Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2016

Microevolutionary analysis of Clostridium difficile PCR ribotype 014 lineage in Australian porcine and humans reveals signatures of long-range intra- and interspecies transmission (#85)

Daniel R Knight 1 , Thomas V Riley 1 2
  1. School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
  2. Department of Microbiology, PathWest Laboratory Medicine, Nedlands, WA, Australia

In the last decade, Clostridium difficile infection (CDI) has reached an epidemic state in some parts of the world with sources outside the healthcare system, particularly livestock, identified as potential reservoirs [1]. PCR ribotype (RT) 014 is a successful lineage of C. difficile and the most common strain-type identified in human and porcine populations in Australia [2,3]. To further define the extent of genetic overlap, whole genome sequencing was performed on RT014 isolates originating from humans with CDI (H strains, n=25) and neonatal pigs (P strains, n=16) from VIC, QLD, SA and NSW in 2012/13.

Genomes were sequenced using illumina chemistry and assembled using de novo and reference-based algorithms. Phylogenies were reconstructed using maximum likelihood inference in three approaches with increasing discriminatory power; (i) in silico MLST, (ii) ortholog detection and strict core genome alignment, and (iii) single nucleotide variant (SNV) analysis [4].

Three sequence types (STs) were identified; ST2 (H=19, P=1), ST13 (H=5, P=10) and ST49 (H=1, P=5). Congruent with the ST population structure, a strict core genome phylogeny (based on alignment of 1260 coding sequences) showed clustering of human and porcine strains, most notably in STs 2 and 13. SNV analysis provided ultra-fine scale resolution of this population. Results were analysed with respect to the previously determined C. difficile molecular clock (~1.4 SNVs per-genome per-year) and date of isolation (2012-13). The SNV phylogeny identified six clonal groups where all isolates differed by 0-2 SNVs. Strikingly, two of the clonal groups included multiple geographically distinct human and porcine strains.

These findings indicate that recent long-range intra- and interspecies transmission of C. difficile RT014 has occurred. Given our current knowledge of C. difficile in piggeries and the livestock industry, it is conceivable that indirect interspecies transmission has occurred through human exposure to contaminated meat or contaminated piggery by-products such as manure and compost.

  1. [1] Knight DR, Elliott B, Chang BJ, Perkins T, Riley TV. Diversity and evolution in the genome of Clostridium difficile. Clin Microbiol Rev 2015 28:721-741.
  2. [2] Knight DR, Squire MM, Riley TV. Clostridium difficile in Australian neonatal pigs; nationwide surveillance study shows high prevalence and heterogeneity of PCR ribotypes. Appl Environ Microbiol 2014 81:119-123.
  3. [3] Cheng AC, Collins DA, Elliott B, Ferguson JK, Paterson DL, Thean S, et al. Laboratory-based surveillance of Clostridium difficile circulating in Australia, September - November 2010. Pathology 2016 48:257-260.
  4. [4] Eyre DW, Tracey L, Elliott B, Slimings C, Huntington PG, Stuart RL, et al. Emergence and spread of predominantly community-onset Clostridium difficile PCR ribotype 244 infection in Australia, 2010 to 2012. Euro Surveill 2015 20:21059.