The Use of Molecular Profiling to Track Equine Reinfection Rates of Cyathostomin Species Following Anthelmintic Administration

Cyathostomins are a multispecies parasite ubiquitous in Equids. Cyathostomins have developed resistance to all but one class of anthelmintics, but species-level sensitivity to anthelmintics has not been shown. This study measured reinfection rates of cyathostomin species following the administration of three commercial dewormers. Nine treated horses were compared with 90 untreated controls during June-September 2017–2019. Ivermectin (IVM) (n = 6), Moxidectin (MOX) (n = 8) or Pyrantel (PYR) (n = 8) were orally administered. Fecal samples were collected every 14 d for 98 d. Fecal egg count reductions (FECR) were calculated using a modified McMaster technique. Nineteen cyathostomin species were identified by 5.8S-ITS-2 profiling using amplicon sequencing. Data were analyzed in QIIME1 and R statistical software using presence/absence methods. MOX had the lowest numbers of species present over the time course, followed by PYR then IVM (7.14, 10.17, 11.09, respectively); however, FECR was fastest for PYR. The presence of seven species: Coronocyclus labiatus, Cyathostomum catinatum, Cyathostomum tetracanthum, Cylicocylus elongatus, Cylicodontophorus bicoronatus, Cylicostephanus minutus, and Cylicostephanus goldi were unaffected by treatment (p > 0.05) points to species-specific differences in dewormer sensitivity and environmental persistence. Identifying resistance patterns at the species level will enable mechanistic understandings of cyathostomin anthelmintic resistance and targeted approaches to control them.

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Detection of anthelmintic resistance in nematodes infecting dairy heifers in Puerto Rico

Archivos Latinoamericanos de Producción Animal ◽

10.53588/alpa.300105 ◽

2021 ◽

Vol 30 (1) ◽

pp. 35-41

Author(s):

Lorraine López-Soberal ◽

Aníbal Ruiz-Lugo ◽

Melvin Pagán-Morales ◽

Esbal Jiménez-Cabán ◽

Guillermo Ortiz-Colón

Keyword(s):

Anthelmintic Resistance ◽

A Priori ◽

Dairy Farm ◽

Anthelmintic Treatment ◽

Nematode Control ◽

Dairy Farmers ◽

Dairy Heifers ◽

Mcmaster Technique ◽

Fecal Egg Count ◽

Integrated Methods

The efficacy of the anthelmintic albendazole (ALB), doramectin (DOR) and ivermectin (IVM) were evaluated in Holstein and Holstein crossbreed dairy heifers using the fecal egg count reduction test (FECRT). Dairy heifers (n=420; ~6 months of age; BW = 149 ± 39.6 kg) were evaluated in 21 dairy farms. All heifers were required to be on pasture and not have been exposed to anthelmintic treatment for a minimum of 3 months. At each dairy farm, a priori, groups of at least 18 heifers were randomly divided to be treated with IVM, or DOR, or ALB following manufacturer's instructions. Fecal samples were collected directly from the rectum 7 days before anthelmintic treatment (d-7), at the time of the treatment (d0), and 14 days after treatment (d14). Only heifers that had an average FEC ³ 100 eggs per gram of feces (average of FEC from day d-7 and d0) were considered in the FECRT. The FECRT was determined by the modified McMaster technique. Of the three-anthelmintic used, ALB (n=142) proved to be the most effective (P < 0.0005) with an efficacy of 67.47% ± 8.43. The efficacy of DOR and IVM did not differ (P = 0.8713). While DOR (n = 130) exhibited a efficacy of 25.50% ± 18.00, IVM (n = 148) exhibited a efficacy of -8.13% ± 19.89 due to an increase in FEC after treatment. Dairy farmers should implement integrated methods of nematode control to preserve the effectiveness of currently available anthelmintics.

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Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates

10.1101/463901 ◽

2018 ◽

Author(s):

Valentina Galata ◽

Cédric C. Laczny ◽

Christina Backes ◽

Georg Hemmrich-Stanisak ◽

Susanne Schmolke ◽

...

Keyword(s):

Antibiotic Resistance ◽

Academic Research ◽

Species Level ◽

Statistical Testing ◽

Clinical Isolates ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Resistance Factors ◽

Resistance Patterns ◽

Resistance Rates

AbstractEmerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly sequenced whole genomes) and culture-based resistance profiles (10,991 of 11,087 isolates were comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns could be observed including increasing resistance rates forAcinetobacter baumanniito carbapenems and forEscherichia colito fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species such as conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene-drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into a resource, GEAR-base, available for academic research use free of charge athttps://gear-base.com.

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Retinitis pigmentosa is associated with shifts in the gut microbiome

Scientific Reports ◽

10.1038/s41598-021-86052-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Oksana Kutsyr ◽

Lucía Maestre-Carballa ◽

Mónica Lluesma-Gomez ◽

Manuel Martinez-Garcia ◽

Nicolás Cuenca ◽

...

