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Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds
2017
Frontiers in Veterinary Science
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When the isolate corresponded to a post-mastitis sample, there were lower odds of resistance when compared with non-clinical isolates (P = 0.01). ...
The results of this study showed the strength of associations between phenotypic AMR resistance of both mastitis pathogens and their genotypic resistome and other epidemiological characteristics. ...
Furthermore, the genomes were annotated using the Rast tool kit found in the Pathosystems Resource Integration Center (PATRIC) (PATRIC 3.2.96), as part of the all-bacteria Bioinformatics Resource Center ...
doi:10.3389/fvets.2017.00063
pmid:28589129
pmcid:PMC5438997
fatcat:pl5qjl2vz5dbfkugwzyyw6zatq
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
2016
Nucleic Acids Research
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The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. ...
PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics. ...
To date, 25 subsystems covering 265 unique functional roles relating to antimicrobial resistance have been encoded. ...
doi:10.1093/nar/gkw1017
pmid:27899627
pmcid:PMC5210524
fatcat:amtvn252r5gixdpbsxatrltt3m
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes
2021
Briefings in Bioinformatics
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Antimicrobial resistance (AMR) is a major global health threat that affects millions of people each year. ...
In addition to using the data to track the evolution and spread of AMR, it also serves as a useful starting point for building machine learning models for predicting AMR phenotypes. ...
Acknowledgments We thank the members of the BV-BRC and iSENTRY teams for their helpful comments. ...
doi:10.1093/bib/bbab313
pmid:34379107
pmcid:PMC8575023
fatcat:z2mxaakqs5earkcz3si33m5msq
Draft Genome Sequence of Extremely Drug-Resistant Pseudomonas aeruginosa (ST357) Strain CMC_VB_PA_B22862 Isolated from a Community-Acquired Bloodstream Infection
2016
Genome Announcements
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Extremely drug-resistant Pseudomonas aeruginosa strains causing severe infections have become a serious concern across the world. ...
Here, we report draft genome sequence of P. aeruginosa with an extremely drug-resistant profile isolated from a patient with community-acquired bloodstream infection in India. ...
ACKNOWLEDGMENT We thank the institutional review board, Christian Medical College, Vellore, for approving the study. ...
doi:10.1128/genomea.01092-16
pmid:27795257
pmcid:PMC5073252
fatcat:6hzuv332vje7bh57hzpdwzmzvu
Current Bioinformatics resources in combating infectious diseases
2018
Bioinformation
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resistance analysis and detection of unknown disease-associated pathogens in clinical specimens. ...
Bioinformatics tools and techniques analyzing next-generation sequencing (NGS) data are increasingly used for the diagnosis and monitoring of infectious diseases. ...
Bioinformatics tools for identifying and combating antimicrobial resistance: The need for rapid, accurate detection and understanding of resistance factors and mechanisms are highly demanded in antimicrobial ...
doi:10.6026/97320630014031
pmid:29497257
pmcid:PMC5818640
fatcat:qmy2m52zkjgavnu3wmban4imfi
Machine Learning for Antimicrobial Resistance
[article]
2016
arXiv
pre-print
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Here we present a work in progress case study performing analysis on antimicrobial resistance (AMR) using standard ensemble machine learning techniques and note the successes and pitfalls such work entails ...
Biological datasets amenable to applied machine learning are more available today than ever before, yet they lack adequate representation in the Data-for-Good community. ...
This allows unique opportunity for large-scale aggregation platforms, such as Pathosystems Resource Integration Center (PATRIC) (Gillespie et al., 2011) to serve a unique role. ...
arXiv:1607.01224v1
fatcat:gyle5odl5jah7hp2vpbp7age6u
Review and Comparison of Antimicrobial Resistance Gene Databases
2022
Antibiotics
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We believe that this knowledge is fundamental for selecting the most appropriate database for a research question and for the development of new tools and resources of resistance gene annotation. ...
As the prevalence of antimicrobial resistance genes is increasing in microbes, we are facing the return of the pre-antibiotic era. ...
As stated by a CDC study, approximately 35,000 people die in the United States yearly due to antibiotic resistance [2] . A recent study, however, draws a more drastic picture. ...
doi:10.3390/antibiotics11030339
pmid:35326803
pmcid:PMC8944830
fatcat:alet6yxlwvb7jceooj2232n7aq
The Notable Achievements and the Prospects of Bacterial Pathogen Genomics
2022
Microorganisms
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A small number of bacterial pathogens are of very high importance, and we also present the wealth of the genomic data for these species (i.e., which ones they are, the number of antimicrobial resistance ...
We have mined and discuss some of the most prominent data/bioinformatics resources such as NCBI pathogens, PATRIC, and Pathogenwatch. ...
Oliver, Department of Biochemistry, Cambridge University, UK, for his useful discussions and critical reading of the manuscript.
