scholarly journals Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview

2021 ◽  
Vol 11 ◽  
Author(s):  
Vinicius A. C. de Abreu ◽  
José Perdigão ◽  
Sintia Almeida
Keyword(s):  
Antimicrobial Resistance ◽  
High Throughput Sequencing ◽  
Genetic Recombination ◽  
Public Health Problem ◽  
Metagenomic Data ◽  
Global Public Health ◽  
Community Based ◽  
Sequencing Technologies ◽  
Antimicrobial Resistance Genes ◽  
Functional Gene Analysis

Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particular, the metagenomic approach has facilitated the identification of community-based antimicrobial resistance. This approach is useful, as it allows access to the genomic data in an environmental sample without the need to isolate and culture microorganisms prior to analysis. Here, we aimed to reflect on the challenges of analyzing metagenomic data in the three main approaches for studying antimicrobial resistance: (i) analysis of microbial diversity, (ii) functional gene analysis, and (iii) searching the most complete and pertinent resistome databases.

scholarly journals Abundance and diversity of resistomes differ between healthy human oral cavities and gut

2019 ◽  
Author(s):  
Victoria R. Carr ◽  
Elizabeth Witherden ◽  
Sunjae Lee ◽  
Saeed Shoaie ◽  
Peter Mullany ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Oral Cavity ◽  
Resistance Genes ◽  
High Throughput Sequencing ◽  
Metagenomic Data ◽  
Microbial Composition ◽  
Healthy Human ◽  
Antimicrobial Resistance Genes ◽  
Stool Samples ◽  
Abundance And Diversity

AbstractThe global threat of the “antimicrobial resistance apocalypse” that has arisen in recent years has driven the use of high-throughput sequencing techniques to monitor the profile of resistance genes, known as the “resistome”, in microbial populations. The human oral cavity contains a poorly explored reservoir of these genes, and little is known about their abundance and diversity, or how their profile compares with antimicrobial resistance genes in the gut. Here we analyse the resistome profiles of 788 oral cavities worldwide and compare these profiles with paired stool samples from shotgun metagenomic data. We find country and body site-specific differences in the prevalence of antimicrobial resistance genes, classes and mechanisms in oral and stool samples. However, the abundance of these antimicrobial resistance classes do not correlate with antibiotic prescription rates. A greater similarity was found in interpersonal resistomes between the same body sites than intrapersonal resistomes across different body sites. Between individuals, the oral cavity contains the highest and lowest abundances of specific antimicrobial resistance genes, but a lower diversity of resistance genes compared to the gut, which is likely influenced by differences in microbial composition and exposure to antimicrobial selection pressures. Co-occurrence analysis shows contrasting ARG-species associations between saliva and stool samples. This is the first study to date that characterises the oral cavity resistome worldwide, identifying its distinctive signatures compared to the gut.Maintenance and persistence of antimicrobial resistance is likely to vary across different body sites. Thus, we highlight the importance of characterising the resistome across body sites to uncover the antimicrobial resistance potential in the human body.

Clin-mNGS: Automated Pipeline for Pathogen Detection from Clinical Metagenomic Data

2020 ◽  
Vol 15 ◽  
Author(s):  
Akshatha Prasanna ◽  
Vidya Niranjan
Keyword(s):  
Antimicrobial Resistance ◽  
High Performance ◽  
Pathogen Detection ◽  
Bacterial Species ◽  
Workflow Management ◽  
Metagenomic Data ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent ◽  
Automated Pipeline ◽  
User Friendly

Background: Since bacteria are the earliest known organisms, there has been significant interest in their variety and biology, most certainly concerning human health. Recent advances in Metagenomics sequencing (mNGS), a culture-independent sequencing technology have facilitated an accelerated development in clinical microbiology and our understanding of pathogens. Objective: For the implementation of mNGS in routine clinical practice to become feasible, a practical and scalable strategy for the study of mNGS data is essential. This study presents a robust automated pipeline to analyze clinical metagenomic data for pathogen identification and classification. Method: The proposed Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the Snakemake workflow management software. The implementation avoids the hassle of manual installation and configuration of the multiple command-line tools and dependencies. The approach directly screens pathogens from clinical raw reads and generates consolidated reports for each sample. Results: The pipeline is demonstrated using publicly available data and is tested on a desktop Linux system and a High-performance cluster. The study compares variability in results from different tools and versions. The versions of the tools are made user modifiable. The pipeline results in quality check, filtered reads, host subtraction, assembled contigs, assembly metrics, relative abundances of bacterial species, antimicrobial resistance genes, plasmid finding, and virulence factors identification. The results obtained from the pipeline are evaluated based on sensitivity and positive predictive value. Conclusion: Clin-mNGS is an automated Snakemake pipeline validated for the analysis of microbial clinical metagenomics reads to perform taxonomic classification and antimicrobial resistance prediction.

