A Longitudinal Study of Escherichia coli Clinical Isolates from the Tracheal Aspirates of a Paediatric Patient-Strain Type Similar to Pandemic ST131

Abstract

Escherichia coli is a Gram-negative bacterium and part of the intestinal microbiota. However, it can cause various diarrhoeal illnesses, i.e., traveller's diarrhoea, dysentery, and extraintestinal infections when the bacteria are translocated from the intestine to other organs, such as urinary tract infections, abdominal and pelvic infections, pneumonia, bacteraemia, and meningitis. It is also an important pathogen in intensive care units where cross-infection may cause intrahospital spread with serious consequences. Within this study, four E. coli isolates from the tracheal aspirates of a tracheotomised paediatric patient on chronic respiratory support were analysed and compared for antibiotic resistance and virulence potential. Genomes of all four isolates (5381a, 5381b, 5681, 5848) were sequenced using Oxford Nanopore Technology. According to PFGE analysis, the clones of isolates 5681 and 5848 were highly similar, and differ from 5381a and 5381b which were isolated first chronologically. All four E. coli isolates belonged to an unknown sequence type, related to the E. coli ST131, a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. All four E. coli isolates in this study exhibited a multidrug-resistant phenotype as, according to MIC data, they were resistant to ceftriaxone, ciprofloxacin, doxycycline, minocycline, and tetracycline. In addition, principal component analyses revealed that isolates 5681 and 5848, which were recovered later than 5381a and 5381b (two weeks and three weeks, respectively) possessed more complex antibiotic resistance genes and virulence profiles, which is concerning considering the short time period during which the strains were isolated.

Keywords: Escherichia coli; antimicrobial drug resistance; respiratory tract infections; virulence factors.

Figure 1

Sample collection and longitudinal bacterial isolation from the hospitalised patient. The first two isolates were not available for this study. TA—Tracheal aspirate. Figure made with Biorender.com, accessed on 27 February 2024.

Figure 2

DNA patterns of E. coli isolates obtained by PFGE (XbaI macrorestriction fingerprint). λ-ladder (λ-concatemers; New England Biolabs), 1—strain 5381a; 2—strain 5381b; 3—strain 5681; 4—strain 5848. The differences between the strains are indicated by the arrows.

Figure 3

Visualisation of the pan-genome constructed using Roary based on the core and accessory genes showing phylogenetic relatedness of the isolates by blue (present) and white (absent) fragments.

Figure 4

Single nucleotide polymorphisms (SNPs) occurring in clinically relevant genes: (a) the number of exclusive and shared mutated genes among the four strains; (b) the number of mutations within each gene, represented as a heatmap.

Figure 5

The individual factor map (a) and variables factor map (b) of PCA on different genetic determinants of antibiotic resistance, detected in genomes by the ResFinder database.

Figure 6

The individual factor map (a) and variables factor map (b) of PCA on different virulence factors, detected in genomes by VFDB.