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/microorganisms10051040
pmid:35630482
fatcat:iukfjmld7jd5fetfptcwyv7t7y
Antimicrobial Susceptibility Profile and Whole-Genome Analysis of a Strong Biofilm-Forming Bacillus Sp. B87 Strain Isolated from Food
2022
Microorganisms
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Moreover, a biofilm allows the exchange of genetic material, such as antimicrobial resistance genes, among the different bacterial strains inside the matrix. ...
The aim of the current study was to genotypically and phenotypically characterize Bacillus sp. B87, a strain that was isolated from food and which exhibited strong biofilm-forming capacity. ...
Acknowledgments: The authors would like to acknowledge Sumet Amonyingcharoen for his assistance with preparing the figures. ...
doi:10.3390/microorganisms10020252
pmid:35208707
pmcid:PMC8876208
fatcat:kjbvm56qdjaajj3hivu2mqsjuq
Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase–Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates
2019
Frontiers in Cellular and Infection Microbiology
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The link between antimicrobial resistance acquired by strains of Klebsiella and their unique metabolic capabilities has not been determined. ...
The emergence and spread of metallo-beta-lactamase-producing multidrug-resistant (MDR) Klebsiella pneumoniae is a serious public health threat, which is further complicated by the increased prevalence ...
., 2011) , as a platform to investigate the metabolic differences amongst our group of isolates. iYL12228 is a reconstruction for K. pneumoniae MGH78578 and provided a valuable resource to link the genetic ...
doi:10.3389/fcimb.2019.00161
fatcat:4ynia46wb5b4pmaz536gpdajle
Antibiotic resistance: Global Health Crisis and Metagenomics
2021
Biotechnology Reports
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Urban wastewater & sewage treatment plants act as the hotspot for the widespread of antimicrobial resistance. Natural environment also plays an important role in the dissemination of resistance. ...
Antibiotic resistance is a global problem which affects human health. ...
The manuscript has been checked for the plagiarism using iThenticate software at the NEERI Knowledge resource center: KRC no.: CSIR-NEERI/KRC/2019/SEP/DRC/1.
Appendix A. ...
doi:10.1016/j.btre.2021.e00604
pmid:33732632
pmcid:PMC7937537
fatcat:jf56rfgoazgk7k6qleri6r3roq
Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences
2021
PLoS Biology
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The open sharing of genomic data provides an incredibly rich resource for the study of bacterial evolution and function and even anthropogenic activities such as the widespread use of antimicrobials. ...
We produced a searchable COmpact Bit-sliced Signature (COBS) index, facilitating the easy interrogation of the entire dataset for a specific sequence (e.g., gene, mutation, or plasmid). ...
We also thank Colman O'Cathail and Nadim Rahman for their help with accession of the assemblies in the ENA. ...
doi:10.1371/journal.pbio.3001421
pmid:34752446
pmcid:PMC8577725
fatcat:vv35flueoban7b3uvr4r7gozae
Identification of nonserotypeable Shigella spp. using genome sequencing: a step forward
2017
Future Science OA
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Sequence types, plasmid types, antimicrobial resistance and virulence genes were also investigated. ...
Antimicrobial resistance, virulence and plasmid incompatibility groups were identified in all the isolates. Sequence types were determined. ...
Acknowledgements The authors gratefully acknowledge the Institutional Review Board for approving the study and the department of Clinical Microbiology for providing lab space and facilities. ...
doi:10.4155/fsoa-2017-0063
pmid:29134117
pmcid:PMC5674244
fatcat:efxeuwdp5nh7noipmz6yx6fkii
Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review
2020
Journal of Antimicrobial Chemotherapy
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Background Antimicrobial resistance (AMR) is a rising health threat with 10 million annual casualties estimated by 2050. ...
Methods We present a systematic evaluation of the performance of publicly available AMR marker databases for resistance prediction on clinical isolates. ...
A number of studies applied genotype to phenotype prediction while relying on a curated subset of markers from CARD, ResFinder and other resources and obtained better overall prediction performance. ...
doi:10.1093/jac/dkaa257
pmid:32658975
fatcat:cbuyany53zewvgobeeribi3sgq
The genomic characterisation and comparison of Bacillus cereus strains isolated from indoor air
2021
Gut Pathogens
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Due to virulence potential of B. cereus and its reported involvement in nosocomial infections, antibiotic resistance analyses were performed and confirmed resistance to ampicillin and fosfomycin, with ...
Background Bacillus cereus is ubiquitous in nature, found in environments such as soil, plants, air, and part of the insect and human gut microbiome. ...
Gaultier for their assistance in sampling and isolation. ...
doi:10.1186/s13099-021-00399-4
pmid:33516253
fatcat:z3gcg4c3wfezdipiervb5zvjaq
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