scholarly journals Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2006
Author(s):  
Anna Y Budkina ◽  
Elena V Korneenko ◽  
Ivan A Kotov ◽  
Daniil A Kiselev ◽  
Ilya V Artyushin ◽  
...  
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Metagenomic Data ◽  
Sequencing Data ◽  
Viral Pathogens ◽  
Genomic Databases ◽  
Bioinformatic Pipeline ◽  
Viral Genomes ◽  
Sequencing Technologies ◽  
Viral Screening

According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes. In this paper, we present a new bioinformatic pipeline, VirIdAl, for detecting and identifying viral pathogens in sequencing data. We also demonstrate the utility of the new software by applying it to viral screening of the feces of bats collected in the Moscow region, which revealed a significant variety of viruses associated with bats, insects, plants, and protozoa. The presence of alpha and beta coronavirus reads, including the MERS-like bat virus, deserves a special mention, as it once again indicates that bats are indeed reservoirs for many viral pathogens. In addition, it was shown that alignment-based methods were unable to identify the taxon for a large proportion of reads, and we additionally applied other approaches, showing that they can further reveal the presence of viral agents in sequencing data. However, the incompleteness of viral databases remains a significant problem in the studies of viral diversity, and therefore necessitates the use of combined approaches, including those based on machine learning methods.

Formula-fed and Clostridium difficile infected neonatal piglets carry a highly diverse and abundant set of antimicrobial resistance genes

2020 ◽  
Author(s):  
Robert Pieper ◽  
Temesgen Dadi ◽  
Lukasz Grzeskowiak ◽  
Laura Pieper ◽  
Britta Siegmund ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Microbial Colonization ◽  
Metagenomic Data ◽  
Neonatal Piglets ◽  
Gut Colonization ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Genes Encoding

Abstract Background: Clostridium difficile infection (CDI) is an increasing zoonotic health threat and has also been documented as a cause of enteritis outbreaks in neonatal pigs. Furthermore, CDI in neonatal piglets cause changes in microbial gut colonization. We hypothesized that an imbalanced microbial colonization in piglets with CDI could be associated with an altered abundance of antimicrobial resistance genes. Results: We analyzed fecal metagenomic data of lactating sows (S), their piglets during suckling (SP), the same piglets two weeks after weaning (WP), 5-day old artificially reared and formula-fed siblings (FP) and FP infected with C. difficile (FP-CD) for microbiota composition and antimicrobial resistance gene abundance. FP and FP-CD piglets had an immature-type microbiota and increased abundance of antimicrobial resistance genes. A co-occurrence of genes encoding for resistance against aminoglycosides (e.g. aph(3”)-lb, aph(6)-ld, ant(2”)-la), β-lactams (blaCTX-M, blaTEM), fluoroquinolones (pat(A) macrolides (mph(A)), sulfonamides (sul1, sul2), polypeptides (e.g. pmrB, pmrC, arnA, bac(A)) and tetracyclines (e.g. tet(A-D),) was observed. Conclusion: Increased abundance of antimicrobial resistance genes in formula feeding and concomitant CDI may be associated with therapeutic resistance later in life and warrant further studies.

scholarly journals Metagenomics: aid to combat antimicrobial resistance in diarrhea

Gut Pathogens ◽  
2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Rituparna De
Keyword(s):  
Antimicrobial Resistance ◽  
Antimicrobial Agents ◽  
Genetic Recombination ◽  
Molecular Taxonomy ◽  
Ecological Niches ◽  
Next Generation ◽  
Genetic Determinants ◽  
Antimicrobial Resistance Genes ◽  
And Function ◽  
Generation Sequencing

Abstract Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for assuaging diarrheal symptoms. Antimicrobial resistance develops when pathogens acquire antimicrobial resistance genes (ARGs) through genetic recombination from commensals and pathogens. These are the constituents of the complex microbiota in all ecological niches. The recombination events may occur in the environment or in the gut. Containment of AMR can be achieved through a complete understanding of the complex and diverse structure and function of the microbiota. Its taxonomic entities serve as focal points for the dissemination of antimicrobial resistance genetic determinants. Molecular methods complemented with culture-based diagnostics have been historically implemented to document these natural events. However, the advent of next-generation sequencing has revolutionized the field of molecular epidemiology. It has revolutionized the method of addressing relevant problems like diagnosis and surveillance of infectious diseases and the issue of antimicrobial resistance. Metagenomics is one such next-generation technique that has proved to be a monumental advancement in the area of molecular taxonomy. Current understanding of structure, function and dysbiosis of microbiota associated with antimicrobial resistance was realized due to its conception. This review describes the major milestones achieved due to the advent and implementation of this new technique in the context of antimicrobial resistance. These achievements span a wide panorama from the discovery of novel microorganisms to invention of translational value.

scholarly journals Editorial: Antimicrobial Resistance as a Global Public Health Problem: How Can We Address It?