Keyword(s):

Retinitis Pigmentosa ◽

Gut Microbiome ◽

Functional Decline ◽

Retinal Disease ◽

Photoreceptor Cells ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sequencing Data ◽

Alpha And Beta Diversity ◽

Potential Biomarker

AbstractThe gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.

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Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽

10.1186/s40168-021-01072-3 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Benjamin J. Callahan ◽

Dmitry Grinevich ◽

Siddhartha Thakur ◽

Michael A. Balamotis ◽

Tuval Ben Yehezkel

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Amplicon Sequencing ◽

Species Level ◽

Full Length ◽

16S Rrna Genes ◽

Rrna Genes ◽

Strain Identification ◽

Long Reads ◽

Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

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Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Nature Communications ◽

10.1038/s41467-021-22203-2 ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 2

Author(s):

Caitlin M. Singleton ◽

Francesca Petriglieri ◽

Jannie M. Kristensen ◽

Rasmus H. Kirkegaard ◽

Thomas Y. Michaelsen ◽

...

Keyword(s):

16S Rrna ◽

Wastewater Treatment Plants ◽

In Situ Hybridisation ◽

Amplicon Sequencing ◽

Rrna Genes ◽

Fluorescence In Situ Hybridisation ◽

Sequencing Data ◽

High Quality ◽

16S Rrna Amplicon Sequencing ◽

Long Read

AbstractMicroorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

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Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia

Communications Biology ◽

10.1038/s42003-021-01723-z ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Anastasiya Börsch ◽

Daniel J. Ham ◽

Nitish Mittal ◽

Lionel A. Tintignac ◽

Eugenia Migliavacca ◽

...

Keyword(s):

Muscle Mass ◽

Inflammatory Responses ◽

Molecular Data ◽

Model Organisms ◽

Sequencing Data ◽

Phenotypic Analysis ◽

Age Related ◽

Analogous Data ◽

Species Specific ◽

And Function

AbstractSarcopenia, the age-related loss of skeletal muscle mass and function, affects 5–13% of individuals aged over 60 years. While rodents are widely-used model organisms, which aspects of sarcopenia are recapitulated in different animal models is unknown. Here we generated a time series of phenotypic measurements and RNA sequencing data in mouse gastrocnemius muscle and analyzed them alongside analogous data from rats and humans. We found that rodents recapitulate mitochondrial changes observed in human sarcopenia, while inflammatory responses are conserved at pathway but not gene level. Perturbations in the extracellular matrix are shared by rats, while mice recapitulate changes in RNA processing and autophagy. We inferred transcription regulators of early and late transcriptome changes, which could be targeted therapeutically. Our study demonstrates that phenotypic measurements, such as muscle mass, are better indicators of muscle health than chronological age and should be considered when analyzing aging-related molecular data.

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PSV-37 Reemergence of cyathostomins species demonstrates anthelmintic resistance following drug administration in horses

Journal of Animal Science ◽

10.1093/jas/skaa278.596 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 335-335

Author(s):

Alexa C Johnson ◽

Amy S Biddle

Keyword(s):

Anthelmintic Resistance ◽

Macrocyclic Lactones ◽

Number Of Species ◽

Molecular Approaches ◽

Pyrantel Pamoate ◽

Drug Classes ◽

Blast Database ◽

Resistance Patterns ◽

Near Future ◽

Ncbi Blast

Abstract Arbitrary administration of anthelmintics to control equine gastrointestinal worms has led to increased resistance to the three broad-spectrum drug classes; benzimidazoles, tetrahydropyrimidines, and macrocyclic lactones. With little promise of new drug classes to target cyathostomins being introduced to the market in the near future, anthelmintic drugs must be administered judiciously to prevent complete anthelmintic parasite resistance. The objective of this study is to determine the reemergence rate of cyathostomins following three commercial horse dewormers during summer. Nine horses housed at two locations were enrolled to the study and was repeated June–September through 2017–2019. Horses were removed from the study if sequencing failed due to low egg recovery for more than 50% of the timepoints. Ivermectin (macrocyclic lactones; n = 6), Moxidectin (macrocyclic lactones; n = 8) and Strongid (pyrantel pamoate; n = 8) were administered to horses and fecal samples were collected every 14d for 98d. Samples were tested using fecal egg counts with a modified McMaster technique and 18S rRNA profiling of the V5.8 and ITS1 regions. Sequences were clustered and taxonomy was assigned against a custom NCBI Blast+ database with the aligned sequences of 19 cyathostomins. Data were analyzed using presence/absence methods in R studio. Treatment and Day significantly impacted the average number of species present (P < 0.001). Moxidectin had the lowest number of species present followed by Strongid then Ivermectin (7.14, 10.17, 11.09, respectively). Equine shedder status had no effect on the average number of species present (P > 0.05). Six species, CO. labiatus, CS. catinatum, CY. auriculatus, CY. elongatus, CT. goldi and CT. longibursatus, showed resistance to the three treatments (P > 0.05). Moxidectin was the most effective at eradicating cyathostomins infestations (P < 0.05). Identifying resistance patterns at the species level will enable mechanistic molecular approaches to determine anthelmintic resistance in cyathostomins.

