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European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures

Identifieur interne : 000C87 ( Main/Exploration ); précédent : 000C86; suivant : 000C88

European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures

Auteurs : H. M. B. Seth-Smith [Suisse] ; Leonor Sánchez Bus ; M. Livingstone ; M. Sait ; S. R. Harris ; K. D. Aitchison ; Evangelia Vretou [Grèce] ; V. I. Siarkou [Grèce] ; K. Laroucau [France] ; K. Sachse [Allemagne] ; D. Longbottom ; N. R. Thomson

Source :

RBID : PMC:5415952

Descripteurs français

English descriptors

Abstract

Background

Chlamydia abortus (formerly Chlamydophila abortus) is an economically important livestock pathogen, causing ovine enzootic abortion (OEA), and can also cause zoonotic infections in humans affecting pregnancy outcome. Large-scale genomic studies on other chlamydial species are giving insights into the biology of these organisms but have not yet been performed on C. abortus. Our aim was to investigate a broad collection of European isolates of C. abortus, using next generation sequencing methods, looking at diversity, geographic distribution and genome dynamics.

Results

Whole genome sequencing was performed on our collection of 57 C. abortus isolates originating primarily from the UK, Germany, France and Greece, but also from Tunisia, Namibia and the USA. Phylogenetic analysis of a total of 64 genomes shows a deep structural division within the C. abortus species with a major clade displaying limited diversity, in addition to a branch carrying two more distantly related Greek isolates, LLG and POS. Within the major clade, seven further phylogenetic groups can be identified, demonstrating geographical associations. The number of variable nucleotide positions across the sampled isolates is significantly lower than those published for C. trachomatis and C. psittaci. No recombination was identified within C. abortus, and no plasmid was found. Analysis of pseudogenes showed lineage specific loss of some functions, notably with several Pmp and TMH/Inc proteins predicted to be inactivated in many of the isolates studied.

Conclusions

The diversity within C. abortus appears to be much lower compared to other species within the genus. There are strong geographical signatures within the phylogeny, indicating clonal expansion within areas of limited livestock transport. No recombination has been identified within this species, showing that different species of Chlamydia may demonstrate different evolutionary dynamics, and that the genome of C. abortus is highly stable.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3657-y) contains supplementary material, which is available to authorized users.


Url:
DOI: 10.1186/s12864-017-3657-y
PubMed: 28472926
PubMed Central: 5415952


Affiliations:


Links toward previous steps (curation, corpus...)


