Evidence map›Paper›PMID 32143704›Full record

ArticleParasites & vectors2020

Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing.

Hediye Nese Cinar, Gopal Gopinath, Helen R Murphy, Sonia Almeria, Mauricio Durigan, Dajung Choi, AhYoung Jang, Eunje Kim, RaeYoung Kim, Seonju Choi and 7 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Parasites & vectors, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
3.5field-weighted citation impact, top 7% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed, 25 citations in OpenAlex.

  1. Article
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  7. Hastening Progress inMicroorganisms · 2022
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors at 5 institutions in 1 country.

Hediye Nese CinarCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA. hediye.cinar@fda.hhs.gov.
Gopal GopinathCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Helen R MurphyCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Sonia AlmeriaCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Mauricio DuriganCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Dajung ChoiCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
AhYoung JangCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Eunje KimCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
RaeYoung KimCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Seonju ChoiCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Jeongu LeeCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Yurim ShinCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Jieon LeeCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Yvonne QvarnstromDivision of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Theresa K BenedictDivision of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Henry S BishopDivision of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Alexandre da SilvaCenter for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
Center for Food Safety and Applied Nutrition · USUnited States Food and Drug Administration · USCenter for Global Health · USCenters for Disease Control and Prevention · USDivision of Parasitic Diseases and Malaria · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundOutbreaks of cyclosporiasis, a diarrheal illness caused by Cyclospora cayetanensis, have been a public health issue in the USA since the mid 1990's. In 2018, 2299 domestically acquired cases of cyclosporiasis were reported in the USA as a result of multiple large outbreaks linked to different fresh produce commodities. Outbreak investigations are hindered by the absence of standardized molecular epidemiological tools for C. cayetanensis. For other apicomplexan coccidian parasites, multicopy organellar DNA such as mitochondrial genomes have been used for detection and molecular typing.

methodsWe developed a workflow to obtain complete mitochondrial genome sequences from cilantro samples and clinical samples for typing of C. cayetanensis isolates. The 6.3 kb long C. cayetanensis mitochondrial genome was amplified by PCR in four overlapping amplicons from genomic DNA extracted from cilantro, seeded with oocysts, and from stool samples positive for C. cayetanensis by diagnostic methods. DNA sequence libraries of pooled amplicons were prepared and sequenced via next-generation sequencing (NGS). Sequence reads were assembled using a custom bioinformatics pipeline.

resultsThis approach allowed us to sequence complete mitochondrial genomes from the samples studied. Sequence alterations, such as single nucleotide polymorphism (SNP) profiles and insertion and deletions (InDels), in mitochondrial genomes of 24 stool samples from patients with cyclosporiasis diagnosed in 2014, exhibited discriminatory power. The cluster dendrogram that was created based on distance matrices of the complete mitochondrial genome sequences, indicated distinct strain-level diversity among the 2014 C. cayetanensis outbreak isolates analyzed in this study.

conclusionsOur results suggest that genomic analyses of mitochondrial genome sequences may help to link outbreak cases to the source.

Indexed as

Base SequenceCluster AnalysisComputational BiologyCyclosporaCyclosporiasisDNA, ProtozoanFecesGenome, MitochondrialGenotyping TechniquesHigh-Throughput Nucleotide SequencingHumansMolecular TypingOocystsPhylogenyPolymerase Chain ReactionPolymorphism, Single NucleotideDNA, ProtozoanCyclospora cayetanensisGenotypingMitochondria genomeNext-generation sequencing

Identifiers

PMID32143704
PMCPMC7060604
OpenAlexW3011360748

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.