Mapping Microbiome Signatures Associated With Antibiotic Usage On A Swine Production Farm Using Amplicon And Shotgun Data

Abstract Background: High antimicrobial usage in swine production has the potential to create reservoirs of antimicrobial resistance (AMR) genes which are transferable to human pathogens via mobile genetic elements. Understanding microbial community responses to antibiotic use is central to unravelling transfer of such resistance genes. Our previous investigation revealed a scenario of optimal antibiotic activity associated with saturation of AMR genes on this farm. Here, we use amplicon and shotgun sequence data to investigate the microbiome signatures that underwrite such a phenomenon.Results: We generated 1.24 and 576 million high quality 16S rRNA gene amplicon and shotgun sequences from 24 porcine faecal samples, respectively. The ratio of taxa detection at genus level between the two methods was 1:24. Using shotgun sequence data, 235 unique AMR genes, 122 modes of action and 17 antibiotic classes were identified using the MEGARes AMR database. Antibiotic usage in growing pigs was significantly associated with microbial and AMR resistome structural and compositional changes detectable two weeks after antibiotic initiation. These were characterised by a down regulation of MDR efflux pumps and an up regulation of macrolide-specific efflux pumps in the growing pigs (treated-group) linked to lower abundance of Verrucomicrobiaeceae. In the sows (non-treated group), a potentially undetected infection, was characterised by a high abundance of pathogenic viral sequences, microbial structural changes i.e. family Alcaligenaceae, and an up regulation of beta-lactamases, including MDR efflux pumps. We assembled 682 near complete bacterial genomes revealing that a large proportion of the resistome is carried by Firmicutes and Proteobacteria, specifically multi-class gene carriage by Clostridium species and Escherichia coli, which occurred exclusively in the treatment group.Conclusion: Microbiome signatures i.e. microbial structure, composition and resistome carriage associated with antibiotic-use can be cost effectively screened with amplicon sequencing but their granularity unravelled using shotgun metagenomic data.

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THE RELATION BETWEEN KNOWLEDGE AND ATTITUDE TOWARD BEHAVIOR OF ANTIBIOTIC USAGE ON SOCIETY IN TALANG JAWA HEALTH CENTER OF SOUTH LAMPUNG AUGUST PERIOD 2019

JFL : Jurnal Farmasi Lampung ◽

10.37090/jfl.v8i2.149 ◽

1970 ◽

pp. 132-141

Author(s):

Lilik Koernia Wahidah

Keyword(s):

Health Center ◽

Significant Relationship ◽

Health Centre ◽

Antibiotic Use ◽

Antibiotic Usage ◽

Bivariate Analysis ◽

Chi Square ◽

Public Health Centre ◽

Knowledge And Attitude ◽

Use Behavior

In developing countries, many antibiotics are used without a doctor's prescription, causing someone to use antibiotics incorrectly. Lack of knowledge about antibiotics is a major factor that triggers an increase in the rate of bacterial resistance to antibiotics. Knowledge and attitude become one of the social cognitive factors that influence antibiotic use behavior.This study aims to determine the relationship of knowladge and attitudes toward of antibiotic usage behavior in community of Talang jawa public health centre. The research is an observasional analytic research using cross sectional study design. sampling using non-probability sampling methode with type purposive sampling and instruments in the form of questionnaires. The data analysis was based univariate and bivariate analysis eqipped with chi square. The study was conducted on 100 community respondents in the Talang Jawa Health Center. The results showed respondents with good knowledge (25%), enough (27%) and less (48%). Respondents with positive attitudes (64%) and negative attitudes (35%). Respondents with positive behavior (43%) and negative behavior (57%). Chi square test result showed that there was a significant relationship between knowladge and antibiotic use behavior (p= 0,000) and there was a significant relationship between attitude and antibiotic use behavior (p= 0,000). This study has a meaningful relationship between and attitudes with antibiotic use behavior in Talang Jawa Health Center. Keywords: Antibiotics,Knowledge, Attitudes, Behavior

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180. Leveraging the Electronic Medical Record as a Method of Antibiotic Stewardship

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.224 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S97-S97

Author(s):

