Extensive genomic divergence among 61 strains ofChlamydia psittaci

Abstract

Chlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains. Initially, poorly assembled genomes in public databases were subjected to clean-up, reassembly and polishing. Multiple sequence alignment of the genome sequences revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Clades 2-4 carry strains from different non-psittacine hosts. We found that clade membership correlates with classification schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin OmpA can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps). Altogether, our study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains.

Whole genome sequencing characteristics of Chlamydia psittaci caprine AMK-16 strain, a promising killed whole cell veterinary vaccine candidate against chlamydia infection

“…It is not clear whether or not some of them could be involved into the protective immune response conferring by the immunization of animal models with the AMK-16. These findings agree with the recent research, in which PZ has been carefully investigated in a number of C. psittaci strains [62].…”

“…The same six genes, encoding: (i) MAC/perforin family protein, (ii) GMP synthase [glutamine-hydrolyzing], amidotransferase subunit (EC 6.3.5.2)/GMP synthase [glutaminehydrolyzing], ATP pyrophosphatase subunit (EC 6.3.5.2), (iii) Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205)/CBS domain, and (iv-vi) three hypothetical proteins were missing in both AMK-16 and the GR9 in contrast to the 6BC (S6 Table in S1 File). In agreement with the recent report [62], similar modifications in the relevant regions were found in four phylogenetically close strains, the Rostinovo-70, the WS/RT/E30, the CPS-QD/LS and the LS-QXC01, but not in the other three more distant strains, the Full127, the Mat116 and the WC (Fig…”

“…Furthermore, the AMK-16 had the GC content typical for C. psittaci [23] and belonged to ST28 which includes a number of C. psittaci strains (Fig 4a). Overall, this clustering was in agreement with the MLST clustering reported earlier [54,62,64,70]. However, the AMK-16 became the second strain after the Rostinovo-70 grouped with the C. psittaci group II, which had initially included mainly the duck strains [54,64].…”

“…The AMK-16 formed a single branch only with another C. psittaci strain, also isolated from small ruminants [22], the C. psittaci Rostinovo-70 (Fig 1). The C. psittaci strain GR9, which was earlier (in 1960) isolated from a mallard in Germany [61], was identified as the closest homologue similarly with another study [62] and used as the reference one. Importantly, the C. psittaci strain 6BC, which was earlier recognized as the reference strain for the majority of C. psittaci representatives [63], formed another separate cluster of 15 relevant homologous strains.…”

Pangenome calculation beyond the species level using RIBAP: A comprehensive bacterial core genome annotation pipeline based on Roary and pairwise ILPs

“…Here we present RIBAP (Roary ILP Bacterial core Annotation Pipeline), a comprehensive bacterial pangenome annotation pipeline based on Roary (Page et al 2015) and pairwise integer linear programs (ILPs) as introduced by (Martinez et al 2015). The development of the pipeline was motivated by our comparative genome studies on different Chlamydia species (Hölzer et al 2020;Vorimore et al 2021;Sachse et al 2022). Here, we could not calculate meaningful core genome sets based on experts' evaluation using the available pangenome tools without lowering the sequence similarity cutoff well below the values recommended by the pipeline authors.…”