A Comparison of Methods for the Extraction of Plasmids Capable of Conferring Antibiotic Resistance in a Human Pathogen From Complex Broiler Cecal Samples

Frontiers in Microbiology
Sarah DelaneyFiona Walsh

Abstract

The direct extraction of plasmid DNA containing antibiotic resistance genes from complex samples is imperative when studying plasmid-mediated antibiotic resistance from a One Health perspective, in order to obtain a wide representation of all the resistance plasmids present in these microbial communities. There are also relatively few bacterial species from natural environments which can be cultured in vitro. Extracting plasmids from the cultivable fraction of these complex microbiomes may only represent a fraction of the total antibiotic resistance plasmids present. We compared different methods of plasmid extraction from broiler cecal samples, whose resistance could be expressed in a human pathogen-Escherichia coli. We found that kits designed for DNA extraction from complex samples such as soil or feces did not extract intact plasmid DNA. Commercial kits specific for plasmid extraction were also generally unsuccessful, most likely due to the complexity of our sample and intended use of the kits with bacterial culture. An alkaline lysis method specific for plasmid extraction was ineffective, even with further optimization. Transposon-aided capture of plasmids (TRACA) allowed for the acquirement of a small range of resistance ...Continue Reading

References

Nov 24, 1979·Nucleic Acids Research·H C Birnboim, J Doly
Jul 1, 1996·Applied and Environmental Microbiology·A GötzK Smalla
Sep 3, 2005·Nature Reviews. Microbiology·Søren J SørensenStefan Wuertz
Sep 3, 2005·Nature Reviews. Microbiology·Christopher M Thomas, Kaare M Nielsen
Nov 28, 2006·Nature Methods·Brian V Jones, Julian R Marchesi
Dec 17, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sébastien HalaryEric Bapteste
Dec 2, 2011·Molecular Biology and Evolution·Manu TamminenMarco Fondi
Jun 5, 2012·Journal of Bacteriology·Eric J Stewart
Feb 15, 2013·The ISME Journal·Vladimir SentchiloJan R van der Meer
Sep 24, 2013·Journal of Microbiological Methods·Aya Brown KavItzhak Mizrahi
Aug 15, 2014·PloS One·Anders NormanSøren Johannes Sørensen
Oct 4, 2014·Current Opinion in Microbiology·Julie Ann PerryGerard D Wright
Feb 7, 2015·Frontiers in Microbiology·Tue S JørgensenLars H Hansen
Mar 3, 2015·Nature Reviews. Microbiology·Michael D J Lynch, Josh D Neufeld
Jun 16, 2015·Frontiers in Microbiology·Julián R DibFriedhelm Meinhardt
Jun 25, 2015·Microbiology Spectrum·María de ToroFernando De La Cruz
Nov 28, 2017·Microbial Genomics·Sergio Arredondo-AlonsoAnita C Schürch

❮ Previous
Next ❯

Citations

Jan 12, 2020·Topics in Current Chemistry·José Raúl Sosa-AcostaAlicia M Díaz-García
Jul 17, 2020·FEMS Microbiology Reviews·Christina C SaakRachel J Dutton
Apr 10, 2021·Frontiers in Microbiology·Alla L Lapidus, Anton I Korobeynikov
Apr 14, 2021·Nature Reviews. Microbiology·Ilana Lauren Brito

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
MDA

Software Mentioned

TRACA
runVIEW

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.