First Complete Genome Sequence of the Dutch Veterinary
            <i>Coxiella burnetii</i>
            Strain NL3262, Originating from the Largest Global Q Fever Outbreak, and Draft Genome Sequence of Its Epidemiologically Linked Chronic Human Isolate NLhu3345937

Kuley, Runa; Smith, Hilde E.; Janse, Ingmar; Harders, Frank; Baas, Frank; Schijlen, Elio; Nabuurs-Franssen, Marrigje H.; Smits, M.A.; Roest, H.I.J.; Bossers, Alex

doi:10.1128/genomea.00245-16

Cited by 16 publications

(19 citation statements)

References 14 publications

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“…The CbNL01 genotype was identified mostly in strains isolated from goats and specifically from human patients, indicating that goats harboring the CbNL01 genotype strain were most likely the source of the large human Q fever outbreak in The Netherlands. These genotyping studies confirmed the earlier observed epidemiological link between an increase in human Q fever cases and a high abortion rate in goats (Enserink, 2010 ; van der Hoek et al, 2010 ; Roest et al, 2011a , b ; Kampschreur et al, 2013 ; Kuley et al, 2016 ). Additionally, the genotyping studies also showed that the CbNL12 genotype was majorly associated with strains originating from cattle and rarely with strains from goat, sheep and humans (Roest et al, 2011a , b ; Tilburg et al, 2012c ; Mori et al, 2013 ).…”

Section: Introductionsupporting

confidence: 86%

“…In the present study we report the new genome sequences of 11 C. burnetii strains. The reconstruction of the genome sequences of the NL3262 and NLhu3345937 strains was described before (Kuley et al, 2016 ). Table 1 is a summary of the main features of the sequenced genomes.…”

Section: Resultsmentioning

confidence: 99%

“…Strain NL3262 and the database strain NL-Limburg clustered closely together (Cluster 1a, Figure 1 ). The genome of strain NL3262 is a complete reconstructed genome derived and curated using different sequencing technologies (Kuley et al, 2016 ). The NL-Limburg genome is a draft genome generated with a single sequencing technology (PacBio) and its assembly constitutes 4 contigs representing the chromosome (Hammerl et al, 2015 ).…”

Section: Resultsmentioning

confidence: 99%

“…The draft genome sequence of the 602 strain was obtained by using Roche 454XL sequencing technology and was de novo assembled by Newbler 2.6. The Dutch outbreak representative strain NL3262 was fully reconstructed using a combination of sequencing technologies (Illumina MiSeq paired-end 250 bp, PacBio RS and Roche 454XL) as described previously (Kuley et al, 2016 ). The contigs of the draft genome sequences were scaffolded and joined into an artificial chromosome based on homology with the closest C. burnetii strain from the database using BLAT synteny tool (Table 1 ; Kent, 2002 ).…”

Section: Methodsmentioning

confidence: 99%

“…Q fever is prevalent throughout the world, but during 2007–2010 an unprecedented Q fever outbreak occurred in The Netherlands and is referred to as the largest outbreak ever reported (Raoult et al, 2005 ; Roest et al, 2011b ; Hammerl et al, 2015 ; Kuley et al, 2016 ). During this epidemic, several isolates from different host species were isolated and cultured.…”

Section: Introductionmentioning

confidence: 99%

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Genome Plasticity and Polymorphisms in Critical Genes Correlate with Increased Virulence of Dutch Outbreak-Related Coxiella burnetii Strains

et al. 2017

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Coxiella burnetii is an obligate intracellular bacterium and the etiological agent of Q fever. During 2007–2010 the largest Q fever outbreak ever reported occurred in The Netherlands. It is anticipated that strains from this outbreak demonstrated an increased zoonotic potential as more than 40,000 individuals were assumed to be infected. The acquisition of novel genetic factors by these C. burnetii outbreak strains, such as virulence-related genes, has frequently been proposed and discussed, but is not proved yet. In the present study, the whole genome sequence of several Dutch strains (CbNL01 and CbNL12 genotypes), a few additionally selected strains from different geographical locations and publicly available genome sequences were used for a comparative bioinformatics approach. The study focuses on the identification of specific genetic differences in the outbreak related CbNL01 strains compared to other C. burnetii strains. In this approach we investigated the phylogenetic relationship and genomic aspects of virulence and host-specificity. Phylogenetic clustering of whole genome sequences showed a genotype-specific clustering that correlated with the clustering observed using Multiple Locus Variable-number Tandem Repeat Analysis (MLVA). Ortholog analysis on predicted genes and single nucleotide polymorphism (SNP) analysis of complete genome sequences demonstrated the presence of genotype-specific gene contents and SNP variations in C. burnetii strains. It also demonstrated that the currently used MLVA genotyping methods are highly discriminatory for the investigated outbreak strains. In the fully reconstructed genome sequence of the Dutch outbreak NL3262 strain of the CbNL01 genotype, a relatively large number of transposon-linked genes were identified as compared to the other published complete genome sequences of C. burnetii. Additionally, large numbers of SNPs in its membrane proteins and predicted virulence-associated genes were identified in all Dutch outbreak strains compared to the NM reference strain and other strains of the CbNL12 genotype. The presence of large numbers of transposable elements and mutated genes, thereof most likely resulted in high level of genome rearrangements and genotype-specific pathogenicity of outbreak strains. Thus, the epidemic potential of Dutch outbreak strains could be linked to increased genome plasticity and mutations in critical genes involved in virulence and the evasion of the host immune system.

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