Dataset Information

Data of de novo genome assembly of the Chlamydia psittaci strain isolated from the livestock in Volga Region, Russian Federation.

ABSTRACT: Chlamydiae are obligate intracellular bacteria globally widespread across humans, wildlife, and domesticated animals. Chlamydia psittaci is a primarily zoonotic pathogen with multiple hosts, which can be transmitted to humans, resulting in psittacosis or ornithosis. Since this pathogen is a well-recognized threat to human and animal health, it is critical to unravel in detail the genetic make-up of this microorganism. Though many genomes of C. psittaci have been studied to date, little is known about the variants of chlamydial organisms causing infection in Russian livestock. This research is the first de novo genome assembly of the C. psittaci strain Rostinovo-70 of zoonotic origin that was isolated in Russian Federation. The results were obtained by using standard protocols of sequencing with the Illumina HiSeq 2500 and Oxford Nanopore MinION technology that generated 3.88 GB and 3.08 GB of raw data, respectively. The data obtained are available in NCBI DataBase (GenBank accession numbers are CP041038.1 & CP041039.1). The Multi-Locus Sequence Typing (MLST) showed that the strain Rostinovo-70 together with C. psittaci GR9 and C. psittaci WS/RT/E30 belong to the sequence type (ST)28 that could be further separated into two different clades. Despite C. psittaci Rostinovo-70 and C. psittaci GR9 formed a single clade, the latter strain did not contain a cryptic plasmid characteristis to Rostinovo-70. Moreover, the genomes of two strains differed significantly in the cluster of 30 genes that in Rostinovo-70 were closer to Chlamydia abortus rather than C. psittaci. The alignment of the genomes of C. psittaci and C. abortus in this area revealed the exact boarders of homologous recombination that occurred between two Chlamydia species. These findings provide evidence for the first time of genetic exchange between closely related Chlamydia species.

SUBMITTER: Feodorova VA

PROVIDER: S-EPMC7015991 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Data of de novo genome assembly of the Chlamydia psittaci strain isolated from the livestock in Volga Region, Russian Federation.

Feodorova Valentina A VA Zaitsev Sergey S SS Khizhnyakova Mariya A MA Saltykov Yury V YV Evstifeev Vitaliy V VV Khusainov Fidail M FM Yakovlev Sergey I SI Larionova Olga S OS Motin Vladimir L VL

Data in brief 20200127

Chlamydiae are obligate intracellular bacteria globally widespread across humans, wildlife, and domesticated animals. Chlamydia psittaci is a primarily zoonotic pathogen with multiple hosts, which can be transmitted to humans, resulting in psittacosis or ornithosis. Since this pathogen is a well-recognized threat to human and animal health, it is critical to unravel in detail the genetic make-up of this microorganism. Though many genomes of C. psittaci have been studied to d ...[more]

PMID: 32071972

Similar Datasets

Project description:BackgroundChlamydia abortus and Chlamydia psittaci are important pathogens of livestock and avian species, respectively. While C. abortus is recognized as descended from C. psittaci species, there is emerging evidence of strains that are intermediary between the two species, suggesting they are recent evolutionary ancestors of C. abortus. Such strains include C. psittaci strain 84/2334 that was isolated from a parrot. Our aim was to classify this strain by sequencing its genome and explore its evolutionary relationship to both C. abortus and C. psittaci.ResultsIn this study, methods based on multi-locus sequence typing (MLST) of seven housekeeping genes and on typing of five species discriminant proteins showed that strain 84/2334 clustered with C. abortus species. Furthermore, whole genome de novo sequencing of the strain revealed greater similarity to C. abortus in terms of GC content, while 16S rRNA and whole genome phylogenetic analysis, as well as network and recombination analysis showed that the strain clusters more closely with C. abortus strains. The analysis also suggested a closer evolutionary relationship between this strain and the major C. abortus clade, than to two other intermediary avian C. abortus strains or C. psittaci strains. Molecular analyses of genes (polymorphic membrane protein and transmembrane head protein genes) and loci (plasticity zone), found in key virulence-associated regions that exhibit greatest diversity within and between chlamydial species, reveal greater diversity than present in sequenced C. abortus genomes as well as similar features to both C. abortus and C. psittaci species. The strain also possesses an extrachromosomal plasmid, as found in most C. psittaci species but absent from all sequenced classical C. abortus strains.ConclusionOverall, the results show that C. psittaci strain 84/2334 clusters very closely with C. abortus strains, and are consistent with the strain being a recent C. abortus ancestral species. This suggests that the strain should be reclassified as C. abortus. Furthermore, the identification of a C. abortus strain bearing an extra-chromosomal plasmid has implications for plasmid-based transformation studies to investigate gene function as well as providing a potential route for the development of a next generation vaccine to protect livestock from C. abortus infection.

Project description:African swine fever (ASF) is an incurable viral disease of domestic and wild pigs. A large-scale spread of ASF began in Eurasia in 2007 and has affected territories from Belgium to the Far East, occurring as both local- and regional-level epidemics. In 2020, a massive ASF epidemic emerged in the southeastern region of European Russia in the Samara Oblast and included 41 outbreaks of ASF in domestic pigs and 40 cases in wild boar. The Samara Oblast is characterized by a relatively low density of wild boar (0.04-0.05 head/km2) and domestic pigs (1.1-1.3 head/km2), with a high prevalence of small-scale productions (household farms). This study aims to understand the driving forces of the disease and perform a risk assessment for this region using complex epidemiological analyses. The socioeconomic and environmental factors of the ASF outbreak were explored using Generalized Linear Logistic Regression, where ASF infection status of the Samara Oblast districts was treated as a response variable. Presence of the virus in a district was found to be most significantly (p < 0.05) associated with the importation of live pigs from ASF-affected regions of Russia (OR = 371.52; 95% CI: 1.58-87290.57), less significantly (p < 0.1) associated with the density of smallholder farms (OR = 2.94; 0.82-10.59), volume of pork products' importation from ASF-affected regions of Russia (OR = 1.01; 1.00-1.02), summary pig population (OR = 1.01; 0.99-1.02), and insignificantly (p > 0.1) associated with presence of a common border with an ASF-affected region (OR = 89.2; 0.07-11208.64). No associations were found with the densities of pig and wild boar populations. The colocation analysis revealed no significant concentration of outbreaks in domestic pigs near cases in wild boar or vice versa. These results suggest that outbreaks notified in low biosecurity household farms were mainly associated with the transportation and trade of pigs and pork products from ASF-affected regions of Russia. The findings underline the importance of taking into account animal transportation data while conducting future studies to develop a risk map for the region and the rest of European Russia.

Dataset Information

Data of de novo genome assembly of the Chlamydia psittaci strain isolated from the livestock in Volga Region, Russian Federation.

Publications

Data of <i>de novo</i> genome assembly of the <i>Chlamydia psittaci</i> strain isolated from the livestock in Volga Region, Russian Federation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets