Journal ArticleDOI
Genomic analysis of methicillin-resistant Staphylococcus aureus isolated from poultry and occupational farm workers in Umgungundlovu District, South Africa.
Daniel G. Amoako,Anou M. Somboro,Akebe Luther King Abia,Mushal Allam,Arshad Ismail,Linda A. Bester,Sabiha Y. Essack +6 more
TLDR
The need to establish appropriate control measures to curb the spread of MDR-MRSA in the food chain is suggested and a human-associated clone, ST612-CC8-t1257-SCCmec_IVd (2B), previously reported in South Africa is suggested.About:
This article is published in Science of The Total Environment.The article was published on 2019-03-09. It has received 29 citations till now. The article focuses on the topics: SCCmec & Methicillin-resistant Staphylococcus aureus.read more
Citations
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SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Journal ArticleDOI
Molecular epidemiology and mechanisms of antibiotic resistance in Enterococcus spp., Staphylococcus spp., and Streptococcus spp. in Africa: a systematic review from a One Health perspective
John Osei Sekyere,Eric Mensah +1 more
TL;DR: Strict infection control measures, antimicrobial stewardship, and periodic One Health epidemiological surveillance studies are needed to monitor and contain the threat of increasing antibiotic resistance in Africa.
Journal ArticleDOI
Genomic Analysis of Carbapenemase - Producing Extensively Drug-Resistant Klebsiella pneumoniae Isolates Reveals the Horizontal Spread of p18-43_01 Plasmid Encoding blaNDM-1 in South Africa
Yogandree Ramsamy,Yogandree Ramsamy,Koleka Mlisana,Koleka Mlisana,Mushal Allam,Daniel G. Amoako,Akebe Luther King Abia,Arshad Ismail,Ravesh Singh,Ravesh Singh,Theroshnie Kisten,Khine Swe Swe Han,Khine Swe Swe Han,David J. J. Muckart,Timothy Craig Hardcastle,Moosa Suleman,Sabiha Y. Essack +16 more
TL;DR: Findings suggest that the acquisition of blaNDM-1-bearing plasmid structure (p18-43_01), horizontal transfer and clonal dissemination facilitate the spread of carbapenemases in South Africa, emphasizing the importance of targeted infection control measures to prevent dissemination.
Journal ArticleDOI
Antibiotic Resistance and Virulence Gene Characteristics of Methicillin-Resistant Staphylococcus aureus (MRSA) Isolated from Healthy Edible Marine Fish.
TL;DR: The findings of this study showed that marine fish contained MDR-MRSA strains that harbour SCCmec types, characteristic of either HA- MRSA or CA-MRsa, but with a low prevalence of enterotoxin and pvl genes, indicating a need for continuous monitoring and implementation of better control strategies within the food chain.
Journal ArticleDOI
Characterisation of Campylobacter spp. Isolated from Poultry in KwaZulu-Natal, South Africa
Stephanie Pillay,Daniel G. Amoako,Akebe Luther King Abia,Anou M. Somboro,Christiana O. Shobo,Keith Perrett,Linda A. Bester,Sabiha Y. Essack +7 more
TL;DR: The numerous permutations of clonality, antibiotic resistance, and virulence profiles evident in Campylobacter spp.
References
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Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI
MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets
TL;DR: The latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine, has been optimized for use on 64-bit computing systems for analyzing larger datasets.
Journal ArticleDOI
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Anton Bankevich,Sergey Nurk,Dmitry Antipov,Alexey Gurevich,Mikhail Dvorkin,Alexander S. Kulikov,Valery M. Lesin,Sergey I. Nikolenko,Son Pham,Andrey D. Prjibelski,Alexey V. Pyshkin,Alexander Sirotkin,Nikolay Vyahhi,Glenn Tesler,Max A. Alekseyev,Pavel A. Pevzner +15 more
TL;DR: SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies.
SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Journal ArticleDOI
The RAST Server: Rapid Annotations using Subsystems Technology
Ramy K. Aziz,Ramy K. Aziz,Daniela Bartels,Aaron A. Best,Matthew DeJongh,Terrence Disz,Terrence Disz,Robert Edwards,Kevin Formsma,Svetlana Gerdes,Elizabeth M. Glass,Michael Kubal,Folker Meyer,Folker Meyer,Gary J. Olsen,Gary J. Olsen,Robert Olson,Robert Olson,Andrei L. Osterman,Ross Overbeek,Leslie Klis McNeil,Daniel Paarmann,Tobias Paczian,Bruce Parrello,Gordon D. Pusch,Claudia I. Reich,Rick Stevens,Rick Stevens,Olga Vassieva,Veronika Vonstein,Andreas Wilke,Olga Zagnitko +31 more
TL;DR: A fully automated service for annotating bacterial and archaeal genomes that identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user.