scholarly journals Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements

2018 ◽  
Vol 94 (9) ◽  
Author(s):  
Robert D Stedtfeld ◽  
Xueping Guo ◽  
Tiffany M Stedtfeld ◽  
Hongjie Sheng ◽  
Maggie R Williams ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
Design Tool ◽  
Environmental Matrices ◽  
Sequence Coverage ◽  
Genetic Elements ◽  
Qpcr Array ◽  
Primer Sets

ABSTRACT The high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic elements to be targeted. Results of validating the updated array with a mock community of strains resulted in over 98% of tested instances incurring true positive/negative calls. Common queries related to sensitivity, quantification and conventional data analysis (e.g. Ct cutoff value, and estimated genomic copies without standard curves) were also explored. A combined list of new and previously used primer sets is provided with a recommended set based on redesign of primer sets and results of validation.

scholarly journals Sludge bio-drying: Effective to reduce both antibiotic resistance genes and mobile genetic elements

2016 ◽  
Vol 106 ◽  
pp. 62-70 ◽  
Author(s):  
Junya Zhang ◽  
Qianwen Sui ◽  
Juan Tong ◽  
Chulu Buhe ◽  
Rui Wang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
Genetic Elements

scholarly journals Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements

2018 ◽  
Author(s):  
Jean Cury ◽  
Pedro H. Oliveira ◽  
Fernando de la Cruz ◽  
Eduardo P.C. Rocha
Keyword(s):  
Antibiotic Resistance ◽  
Horizontal Gene Transfer ◽  
Host Range ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
The Other ◽  
Microbial Populations ◽  
Dna Repeats ◽  
Genetic Elements ◽  
Integrative And Conjugative Elements

AbstractSelf-transmissible mobile genetic elements drive horizontal gene transfer between prokaryotes. Some of these elements integrate in the chromosome, whereas others replicate autonomously as plasmids. Recent works showed the existence of few differences, and occasional interconversion, between the two types of elements. Here, we enquired on why evolutionary processes have maintained the two types of mobile genetic elements by comparing integrative and conjugative elements (ICE) with extrachromosomal ones (conjugative plasmids) of the highly abundant MPFT conjugative type. We observed that plasmids encode more replicases, partition systems, and antibiotic resistance genes, whereas ICEs encode more integrases and metabolism-associated genes. ICEs and plasmids have similar average sizes, but plasmids are much more variable, have more DNA repeats, and exchange genes more frequently. On the other hand, we found that ICEs are more frequently transferred between distant taxa. We propose a model where differential plasticity and transmissibility range explain the co-occurrence of integrative and extra-chromosomal elements in microbial populations. In particular, the conversion from ICE to plasmid allows ICE to be more plastic, while the conversion from plasmid to ICE allows the expansion of the element‘s host range.

scholarly journals The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance

2016 ◽  
Author(s):  
Katherine H Tanaka ◽  
Antony T Vincent ◽  
Mélanie V Trudel ◽  
Valérie E Paquet ◽  
Michel Frenette ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
Aeromonas Salmonicida ◽  
Genomic Plasticity ◽  
Genetic Elements ◽  
Resistance Patterns ◽  
Antibiotic Resistance Patterns

Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible existence of alternative forms of pAsa4, a large plasmid found in A. salmonicida subsp. salmonicida and bearing multiple antibiotic resistance genes. The present study reveals the existence of two newly detected pAsa4 variants, pAsa4b and pAsa4c. We present the extensive characterization of the genomic architecture, the mobile genetic elements and the antimicrobial resistances genes of these plasmids in addition to the reference pAsa4 from the strain A449. The analysis showed differences between the three architectures with consequences on the content of resistance genes. The genomic plasticity of the three pAsa4 variants could be partially explained by the action of mobile genetic elements like insertion sequences. Isolates from Canada and Europe that bore similar antibiotic resistance patterns than pAsa4-bearing strains were genotyped and specific pAsa4 variants could be attributed to phenotypic profiles. pAsa4 and pAsa4c were found in Europe, while pAsa4b was found in Canada. The plasticity of pAsa4 variants related to the acquisition of antibiotic resistance indicates that these plasmids may pose a threat in terms of the dissemination of antimicrobial-resistant A.salmonicida subsp. salmonicida bacteria.

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