The use of whole-genome based phylogenetic analysis may better track Clostridium difficile transmission and reinfection, according to a study published in Clinical Infectious Diseases.

Nitin Kumar, PhD, of the Wellcome Trust Sanger Institute in Hinxton, UK and colleagues examined adult patients ≥18 from July 2008 to May 2010 at the Royal Liverpool and Broadgreen University Hospitals National Health Service (NHS) Trust. To qualify, patients had to have been diagnosed with healthcare-associated diarrhea, tested positive on a C difficile toxin test, and were diagnosed by independent clinicians.

The researchers implemented whole-genome and phylogenetic analysis of 108 strains alongside comprehensive epidemiological data to track C. difficile 027/ST1 (CDI) transmission and persistence.

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Researchers examined more than 10 580 samples from 7048 patients and found an infection rate of 7.6%. Patients in the hospital made up 616 of these samples – of this group, 453 were nosocomial infections and 163 were community associated. Researchers obtained 446 isolates from these samples, which were PCR ribotyped.

“During the entire sampling period, C difficile 027/ST1 was the most prevalent PCR ribotype, ranging from 50% in 2008 to 31% in 2010. Of these C difficile 027/ST1 samples, 108 (34%) were sampled and sequenced from 87 patients with confirmed C difficile infection, including multiple samples from 14 patients with recurrent infection,” Dr Kumar and colleagues reported.

The researchers explained that their method of whole-genome single nucleotide polymorphism (SNP) phylogenetic analysis identified 27 separate SNP genotypes, “with patient movement and contact data identified 32 plausible transmission events, including ward-based contamination (66%) or direct donor–recipient contact (34%).”

In an editorial commentary, Dale N. Gerding, MD, of the Research Service at Hines VA Hospital in Hines, Illinois, said that this method will “help untangle the complex transmission epidemiology” of CDI that has only been partly obtainable to this point. The typing used by these researchers is more sensitive than previous methods, Dr Gerding noted.

The study researchers noted some limitations of the study, which were the small (34%) sample of CDI strain isolates and no collection of specimens from colonized patients who were asymptomatic. Dr Gerding also noted another limitation to the study – that “current hypothetical definitions for transmission that may or may not be indicative of actual transmissions,” and that “current WGS studies leave too many unknowns regarding sources of transmission such as asymptomatic colonized patients and the environment, or even hands of healthcare workers.”


1. Kumar N, Miyajima F, He M et al. Genome-based infection tracking reveals dynamics of Clostridium difficile transmission and disease recurrence. Clin Infect Dis. 2016;62(6): 746-752. doi: 10.1093/cid/civ1031. Published Online December 18, 2015. Accessed March 23, 2016.