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Additional file 4: Figure S4. Heatmap analysis with annotation for disease duration in months and active GPA and inactive GPA disease stage using top 28 species with a minimum abundance of 0.5% in at least one sample in the bacterial 16S rRNA dataset. (PDF 75 kb)

Additional file 2: Figure S2. NMDS analysis of bacterial 16S marker gene sequenced species. a. NMDS plot reveals that healthy controls (HC) form a cluster separating them from inactive [green ellipse] and active GPA patients [orange ellipse]. The two disease controls (EGPA) are within the inGPA and aGPA clusters. The overall cluster separation is not statistically different (PERMANOVA test: P value > 0.05). b. The inGPA and aGPA samples were grouped into one cluster [GPA cluster, orange ellipse]. PERMANOVA test between the three groups revealed that samples from the combined GPA patients are statistically different from the healthy control (HC) samples (PERMANOVA P value = 0.039, F value = 1.739). (PDF 155 kb)

Additional file 3: Figure S3. Taxonomic annotation of longitudinal case studies using bacterial 16S marker gene sequenced species. Bacterial diversity in six patients with follow up sampling one month (n = 6) and 3 months later (n = 1) is shown. In two case studies, household controls at the initial sampling time point (n = 2) and one month later (n = 1) were also available. For comparisons, seven healthy controls are shown at the bottom of the figure. The abundance of the top 27 species with a minimum 0.1% contribution in samples from longitudinal case studies with matching species from healthy controls are shown on the x axis. (PDF 629 kb)

Additional file 8: Table S3. Relative abundance of S. aureus in the bacterial 16S dataset and in the shot gun metagenomic dataset. (DOCX 16 kb)

Additional file 1: Figure S1. 31 cultured Staphylococcus isolates were sequenced and their assembled genomes were used for phylogenetic tree construction. a. Bacterial 16S marker gene sequenced species were matched with cultured S. aureus isolates in their phylogenetic tree. The top 22 species with a minimum abundance of 0.1% were used for the stack bar chart presentation. The top 22 species represented 98.91% of all reads. Please note: a bacterial 16S profile was not available from all samples from which an isolate was sequenced. b. Shotgun sequenced Staphylococcus species were matched with cultured S. aureus isolates in their phylogenetic tree. The top 28 taxa with a minimum abundance of 0.1% were used for the stack bar chart presentation. The top 28 taxa represented 97.25% of all reads. Please note: A Staphylococcus profile was not available from all samples from which an isolate was sequenced. (PDF 8765 kb)

Figures and descriptions of Supplemental Figures S1â S6 mentioned throughout the manuscript. (DOCX 1927Â kb)

Predominant STs of ESBL-producing E. coli isolated from clinical and environmental origins in Thailand. Graph showing the prevalence of the eight most frequently identified STs among each of the clinical or environmental Thai ESBL-producing E. coli isolates, split by source of isolation. The total adds up to 12 since four of the top eight most frequent in each category did not overlap. The presence of all isolates in each of the 12 STs is shown. Figure S2. Phylogeny of CTX-M genes identified in Thai ESBL-producing E. coli. Phylogeny of the seven CTX-M gene variants identified in the 149 study genomes. Figure S3. Phylogeny of Thai ESBL-producing E. coli in a global context. Maximum-likelihood tree of the 149 study genomes and 514 global genomes based on 222,900 SNPs in the 1983 core genes. Inner ring shows origin of isolate, middle ring shows country of isolation and outer ring indicates the study isolates (black). Scale bar indicates ~ 20,000 SNPs. Figure S4. Virulence gene comparison between ST131 and non-ST131 isolates. Graph showing the prevalence of virulence factors in ST131 (n 26) compared to non-ST131 (n 123) in the study isolates. Using Fisher’s exact test at a p value of 0.05, only those factors over-represented between the two groups are shown. (DOCX 2381 kb)

