Table 1.
Characteristics of the included first unique ESBL-producing E. coli and K. pneumoniae isolates from humans, the human-polluted environment, and food.
Table 2.
Detected antimicrobial resistance gene (ARG) types grouped per antimicrobial class of conferred resistance.
Fig 1.
Proportions (95% CI) of the ten most frequent antimicrobial resistance gene types per isolate.
Panel (a) beta-lactamases, panel (b) ESBLs, panel (c) fluoroquinolones, panel (d) aminoglycosides.
Fig 2.
Czekanowski’s proportional similarity index (PSI) (95% confidence interval) of detected antimicrobial resistance gene (ARG) types.
Panel (a) beta-lactamases conferring resistance to penicillins only (small and broad spectrum), panel (b) ESBL, panel (c) fluoroquinolones, and panel (d) aminoglycosides. The PSI is calculated with the following formula: where p corresponded to the relative frequency of gene type k (e.g. blaCTX-M-15) in reservoir n (e.g., ESBL-E. coli from humans), and q corresponded to the relative frequency of the same gene type in reservoir nx (e.g., ESBL-K. pneumoniae from humans). The numerator of the relative frequency was the count of each ARG type. The denominator of the relative frequency was the total number of genes of the corresponding ARG class. The PSI is a proportion, with 0 interpreted as no overlap, and 1 as perfect overlap in ARG type distributions between two reservoirs. 95% confidence intervals were calculated with 5,000 bootstrap iterations. PSI analysis for fosfomycin, trimethoprim, and sulfonamides ARGs are described in the supplement (S1 Fig 4 in S1 Appendix).
Fig 3.
Visualization of clonally related isolate pairs.
Nodes represent isolates and are grouped based on epidemiological setting, lines represent genetically similar isolate pairs. Panel (a) ESBL-producing E. coli (ESBL-Ec), panel (b) ESBL-producing K. pneumoniae (including seven K. variicola isolates) (ESBL-Kp), panel (c) ESBL-Ec Seville, panel (d) ESBL-Kp Seville. Grey boxes I and II are displayed enlarged in S1 Fig 5 in S1 Appendix, I: Panel A, II panel B.
Fig 4.
Maximum likelihood core genome phylogenies.
Panel (a) ESBL-producing E. coli (ESBL-Ec) (n = 475 isolates), panel (b) ESBL-producing K. pneumoniae (ESBL-Kp) (n = 171 isolates, including seven K. variicola isolates). Online access interactive trees: ESBL-Ec: https://microreact.org/project/wSXSAfjgAH1Xr9af46Hbcb-modern-project-esbl-e-coli-n475.