Christina M Kaul ◽

Eric Molina ◽

Donna Armellino ◽

Mary Ellen Schilling ◽

Mark Jarrett

Keyword(s):

Medical Record ◽

Electronic Medical Record ◽

Antibiotic Stewardship ◽

Antibiotic Use ◽

Antibiotic Usage ◽

P Value ◽

Inpatient Setting ◽

Post Intervention ◽

Paired Samples ◽

Viable Method

Abstract Background Overutilization of antibiotics remains an issue in the inpatient setting. What is more, many protocols geared toward curbing improper antibiotic use rely heavily on resource- and personnel-intensive interventions. Thus, the potential for using the EMR to facilitate antibiotic stewardship remains largely unexplored. Methods We implemented a novel change for ordering certain antibiotics in our EMR: ceftriaxone, daptomycin, ertapenem, imipenem, meropenem, and piperacillin-tazobactam. When ordering one of these antibiotics, providers had to note a usage indication, which assigned a usage duration as per our Antibiotic Stewardship Committee guidelines. Pre-intervention, manual discontinuation was required if a provider did not enter a duration. The intervention was enacted August 2019 in 13 hospitals. Data was collected from January 2018 to February 2020. Antibiotic usage was reported monthly as rate per 1000-patient days. Monthly pre- and post-intervention rates were averaged, respectively. Paired samples t-tests were used to compare pre- and post-intervention rates per unit type per hospital. A p-value of less than 0.05 was considered significant. Units with minimal usage, as defined by a pre- or post-intervention mean of 0, were excluded from analysis. Example of Ordering an Antibiotic Prior to Intervention Example of Ordering an Antibiotic After Intervention Results Ertapenem was noted to have a statistically significant decrease in utilization in seven units at three hospitals. Piperacillin-tazobactam was found to have a decrease in utilization in 19 units at eight hospitals. Daptomycin was found to have a decrease in utilization in one unit. Significant decreases in the utilization of ceftriaxone, imipenem, and meropenem were not noted. Example of Statistically Significant Decreased Utilization in Piperacillin-Tazobactam on a Medical-Surglcal Unit Conclusion Our study showed a statistically significant decrease in use of ertapenem, piperacillin-tazobactam and daptomycin using a simple built-in EMR prompt that curtails provider error. This should allow for an increased ease of integration, as the protocol does not require a host of resources for maintenance. Of note is decreased utilization of piperacillin-tazobactam and ertapenem across multiple hospitals, most notably on the medical and surgical wards. Thus, usage of the EMR without personnel-intensive protocols is a viable method for augmenting antibiotic stewardship in health systems. Disclosures All Authors: No reported disclosures

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Microbial drivers of methane emissions from unrestored industrial salt ponds

The ISME Journal ◽

10.1038/s41396-021-01067-w ◽

2021 ◽

Author(s):

Jinglie Zhou ◽

Susanna M. Theroux ◽

Clifton P. Bueno de Mesquita ◽

Wyatt H. Hartman ◽

Ye Tian ◽

...

Keyword(s):

Microbial Communities ◽

Methane Flux ◽

Methane Emissions ◽

Metagenomic Data ◽

Rrna Gene ◽

Salt Ponds ◽

Salt Pond ◽

Reference Wetlands ◽

Reference Wetland ◽

The Impact

AbstractWetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.01541-09 ◽

2009 ◽

Vol 75 (23) ◽

pp. 7537-7541 ◽

Cited By ~ 11597

Author(s):

Patrick D. Schloss ◽

Sarah L. Westcott ◽

Thomas Ryabin ◽

Justine R. Hall ◽

Martin Hartmann ◽

...

