“Population structure of drug-susceptible,—resistant and ESBL-producing Escherichia coli from community-acquired urinary tract”

Distributions of a-MLVA codes and sequence types in the three E. coli populations are found in detail in Supplementary materials 1-3. We show: 1) The number of isolates found in each cluster of sequence types and a-MLVA codes 2) The sequence type and the corresponding a-MLVA code (or a-MLVA codes in case more than one a-MLVA code was identified for the specific ST) 3) We also show cases where more than one ST was identified by the same a-MLVA (shown as ST10/ST617, for example) 4) Finally, for the ESBL-population, we show the ESBL genotype identified within the a-MLVA code Abbreviated-MLVA codes PCR amplification of the six MLVA alleles was done as described in the primary manuscript and this abbreviated MLVA (a-MLVA) was used to type the three strain collections. As such, all isolates (100%) were typable by this a-MLVA method. All but one isolate, selected for MLST, had the alleles successfully sequenced. However, a single isolate with a unique a-MLVA code was not sent for MLST. In these three populations we found a total of 83 a-MLVA-codes and 72 sequence types. Thirteen a-MLVA´s and 13 ST´s were found in two out of three populations. Six a-MLVA´s and seven ST´s were found in all three populations. Ten a-MLVA codes were unique and classified as " unknown " sequence types (in Supplementary material classified as " New STs "). Overall, ST131 constituted 23% of all isolates and ST69 constituted 10%. ST73 was found to constitute 9%. Of the found a-MLVA codes, 74 identified just one sequence type. Yet, in quite a few situations one specific ST was subdivided by more than one a-MLVA code. More complex situations were seen where several different ST´s were assigned the same a-MLVA code.