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. Author manuscript; available in PMC: 2021 Apr 26.
Published in final edited form as: Nat Microbiol. 2020 Oct 26;6(1):103–111. doi: 10.1038/s41564-020-00806-7

Table 1. Genomic and epidemiological evidence of nosocomial E. faecium transmission.

Number of
subtypes
(patients)		 Median SNP
distance
(IQR)		 Strong
environme
links3
Acquired subtypes 111 (64)1 - 41/111
  Genetically unlinked 22 (19) - 1/22
  Genetically linked to 89 (56) - 40/89
   Future sampled patients 11 (9) - 1/11
   Previously sampled patients 78 (52) 0 (0-2) 39/78
    With weak epidemiological links 17 (15) 2 (0-2) 7/17
    With strong epidemiological links 61(43) 0 (0-1) 32/61
     Same bay or room, same time 16 (11) 0 (0-0) 13/16
     Same bay within 7 days 5 (5) 0 (0-1) 4/5
     Same ward, same time 32 (24) 0 (0-1) 11/32
     Same ward within 7 days 8 (8) 2.5 (0-3) 4/8
 Index subtypes 116 (80)4 - 24/116
  Genetically unlinked2 37 (32) - 4/37
  Genetically linked to 79 (50) - 20/79
   Future sampled patients 28 (24) - 5/28
   Previously sampled patients 51 (43) 1 (0-3) 15/51
    With weak epidemiological links 20 (20) 2 (0-3) 5/20
    With strong epidemiological links 31 (25) 1 (0-2) 10/31
     Same bay or room, same time 13 (11) 0 (0-2) 4/13
     Same bay within 7 days 2 (2) 1 (0-2) 1/2
     Same ward, same time 16 (14) 1 (0-2.5) 5/16
     Same ward within 7 days - - -

A total of 227 unique subtype-patient combinations were identified in 111 patients positive for clade A1, 38 of whom carried a single subtype and 73 carried multiple subtypes. Of the 227 subtype-patient combinations, 111 were acquired based on consecutive sampling and 116 were detected in the first available stool sample. For each subtype in each patient, evidence of nosocomial transmission was supported by genetic links to E. faecium isolates sampled in previous patients or environmental locations. Epidemiological data provided a second level of evidence of hospital transmission.

1

Among patients with at least two available stool samples (n=101).

2

Using a cut-off of 6 SNPs to detect recent transmission of E. faecium subtypes during the study period.

3

Genetically linked and with strong epidemiological links to previously sampled environmental sites.

4

Among all patients positive for the hospital- adapted clade (n=111).