Multi Locus Sequence Typing of Chlamydia Reveals an Association between Chlamydia psittaci Genotypes and Host Species

Abstract

Chlamydia comprises a group of obligate intracellular bacterial parasites responsible for a variety of diseases in humans and animals, including several zoonoses. Chlamydia trachomatis causes diseases such as trachoma, urogenital infection and lymphogranuloma venereum with severe morbidity. Chlamydia pneumoniae is a common cause of community-acquired respiratory tract infections. Chlamydia psittaci, causing zoonotic pneumonia in humans, is usually hosted by birds, while Chlamydia abortus, causing abortion and fetal death in mammals, including humans, is mainly hosted by goats and sheep. We used multi-locus sequence typing to asses the population structure of Chlamydia. In total, 132 Chlamydia isolates were analyzed, including 60 C. trachomatis, 18 C. pneumoniae, 16 C. abortus, 34 C. psittaci and one of each of C. pecorum, C. caviae, C. muridarum and C. felis. Cluster analyses utilizing the Neighbour-Joining algorithm with the maximum composite likelihood model of concatenated sequences of 7 housekeeping fragments showed that C. psittaci 84/2334 isolated from a parrot grouped together with the C. abortus isolates from goats and sheep. Cluster analyses of the individual alleles showed that in all instances C. psittaci 84/2334 formed one group with C. abortus. Moving 84/2334 from the C. psittaci group to the C. abortus group resulted in a significant increase in the number of fixed differences and elimination of the number of shared mutations between C. psittaci and C. abortus. C. psittaci M56 from a muskrat branched separately from the main group of C. psittaci isolates. C. psittaci genotypes appeared to be associated with host species. The phylogentic tree of C. psittaci did not follow that of its host bird species, suggesting host species jumps. In conclusion, we report for the first time an association between C. psittaci genotypes with host species.

Multilocus Sequence Analysis Provides Insights into Molecular Epidemiology of Chlamydia pecorum Infections in Australian Sheep, Cattle, and Koalas

“…This limited diversity of the C. pecorum species is consistent with the diversity observed in other members of the genus Chlamydia, particularly that observed from MLSA and MLST analysis of the closely related chlamydial species C. pneumoniae (30,49). The number of synonymous substitutions detected in C. pecorum was comparable to those observed in Chlamydia abortus and C. psittaci (31). Our Australian C. pecorum strains had diversity of 0.4 ST/per strain, which is consistent with observations across the Chlamydiae in general (31,44).…”

“…Diversity within livestock and koala C. pecorum populations as assessed by MLSA. MLSA of Chlamydia HK genes has previously been shown to reflect the level of genetic diversity present across the genome among representative species of Chlamydiae (30,31,46). To confirm whether similar observations could be made for C. pecorum, we analyzed the genetic diversity within and between C. pecorum isolates by assessing d n /d s ratios, the number of sequence types (STs), and divergence between different C. pecorum populations based on their respective hosts and/or biogeographical origins.…”

“…A number of studies have reported the use of multilocus sequence typing (MLST) (28) and multilocus sequence analysis (MLSA) to elucidate intraspecies relationships between members of the genus Chlamydia (29,30), including analyses of strains from the same species that infect multiple animal hosts (31). These methods utilize the concatenation of four to 12 evolutionarily conserved housekeeping (HK) gene sequence fragments.…”

Improving the molecular diagnosis of Chlamydia psittaci and Chlamydia abortus infection with a species-specific duplex real-time PCR

“…Despite their distinct host and tissue tropism, C. psittaci and C. abortus are phylogenetically so closely related that it is difficult to design a species-specific PCR targeting housekeeping genes, such as the 16S rRNA gene (Pannekoek et al, 2010;Lienard et al, 2011). Thus, the aim of this study was to develop a new RT-PCR-based method that could reliably detect and differentiate these two pathogens in clinical samples that could be used in routine diagnostic laboratories.…”

Multilocus Variable-Number Tandem-Repeat Analysis Scheme for Chlamydia felis Genotyping: Comparison with Multilocus Sequence Typing

“…MLST based on the partial sequences of seven housekeeping genes was recently used to understand the population genetic structure of C. trachomatis, C. pneumoniae (24), and C. psittaci (25). Results of cluster analyses of concatenated sequences of the seven housekeeping genes validated the proposed typing system for all chlamydial species.…”