Genomic analysis of extended-spectrum beta-lactamase (ESBL)
producing Escherichia coli colonising adults in Blantyre, Malawi
reveals previously undescribed diversity
Supplementary material
This study
473 genomes
473 genomes
Musicha et al
93 genomes
97 genomes
4 excluded:
failed QC
3342 genomes
Horesh et al
50 largest popPUNK clusters:
• 500 representative
genomes as selected in
original publication
Other popPUNK clusters: 2776 genomes
• All isolates if ≤ 10 isolates
• 10 randomly selected
isolates if > 10 isolates
Supplementary Figure 1: Flowchart of included contextualising isolates.
, A
2
No. of STs per participant
5
No. of
Participants
4 10 5
75
3 22 10 4
50
2 62 7 4 0 25
1 99 4 0 1 0 0
1 2 3 4 5
No. of samples per participant
B
Between−participant, same ST Within−participant, same ST
8
Number of sample−pairs
300
6
200
4
100
2
0 0
0 50 100 150 200 0 50 100 150 200
Core genome SNP distance
Supplementary figure 2: Describing within-participant diversity. A: Heatmap
showing number of participants with a given number of samples and number of STs
per participant. Most (195/230, 85%) participants do not contribute samples with a
duplicated ST. B: Histogram of distribution of pairwise core genome SNP distance,
considering only sample pairs of the same ST, and stratified by whether sample pair
is between- or within-participant. Distributions are similar, justifying keeping all
samples in the analysis. Histogram has bin size 4 SNPs and x-axis is restricted to ≤
200 SNPs to show closely related isolates.
producing Escherichia coli colonising adults in Blantyre, Malawi
reveals previously undescribed diversity
Supplementary material
This study
473 genomes
473 genomes
Musicha et al
93 genomes
97 genomes
4 excluded:
failed QC
3342 genomes
Horesh et al
50 largest popPUNK clusters:
• 500 representative
genomes as selected in
original publication
Other popPUNK clusters: 2776 genomes
• All isolates if ≤ 10 isolates
• 10 randomly selected
isolates if > 10 isolates
Supplementary Figure 1: Flowchart of included contextualising isolates.
, A
2
No. of STs per participant
5
No. of
Participants
4 10 5
75
3 22 10 4
50
2 62 7 4 0 25
1 99 4 0 1 0 0
1 2 3 4 5
No. of samples per participant
B
Between−participant, same ST Within−participant, same ST
8
Number of sample−pairs
300
6
200
4
100
2
0 0
0 50 100 150 200 0 50 100 150 200
Core genome SNP distance
Supplementary figure 2: Describing within-participant diversity. A: Heatmap
showing number of participants with a given number of samples and number of STs
per participant. Most (195/230, 85%) participants do not contribute samples with a
duplicated ST. B: Histogram of distribution of pairwise core genome SNP distance,
considering only sample pairs of the same ST, and stratified by whether sample pair
is between- or within-participant. Distributions are similar, justifying keeping all
samples in the analysis. Histogram has bin size 4 SNPs and x-axis is restricted to ≤
200 SNPs to show closely related isolates.
