Distribution of genes encoding MSCRAMM-like proteins, putative

virulence genes, antibiotic resistance determinants, and CRISPRs Previous studies of E. faecium TX16 identified 15 genes encoding LPXTG family cell-wall anchored proteins with MSCRAMM-like features, such as immunoglobulin-like folding; 11 of these were found in four gene clusters, each predicted/demonstrated to encode a different pilus, and four were found as individual MSCRAMM-encoding genes [18, 21, 22]. Our search for these genes in 21 unique E. faecium draft genomes in this study found all of the MSCRAMM-encoding genes to be widely distributed except fms18 (ecbA) and fms15 which were only in HA-clade isolates (although some are present as variants or pseudogenes Linsitinib clinical trial within the HA-clade) (Additional file 8: Table S5). Moreover, our analysis revealed that ebpA-ebpB-ebpC fm fms14-fms17-fms13 fms20, scm, and fms18 (the latter present in only HA isolates) all have sequence variants in some of the 21 strains, with identities of the encoded variant proteins ranging from 39% (fms20 homolog) to 94% (ebpC) versus their counterparts in TX16 (Additional file 8: Table S5). In general, most of the MSCRAMMS followed the CA/HA clade groupings

with a variant representing each clade. Variant 1 of the fms11-fms19-fms16 locus was strictly found in the HA-clade, and variant 2 in the CA-clade except for 1,231,501 which only had one of the three proteins (fms16) as a CA-variant, suggesting recombination by this isolate. Variant 1 of Dichloromethane dehalogenase fms14-fms17-fms13 find more was found in all but one HA clade isolate (1,231,408, a hybrid of HA and CA clades, has variant 2) and variant 2 in all 5 CA-clade strains. Variant 1 of scm was found to be exclusively carried by all 16 HA clade strains and variant 2 by 4 of the 5 CA clade strains. Although the differences between these MSCRAMMs in CA- vs. HA-clade strains are generally greater (ranging from 2 to 27% with an average of 10%) than the differences (3–4%) previously reported for the clade-specific differences in a set of core genes that excluded predicted surface proteins,

they are comparable to the differences seen in several other surface proteins that have been studied [33, 57]. Interestingly, the majority of HA clade strains (12/16, including TX16) were found to have variant 1 of the ebp pilus operon, while variant 2 was exclusively found in the 5 CA-clade strains in addition to variant 1 in three of the five isolates. In contrast, variation within fms20 was restricted to the HA clade; all CA clade isolates carried fms20 variant 1, but the percent identity between these two variants is much smaller (39%), possibly indicating the need for a new gene name. Also of note was the acm gene, which is present as a pseudogene in all of the CA-clade isolates except 1,141,733 which is the only CA-clade isolate that is from a hospitalized patient; acm pseudogenes were also found in non-CC17 HA-clade isolates.