CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
Brian Alcock,Amogelang R. Raphenya,Tammy T. Y. Lau,Kara K. Tsang,Mégane Bouchard,Arman Edalatmand,William Huynh,Anna-Lisa V. Nguyen,Annie A. Cheng,Sihan Liu,Sally Y. Min,Anatoly Miroshnichenko,Hiu-Ki R Tran,Rafik El Werfalli,Jalees A. Nasir,Martins Oloni,David Speicher,Alexandra Florescu,Bhavya Singh,Mateusz Faltyn,Anastasia Hernández-Koutoucheva,Arjun N. Sharma,Emily Bordeleau,Andrew C. Pawlowski,Haley L. Zubyk,Damion M. Dooley,Emma Griffiths,Finlay Maguire,Geoffrey L. Winsor,Robert G. Beiko,Fiona S. L. Brinkman,William W. L. Hsiao,William W. L. Hsiao,Gary Van Domselaar,Gary Van Domselaar,Andrew G. McArthur +35 more
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TLDR
A new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes, able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants.Abstract:
The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD's Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.read more
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Comparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus.
Zheng Huang,Xingya Zhou,Catherine Stanton,Catherine Stanton,Catherine Stanton,R.P. Ross,R.P. Ross,Jianxin Zhao,Hao Zhang,Bo Yang,Wei Chen +10 more
TL;DR: In this paper, 46 Lactobacillus acidophilus species were compared at the genomic level and the results showed that all the L. acidphilus strains were divided into two clusters based on ANI values, phylogenetic analysis and whole genome comparison, due to the difference of their predicted gene composition.
Journal ArticleDOI
Comparative study of gut microbiota from captive and confiscated-rescued wild pangolins
TL;DR: In this paper, the effects of different periods of captivity and captivity with and without antibiotic treatment are considered, and it is shown that different diets and periods of confinement, as well as the application of antibiotic therapy, can alter gut community composition and abundance in pangolins.
Journal ArticleDOI
Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis
P K Vishnu Prasoodanan,Ashok K. Sharma,Ashok K. Sharma,Shruti Mahajan,Darshan B. Dhakan,Abhijit Maji,Abhijit Maji,Joy Scaria,Vineet K. Sharma +8 more
TL;DR: A population-wide analysis was carried out on 586 healthy samples from western and non-western populations including the largest Indian cohort comprising of 200 samples, and 189 Inflammatory Bowel Disease (IBD)-associated Prevotella species from western populations as mentioned in this paper.
Journal ArticleDOI
Profiles of antibiotic resistome and microbial community in groundwater of CKDu prevalence zones in Sri Lanka
Titus Cooray,Junya Zhang,Hui Zhong,Libing Zheng,Yuansong Wei,S. K. Weragoda,Kbsn Jinadasa,Rohan Weerasooriya +7 more
TL;DR: Results showed that CKDu prevalence significantly influenced the distribution of antibiotic resistome and microbial community composition in the groundwater, and MGEs contributed to the occurrence of mexF, while the enrichment of cphA could be attributed to the increase of Aeromonas.
Journal ArticleDOI
Genomic islands mediate environmental adaptation and the spread of antibiotic resistance in multiresistant Enterococci - evidence from genomic sequences.
Weiwei Li,Ailan Wang +1 more
TL;DR: In this article, the authors investigated the spread of genomic islands (GIs) between Enterococcus strains and their correlation with antibiotic resistance genes (ARGs) using bitsliced Genomic Signature Indexes (BIGSI) to screen the NCBI Sequence Read Archive (SRA) for multiple resistant enterococcus.
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