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cgMLST detected clusters not detected by PGFE, which enabled elimination of several pseudoclusters defined by PFGE and detection of closely related isolates with different PFGE profiles caused by phage insertions or deletions.
PGFE analysis showed a high diversity of genotypes: 8 clones for 8 CTX-M-1-positive isolates, 4 clones for 4 CTX-M-9-positive isolates, 13 clones for 17 CTX-M-15-positive isolates, and 14 clones for 15 CTX-M-32-positive isolates (data not shown).
MSSA isolates belonged to spa type t011 or t034 corresponding to ST398 (n = 3) and to 7 PGFE types and 12 spa types (n = 19).
An identical PGFE pattern was also found for 80 (4.5%) isolates from epidemiologically unrelated patients; these isolates were further characterized by sequence-based typing and MAb subgrouping.
Therefore, when indistinguishable STEC O157:H7 PGFE subtypes occurred at the same fairs, we could not tell if matches were linked to animals from the same farm, if the same subtype occurred simultaneously on 2 geographically isolated farms, or if the clone was transmitted between animals at the fair.
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