Fig. 2

Phylogenetic relationship and antimicrobial resistance prediction of genome sequences from Escherichia coli isolated during admission and reassessment. The isolates were clustered based on core genome SNPs identified using ParSNP [12, 20], with the phylogroups B2, F, A, B1 and D indicated at the appropriate branching points in the tree. Sample names are provided, with red labeled text highlighting samples obtained from mothers, dark blue highlighting samples obtained from infants, with the column “Adm” showing E. coli isolated from samples obtained at initial admission (black) or reassessment (white). Antimicrobial genotypes were predicted using AMRfinder, and grouped per class of antibiotics, with multidrug resistance (MDR, predicted resistance to ≥ 3 classes of antibiotics). All isolates were predicted to contain extended spectrum β-lactamases (ESBL), with the next two columns indicating the presence (black) or absence (white) of blaCTX-M and blaTEM genes. The final ten bars show the presence (black) and absence (white) of individual classes of antibiotic resistances (Ag, aminoglycoside; BL, β-lactam; Co, colistin; Fo, fosfomycin; Ma, macrolide; Ph, phenicol; Qn, quinolone; Su, sulfonamide; Te, tetracycline; Tp, trimethoprim). Full data with individual resistance genes and mutations can be found in Additional File 2: Table S8. Grey ellipses and stripes indicate the mothers and/or infants that are clonally related (nomenclature: M = mother, B = infant, A = admissions, X = reassessment, number = household ID)