 gene copies [GC] per ml) and in 94.0% of animal wastewater samples of several origins (10 to 1010 GC per ml). Eighty-nine percent of cattle fecal samples were positive for Stx phages (10 to 105 GC per g of sample), as were 31.8% of other fecal samples of various origins (10 to 104 GC per g of sample). The stx 2 genes and stx 2 variants were detected in the viral fraction of some of the samples after sequencing of stx 2 fragments amplified by conventional PCR. The occurrence and abundance of Stx phages in the extraintestinal environment confirm the role of Stx phages as a reservoir of stx in the environment.

scholarly journals Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages are not vectors of antibiotic resistance genes

2021 ◽  
Author(s):  
Maud Billaud ◽  
Quentin Lamy-Besnier ◽  
Julien Lossouarn ◽  
Elisabeth Moncaut ◽  
Moira B. Dion ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Genetic Maps ◽  
Human Pathogens ◽  
Bacterial Dna ◽  
Fecal Samples ◽  
Viral Particles ◽  
First Time ◽  
Animal Reservoirs

Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles.

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