A critical review on the antimicrobial resistance, antibiotic residue and metagenomics‐assisted antimicrobial resistance gene detection in freshwater aquaculture environment

2021 ◽  
Author(s):  
Hemamalini Nallaiah ◽  
Shanmugam Seerappalli Aran ◽  
Kathirvelpandian Ayyathurai ◽  
Deepak Agarwal ◽  
Kaliyamurthi Venkatachalam ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Critical Review ◽  
Gene Detection ◽  
Freshwater Aquaculture ◽  
Antimicrobial Resistance Gene ◽  
Antibiotic Residue

scholarly journals Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates

2017 ◽  
Vol 55 (12) ◽  
pp. 3530-3543 ◽  
Author(s):  
Jamie K. Lemon ◽  
Pavel P. Khil ◽  
Karen M. Frank ◽  
John P. Dekker
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Plasmid Dna ◽  
Clinical Isolates ◽  
Clinical Microbiology Laboratory ◽  
Nanopore Sequencing ◽  
Gene Detection ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene

ABSTRACTRecent advances in nanopore sequencing technology have led to a substantial increase in throughput and sequence quality. Together, these improvements may permit real-time benchtop genomic sequencing and antimicrobial resistance gene detection in clinical isolates. In this study, we evaluated workflows and turnaround times for a benchtop long-read sequencing approach in the clinical microbiology laboratory using the Oxford Nanopore Technologies MinION sequencer. We performed genomic and plasmid sequencing of three clinical isolates with both MinION and Illumina MiSeq, using different library preparation methods (2D and rapid 1D) with the goal of antimicrobial resistance gene detection. We specifically evaluated the advantages of using plasmid DNA for sequencing and the value of supplementing MinION sequences with MiSeq reads for increasing assembly accuracy. Resequencing of three plasmids in a referenceKlebsiella pneumoniaeisolate demonstrated ∼99% accuracy of draft MinION-only assembly and >99.9% accuracy of assembly polished with MiSeq reads. Plasmid DNA sequencing of previously uncharacterized clinical extended-spectrum β-lactamase (ESBL)-producingEscherichia coliandK. pneumoniaeisolates using MinION allowed successful identification of antimicrobial resistance genes in the draft assembly corresponding to all classes of observed plasmid-based phenotypic resistance. Importantly, use of plasmid DNA enabled lower depth sequencing, and assemblies sufficient for full antimicrobial resistance gene annotation were obtained with as few as 2,000 to 5,000 reads, which could be acquired in 20 min of sequencing. With a MinION-only workflow that balances accuracy against turnaround time, full annotation of plasmid resistance gene content could be obtained in under 6 h from a subcultured isolate, less time than traditional phenotypic susceptibility testing.

Benchmarking of Antimicrobial Resistance Gene Detection Tools in Assembled Bacterial Whole Genomes

2021 ◽  
Author(s):  
Eman Abdelrazik ◽  
Mariam Oweda ◽  
Mohamed El-Hadidi
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Gene Detection ◽  
Antimicrobial Resistance Gene ◽  
Whole Genomes

scholarly journals Variations in bacterial community structure and antimicrobial resistance gene abundance in cattle manure and poultry litter

2021 ◽  
Vol 197 ◽  
pp. 111011
Author(s):  
Biyensa Gurmessa ◽  
Amanda J. Ashworth ◽  
Yichao Yang ◽  
Mary Savin ◽  
Philip A. Moore ◽  
...  
Keyword(s):  
Community Structure ◽  
Antimicrobial Resistance ◽  
Bacterial Community ◽  
Resistance Gene ◽  
Bacterial Community Structure ◽  
Poultry Litter ◽  
Cattle Manure ◽  
Gene Abundance ◽  
Antimicrobial Resistance Gene

scholarly journals Soil bacteriological pollution in pig farm vicinity: Assessment of bacterial dynamics and detection of antimicrobial resistance gene

2016 ◽  
Vol 10 (38) ◽  
pp. 1625-1636 ◽  
Author(s):  
Shirley-may Matjuda Dikonketso ◽  
Ayobami Aiyegoro Olayinka
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Bacterial Dynamics ◽  
Antimicrobial Resistance Gene ◽  
Pig Farm

scholarly journals Microarray-based detection of extended virulence and antimicrobial resistance gene profiles in phylogroup B2 Escherichia coli of human, meat and animal origin

2011 ◽  
Vol 60 (10) ◽  
pp. 1502-1511 ◽  
Author(s):  
Lotte Jakobsen ◽  
Philippe Garneau ◽  
Azra Kurbasic ◽  
Guillaume Bruant ◽  
Marc Stegger ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Animal Origin ◽  
Gene Profiles ◽  
Antimicrobial Resistance Gene

Author response for "Faecal microbiota and antimicrobial resistance gene profiles of healthy foals"

2020 ◽  
Author(s):  
Yuhong Liu ◽  
Kirsten E. Bailey ◽  
Michael Dyall‐Smith ◽  
Marc S. Marenda ◽  
Laura Y. Hardefeldt ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Author Response ◽  
Faecal Microbiota ◽  
Gene Profiles ◽  
Antimicrobial Resistance Gene

scholarly journals Faecal microbiota and antimicrobial resistance gene profiles of healthy foals

2020 ◽  
Author(s):  
Yuhong Liu ◽  
Kirsten E. Bailey ◽  
Michael Dyall‐Smith ◽  
Marc S. Marenda ◽  
Laura Y. Hardefeldt ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Faecal Microbiota ◽  
Gene Profiles ◽  
Antimicrobial Resistance Gene

scholarly journals Heterogeneity among Virulence and Antimicrobial Resistance Gene Profiles of Extraintestinal Escherichia coli Isolates of Animal and Human Origin

2004 ◽  
Vol 42 (12) ◽  
pp. 5444-5452 ◽  
Author(s):  
C. Maynard ◽  
S. Bekal ◽  
F. Sanschagrin ◽  
R. C. Levesque ◽  
R. Brousseau ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Human Origin ◽  
Gene Profiles ◽  
Antimicrobial Resistance Gene
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