Identification of the taxonomic affiliation of Cryptosporidium spp. in piglets in the conditions of the north-west of the Russian Federation using molecular genetic methods

Kryazhev, A. L.; Новиков, А С

doi:10.31016/1998-8435-2023-17-1-84-90

Cited by 3 publications

(2 citation statements)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The identification of cryptosporidia to a species in fecal samples of farm animals was carried out according to a previously developed technique [16] using two rounds of highperformance sequencing of amplicon libraries of fragments of the 18S rRNA gene obtained as a result of nested PCR using specialized methods [18][19] followed by demultiplexing of samples, "denoising", combining sequences (minimum overlap in 12 nucleotides), restoration of the original phylotypes (ASV, (Amplicon sequence variant)) and removal of chimeric readings [20]. The taxonomic affiliation of the sequences was determined using blastn in the GenBank database [16].…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

RETRACTED: Features of prevalence of ASV types of Cryptosporidium scrofarum in pig farms in the Northwestern of Russia

Kryazhev,

Novikov

2024

BIO Web Conf.

View full text Add to dashboard Cite

For the first time in the Russian Federation, using the example of the Vologda region of the North-West of the Russian Federation in pig farms by high-performance sequencing of amplicon libraries of fragments of the 18S rRNA gene obtained as a result of nested PCR, we have established parasitization of Cryptosporidium scrofarum in pigs of all age groups. The infection rate of animals kept in pig farms was 34%, in farms – 32.4%. Piglets that are fattening at the age of 13-24 weeks are most susceptible to infection. The analysis of the taxonomic affiliation of ASV carried out using phylogenetic analysis, supplemented by analysis using the blastn algorithm in the GenBank database, showed that in total, 10 ASV types (amplicon sequence variant) with high similarity to sequences deposited in GenBank as fragments of the Cryptosporidium scrofarum 18S rRNA gene are present in all the samples studied. It was found that the ASV1 and ASV2 types detected in various geographical regions of the world from Portugal and Great Britain to China, India and Australia were identified in all surveyed farms, although in significantly different quantities. The remaining ASVS belong to local populations of C. scrofarum subspecies. A unique sequence of the genus Cryptosporidium of type ASV 8 has been discovered, which can later be described as a new species. The nucleotide sequences we have discovered are unique. Each of them was deposited in GenBank with the assignment of identifiers (Sequence ID: OR649139, OR654022, OR654023, OR661243, OR661244, OR654051, OR654052, OR654083, OR654084, OR654106).

show abstract

Section: Methodsmentioning

confidence: 99%

“…Earlier, we used molecular genetic studies to study the taxonomic affiliation of pig cryptosporidia in the conditions of the Northwestern Federal District of the Russian Federation and identified the species Cryptosporidium scrofarum [16].…”

Section: Introductionmentioning

confidence: 99%

RETRACTED: Features of prevalence of ASV types of Cryptosporidium scrofarum in pig farms in the Northwestern of Russia

Kryazhev,

Novikov

2024

BIO Web Conf.

View full text Add to dashboard Cite

show abstract

ASV (Amplicon Sequence Variant) taxonomic affiliation analysis of <i>Cryptosporidium scrofarum</i> species in pigs in the Vologda Region, the Northwestern Federal District of the Russian Federation

Kryazhev,

Novikov

2024

Ross. parazitol. ž..

View full text Add to dashboard Cite

The purpose of the research is isolation, identification, and analysis of ASV (Amplicon Sequence Variant) types of Cryptosporidia spp. in pigs in the Vologda Region of the Russian Federation.Materials and methods. The research has been conducted in the Russian Federation for the first time. The research was conducted on pig farms in the Vologda Region of the Northwestern Federal District of the Russian Federation from January to October 2023. Feces were taken from piglets of various age groups, as well as milking sows. The samples were studied using the equipment of the resource center “Genomic Technologies, Proteomics and Cell Biology” of ARRIAM. Species of the genus Cryptosporidia were identified in fecal samples using high-throughput sequencing of 18S rRNA gene fragment amplicon libraries as obtained from nested PCR followed by “denoising”, sequence combining, and restoring the original phylotypes (ASV, (Amplicon Sequence Variant)).Results and discussion. Cryptosporidia spp. species were identified in each age group studied. As a result of high-throughput sequencing of the libraries using the Illumina technology, 20 to 100 thousand nucleotide sequences (reads) were obtained for each sample after processing of which a total of 2,372 ASVs were identified. The analysis of the ASV taxonomic affiliation performed with phylogenetic analysis supplemented by an analysis using the blastn algorithm in the GenBank database showed that, in total, 10 ASVs were only present in all studied samples that had high similarity to sequences deposited in the GenBank as 18S rRNA gene fragments of Cryptosporidium scrofarum. Eight ASV types were unique and did not repeat from farm to farm. Probably, these sequences belong to local populations of C. scrofarum subspecies. Of interest is the discovery of a unique Cryptosporidium sequence of ASV8 type which is only 91.47% similar to the closest relative of the genus, which may indicate a rather distant taxonomic relationship. This type of nucleotide sequence can be further described as a new species. All identified unique ASV nucleotide sequences were deposited in GenBank.

show abstract

Molecular characteristics of Cryptosporidium scrofarum in pig farms of the Vologda region of the Northwestern Federal District of the Russian Federation

Kryazhev,

Novikov

2023

jour

View full text Add to dashboard Cite

The purpose of these studies was to identify, identify, analyze and study the distribution of Cryptosporidium scrofarum in pigs in the farms of the Vologda Region of the Northwestern Federal District of the Russian Federation.For the first time in the Russian Federation, using the example of the Vologda Oblast of the Northwestern Federal District in pig farms of various types using the latest molecular genetic methods, namely using high-throughput sequencing of amplicon libraries of fragments of the 18S rRNA gene obtained because of nested PCR, we have established the infection of C. scrofarum in all age groups of examined animals. The contamination of animals kept in pig farms was 34%, in farms - 32.4%. Animals that are fattened at the age of 13-24 weeks are most susceptible to infection.Analysis of ASV taxonomic affiliation using phylogenetic analysis, supplemented by analysis using the blastn algorithm in the GenBank database, showed that a total of 10 ASV types (amplicon sequence variant) are present in all tested samples, which have high similarity to sequences deposited in GenBank as fragments of the 18S p gene Cryptosporidium scrofarum RNA. It has been established that the types of ASV1 and ASV2 detected in various geographical regions of the world from Portugal and Great Britain to China, India and Australia are identified in all examined farms, although in significantly different quantities. The remaining ASVs are present in much smaller numbers and do not repeat from farm to farm. These sequences probably belong to local populations of subspecies Cryptosporidium scrofarum. It is interesting to find a unique sequence of the genus Cryptosporidium of type ASV8, which can later be described as a new species.

show abstract

Identification of the taxonomic affiliation of Cryptosporidium spp. in piglets in the conditions of the north-west of the Russian Federation using molecular genetic methods

Cited by 3 publications

References 7 publications

RETRACTED: Features of prevalence of ASV types of Cryptosporidium scrofarum in pig farms in the Northwestern of Russia

RETRACTED: Features of prevalence of ASV types of Cryptosporidium scrofarum in pig farms in the Northwestern of Russia

ASV (Amplicon Sequence Variant) taxonomic affiliation analysis of <i>Cryptosporidium scrofarum</i> species in pigs in the Vologda Region, the Northwestern Federal District of the Russian Federation

Molecular characteristics of Cryptosporidium scrofarum in pig farms of the Vologda region of the Northwestern Federal District of the Russian Federation

Contact Info

Product

Resources

About