Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian, EH26 0PZ, UK.
Biomathematics and Statistics Scotland, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
BMC Genomics. 2021 Mar 6;22(1):159. doi: 10.1186/s12864-021-07477-6.
Chlamydia 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.
In 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.
Overall, 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.
鹦鹉热衣原体和流产衣原体分别是家畜和禽类的重要病原体。虽然已确认流产衣原体是从鹦鹉热衣原体物种中衍生而来的，但有越来越多的证据表明存在两种物种之间的中间菌株，这表明它们是流产衣原体的最近进化祖先。这些菌株包括从鹦鹉中分离出的鹦鹉热衣原体菌株 84/2334。我们的目的是通过测序其基因组对该菌株进行分类，并探讨其与流产衣原体和鹦鹉热衣原体的进化关系。
在这项研究中，基于七个管家基因的多位点序列分型（MLST）方法和五种物种鉴别蛋白的分型方法表明，菌株 84/2334 与流产衣原体物种聚类。此外，该菌株的全基因组从头测序显示，在 GC 含量方面与流产衣原体更为相似，而 16S rRNA 和全基因组系统发育分析以及网络和重组分析表明，该菌株与流产衣原体菌株聚类更为密切。该分析还表明，与其他两种中间禽类流产衣原体菌株或鹦鹉热衣原体菌株相比，该菌株与主要流产衣原体谱系之间的进化关系更为密切。对基因（多态性膜蛋白和跨膜头部蛋白基因）和基因座（可塑性区）的分子分析，这些基因座和基因座存在于与种内和种间多样性最大相关的关键毒力相关区域，表明与已测序的流产衣原体基因组相比，该菌株具有更大的多样性，并且与流产衣原体和鹦鹉热衣原体物种具有相似的特征。该菌株还具有染色体外质粒，这在大多数鹦鹉热衣原体物种中发现，但在所有已测序的经典流产衣原体菌株中均不存在。
总的来说，结果表明，鹦鹉热衣原体菌株 84/2334 与流产衣原体菌株非常密切聚类，并且与该菌株是流产衣原体的最近祖先物种一致。这表明该菌株应重新分类为流产衣原体。此外，鉴定出携带染色体外质粒的流产衣原体菌株，这对基于质粒的转化研究具有重要意义，可用于研究基因功能，并为保护家畜免受流产衣原体感染提供下一代疫苗的潜在途径。
