Appendix A: Supplementary data

Table S1. List of non-redundant genes included in the P. aeruginosa enrichment capture panel.

Table S2.  List of natural polymorphisms in the resistance and mutability genes included in the enrichment panel.

Table S3 - Normalized sequencing depth of all tested reference strains (PAO1, LESB58 and PA14) and of the ST175 P. aeruginosa mix (1:100) replicates obtained with and without (mWGS) the enrichment hybridisation step in the genomic regions captured with the resistome enrichment panel.

Table S4 - Comparison of the mutations detected within the enriched genomic regions for each individual ST175 P. aeruginosa strain (106-G2 and 107–H4) and for the ST175 P. aeruginosa mix (1:100) replicates with and without (mWGS) the enrichment hybridisation step. Number of aligned bases supporting the indicated mutation and number of total aligned bases in that specific nucleotide position are shown for missense and nonsense mutations potentially involved in resistance. First sheet (clean) collects all mutations and aminoacid substitutions, whereas sheet 2 (all) additionally includes all natural polymorphisms. In light red, variants detected in the totalpileup files are indicated.

Table S5 - Complete phenotypic and genomic data for patients ICU-06, ICU-08, ICU-09 and CF-02. First sheet for each patient (clean) collects all mutations and aminoacid substitutions, whereas the second one (all) additionally includes all natural polymorphisms. In light red, variants detected in the totalpileup files are indicated.


Figure S1 - Phenotypic vs genomic antibiogram. Results for genotypic scores (gScores) obtained for isolated colonies and captured libraries for each respiratory sample and each patient are shown. Colors code: Red indicates a resistant phenotype (EUCAST R) or resistant genotype (gScore ≥1). Yellow indicates a susceptible increased exposure phenotype for meropenem (EUCAST I) or an intermediate resistant genotype (gScore 0.5-<1). Green indicates a susceptible (EUCAST S) or a susceptible increased exposure phenotype (EUCAST I) for ceftazidime and ciprofloxacin or a susceptible genotype (gScore <0.5).

Figure S2 - Comparative analysis of the mutations detected in mutS with the enrichment panel and in the isolated colonies. In bars, the number of colonies in which a specific mutation was detected are represented; lines indicate the percentage of aligned bases supporting that specific mutation in each respiratory sample obtained with the enrichment panel.