From genomes to genotypes: molecular epidemiological analysis of Chlamydia gallinacea reveals a high level of genetic diversity for this newly emerging chlamydial pathogen

Guo Weina; Martina Jelocnik; Jing Li; Konrad Sachse; Adam Polkinghorne; Yvonne Pannekoek; Bernhard Kaltenboeck; Jiansen Gong; Jinfeng You; Chengming Wang

doi:10.1186/s12864-017-4343-9

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From genomes to genotypes: molecular epidemiological analysis of Chlamydia gallinacea reveals a high level of genetic diversity for this newly emerging chlamydial pathogen

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From genomes to genotypes: molecular epidemiological analysis of Chlamydia gallinacea reveals a high level of genetic diversity for this newly emerging chlamydial pathogen

Guo Weina, Martina Jelocnik, Jing Li, Konrad Sachse, Adam Polkinghorne, Yvonne Pannekoek, Bernhard Kaltenboeck, Jiansen Gong, Jinfeng You and Chengming Wang

BMC Genomics, Vol.18, 949

2017

DOI: https://doi.org/10.1186/s12864-017-4343-9

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Abstract

chlamydia gallinacea

comparative genomics analysis

MLST

phylogenetic analysis

whole-genome sequence

Background: Chlamydia (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. Results: The 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.* Conclusions: In 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

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Title: From genomes to genotypes: molecular epidemiological analysis of Chlamydia gallinacea reveals a high level of genetic diversity for this newly emerging chlamydial pathogen
Authors: Guo Weina (Author) - Anhui Science and Technology University, China
Martina Jelocnik (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Jing Li (Author) - Yangzhou University College of Veterinary Medicine, China
Konrad Sachse (Author) - Friedrich-Schiller-Universität Jena, Germany
Adam Polkinghorne (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Yvonne Pannekoek (Author) - University of Amsterdam, Netherlands
Bernhard Kaltenboeck (Author) - Auburn University, United States
Jiansen Gong (Author) - Chinese Academy of Agricultural Sciences, China
Jinfeng You (Author) - Yangzhou University College of Veterinary Medicine, China
Chengming Wang (Author) - Auburn University, United States
Publication details: BMC Genomics, Vol.18, 949; 12
Publisher: BioMed Central Ltd.
Date published: 2017
DOI: 10.1186/s12864-017-4343-9
ISSN: 1471-2164
Copyright note: Copyright © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated
Organisation Unit: University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99450610202621
Output Type: Journal article

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