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Background  The rapid spread of  Clostridium difficile  NAP1/BI/027 ( C. difficile  027) has become one of the leading threats of healthcare-associated infections worldwide. However,  C. difficile  027 infections have been rarely reported in Asia, particularly in China.    Results  In this study, we identified a rare  C. difficile  bloodstream infection (BSI) from three isolates of a patient during repeated hospital admission. This finding triggered a retrospective epidemiological study to scan all cases and strains emerged from this ward during the past three years. Using medical personnel interviews, medical record reviews and the genomic epidemiology, two outbreaks in 2012 and 2013–2014 were identified. Through using whole genome sequencing, we succeeded to trace the origin of the BSI strain. Surprisingly, we found the genome sequences were similar to  C. difficile  027 strain R20291, indicating the occurrence of a rare  C. difficile  027 strain in China. Integrated epidemiological investigation and whole genome sequencing of all strains, we constructed a nosocomial transmission map of these two  C. difficile  027 outbreaks and traced the origin of the infection.    Conclusions  By genome sequencing, spatio-temporal analysis and field epidemiology investigation, we can estimate their complex transform network and reveal the possible modes of transmission in this ward. Based on their genetic diversity, we can assume that the toilets, bathroom, and janitor’s equipment room may be contaminated area, which may be suggested to improve infection control measures in the following health care.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2708-0) contains supplementary material, which is available to authorized users.

Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012–2014, traced by whole genome sequencing