Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana.
Stefan P. W. de Vries,Moses Vurayai,Mark A. Holmes,Srishti Gupta,Michael D. Bateman,David M. Goldfarb,David M. Goldfarb,Duncan J. Maskell,Maitshwarelo Ignatius Matsheka,Andrew J. Grant +9 more
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Insight is provided into Campylobacter spp.Abstract:
Campylobacter spp. are a leading cause of bacterial enteritis worldwide, including countries in Africa, and have been identified by the World Health Organisation (WHO) as one of the high priority antimicrobial resistant pathogens. However, at present there is little knowledge on the prevalence, molecular epidemiology or antimicrobial susceptibility of Campylobacter spp. isolates in Botswana, both in patients and in the zoonotic context. Some data indicate that ~14% of diarrhoeal disease cases in a paediatric setting can be ascribed to Campylobacter spp., urging the need for the magnitude of Campylobacter-associated diarrhoea to be established. In this survey, we have characterised the genomic diversity of Campylobacter spp. circulating in Botswana isolated from cases of diarrhoeal disease in humans (n = 20) and from those that colonised commercial broiler (n = 35) and free-range (n = 35) chickens. Phylogeny showed that the Campylobacter spp. isolated from the different poultry and human sources were highly related, suggesting that zoonotic transmission has likely occurred. We found that for Campylobacter spp. isolated from humans, broilers and free-range chickens, 52% was positive for tetO, 47% for gyrA-T86I, 72% for blaOXA-61, with 27% carrying all three resistance determinants. No 23S mutations conferring macrolide resistance were detected in this survey. In summary, our study provides insight into Campylobacter spp. in poultry reservoirs and in diarrhoeal patients, and the relevance for treatment regimens in Botswana.read more
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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
Global trends in antimicrobial resistance in animals in low- and middle-income countries
Thomas P. Van Boeckel,Thomas P. Van Boeckel,João Pires,Reshma Silvester,Cheng Zhao,Julia Song,Nicola G. Criscuolo,Marius Gilbert,Sebastian Bonhoeffer,Ramanan Laxminarayan,Ramanan Laxminarayan,Ramanan Laxminarayan +11 more
TL;DR: The current study provides a much-needed baseline model for low- and middle-income countries and provides a “one health” perspective to which future data can be added, and produces global maps of AMR in LMICs to give policy-makers—or a future international panel—a baseline for monitoring AMR levels in animals and target interventions in the regions most affected by the rise of resistance.
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Human campylobacteriosis: A public health concern of global importance.
Aboi Igwaran,Anthony I. Okoh +1 more
TL;DR: The emergence of some Campylobacter species as one of the main causative agent of diarrhea and the propensity of these bacteria species to resist the actions of antimicrobial agents position them as a serious threat to the public health.
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Systematic Review of Important Bacterial Zoonoses in Africa in the Last Decade in Light of the ‘One Health’ Concept
TL;DR: It was found that zoonoses such as leptospirosis, brucellosis, Q fever and rickettsiosis among others are frequently under/misdiagnosed in febrile patients seeking treatment at healthcare centres, leading to overdiagnoses of more familiar febRIle conditions such as malaria and typhoid fever.
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Molecular characterization of Campylobacter causing human clinical infection using whole-genome sequencing: Virulence, antimicrobial resistance and phylogeny in Ireland.
TL;DR: Virulence genes in clinical Campylobacter infections in Ireland were similar to those known previously, and high prevalence of quinolone resistance markers has been found, which has implications for antimicrobial stewardship.
References
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh,Daron M. Standley +1 more
TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
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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.
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
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Prokka: Rapid Prokaryotic Genome Annotation
TL;DR: Prokka is introduced, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer, and produces standards-compliant output files for further analysis or viewing in genome browsers.
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).