Genomic Analysis of Clostridioides difficile in 2 Regions of the United States Reveals a Diversity of Strains and Limited Transmission

• Published in: The Journal of infectious diseases Vol. 225; no. 1; pp. 121 - 129
• Main Authors: Pecora, Nicole, Holzbauer, Stacy, Wang, Xiong, Gu, Yu, Taffner, Samantha, Hatwar, Trupti, Hardy, Dwight, Dziejman, Michelle, D’Heilly, Paige, Pung, Kelly, Guh, Alice, Qiu, Xing, Gill, Steven, Dumyati, Ghinwa
• Format: Journal Article
• Language: English
• Published: US Oxford University Press 05.01.2022
• Subjects: Bacterial infections; Catchment areas; Clostridioides; Clostridioides difficile; Clostridioides difficile - genetics; Clostridium Infections - epidemiology; Clostridium Infections - microbiology; Clostridium Infections - transmission; Cross Infection - epidemiology; Disease transmission; Epidemiology; Genome; Genomes; Genomic analysis; Genomics; Gram-positive bacteria; Hospitalization - statistics & numerical data; Humans; Infectious Disease Transmission, Patient-to-Professional; Infectious Disease Transmission, Professional-to-Patient; Minnesota - epidemiology; Multilocus Sequence Typing; New York - epidemiology; Patients; Population Surveillance; United States - epidemiology; Whole Genome Sequencing; New York; United States; Minnesota; United States > US; NAP1; transmission; MLST; whole-genome sequencing; Clostridioides difficile
• ISSN: 0022-1899; 1537-6613
• DOI: 10.1093/infdis/jiab294

Abstract Background The distribution of Clostridioides difficile strains and transmission dynamics in the United States are not well defined. Whole-genome sequencing across 2 Centers for Disease Control and Prevention Emerging Infections Program C. difficile infection (CDI) surveillance regions (Minnesota and New York) was performed to identify predominant multilocus sequence types (MLSTs) in community-associated (CA) and healthcare-associated (HCA) disease and assess transmission. Methods Whole-genome sequencing was performed on C. difficile isolates from patients with CDI over 3 months between 2016 and 2017. Patients were residents of the catchment area without a positive C. difficile test in the preceding 8 weeks. CDI cases were epidemiologically classified as HCA or CA. Results Of 422 isolates, 212 (50.2%) were HCA and 203 (48.1%) were CA. Predominant MLSTs were sequence type (ST) 42 (9.3%), ST8 (7.8%), and ST2 (8.1%). MLSTs associated with HCA-CDI included ST1 (76%), ST53 (83.3%), and ST43 (80.0%), while those associated with CA-CDI included ST3 (76.9%) and ST41 (77.8%). ST1 was more frequent in New York than in Minnesota (10.8% vs 3.1%). Thirty-three pairs were closely related genomically, 14 of which had potential patient-to-patient transmission supported by record review. Conclusions The genomic epidemiology of C. difficile across 2 regions of the United States indicates the presence of a diverse strain profile and limited direct transmission. Whole-genome sequencing of 422 Clostridioides difficile strains from healthcare and community settings across 2 sites over a 3-month period demonstrated a diverse group of strain types and very little evidence of direct transmission.