We performed NGS based sequencing of 98 cgMLST loci using the protocol described by Beveridge and colleagues22, to investigate the diversity between strains investigated in this study. Nine loci (i.e. lmo2152, lmo2106, lmo212, lmo2351, lmo2896, lmo0890, lmo0950, lmo1889, lmo0646) were absent from the dataset, whereas for the other 89 loci, about 63 % of the full length of each locus was retrieved from the datasets (Additional file 2). Analysis reveals a high number of redundant core repeat (CR) loci (25.5 %) of S. maltophilia. Interestingly, the CR locus lmo0950 (EC 188.8.131.52) encodes a d-dopachrome decarboxylase that is responsible for the biosynthesis of dark pigments of pyomelanin and homogentisic acid in S. maltophilia. lmo2290 is a predicted methyl lysine methyltransferase. Although lmo2290 is highly conserved in S. maltophilia, the rest of the phylogeny reveals that lmo2290 is yet to be sequenced in one of the available draft genomes from NCBI. Nitrite/nitrate respiratory nitrate reductase encoded by lmo2896 is found in all strains investigated in this study. Strains belonging to group II showed a higher number of CR loci (73.3 %) and chromosomal repeat (CRT) loci (7.2 %) compared to strains from group I (52.0 % and 4.5 %, respectively).
Clustering of clustered regularly interspaced short palindromic repeat (CRISPR) loci was performed to identify CRISPR-associated (Cas) genes (Additional file 1C). S. maltophilia had at least two copies of Csr3, which controls Cse2-Cas subtype II-E and II-F activity, as well as Cri1 of Cri1-Cas subtype II-A. S. maltophilia had also at least one copy of Cas9, which controls Cse2-Cas II-E activity and Cri1 activity. Two copies of Cas2a4 are present in S.
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