The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies

The impact of treatment strategies on the epidemiological dynamics of plasmid-conferred antibiotic resistance

The issue of antibiotic resistance is a critical concern for public health, prompting numerous investigations into the impact of treatment strategies on preventing or slowing down the emergence of resistance. While existing studies have predominantly focused on chromosomal resistance mutations, the consequences of often clinically more relevant plasmid-conferred resistance remain insufficiently explored. To address this gap, we conducted three extensive in vitro experiments utilizing a liquid-handling platform. These experiments evaluated the efficacy of five distinct treatment strategies using two antibiotics (tetracycline and ceftazidime) along with two horizontally transmissible clinical resistance plasmids conferring the respective resistances. Among the experimentally investigated treatment strategies, combination therapy proved to be the most effective in preventing the emergence of double resistance while minimizing the number of infections. To verify the reliability of these findings, we constructed a computational model of our experiments that we parameterized using the experimental data. We employed this model to augment the experimental data by conducting an in silico parameter sensitivity analysis. The sensitivity analysis corroborated our experimental results, demonstrating that combination therapy consistently outperformed other treatment strategies across a range of parameter values.

Short- and Long-Read Sequencing Reveals the Presence and Evolution of an IncF Plasmid Harboring blaCTX-M-15 and blaCTX-M-27 Genes in Escherichia coli ST131

Escherichia coli sequence type 131 (ST131) has contributed to the spread of extended-spectrum beta-lactamase (ESBL) and has emerged as the dominant cause of hospital- and community-acquired urinary tract infections. Here, we report for the first time an in-depth analysis of whole-genome sequencing (WGS) of 4 ESBL-producing E. coli ST131 isolates recovered from patients in two hospitals in Armenia using Illumina short-read sequencing for accurate base calling to determine their genotype and to infer their phylogeny and using Oxford Nanopore Technologies long-read sequencing to resolve plasmid and chromosomal genetic elements. Genotypically, the four Armenian isolates were identified as part of the H30Rx/clade C2 (n = 2) and H41/clade A (n = 2) lineages and were phylogenetically closely related to isolates from the European Nucleotide Archive (ENA) database previously recovered from patients in the United States, Australia, and New Zealand. The Armenian isolates recovered in this study had chromosomal integration of the blaCTX-M-15 gene in the H30Rx isolates and a high number of virulence genes found in the H41 isolates associated with the carriage of a rare genomic island (in the context of E. coli ST131) containing the S fimbrial, salmochelin siderophore, and microcin H47 virulence genes. Furthermore, our data show the evolution of the IncF[2:A2:B20] plasmid harboring both blaCTX-M-15 and blaCTX-M-27 genes, derived from the recombination of genes from an IncF[F2:A-:B-] blaCTX-M-15-associated plasmid into the IncF[F1:A2:B20] blaCTX-M-27-associated plasmid backbone seen in two genetically closely related H41 Armenian isolates. IMPORTANCE Combining short and long reads from whole-genome sequencing analysis provided a genetic context for uncommon genes of clinical importance to better understand transmission and evolutionary features of ESBL-producing uropathogenic E. coli (UPEC) ST131 isolates recovered in Armenia. Using hybrid genome assembly in countries lacking genomic surveillance studies can inform us about new lineages not seen in other countries with genes encoding high virulence and antibiotic resistance harbored on mobile genetic elements.