Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens DOI Creative Commons
Richard M. Leggett,

Cristina Alcon‐Giner,

Darren Heavens

и другие.

Nature Microbiology, Год журнала: 2019, Номер 5(3), С. 430 - 442

Опубликована: Дек. 16, 2019

The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used coupled to NanoOK RT software package perform shotgun metagenomic and profile mock communities faecal samples from healthy ill preterm infants. Using Nanopore data, we reliably classified a 20-species community captured diversity immature gut microbiota over time response interventions such as probiotic supplementation, antibiotic treatment episodes suspected sepsis. also performed rapid runs assess gut-associated microbial critically infants, facilitated by package, which analysed sequences they were generated. Our pipeline identified pathogenic bacteria (that is, Klebsiella pneumoniae Enterobacter cloacae) their corresponding antimicrobial resistance gene profiles within little 1 h sequencing. Results confirmed using pathogen isolation, whole-genome susceptibility testing, well with known genes. results demonstrate that (including cost-effective Flongle flow cells) can process rich dataset < 5 h, creates future studies aimed at developing these tools approaches settings focus on providing tailored patient options.

Язык: Английский

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database DOI Creative Commons
Brian Alcock, Amogelang R. Raphenya,

Tammy T. Y. Lau

и другие.

Nucleic Acids Research, Год журнала: 2019, Номер unknown

Опубликована: Окт. 9, 2019

The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses high-quality data sequences within controlled vocabulary, Ontology (ARO), designed by biocuration team to integrate with software development efforts for resistome analysis prediction, such as CARD's Gene Identifier (RGI) software. Since 2017, has expanded through extensive curation revision ontological structure, over 500 new AMR models, classification paradigm expansion analytical tools. Most notably, Resistomes & Variants module provides statistical summary in silico predicted variants from 82 pathogens 100 000 genomes. By adding these CARD, we are able summarize using information included identify trends mobility determine previously undescribed novel variants. Here, describe updates recent expansions its process, including resources community data.

Язык: Английский

Процитировано

2803
Antibiotic resistance in Pseudomonas aeruginosa – Mechanisms, epidemiology and evolution DOI
João Botelho, Filipa Grosso,

Luı́sa Peixe

и другие.

Drug Resistance Updates, Год журнала: 2019, Номер 44, С. 100640 - 100640

Опубликована: Май 1, 2019

Язык: Английский

Процитировано

428
Using Genomics to Track Global Antimicrobial Resistance DOI Creative Commons
René S. Hendriksen, Valeria Bortolaia,

Heather Tate

и другие.

Frontiers in Public Health, Год журнала: 2019, Номер 7

Опубликована: Сен. 4, 2019

The recent advancements in rapid and affordable DNA sequencing technologies have revolutionized diagnostic microbiology microbial surveillance. availability of bioinformatics tools online accessible databases has been a prerequisite for this. We conducted scientific literature review here we present description examples available AMR detection provide future perspectives recommendations. At least 47 resources antimicrobial resistance (AMR) determinants or amino acid sequence data developed to date. These include, among others but not limited to, ARG-ANNOT, CARD, SRST2, MEGARes, Genefinder, ARIBA, KmerResistance, AMRFinder ResFinder. Bioinformatics differ several parameters including type accepted input data, presence/absence software search within database that can be specific tool cloned from other resources, the approach employed, which based on mapping alignment. As consequence, each strengths limitations sensitivity specificity application, some highlighted benchmarking exercises articles. identified are either at public genome centers, GitHub run locally online. NCBI ENA possibilities submission both accompanying phenotypic susceptibility allowing researchers further analyze develop test new tools. advancement whole application real-time is essential control prevention strategies combat increasing threat AMR. Accessible expanding establish global pathogen surveillance tracking genomics. There however, need standardization pipelines as well predictions data.

Язык: Английский

Процитировано

381
Surveillance of antimicrobial resistance in low- and middle-income countries: a scattered picture DOI Creative Commons
Katia Iskandar, Laurent Molinier, Souheil Hallit

и другие.

