Unusual Genotype of a Uropathogenic Escherichia coli Strain Assigned to the B2 Phylogenetic Group

LETTER

Extraintestinal pathogenic Escherichia coli (ExPEC) strains cause infections such as urinary tract infections, septicemia, and meningitis. Knowledge of the phylogeny of the strains contributes to the recognition of their virulence potential and clinical outcome. ExPEC virulence factors are often clustered in pathogenicity-associated islands (PAIs) (2). Pathogenic ExPEC strains belong to the B2 and, to a lesser extent, D phylogenetic groups, whereas commensal isolates are assigned to groups A and B1. The triplex PCR method is often used to assess phylogenetic groups (1). The accuracy with which this method assigns strains to their correct multilocus sequence typing (MLST)-based phylogroup is good (4).

As part of a project investigating antimicrobial resistance, virulence, and phylogeny, we used this method (1) to determine the phylogroup of E. coli isolates collected at a university hospital. E. coli strain HUC270 was isolated in 2007 from the urine of a 52-year-old man hospitalized in a medical ward. The antimicrobial susceptibility testing was performed with the Vitek 2 Advanced Expert System (AES) (bioMérieux, France). Eight PAIs were screened by a multiplex PCR (6). The amplification products were sequenced (Macrogen). MLST was used to determine the sequence type (7).

E. coli HUC270 was resistant only to ampicillin and cephalothin, being susceptible to amoxicillin-clavulanic acid, piperacillin-tazobactam, cefotaxime, ceftazidime, levofloxacin, ciprofloxacin, gentamicin, trimethoprim-sulfamethoxazole, and nitrofurantoin. An inverted relationship between the presence of virulence factors and susceptibility to quinolones has been reported in uropathogenic E. coli, which may suggest a possible association of E. coli HUC270 with a virulent phylogenetic group like B2 (5). The majority of uropathogenic strains belonging to the B2 phylogroup contain three or more PAIs (6). Indeed, E. coli HUC270 encoded different virulence determinants in PAIs: in PAI III₅₃₆, S-fimbriae and an iron siderophore system; in PAI IV₅₃₆, the yersiniabactin siderophore system; and in PAI II_CFT073, P-fimbriae and iron-regulated genes. However, it was not possible to cluster the strain in the major phylogenetic groups or subgroups (1, 3). The chuA gene was not amplified, but the yjaA and DNA fragment tspE4.C2 genes were present in the genome (Fig. 1). The result was reproducible and consistent for six colonies submitted to triplex PCR to avoid the hypothesis of a mix of strains belonging to the A₀ or A₁ (3) and B1 phylogroups. According to the MLST scheme (MLST databases at the Environmental Research Institute [ERI], University College Cork), E. coli HUC270 revealed a new sequence type (ST2084), which was related to the B2 reference E. coli strain (ST127) by five housekeeping genes (adk, gyrB, icd, mdh, and recA). These findings suggested that this unusual genotype profile may be included in phylogroup B2 and not considered as a “hybrid” strain like E. coli reference strain 70 (ECOR 70), in which some housekeeping genes exhibit nucleotide sequences shared by group A ECOR strains and some show sequences from B1 ECOR strains (1).

Fig. 1.

Triplex PCR profiles specific for E. coli phylogenetic groups. Lanes 1 and 2, group A; lane 3, group B1; lanes 4 and 5, group D; lanes 6 and 7, group B2; lane 8, E. coli HUC270 profile. Lane M contains a 100-bp marker.

To our knowledge, the combination of yjaA and DNA fragment tspE4.C2 genes reported here has not been described previously. A study correlating phylogroup with MSLT results for 600 E. coli strains did not report this phylogenetic profile (4), suggesting that it is uncommon. Also, it could not be assigned to one of the seven groups defined by Escobar-Páramo et al. (3). On the basis of the results of PAI determination, MLST profile, and susceptibility to quinolones, we suggest that E. coli strains showing this combination of genes by the triplex PCR method should be assigned to the major phylogenetic group B2 and considered potentially pathogenic.