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The selected S. maltophilia isolates represented timeframes 2011-2019 and included 25 host species, among which dogs and cats were over-represented (n = 14, 53%, respectively). We sequenced 10 S. maltophilia isolates from 10 different host species in a cluster or outbreak for which WGS data were primarily published (Fig. 5). The WGS data ranged from 3 to 5.3 Mrd for a median of 4.1 Mrd reads: S. maltophilia isolates originating from a cat and a dog had a similar genome size of 2.98-3.38 Mrd
We used a set of 1740 core orthologous genes (Fig. 3) as defined within the PubMLST database in order to assign strain-specific alleles and cgMLST alleles to each isolate. For the large majority of genes, the same allele was found in each S. maltophilia WGS. For single locus variants, mean gene sequence identity was available from the database. For insertions and deletions (indels), reference sequences were available from the database, therefore calculating the corresponding indel matrix. When the latter was available, we attempted to use it instead of WGS for which indels were not supported. For instance, the reference sequence for the indel locus identified in publications printed in the past was used when the in silico predicted indel (indel-server) from the PubMLST database could not be used. For the third round of reannotation (PubMLST version 2019, which had not been released at the time this study was performed), each indel was supported by previously unannotated loci. Of all 1740 core loci, 85.7% (1538) had the same alleles in each of the 10 S. maltophilia WGS. Within the 10 S. maltophilia WGS, 757 cgMLST (sequential replacements) loci were represented by a single nucleotide difference, the median number of nucleotides difference per locus was 0.25M (range 0-1M). Single base pair substitutions accounted for 2.4% of the total number of cgMLST alleles. Mean sequence identity for single nucleotide polymorphisms (SNPs) in S. maltophilia was 97.1%. d2c66b5586