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From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data

GigaScience ◽

10.1093/gigascience/giw017 ◽

2017 ◽

Vol 6 (2) ◽

Cited By ~ 16

Author(s):

Mohamed Mysara ◽

Mercy Njima ◽

Natalie Leys ◽

Jeroen Raes ◽

Pieter Monsieurs

Keyword(s):

Amplicon Sequencing ◽

Sequencing Data ◽

Operational Taxonomic Units ◽

Processing Pipeline

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Pulmonary cytochrome P-450 monooxygenase system and Clara cell differentiation in rats

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.1995.269.3.l394 ◽

1995 ◽

Vol 269 (3) ◽

pp. L394-L402 ◽

Cited By ~ 4

Author(s):

C. M. Ji ◽

W. V. Cardoso ◽

A. Gebremichael ◽

R. M. Philpot ◽

A. R. Buckpitt ◽

...

Keyword(s):

Protein Expression ◽

Time Course ◽

Smooth Endoplasmic Reticulum ◽

Volume Density ◽

Clara Cell ◽

Developmental Expression ◽

Monooxygenase System ◽

Clara Cells ◽

Developmental Patterns ◽

Species Specific

Because a number of studies suggest that the developmental expression of cytochrome P-450s (CYP) in Clara cells is species specific, this study was designed to compare the developmental patterns of the isoform CYP2B and NADPH reductase protein expression and CYP2B activity with the time course of smooth endoplasmic reticulum (SER) formation in Clara cells of rat lung. Pulmonary CYP2B activity measured as pentoxyresorufin O-dealkylation in lung homogenates was not detectable before 7 days postnatal age, but was detectable at adult levels at 50 days postnatal age. In Clara cells, CYP2B and NADPH reductase were detected immunohistochemically at 4 days postnatal age and at adult levels at 10 days postnatal age. The volume density of SER in Clara cells of terminal bronchioles measured morphometrically increased significantly with postnatal age. We conclude that in the rat 1) CYP2B and NADPH reductase distribution and CYP2B activity are age dependent; 2) the increase in Clara cell SER precedes the expression of CYP2B protein; 3) cellular appearance of CYP2B protein precedes CYP activity; and 4) SER appearance and P-450 protein expression do not occur uniformly in differentiating Clara cells, even within the same bronchiole.

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Drug resistance and plasmid profile of shigellae in Taiwan

Epidemiology and Infection ◽

10.1017/s0950268800049530 ◽

1992 ◽

Vol 108 (1) ◽

pp. 87-97 ◽

Cited By ~ 7

Author(s):

S.-R. Lin ◽

S.-F. Chang

Keyword(s):

Drug Resistance ◽

Antimicrobial Agents ◽

Plasmid Profile ◽

Resistance Pattern ◽

Multiple Resistance ◽

College Hospital ◽

Medical College ◽

Transmissible Plasmid ◽

Resistance Patterns ◽

Species Specific

SUMMARYOne hundred and twenty-eight shigella strains isolated from newborn and infant human faecal specimens at Kaohsiung Medical College Hospital in Taiwan were serogrouped, serotyped and examined for drug-resistance patterns and for the presence of plasmids. Forty-seven pre cent of the isolates were found to belong to theShigella sonneiserogroup, 41%to theS.flexnerigroup,9%to theS.boydiigroup and 3%to theS.dysenteriaegroup.The serotype with the greatest number of strains wasS.sonneiI. (29 %) followed byS. flexneri1 (27%). Each strain was tested for resistance to 11 antimicrobial agents. Eighty-eight per cent of the strains were resistant to tetracycline, 87% to chloramphenicol, 84% to streptomycin, 52% to ampicillin, 25% to nalidixic acid, 29% to kanamycin, 11 % to cephalothin, 11% to neomycin, 10% to cotrimoxazole, 1% to amikacin and none to gentamicin. The most prevalent resistance pattern was ApCmSmTc (28%). Clinical isolates demonstrating multiple resistance were found to harbour a large transmissible plasmid of 45–75 MDa while isolates without multiple resistance did not. Two large virulence plasmids of 123 and 110 MDa were found in 12 strains ofS. flexneriand 4 strains ofS. sonneiphase I. Small plasmids of 4·5, 4·2, 3·5, 2·8, 2·5. 2·0 and 1·5 MDa were also present in all strains. These small plasmids were species specific and can be used as marker plasmids to identify species.

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