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<title xml:lang="en" level="a" type="main">European
<italic>Chlamydia abortus</italic>
livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures</title>
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<name sortKey="Seth Smith, H M B" sort="Seth Smith, H M B" uniqKey="Seth Smith H" first="H. M. B." last="Seth-Smith">H. M. B. Seth-Smith</name>
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</author>
<author>
<name sortKey="Longbottom, D" sort="Longbottom, D" uniqKey="Longbottom D" first="D." last="Longbottom">D. Longbottom</name>
<affiliation>
<nlm:aff id="Aff2">Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Midlothian EH26 0PZ UK</nlm:aff>
<wicri:noCountry code="subfield">Midlothian EH26 0PZ UK</wicri:noCountry>
</affiliation>
</author>
<author>
<name sortKey="Thomson, N R" sort="Thomson, N R" uniqKey="Thomson N" first="N. R." last="Thomson">N. R. Thomson</name>
<affiliation>
<nlm:aff id="Aff1">
<institution-wrap>
<institution-id institution-id-type="ISNI">0000 0004 0606 5382</institution-id>
<institution-id institution-id-type="GRID">grid.10306.34</institution-id>
<institution>Pathogen Genomics, Wellcome Trust Sanger Institute,</institution>
<institution>Wellcome Trust Genome Campus,</institution>
</institution-wrap>
Hinxton, Cambridgeshire CB10 1SA UK</nlm:aff>
<wicri:noCountry code="subfield">Cambridgeshire CB10 1SA UK</wicri:noCountry>
</affiliation>
</author>
</analytic>
<series>
<title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint>
<date when="2017">2017</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass>
<keywords scheme="KwdEn" xml:lang="en">
<term>Animals</term>
<term>Chlamydia (genetics)</term>
<term>Chlamydia Infections (microbiology)</term>
<term>Chlamydia Infections (veterinary)</term>
<term>Europe</term>
<term>Genetic Variation</term>
<term>Genome, Bacterial</term>
<term>Genomic Instability</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Molecular Sequence Annotation</term>
<term>Phylogeography</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Recombination, Genetic</term>
<term>Sequence Analysis, DNA</term>
<term>Sheep</term>
<term>Sheep Diseases (microbiology)</term>
<term>Sheep, Domestic (microbiology)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Analyse de séquence d'ADN</term>
<term>Animaux</term>
<term>Annotation de séquence moléculaire</term>
<term>Chlamydia (génétique)</term>
<term>Europe</term>
<term>Génome bactérien</term>
<term>Infections à Chlamydia (microbiologie)</term>
<term>Infections à Chlamydia (médecine vétérinaire)</term>
<term>Instabilité du génome</term>
<term>Maladies des ovins (microbiologie)</term>
<term>Ovis</term>
<term>Ovis aries (microbiologie)</term>
<term>Phylogéographie</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Recombinaison génétique</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Variation génétique</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Chlamydia</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Chlamydia</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr">
<term>Infections à Chlamydia</term>
<term>Maladies des ovins</term>
<term>Ovis aries</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiology" xml:lang="en">
<term>Chlamydia Infections</term>
<term>Sheep Diseases</term>
<term>Sheep, Domestic</term>
</keywords>
<keywords scheme="MESH" qualifier="médecine vétérinaire" xml:lang="fr">
<term>Infections à Chlamydia</term>
</keywords>
<keywords scheme="MESH" qualifier="veterinary" xml:lang="en">
<term>Chlamydia Infections</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Animals</term>
<term>Europe</term>
<term>Genetic Variation</term>
<term>Genome, Bacterial</term>
<term>Genomic Instability</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Molecular Sequence Annotation</term>
<term>Phylogeography</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Recombination, Genetic</term>
<term>Sequence Analysis, DNA</term>
<term>Sheep</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Analyse de séquence d'ADN</term>
<term>Animaux</term>
<term>Annotation de séquence moléculaire</term>
<term>Europe</term>
<term>Génome bactérien</term>
<term>Instabilité du génome</term>
<term>Ovis</term>
<term>Phylogéographie</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Recombinaison génétique</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Variation génétique</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<sec>
<title>Background</title>
<p>
<italic>Chlamydia abortus</italic>
(formerly
<italic>Chlamydophila abortus</italic>
) is an economically important livestock pathogen, causing ovine enzootic abortion (OEA), and can also cause zoonotic infections in humans affecting pregnancy outcome. Large-scale genomic studies on other chlamydial species are giving insights into the biology of these organisms but have not yet been performed on
<italic>C. abortus</italic>
. Our aim was to investigate a broad collection of European isolates of
<italic>C. abortus</italic>
, using next generation sequencing methods, looking at diversity, geographic distribution and genome dynamics.</p>
</sec>
<sec>
<title>Results</title>
<p>Whole genome sequencing was performed on our collection of 57
<italic>C. abortus</italic>
isolates originating primarily from the UK, Germany, France and Greece, but also from Tunisia, Namibia and the USA. Phylogenetic analysis of a total of 64 genomes shows a deep structural division within the
<italic>C. abortus</italic>
species with a major clade displaying limited diversity, in addition to a branch carrying two more distantly related Greek isolates, LLG and POS. Within the major clade, seven further phylogenetic groups can be identified, demonstrating geographical associations. The number of variable nucleotide positions across the sampled isolates is significantly lower than those published for
<italic>C. trachomatis</italic>
and
<italic>C. psittaci</italic>
. No recombination was identified within
<italic>C. abortus</italic>
, and no plasmid was found. Analysis of pseudogenes showed lineage specific loss of some functions, notably with several Pmp and TMH/Inc proteins predicted to be inactivated in many of the isolates studied.</p>
</sec>
<sec>
<title>Conclusions</title>
<p>The diversity within
<italic>C. abortus</italic>
appears to be much lower compared to other species within the genus. There are strong geographical signatures within the phylogeny, indicating clonal expansion within areas of limited livestock transport. No recombination has been identified within this species, showing that different species of
<italic>Chlamydia</italic>
may demonstrate different evolutionary dynamics, and that the genome of
<italic>C. abortus</italic>
is highly stable.</p>
</sec>
<sec>
<title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s12864-017-3657-y) contains supplementary material, which is available to authorized users.</p>
</sec>
</div>
</front>
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<li>Grèce</li>
<li>Suisse</li>
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