Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli

Abstract

Supplementary figure legends.Supplementary Fig. 1 Number of antibiotic resistance genes (ARG) according to the phylogenetic group among E. coli ST410 isolates. The horizontal lines in the boxes represent the median number of ARG associated to the three clades: Basal (n=22); FQR clade (n=92) and OXA-181 subclade (n=41). The box boundaries represent the first and third quartiles of the distribution and box-plot whiskers span 1.5 times the interquartile range of the distribution. Outliers are denoted as black dots outside whiskers. Statistical significances were tested with a one-sided Wilcoxon rank-sum test. ***, P < 0.001. Supplementary Fig. 2. Recombination events in isolates of the E. coli ST410 FQR clade. Phylogeny of the E. coli ST410 FQR clade (left). On the right side, the recombined blocks identified by Gubbins 1 are highlighted in red when they occurred in an internal branch and affect more than one isolate and in blue when they occurred in a terminal branch affecting a single isolate. The core genome of E. coli ST410 FQR strains is represented above the figure and annotated genes correspond to the limits of major recombination events. Supplementary Fig. 3. Phylogeny and mutations in non-redundant CP-Ec isolates of ST167, ST101 and ST156. ML phylogenies were estimated as for Fig. 1, using 5,843, 21,810, and 18,746 non-recombinant SNPs for a. Ec ST167, rooted with the ST10 strain MG1655 (NC_00913) b. Ec ST101, and c. Ec ST156 respectively, both rooted with the ST1128 strain IAI1 (NC_011741). 14 distantly related non-CP-Ec ST156 isolates have been removed from the phylogenetic analysis. Branch tips indicates the presence and the type of carbapenemase according to the figure key on the left. On the right side of the tree are represented, from left to right: blaCTX-M ESBL, gyrA and parC QRDR mutations, mutations in the ftsI gene, and genetic events affecting ompF and ompC according to the figure key at the bottom. SNPs in the dcw region are represented by small vertical red bars. Genes from the dcw locus are indicated by arrows and the ftsI gene in red. Black arrowheads indicate isolates used as reference for SNPs mapping in the dcw gene cluster.

Collateral sensitivity interactions between antibiotics depend on local abiotic conditions

“…Note our study included only chromosomal mutants derived from a single strain, albeit of an important commensal and opportunistically pathogenic species. Nevertheless, some of the resistance mechanisms we identified are known to be important in natural and clinical populations, such as mutations in genes for efflux pumps ( acr ) 38 , global regulators (marR, phoPQ ) 39–41 and specific antibiotic targets ( ftsI and rpsL ) 42–44 , suggesting our findings are relevant beyond laboratory studies. A key question for future work is whether collateral effects of resistance encoded on plasmids 45,46 , which is common in clinics, show similar sensitivity to abiotic conditions as we saw here.…”

Molecular characteristics of carbapenemase-producing Enterobacterales in the Netherlands; results of the 2014–2018 national laboratory surveillance

“…The predominant classical MLST type among bla OXA-181carrying K. pneumoniae and E. coli isolates were ST147 and ST410, respectively. These sequence types are known to circulate around the world [20,21], which might be reflected by the increasing occurrence of bla OXA-181 in the Netherlands. Another carbapenemase allele worth noting is bla VIM-1 , which until 2016 was found rarely among Enterobacterales in the Netherlands and globally [22], but was found 25 times in 2017, 11 of which belonged to an outbreak.…”

Occurrence and Diversity of CTX-M-Producing Escherichia coli From the Seine River

“…We also identified one ST410 isolate. This clone has recently attracted not only the light by its association with the spread of the carbapenemase OXA-181 ( Patiño-Navarrete et al, 2020 ) but also for its isolation in animals ( Yang et al, 2019 ). Of note, two isolates of ST162 were recovered in this study.…”