Antimicrobial Resistance and Infection Control, Год журнала: 2021, Номер 10(1)

Опубликована: Март 31, 2021

Abstract Data on comprehensive population-based surveillance of antimicrobial resistance is lacking. In low- and middle-income countries, the challenges are high due to weak laboratory capacity, poor health systems governance, lack information systems, limited resources. Developing countries struggle with political social dilemma, bear a economic burden communicable diseases. Available data fragmented representativeness which limits their use advice policy makers orientate efficient allocation funding financial resources programs mitigate resistance. Low-quality means soaring rates inability track map spread resistance, detect early outbreaks, set national tackle Here, we review barriers limitations conducting effective surveillance, highlight multiple incremental approaches that may offer opportunities strengthen if tailored context each country.

Язык: Английский

Процитировано

279
Innovative and rapid antimicrobial susceptibility testing systems DOI
Alex van Belkum, Carey‐Ann D. Burnham, John W. A. Rossen

и другие.

Nature Reviews Microbiology, Год журнала: 2020, Номер 18(5), С. 299 - 311

Опубликована: Фев. 13, 2020

Язык: Английский

Процитировано

273
Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges DOI
Quỳnh Anh Nguyễn,

Hang P. Vu,

Luong N. Nguyen

и другие.

The Science of The Total Environment, Год журнала: 2021, Номер 783, С. 146964 - 146964

Опубликована: Апрель 7, 2021

Язык: Английский

Процитировано

237
Label-free terahertz microfluidic biosensor for sensitive DNA detection using graphene-metasurface hybrid structures DOI
Ruiyun Zhou, Chen Wang, Yuxin Huang

и другие.

Biosensors and Bioelectronics, Год журнала: 2021, Номер 188, С. 113336 - 113336

Опубликована: Май 14, 2021

Язык: Английский

Процитировано

174
Bacterial defences: mechanisms, evolution and antimicrobial resistance DOI
William P. J. Smith, Benjamin R. Wucher, Carey D. Nadell

и другие.

Nature Reviews Microbiology, Год журнала: 2023, Номер 21(8), С. 519 - 534

Опубликована: Апрель 24, 2023

Язык: Английский

Процитировано

167
BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking DOI Creative Commons
Ye Feng,

Shengmei Zou,

Hangfei Chen

и другие.

Nucleic Acids Research, Год журнала: 2020, Номер 49(D1), С. D644 - D650

Опубликована: Сен. 17, 2020

Abstract An increasing prevalence of hospital acquired infections and foodborne illnesses caused by pathogenic multidrug-resistant bacteria has stimulated a pressing need for benchtop computational techniques to rapidly accurately classify from genomic sequence data, based on that, trace the source infection. BacWGSTdb (http://bacdb.org/BacWGSTdb) is free publicly accessible database we have developed bacterial whole-genome typing tracking. This incorporates extensive resources genome sequencing data corresponding metadata, combined with specialized bioinformatics tools that enable systematic characterization isolates recovered infections. Here, present 2.0, which encompasses several major updates, including (i) integration core multi-locus (cgMLST) approach, highly scalable appropriate belonging different lineages; (ii) addition multiple analysis module can process dozens user uploaded sequences in batch mode; (iii) new tracking comparing plasmid those deposited public databases; (iv) number species encompassed 2.0 increased 9 20, represents pathogens medical importance; (v) newly designed, user-friendly interface set visualization providing convenient platform users are also included. Overall, updated bears great utility continuing provide users, epidemiologists, clinicians bench scientists, one-stop solution analysis.

Язык: Английский

Процитировано

164
Antimicrobial Resistance Threats in the emerging COVID-19 pandemic: Where do we stand? DOI Creative Commons
Soumya Ghosh, Charné Bornman, Mai M. Zafer

и другие.

Journal of Infection and Public Health, Год журнала: 2021, Номер 14(5), С. 555 - 560

Опубликована: Март 7, 2021

Antimicrobial resistance (AMR) continues to exert a substantial toll on the global health and world economy is now expected be hidden by COVID-19 for while. The wrong consumption of antibiotics during pandemic will raise disastrous effects AMR management antibiotic stewardship programs. This related concerns extrapolated due an increase in mortality rates patients with bacterial coinfections. Importantly, immune system regions high may fighting two fronts altogether, virus MDR bacteria. Current control policies manage prioritization plans are mandatory this pandemic. review aims discuss rising excess use highlighting role coinfections these patients. Types prescribed development addressed as well.

Язык: Английский

Процитировано

160