The complete genome sequence of the crayfish pathogen Candidatus
Paracoxiella cheracis
n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family
ABSTRACT
The Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poorly characterized obligate intracellular bacteria. The zoonotic pathogen and causative agent of human Q fever,
Coxiella burnetii
, represents the best-characterized member of this family. Coxiellaceae establish replicative niches within diverse host cells and rely on their host for survival, making them challenging to isolate and cultivate within a laboratory setting. Here, we describe a new genus within the Coxiellaceae family that has been previously shown to infect economically significant freshwater crayfish. Using culture-independent long-read metagenomics, we reconstructed the complete genome of this novel organism and demonstrate that the species previously referred to as Candidatus
Coxiella cheraxi
represents a novel genus within this family, herein denoted Candidatus
Paracoxiella cheracis
. Interestingly, we demonstrate that Candidatus
P. cheracis
encodes a complete, putatively functional Dot/Icm type 4 secretion system that likely mediates the intracellular success of this pathogen.
In silico
analysis defined a unique repertoire of Dot/Icm effector proteins and highlighted homologs of several important
C. burnetii
effectors, including a homolog of CpeB that was demonstrated to be a Dot/Icm substrate in
C. burnetii
.
IMPORTANCE
Using long-read sequencing technology, we have uncovered the full genome sequence of Candidatus
Paracoxiella cheracis
, a pathogen of economic importance in aquaculture. Analysis of this sequence has revealed new insights into this novel member of the Coxiellaceae family, demonstrating that it represents a new genus within this poorly characterized family of intracellular organisms. Importantly, the genome sequence reveals invaluable information that will support diagnostics and potentially both preventative and treatment strategies within crayfish breeding facilities. Candidatus
P. cheracis
also represents a new member of Dot/Icm pathogens that rely on this system to establish an intracellular niche. Candidatus
P. cheracis
possesses a unique cohort of putative Dot/Icm substrates that constitute a collection of new eukaryotic cell biology-manipulating effector proteins.