Interrelation Between Pathoadaptability Factors and Crispr-Element Patterns in the Genomes of Escherichia coli Isolates Collected from Healthy Puerperant Women in Ural Region, Russia

Abstract

Escherichia coli is a commensal and opportunistic bacterium widely distributed around the world in different niches including intestinal of humans and animals, and its extraordinary genome plasticity led to the emergence of pathogenic strains causing a wide range of diseases. E. coli is one of the monitored species in maternity hospitals, being the main etiological agent of urogenital infections, endometriosis, puerperal sepsis, and neonatal diseases. This study presents a comprehensive analysis of E. coli isolates obtained from the maternal birth canal of healthy puerperant women 3-4 days after labor. According to whole genome sequencing data, 31 sequence types and six phylogenetic groups characterized the collection containing 53 isolates. The majority of the isolates belonged to the B2 phylogroup. The data also includes phenotypic and genotypic antibiotic resistance profiles, virulence factors, and plasmid replicons. Phenotypic and genotypic antibiotic resistance testing did not demonstrate extensive drug resistance traits except for two multidrug-resistant E. coli isolates. The pathogenic factors revealed in silico were assessed with respect to CRISPR-element patterns. Multiparametric and correlation analyses were conducted to study the interrelation of different pathoadaptability factors, including antimicrobial resistance and virulence genomic determinants carried by the isolates under investigation. The data presented will serve as a valuable addition to further scientific investigations in the field of bacterial pathoadaptability, especially in studying the role of CRISPR/Cas systems in the E. coli genome plasticity and evolution.

Keywords: CRISPR/Cas system; Escherichia coli; WGS; antibiotic resistance genes; pathoadaptability; pathogenic potential; virulence factors.

Figure 1

Sequence type distribution among different groups (“No CRISPR/No Cas”, “CRISPR/No Cas”, “Type I-E”, and “Type I-F”) of Crie-Pu E. coli isolates.

Figure 2

Phylogenetic groups’ distribution within different CRISPR-elements groups (“No CRISPR/No Cas”, “CRISPR/No Cas”, “Type I-E”, and “Type I-F”) for Crie-Pu E. coli isolates. (a) Crie-Pu isolates bearing neither CRISPR array, nor cas cassette; (b) Crie-Pu isolates with confirmed CRISPR arrays, but without cas cassettes; (c) Crie-Pu isolates with Type I-E CRISPR/Cas systems; (d) Crie-Pu isolates with Type I-F CRISPR/Cas systems.

Figure 3

Maximum likelihood phylogenetic tree of the full-length Type I-E cas3 gene sequences of clinical Crie-Pu E. coli isolates (shown as ‘Pu’ for brevity) and reference Escherichia isolates obtained from CRISPRCasdb. Bootstrap test (1000 replicates) was applied. Bootstrap values are indicated at the branch nodes. Antibiotic-resistant Crie-Pu E. coli isolates are marked with black triangles, antibiotic-sensitive Crie-Pu E. coli isolates are marked with white triangles. The genes identified in this study are indicated by the short isolate names, and the reference sequences are shown by GenBank accession number and strain name.

Figure 4

Maximum likelihood phylogenetic tree of the full-length Type I-F cas3 gene sequences of clinical Crie-Pu E. coli isolates (shown as ‘Pu’ for brevity) and reference Escherichia isolates obtained from CRISPRCas database. Bootstrap test (1000 replicates) was applied. Bootstrap values are indicated at the branch nodes. Antibiotic-resistant Crie-Pu E. coli isolates are marked with black triangles, antibiotic-sensitive Crie-Pu E. coli isolates are marked with white triangles. The genes identified in this study are indicated by the short isolate names, and the reference sequences are shown by GenBank accession number and strain name.

Figure 5

The number of antibiotic resistance genes in the analyzed groups of the Crie-Pu E. coli isolates. Asterisks denote significant difference (** p ≤ 0.01).

Figure 6

Virulence genes number in the analyzed groups of the Crie-Pu E. coli isolates. Asterisk denotes significant difference (* p ≤ 0.05).

Figure 7

Plasmid replicons number in the analyzed groups of the Crie-Pu E. coli isolates. Asterisk denotes significant difference (* p ≤ 0.05).

Figure 8

The CRISPR arrays spacers count in the analyzed groups of the Crie-Pu E. coli isolates. Asterisks denote significant differences (** p ≤ 0.01, **** p ≤ 0.0001).

Figure 9

CRISPR array spacers distribution in Type I-E and Type I-F Crie-Pu E. coli isolates according to CRISPRTarget web service. Asterisks denote significant differences (*** p ≤ 0.001, **** p ≤ 0.0001).