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Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds

Julián Reyes Vélez, Marguerite Cameron, Juan Carlos Rodríguez-Lecompte, Fangfang Xia, Luke C. Heider, Matthew Saab, J. Trenton McClure, Javier Sánchez
2017 Frontiers in Veterinary Science  
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

Alice R. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, Terry Disz, Joseph L. Gabbard, Svetlana Gerdes, Christopher S. Henry (+16 others)
2016 Nucleic Acids Research  
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

Margo VanOeffelen, Marcus Nguyen, Derya Aytan-Aktug, Thomas Brettin, Emily M Dietrich, Ronald W Kenyon, Dustin Machi, Chunhong Mao, Robert Olson, Gordon D Pusch, Maulik Shukla, Rick Stevens (+5 others)
2021 Briefings in Bioinformatics  
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

Agila Kumari Pragasam, Francis Yesurajan, George Priya Doss C, Biju George, Naveen Kumar Devanga Ragupathi, Kamini Walia, Balaji Veeraraghavan
2016 Genome Announcements  
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

Amr T. M. Saeb
2018 Bioinformation  
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]

John W. Santerre, James J. Davis, Fangfang Xia, Rick Stevens
2016 arXiv   pre-print
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

Márton Papp, Norbert Solymosi
2022 Antibiotics  
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

Grigorios D. Amoutzias, Marios Nikolaidis, Andrew Hesketh
2022 Microorganisms  
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

Phornphan Sornchuer, Kritsakorn Saninjuk, Parisa Prathaphan, Rattana Tiengtip, Suphot Wattanaphansak
2022 Microorganisms  
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

Charles J. Norsigian, Heba Attia, Richard Szubin, Aymen S. Yassin, Bernhard Ø. Palsson, Ramy K. Aziz, Jonathan M. Monk
2019 Frontiers in Cellular and Infection Microbiology  
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

Shailendra Yadav, Atya Kapley
2021 Biotechnology Reports  
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

Grace A. Blackwell, Martin Hunt, Kerri M. Malone, Leandro Lima, Gal Horesh, Blaise T. F. Alako, Nicholas R. Thomson, Zamin Iqbal, William P. Hanage
2021 PLoS Biology  
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

Muthuirulandi Sethuvel Dhiviya Prabaa, Devanga Ragupathi Naveen Kumar, Inbanathan Francis Yesurajan, Shalini Anandan, Walia Kamini, Veeraraghavan Balaji
2017 Future Science OA  
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

Norhan Mahfouz, Inês Ferreira, Stephan Beisken, Arndt von Haeseler, Andreas E Posch
2020 Journal of Antimicrobial Chemotherapy  
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

Balakrishnan N. V. Premkrishnan, Cassie E. Heinle, Akira Uchida, Rikky W. Purbojati, Kavita K. Kushwaha, Alexander Putra, Puramadathil Sasi Santhi, Benjamin W. Y. Khoo, Anthony Wong, Vineeth Kodengil Vettath, Daniela I. Drautz-Moses, Ana Carolina M. Junqueira (+1 others)
2021 Gut Pathogens  
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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