Sequencing-based methods and resources to study antimicrobial resistance.
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ABSTRACT:
SUBMITTER: Boolchandani M
PROVIDER: S-EPMC6525649 | biostudies-literature | 2019 Jun
REPOSITORIES: biostudies-literature
Publications
Sequencing-based methods and resources to study antimicrobial resistance.
Boolchandani Manish M D'Souza Alaric W AW Dantas Gautam G
Nature reviews. Genetics 20190601 6
Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial resistance are imperative for clinical practice to treat resistant infections and for public health efforts to limit the spread of resistance. Technologies such as next-generation sequencing are expanding our abilities to detect and study antimicrobial resistance. This Review provides a detailed overview of antimicrobial re ...[more]
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Project description:ObjectivesAntimicrobial resistance (AMR) is a significant threat to global public health. Many medical curricula have limited clinical cases and materials focused on AMR, yet enhanced AMR education and training are needed to support antimicrobial stewardship programmes. We used crowdsourcing methods to develop open-access, learner-centred AMR resources. Crowdsourcing is the process of having a large group, including experts and non-experts, solve a problem and then share solutions with the public.MethodsWe organised a global crowdsourcing contest soliciting AMR-related multiple-choice questions, infographics, and images. First, we convened a diverse steering committee group to finalise a call for entries. Second, we launched the contest and disseminated the call for entries using social media, blog posts, email, and an in-person event. Partner institutions included two digital healthcare platforms: Figure 1® and Ding Xiang Yuan. Both organizations serve as online communities for healthcare specialists and professionals to report and comment on clinical information. At the end of the call, solicited entries were screened for eligibility and judged on merit and relevance to AMR learning and education. Exceptional entries were recognised, awarded prizes, and further reviewed for sharing with the public via open-access platforms.ResultsWe received 59 entries from nine countries. These included 54 multiple-choice questions, four infographics, and one image. Eligible entries (n = 56) were reviewed and assigned a score on a 1-10 scale. Eight entries received mean scores greater than 6.0 and were selected as finalists. The eight finalist entries consisted of three infographics and five multiple-choice questions. They were disseminated through open-access publications and online medical communities. Although we launched a global call, we relied heavily on medical student groups and the entries received were not entirely globally representative.ConclusionsWe demonstrate that crowdsourcing challenge contests can be used to identify infectious disease teaching materials. Medical educators and curriculum developers can adapt this method to solicit additional teaching content for medical students.
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Project description:Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due to their potential to generate long reads. Nevertheless, there is a lack of updated and systematic studies evaluating the performance of different assembly tools on nanopore data. In this study, we have benchmarked the ability of different assemblers to reconstruct two different commercially-available mock communities that have been sequenced using Oxford Nanopore Technologies platforms. Among the tested tools, only metaFlye, Raven, and Canu performed well in all the datasets. These tools retrieved highly contiguous genomes (or even complete genomes) directly from the metagenomic data. Despite the intrinsic high error of nanopore sequencing, final assemblies reached high accuracy (~?99.5 to 99.8% of consensus accuracy). Polishing strategies demonstrated to be necessary for reducing the number of indels, and this had an impact on the prediction of biosynthetic gene clusters. Correction with high quality short reads did not always result in higher quality draft assemblies. Overall, nanopore metagenomic sequencing data-adapted to MinION's current output-proved sufficient for assembling and characterizing low-complexity microbial communities.
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Project description:Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customizable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods.
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Project description:The surveillance of antimicrobial-resistant isolates has proven to be one of the most valuable tools to understand the global rise of multidrug-resistant bacterial pathogens. We report the first insights into the current situation in the Caribbean, where a pilot project to monitor antimicrobial resistance (AMR) through phenotypic resistance measurements combined with whole-genome sequencing was set up in collaboration with the Caribbean Public Health Agency (CARPHA). Our first study focused on Klebsiella pneumoniae, a highly relevant organism amongst the Gram-negative opportunistic pathogens worldwide causing hospital- and community-acquired infections. Our results show that not only carbapenem resistance, but also hypervirulent strains, are circulating in patients in the Caribbean. Our current data does not allow us to infer their prevalence in the population. We argue for the urgent need to further support AMR surveillance and stewardship in this almost uncharted territory, which can make a significant impact on the reduction of antimicrobial usage. This article contains data hosted by Microreact (https://microreact.org).