Keyword(s):

16S Rrna ◽

Software Package ◽

Sequence Data ◽

Rrna Gene ◽

Sequencing Data ◽

Laptop Computer ◽

Operational Taxonomic Units ◽

Β Diversity ◽

Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

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Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.054171-0 ◽

2014 ◽

Vol 64 (Pt_2) ◽

pp. 316-324 ◽

Cited By ~ 258

Author(s):

Jongsik Chun ◽

Fred A. Rainey

Keyword(s):

Genomic Sequence ◽

Sequence Data ◽

Original Research ◽

Rrna Gene ◽

New Taxon ◽

Genome Sequences ◽

Microbial World ◽

Content Type ◽

Link Type ◽

Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

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Informing the development of a standardised approach to measure antibiotic use in secondary care: a systematic review protocol

BMJ Open ◽

10.1136/bmjopen-2018-026792 ◽

2019 ◽

Vol 9 (5) ◽

pp. e026792

Author(s):

Selina Patel ◽

Arnoupe Jhass ◽

Susan Hopkins ◽

Laura Shallcross

Keyword(s):

Secondary Care ◽

Scale Up ◽

Antibiotic Use ◽

Antibiotic Consumption ◽

Antibiotic Usage ◽

Prescribing Patterns ◽

Primary Data ◽

Antibiotic Prescribing ◽

Cochrane Central Register ◽

Antibiotic Consumption Surveillance

IntroductionEcological and individual-level evidence indicates that there is an association between level of antibiotic exposure and the emergence and spread of antibiotic resistance. The Global Point Prevalence Survey in 2015 estimated that 34.4% of hospital inpatients globally received at least one antimicrobial. Antimicrobial stewardship to optimise antibiotic use in secondary care can reduce the high risk of patients acquiring and transmitting drug-resistant infections in this setting. However, differences in the availability of data on antibiotic use in this context make it difficult to develop a consensus of how to comparably monitor antibiotic prescribing patterns across secondary care. This review will aim to document and critically evaluate methods and measures to monitor antibiotic use in secondary care.Methods and analysisWe will search Medline (Ovid), Embase (Ovid), Cumulative Index to Nursing and Allied Health Literature, Cochrane Central Register of Controlled Trials and websites of key organisations for published reports where an attempt to measure antibiotic usage among adult inpatients in high-income hospital settings has been made. Two independent reviewers will screen the studies for eligibility, extract data and assess the study quality using the Newcastle-Ottawa scale. A description of the methods and measures used in antibiotic consumption surveillance will be presented. An adaptation of the Affordability, Practicability, Effectiveness, Acceptability, Side-effects Equity framework will be used to consider the practicality of implementing different approaches to measuring antibiotic usage in secondary care settings. A descriptive comparison of definitions and estimates of (in)appropriate antibiotic usage will also be carried out.Ethics and disseminationEthical approval is not required for this study as no primary data will be collected. The results will be published in relevant peer-reviewed journals and presented at relevant conferences or meetings where possible. This review will inform future approaches to scale up antibiotic consumption surveillance strategies to attempt to maximise impact through standardisation.PROSPERO registration numberCRD42018103375

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A new species of trypanosome, Trypanosoma desterrensis sp. n., isolated from South American bats

Parasitology ◽

10.1017/s0031182003003536 ◽

2003 ◽

Vol 127 (3) ◽

pp. 265-271 ◽

Cited By ~ 17

Author(s):

E. C. GRISARD ◽

N. R. STURM ◽

D. A. CAMPBELL

Keyword(s):

New Species ◽

Dna Sequence ◽

Sequence Data ◽

Rrna Gene ◽

South American ◽

Sequence Variability ◽

Dna Sequence Data ◽

Hybridization Probes ◽

5S Rrna Gene ◽

A New Species

Trypanosomes isolated from South American bats include the human pathogen Trypanosoma cruzi. Other Trypanosoma spp. that have been found exclusively in bats are not well characterized at the DNA sequence level and we have therefore used the SL RNA gene to differentiate and characterize kinetoplastids isolated from bats in South America. A Trypanosoma sp. isolated from bats in southern Brazil was compared with the geographically diverse isolates T. cruzi marinkellei, T. vespertilionis, and T. dionisii. Analysis of the SL RNA gene repeats revealed size and sequence variability among these bat trypanosomes. We have developed hybridization probes to separate these bat isolates and have analysed the DNA sequence data to estimate their relatedness. A new species, Trypanosoma desterrensis sp. n., is proposed, for which a 5S rRNA gene was also found within the SL RNA repeat.

