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. 2024 Apr 16;12:RP91853. doi: 10.7554/eLife.91853

Figure 1. Maximum likelihood phylogram displaying the relationship of the NMEC isolates with their associated serotype and virulence factor profile.

Non-NMEC isolates used in the analysis for referencing are italicised. The phylogram was built and recombination regions removed employing Parsnp, using 185,911 core single-nucleotide polymorphisms (SNPs) and NMEC strain IHE3034 as the reference. The scale bar indicates branch lengths in numbers of SNPs. NMEC isolates with available complete genomes are bold-italicised, while NMEC isolates that were completely sequenced in this study are indicated in bold and marked with an asterisk. The NMEC isolates that caused recrudescent invasive infection in this study are indicated in red. Branches are coloured according to phylogroups: orange, phylogroup F; red, phylogroup C; green, phylogroup A; violet, phylogroup D; and blue, phylogroup B2. The presence of specific virulence factors is indicated in dark blue. The phylogeny can be viewed interactively at https://microreact.org/project/oNfA4v16h3tQbqREoYtCXj-high-risk-escherichia-coli-clones-that-cause-neonatal-meningitis.

Figure 1.

Figure 1—figure supplement 1. Number of human-derived E. coli strains from ST95, ST1193, ST38, ST131, ST73, ST10, and ST69 available in the Enterobase database.

Figure 1—figure supplement 1.

Strains were stratified based on their year of isolation, spanning the periods before 2000, 2001–2005, 2006–2010, 2011–2015, and 2016–2022.
Figure 1—figure supplement 2. Antibiotic resistance gene profile of NMEC strains in the collection.

Figure 1—figure supplement 2.

The presence of each resistance gene is denoted by black shading.
Figure 1—figure supplement 3. ST95 NMEC strains contain more virulence factors than ST1193 NMEC strains.

Figure 1—figure supplement 3.

(A) The number of virulence genes (grouped as in Figure 1) for each strain within each sequence type (ST). (B) The number of virulence genes grouped by their functions in ST95 versus ST1193 strains. p-value was calculated using Mann–Whitney two-tailed unpaired test.
Figure 1—figure supplement 4. K1 capsule production in NMEC.

Figure 1—figure supplement 4.

K1 capsule production was detected by ELISA using a monoclonal antibody specific for polysialic acid. Strains with an OD420 >0.133 (mean + 3 standard deviations of a negative control kpsD mutant; dashed line) were considered positive for K1 capsule production. Data points represent independent biological replicates with horizontal lines as the mean.