Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry.

Liljana Petrovska,Yue Tang,Samuel K Sheppard,Javier Nunez,Tim R Crawshaw,Melissa J Jansen Van Rensburg,Richard M Irvine,Shaun Cawthraw,Richard J Ellis,Adrian M Whatmore

doi:10.3389/fcimb.2017.00354

Abstract

The term “spotty liver disease” (SLD) has been used since the late 1990s for a condition seen in the UK and Australia that primarily affects free range laying hens around peak lay, causing acute mortality and a fall in egg production. A novel thermophilic SLD-associated Campylobacter was reported in the United Kingdom (UK) in 2015. Subsequently, similar isolates occurring in Australia were formally described as a new species, Campylobacter hepaticus. We describe the comparative genomics of 10 C. hepaticus isolates recovered from 5 geographically distinct poultry holdings in the UK between 2010 and 2012. Hierarchical gene-by-gene analyses of the study isolates and representatives of 24 known Campylobacter species indicated that C. hepaticus is most closely related to the major pathogens Campylobacter jejuni and Campylobacter coli. We observed low levels of within-farm variation, even between isolates collected over almost 3 years. With respect to C. hepaticus genome features, we noted that the study isolates had a ~140 Kb reduction in genome size, ~144 fewer genes, and a lower GC content compared to C. jejuni. The most notable reduction was in the subsystem containing genes for iron acquisition and metabolism, supported by reduced growth of C. hepaticus in an iron depletion assay. Genome reduction is common among many pathogens and in C. hepaticus has likely been driven at least in part by specialization following the occupation of a new niche, the chicken liver.

Highlights

Spotty liver disease (SLD) is an important concern for the poultry egg and meat industries
With reference to published Campylobacter genomes, we identified potential genetic components that contributed to the diversification of the SLD-associated Campylobacter from closely related species and features associated with niche specialization
C. hepaticus has been identified as the cause of SLD (Crawshaw et al, 2015; Van et al, 2016, 2017), and the disease pathology reproduced in specific pathogen-free (SPF) birds in the United Kingdom (UK) and mature layer hens in Australia; our understanding of the genomics and evolution of this emerging pathogen remain limited

Summary

Introduction

Spotty liver disease (SLD) is an important concern for the poultry egg and meat industries. The disease is sporadic in nature and predominantly affects free-range laying hens, causing a drop in egg production, and up to 10% mortality in some flocks (Grimes and Reece, 2011; Jennings et al, 2011; Crawshaw et al, 2015). SLD is characterized by the appearance of 1–2 mm gray/white foci in the liver, described as multifocal fibrinogranulocytic necrotising hepatitis when examined microscopically (Crawshaw et al, 2015). A Vibrio-like organism was isolated from cases of vibrionic hepatitis and disease was reproduced (Delaplane et al, 1955; Winterfield and Sevoian, 1957); the organism was never fully characterized and questions remain about the nature of this disease and how it relates to the contemporary manifestations of SLD

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