Correlating Genotyping Data of Coxiella burnetii with Genomic Groups.

Claudia M. Hemsley,Richard W. Titball,Isobel H. Norville,Angela Essex-Lopresti

doi:10.3390/pathogens10050604

Abstract

Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. Several distinct genetic lineages or genomic groups have been shown to exist, with evidence for different virulence potential of these lineages. Multispacer Sequence Typing (MST) and Multiple-Locus Variable number tandem repeat Analysis (MLVA) are being used to genotype strains. However, it is unclear how these typing schemes correlate with each other or with the classification into different genomic groups. Here, we created extensive databases for published MLVA and MST genotypes of C. burnetii and analysed the associated metadata, revealing associations between animal host and human disease type. We established a new classification scheme that assigns both MST and MLVA genotypes to a genomic group and which revealed additional sub-lineages in two genomic groups. Finally, we report a novel, rapid genomotyping method for assigning an isolate into a genomic group based on the Cox51 spacer sequence. We conclude that by pooling and streamlining existing datasets, associations between genotype and clinical outcome or host source were identified, which in combination with our novel genomotyping method, should enable an estimation of the disease potential of new C. burnetii isolates.

Highlights

Coxiella burnetii is an obligate intracellular, zoonotic pathogen that causes the disease Q fever in humans [1]
Jäger et al [17] later showed that these restriction fragment length polymorphism patterns corresponded to the geographical origin of the isolates, and later the term “geotype” was coined, i.e., genetic lineages and genotypes that have originated in a certain geographic location, some of which have remained locally whilst others are spreading across the globe [18]
We previously reported the distinction of genomic groups” (GGs) II-a (MST18 and 25-like) and GG II-b (MST33-like) based on core single-nucleotide polymorphisms (SNPs) and genome content [21], whereas the third cluster, GG II-c, contained sequenced strains which we had previously determined to represent the MST32 genotype

Summary

Introduction

Coxiella burnetii is an obligate intracellular, zoonotic pathogen that causes the disease Q fever in humans [1]. Jäger et al [17] later showed that these restriction fragment length polymorphism patterns corresponded to the geographical origin of the isolates, and later the term “geotype” was coined, i.e., genetic lineages and genotypes that have originated in a certain geographic location, some of which have remained locally whilst others are spreading across the globe [18] This concept of genomic groups was later confirmed by other genotyping methods, including microarray or whole-genome sequence analyses, with four additional groups (GG VII–X) having been proposed and GG IV and GG II subsequently having been divided into further subgroups [19,20,21]

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