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MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

F1000Research ◽

10.12688/f1000research.18866.2 ◽

2019 ◽

Vol 8 ◽

pp. 726

Author(s):

Mike W.C. Thang ◽

Xin-Yi Chua ◽

Gareth Price ◽

Dominique Gorse ◽

Matt A. Field

Keyword(s):

Microbial Communities ◽

Sequence Data ◽

Metagenomic Data ◽

Marker Genes ◽

Metagenomic Sequencing ◽

Differential Analysis ◽

Biomedical Sciences ◽

Metagenomic Sequence ◽

Differential Abundance ◽

Differential Abundance Analysis

Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences. While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs. Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics. MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.

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META-pipe cloud setup and execution

F1000Research ◽

10.12688/f1000research.13204.1 ◽

2017 ◽

Vol 6 ◽

pp. 2060

Author(s):

Aleksandr Agafonov ◽

Kimmo Mattila ◽

Cuong Duong Tuan ◽

Lars Tiede ◽

Inge Alexander Raknes ◽

...

Keyword(s):

Functional Annotation ◽

High Performance ◽

Sequence Data ◽

Metagenomic Data ◽

Taxonomic Profiling ◽

Geographically Distributed ◽

Computationally Intensive ◽

High Performance Computing Cluster ◽

And Storage ◽

Performance Computing

META-pipe is a complete service for the analysis of marine metagenomic data. It provides assembly of high-throughput sequence data, functional annotation of predicted genes, and taxonomic profiling. The functional annotation is computationally demanding and is therefore currently run on a high-performance computing cluster in Norway. However, additional compute resources are necessary to open the service to all ELIXIR users. We describe our approach for setting up and executing the functional analysis of META-pipe on additional academic and commercial clouds. Our goal is to provide a powerful analysis service that is easy to use and to maintain. Our design therefore uses a distributed architecture where we combine central servers with multiple distributed backends that execute the computationally intensive jobs. We believe our experiences developing and operating META-pipe provides a useful model for others that plan to provide a portal based data analysis service in ELIXIR and other organizations with geographically distributed compute and storage resources.

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Epipelic cyanobacterial diversity in Pinang River basin, Malaysia, revealed by 16S-based metagenomic approach

Algologia ◽

10.15407/alg31.01.093 ◽

2021 ◽

Vol 31 (1) ◽

pp. 93-113

Author(s):

A.R. Nur Fadzliana ◽

◽

W.O. Wan Maznah ◽

S.A.M. Nor ◽

Choon Pin Foong ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

River Basin ◽

Sequence Data ◽

Diversity Index ◽

Saline Water ◽

Illumina Miseq ◽

Rrna Gene ◽

Cyanobacterial Community ◽

Upstream Station

Cyanobacteria are the most widespread group of photosynthetic prokaryotes. They are primary producers in a wide variety of habitats and are able to thrive in harsh environments, including polluted waters; therefore, this study was conducted to explore the cyanobacterial populations inhabiting river tributaries with different levels of pollution. Sediment samples (epipelon) were collected from selected tributaries of the Pinang River basin. Air Terjun (T1) and Air Itam rivers (T2) represent the upper streams of Pinang River basin, while Dondang (T3) and Jelutong rivers (T4) are located at in the middle of the river basin. The Pinang River (T5) is located near the estuary and is subjected to saline water intrusion during high tides. Cyanobacterial community was determined by identifying the taxa via 16S rRNA gene amplicon sequence data. 16S rRNA gene amplicons generated from collected samples were sequenced using illumina Miseq, with the targeted V3 and V4 regions yielding approximately 1 mln reads per sample. Synechococcus, Phormidium, Arthronema and Leptolyngbya were found in all samples. Shannon-Weiner diversity index was highest (H’ = 1.867) at the clean upstream station (T1), while the moderately polluted stream (T3) recorded the lowest diversity (H’ = 0.399), and relatively polluted stations (T4 and T5) recorded fairly high values of H’. This study provides insights into the cyanobacterial community structure in Pinang River basin via cultivation-independent techniques using 16S rRNA gene amplicon sequence. Occurrence of some morphospecies at specific locations showed that the cyanobacterial communities are quite distinct and have specific ecological demands. Some species which were ubiquitous might be able to tolerate varied environmental conditions.

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