Phylogenomic analysis ofClostridiodes difficileribotype 106 strains reveals novel genetic islands and emergent phenotypes

Abstract

27Background: Clostridioides difficile RT106 has emerged as a dominant molecular type 28 in the USA in recent years, but the underlying factors contributing to its predominance 29 remain undefined. As part of our ongoing C. difficile infection (CDI) surveillance in 30 Arizona, we monitored RT106 frequency and characterized the genomic and phenotypic 31 properties of the recovered isolates. 32Results: From 2015-2018, RT106 was the second-most prevalent molecular type 33 isolated from CDI patients in our surveillance. A representative RT106 strain displayed 34 robust virulence and 100% lethality in the hamster model of acute CDI. We identified a 35 unique 46 KB genomic island (GI1) in all RT106 strains, including those in public 36 databases. GI1 was not found in its entirety in any other C. difficile clade, or indeed in any 37 other microbial genome; however, smaller segments were detected in select 38 Enterococcus faecium strains. Molecular clock analyses suggest that GI1 was 39 horizontally acquired and sequentially assembled over time. Consistent with the presence 40 of genes encoding homologs of VanZ and a SrtB-anchored collagen-binding adhesin in 41 GI1, all tested RT106 strains had increased teicoplanin resistance and a majority 42 displayed collagen-dependent biofilm formation. Two additional genomic islands (GI2 and 43 GI3) were also present in a subset of RT106 strains. All three islands have features of 44 mobile genetic elements and encode several putative virulence factors. 45 Conclusions: Consistent with the known genetic plasticity of C. difficile, strains belonging 46 to the RT106 clade harbor unique genetic islands. Correspondingly, emergent phenotypic 47 properties may contribute to the relatively rapid shifts of strain distribution in patient 48 populations. 49 Keywords: Clostridioides difficile, RT106, teicoplanin, VanZ, SrtB-anchored collagen-50 binding adhesin, genomic island 51 52 BACKGROUND 53The Gram-positive and spore-forming anaerobic bacterium Clostridioides difficile 54 (formerly named Clostridium difficile) is a leading cause of antibiotic-associated diarrhea 55 that may be self-limiting, or progress to severe and fulminant (pseudomembranous) colitis 56 or toxic megacolon (1-4). There has been an increased incidence of C. difficile infection 57 (CDI) over the past two decades (5-8) and, in the USA, this coincides with the emergence 58 and spread of ribotype 027 strains [also called RT027 or BI or NAP1 based on the 59 phylogenetic test (9, 10)]. While RT027 remains the most prevalent healthcare-associated 60 C. difficile ribotype, its frequency has been steadily declining (11). Multiple surveillance 61 studies indicate a changing trend in the C. difficile ribotype frequency distribution, 62 particularly the emergence of RT106 (also called Group "DH" or "NAP11") in regions 63 where it was previously rarely found. In 2008, RT106 was second to RT027 as the most 64 dominant ribotype in England, and was also identified in neighboring European countries 65 including . Howeve...