Predominant STs of ESBL-producing E. coli isolated from clinical and environmental origins in Thailand. Graph showing the prevalence of the eight most frequently identified STs among each of the clinical or environmental Thai ESBL-producing E. coli isolates, split by source of isolation. The total adds up to 12 since four of the top eight most frequent in each category did not overlap. The presence of all isolates in each of the 12 STs is shown. Figure S2. Phylogeny of CTX-M genes identified in Thai ESBL-producing E. coli. Phylogeny of the seven CTX-M gene variants identified in the 149 study genomes. Figure S3. Phylogeny of Thai ESBL-producing E. coli in a global context. Maximum-likelihood tree of the 149 study genomes and 514 global genomes based on 222,900 SNPs in the 1983 core genes. Inner ring shows origin of isolate, middle ring shows country of isolation and outer ring indicates the study isolates (black). Scale bar indicates ~ 20,000 SNPs. Figure S4. Virulence gene comparison between ST131 and non-ST131 isolates. Graph showing the prevalence of virulence factors in ST131 (n 26) compared to non-ST131 (n 123) in the study isolates. Using Fisher’s exact test at a p value of 0.05, only those factors over-represented between the two groups are shown. (DOCX 2381 kb)

Phylogeny of CC22 MRSA in the Cambridge LTCF with bootstrap values. Bootstrap values for branches are shown in grey. (PDF 224 kb)

Phylogeny of CC5 MRSA in the Galway study. Maximum likelihood tree generated from core genome SNPs of CC5 MRSA isolates from the Galway LTCF residents (blue) and isolates from Galway University Hospital (red). Bootstrap values for branches are shown in grey. (PDF 266 kb)

Phylogeny of CC22 MRSA in the Cambridge LTCF with bootstrap values. Bootstrap values for branches are shown in grey. (PDF 224 kb)

Figure depicting the phylogeny and relatedness of VRE and VSE carried in stool by study participants. (PDF 167 kb)

Phylogeny of CC5 MRSA in the Galway study. Maximum likelihood tree generated from core genome SNPs of CC5 MRSA isolates from the Galway LTCF residents (blue) and isolates from Galway University Hospital (red). Bootstrap values for branches are shown in grey. (PDF 266 kb)

Additional file 5: Figure S5. Heatmap analysis with annotation for disease duration in months and active GPA, inactive GPA, and disease control using top 18 Staphylococcus species with a minimum abundance of 0.5% in at least one sample in the shotgun sequenced dataset. (PDF 83 kb)

Additional file 11. Supplementary Material and Method (DOCX 92 kb)

Phylogeny of ST45 MRSA in the Galway study. a Maximum likelihood tree generated from core genome SNPs of ST45 MRSA isolates from the Galway LTCF environment (black) and the isolate from Galway University Hospital (red). b Zoomed in view of the isolates from the Galway LTCF. Bootstrap values for branches are shown in grey. (PDF 23 kb)

Supplementary figures. (PDF 920 kb)

Additional file 12. Bioinformatics Analysis (DOCX 45 kb)

Additional file 11. Supplementary Material and Method (DOCX 92 kb)

Additional file 6: Table S1. Antimicrobial susceptibility testing of S. aureus isolates. (DOCX 18 kb)

Additional file 6: Table S1. Antimicrobial susceptibility testing of S. aureus isolates. (DOCX 18 kb)

Figure depicting the phylogeny and relatedness of VRE and VSE carried in stool by study participants. (PDF 167 kb)

Phylogeny of CC22 MRSA in the Galway study facility with bootstrap values. Bootstrap values for branches are shown in grey. (PDF 197 kb)

Additional file 5: Figure S5. Heatmap analysis with annotation for disease duration in months and active GPA, inactive GPA, and disease control using top 18 Staphylococcus species with a minimum abundance of 0.5% in at least one sample in the shotgun sequenced dataset. (PDF 83 kb)

Additional file 12. Bioinformatics Analysis (DOCX 45 kb)

Phylogeny of ST45 MRSA in the Galway study. a Maximum likelihood tree generated from core genome SNPs of ST45 MRSA isolates from the Galway LTCF environment (black) and the isolate from Galway University Hospital (red). b Zoomed in view of the isolates from the Galway LTCF. Bootstrap values for branches are shown in grey. (PDF 23 kb)

Phylogeny of CC22 MRSA in the Galway study facility with bootstrap values. Bootstrap values for branches are shown in grey. (PDF 197 kb)

Supplementary figures. (PDF 920 kb)