2020 ◽  
Vol 8 ◽  
Author(s):  
Luciene Andrade Da Rocha Minarini ◽  
Leonardo Neves de Andrade ◽  
Eliana De Gregorio ◽  
Filipa Grosso ◽  
Thierry Naas ◽  
...  
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Health Problem ◽  
Public Health Problem ◽  
Global Public Health ◽  
Global Public Health Problem

scholarly journals Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry

2019 ◽  
Vol 16 (24) ◽  
pp. 4896
Author(s):  
Na Li ◽  
Chong Liu ◽  
Zhiguo Zhang ◽  
Hongna Li ◽  
Tingting Song ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
High Throughput Sequencing ◽  
Animal Husbandry ◽  
Control Measures ◽  
Research Progress ◽  
Future Research ◽  
Resistant Bacteria ◽  
Technological Advances ◽  
Antimicrobial Resistance Genes

The extensive use of antimicrobials in animal farms poses serious safety hazards to both the environment and public health, and this trend is likely to continue. Antimicrobial resistance genes (ARGs) are a class of emerging pollutants that are difficult to remove once introduced. Understanding the environmental transfer of antimicrobial-resistant bacteria (ARB) and ARGs is pivotal for creating control measures. In this review, we summarize the research progress on the spread and detection of ARB and ARG pollution related to animal husbandry. Molecular methods such as high-throughput sequencing have greatly enriched the information about ARB communities. However, it remains challenging to delineate mechanisms regarding ARG induction, transmission, and tempo-spatial changes in the whole process, from animal husbandry to multiple ecosystems. As a result, future research should be more focused on the mechanisms of ARG induction, transmission, and control. We also expect that future research will rely more heavily on metagenomic -analysis, metatranscriptomic sequencing, and multi-omics technologies

scholarly journals 2547. Prioritizing Antimicrobial Resistance Learning Objectives Through a Modified, Two-Round, One-Day Delphi at a Multidisciplinary Conference

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S885-S885 ◽  
Author(s):  
Jehan Budak ◽  
Eneyi E Kpokiri ◽  
Emily Abdoler ◽  
Joseph Tucker ◽  
Brian Schwartz ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Financial Institution ◽  
Medical Profession ◽  
Public Health Problem ◽  
Delphi Process ◽  
Learning Objectives ◽  
World Health ◽  
Global Public Health ◽  
Health Administrator ◽  
International Financial Institution

Abstract Background Antimicrobial resistance (AMR) is a global public health problem, but the learning needs of the medical profession on this topic are not well understood. The World Health Organization has called for better educational resources on AMR. Thus, we aimed to identify AMR learning objectives for physicians and medical trainees. Methods We designed a modified, two-round Delphi process to build consensus around these objectives, recruiting attendees at a one-day, multidisciplinary, international AMR symposium. Through review of the literature and discussion with experts in AMR, we generated an initial list of 17 objectives. We asked participants to rate the importance of including each objective in an AMR curriculum for physicians on a 5-point Likert scale, which ranged from “do not include” (1) to “very important to include” (5). Consensus for inclusion was predefined as ≥ 80% of participants rating the objective ≥ 4. Results The first round was completed by 30 participants, and the second by 21. Nobody declined to participate, but several people had to leave between rounds. Participants included physicians, researchers, graduate students, and a pharmacist, foundation manager, patient advocate, leader of an international financial institution, health administrator, and biomedical scientist. After the first round, 16 objectives met the consensus criteria, and participants suggested five additional topics. After the second round, 12 objectives met the consensus criteria (see Table 1). Objectives related to treatment of AMR most frequently met consensus criteria. Specific objectives with the highest consensus ratings were related to identifying infections not requiring antibiotics and recognizing the importance of using the narrowest spectrum antibiotic for the shortest period of time. Conclusion We successfully employed a modified, one-day Delphi process at an international, multidisciplinary AMR symposium to build consensus among experts and stakeholders regarding key learning objectives for AMR. This technique may be useful for guideline committees and other taskforces in the Infectious Diseases community. Our generated list may be useful for those developing AMR training materials for medical students and physicians. Disclosures All authors: No reported disclosures.

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