Abstract
BackgroundChlamydia (C.) gallinacea is a recently identified bacterium that mainly infects domestic chickens. Demonstration of C. gallinacea in human atypical pneumonia suggests its zoonotic potential. Its prevalence in chickens exceeds that of C. psittaci, but genetic and genomic research on C. gallinacea is still at the beginning. In this study, we conducted whole-genome sequencing of C. gallinacea strain JX-1 isolated from an asymptomatic chicken, and comparative genomic analysis between C. gallinacea strains and related chlamydial species.ResultsThe genome of C. gallinacea JX-1 was sequenced by single-molecule, real-time technology and is comprised of a 1,059,522-bp circular chromosome with an overall G + C content of 37.93% and sequence similarity of 99.4% to type strain 08-1274/3. In addition, a plasmid designated pJX-1, almost identical to p1274 of the type strain, except for two point mutations, was only found in field strains from chicken, but not in other hosts. In contrast to chlamydial species with notably variable polymorphic membrane protein (pmp) genes and plasticity zone (PZ), these regions were conserved in both C. gallinacea strains. There were 15 predicted pmp genes, but only B, A, E1, H, G1 and G2 were apparently intact in both strains. In comparison to chlamydial species where the PZ may be up to 50 kbp, C. gallinacea strains displayed gene content reduction in the PZ (14 kbp), with strain JX-1 having a premature STOP codon in the cytotoxin (tox) gene, while tox gene is intact in the type strain. In multilocus sequence typing (MLST), 15 C. gallinacea STs were identified among 25 strains based on cognate MLST allelic profiles of the concatenated sequences. The type strain and all Chinese strains belong to two distinct phylogenetic clades. Clade of the Chinese strains separated into 14 genetically distinct lineages, thus revealing considerable genetic diversity of C. gallinacea strains in China.ConclusionsIn this first detailed comparative genomic analysis of C. gallinacea, we have provided evidence for substantial genetic diversity among C. gallinacea strains. How these genetic polymorphisms affect C. gallinacea biology and pathogenicity should be addressed in future studies that focus on phylogenetics and host adaption of this enigmatic bacterial agent.
Highlights
Chlamydia (C.) gallinacea is a recently identified bacterium that mainly infects domestic chickens
Recent reports showed that C. gallinacea and C. avium are two emerging chlamydial agents that can be involved in avian chlamydiosis [1]
We describe the second wholegenome sequence (WGS) of C. gallinacea, which originates from the Chinese chicken isolate JX-1, and report findings from comparative genomic analysis between C. gallinacea strains and closely related species in the genus Chlamydia
Summary
Chlamydia (C.) gallinacea is a recently identified bacterium that mainly infects domestic chickens. Chlamydia (C.) psittaci, an avian pathogen with well-documented zoonotic potential, was considered the only chlamydial species infecting domestic and wild birds. The high prevalence of C. gallinacea in poultry flocks across Europe and China determined by PCRs surpassed that of C. psittaci [4, 5]. This organism is known to occasionally be in transmission with C. psittaci in the same flock and can co-infect individuals [6, 7]. Beyond the potential role of this emerging pathogen in animal health, an earlier study of an outbreak of atypical pneumonia in a slaughterhouse, where workers were exposed to C. gallinacea-infected chickens, raised questions over its zoonotic potential as well [8]
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