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Project description:INTRODUCTION:The global nephrology workforce is shrinking and, in many countries, is unable to meet healthcare needs. Accurate data pertaining to human resources in nephrology in South Africa is lacking. This data is critical for the planning and delivery of renal services and the training of nephrologists in South Africa to meet the challenge of the growing burden of chronic kidney disease. METHODS:A cross-sectional study of adult and paediatric nephrologists currently delivering nephrology services in South Africa was conducted. Participants were identified using various data sources, including the register of the Health Professions Council of South Africa. This cohort of doctors was described in terms of their demographics and distribution. A survey was then conducted among these nephrologists to collect additional information on their training, scope of practice, job satisfaction, challenges and future plans. Finally, two focus group interviews were conducted to probe themes identified from the survey data. RESULTS:A total of 120 adult nephrologists and 22 paediatric nephrologists were identified (an overall density of 2.5 per million population). There is a male predominance (66%) and the median age is 45 years. The bulk of the workforce (128 nephrologists, 92%) is distributed in three of the nine South African provinces, and two provinces have no nephrologist at all. The survey was completed by 57% of the nephrologists. Most reported positive attitudes to their chosen profession; however, 35 nephrologists (43%) reported an excessive workload, 9 (11%) were planning emigration and 15 (19%) were planning early retirement. A higher frequency of dissatisfaction regarding remuneration (39% vs. 15%) and unsatisfactory work conditions (35% vs. 13%) was observed amongst nephrologists working in the public sector compared to the private sector. A total of 13 nephrologists participated in the focus group interviews. The themes which were identified included that of a rewarding profession, an overall shortage of nephrologists, poor career planning, a need for changes to nephrologists' training, excessive workloads with inadequate remuneration, and challenging work environments. CONCLUSION:There are insufficient numbers of nephrologists in South Africa, with a markedly uneven distribution amongst the provinces and healthcare sectors. Qualitative data indicate that South African nephrologists are faced with the challenges of a high workload, obstructive policies and unsatisfactory remuneration. In the public sector, a chronic lack of nephrologist posts and other resources are additional challenges. A substantial proportion of the workforce is contemplating emigration.
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Project description:Whole-genome sequencing (WGS) could potentially provide a single platform for extracting all the information required to predict an organism's phenotype. However, its ability to provide accurate predictions has not yet been demonstrated in large independent studies of specific organisms. In this study, we aimed to develop a genotypic prediction method for antimicrobial susceptibilities. The whole genomes of 501 unrelated Staphylococcus aureus isolates were sequenced, and the assembled genomes were interrogated using BLASTn for a panel of known resistance determinants (chromosomal mutations and genes carried on plasmids). Results were compared with phenotypic susceptibility testing for 12 commonly used antimicrobial agents (penicillin, methicillin, erythromycin, clindamycin, tetracycline, ciprofloxacin, vancomycin, trimethoprim, gentamicin, fusidic acid, rifampin, and mupirocin) performed by the routine clinical laboratory. We investigated discrepancies by repeat susceptibility testing and manual inspection of the sequences and used this information to optimize the resistance determinant panel and BLASTn algorithm. We then tested performance of the optimized tool in an independent validation set of 491 unrelated isolates, with phenotypic results obtained in duplicate by automated broth dilution (BD Phoenix) and disc diffusion. In the validation set, the overall sensitivity and specificity of the genomic prediction method were 0.97 (95% confidence interval [95% CI], 0.95 to 0.98) and 0.99 (95% CI, 0.99 to 1), respectively, compared to standard susceptibility testing methods. The very major error rate was 0.5%, and the major error rate was 0.7%. WGS was as sensitive and specific as routine antimicrobial susceptibility testing methods. WGS is a promising alternative to culture methods for resistance prediction in S. aureus and ultimately other major bacterial pathogens.
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