Unusual genotype of a Uropathogenic Escherichia coli strain assigned to the B2 phylogenetic group.
ABSTRACT Extraintestinal pathogenic Escherichia coli (ExPEC) cause infections such as urinary tract infections, septicemia and meningitis.…
- SourceAvailable from: ncbi.nlm.nih.gov[show abstract] [hide abstract]
ABSTRACT: Phylogenetic analysis has shown that Escherichia coli is composed of four main phylogenetic groups (A, B1, B2, and D) and that virulent extra-intestinal strains mainly belong to groups B2 and D. Actually, phylogenetic groups can be determined by multilocus enzyme electrophoresis or ribotyping, both of which are complex, time-consuming techniques. We describe a simple and rapid phylogenetic grouping technique based on triplex PCR. The method, which uses a combination of two genes (chuA and yjaA) and an anonymous DNA fragment, was tested with 230 strains and showed excellent correlation with reference methods.Applied and Environmental Microbiology 11/2000; 66(10):4555-8. · 3.68 Impact Factor
- [show abstract] [hide abstract]
ABSTRACT: It is well recognized that Escherichia coli consists of a number of distinct phylo-groups and that strains of the different phylo-groups vary in their ecological niches, life-history characteristics and propensity to cause disease. Consequently, much can be learnt by assigning a strain of E. coli to one of the recognized phylo-groups. A triplex PCR-based method that enables strains of E. coli to be assigned to a phylo-group using a dichotomous key approach based on the presence or absence of two genes (chuA and yjaA) and an anonymous DNA fragment (TSPE4.C2) has been developed. However, the accuracy with which this method assigns strains to their correct phylo-group has not been adequately evaluated. Consequently, 662 strains of E. coli were characterized using a multi-locus sequence typing approach. Unsupervised population assignment algorithms were used to assign strains to phylo-groups based on the multi-locus sequence typing data. The analyses revealed that 85-90% of E. coli strains can be assigned to a phylo-group and that 80-85% of the phylo-group memberships assigned using the Clermont method are correct. However, the accuracy with which strains are assigned to the correct phylo-group depends on their Clermont genotype. For example, strains yielding a Clermont genotype consistent with phylo-groups B1 and B2 are assigned correctly 95% of the time. Strains failing to yield any PCR products using the Clermont method are seldom members of phylo-group A and strains with such a genotype should not be assigned to a phylo-group.Environmental Microbiology 10/2008; 10(10):2484-96. · 5.76 Impact Factor
- [show abstract] [hide abstract]
ABSTRACT: The virulence of many human pathogens does not seem to be an evolutionarily selected trait, but an accidental by-product of the selection that operates in another ecological context. We investigated the possibility that virulence of the extraintestinal pathogenic Escherichia coli (ExPEC) strains, which frequently cause disease in the host in which they asymptomatically colonize the intestine, is the consequence of commensalism. Most of the ExPEC virulence factors are clustered on genomic islands called pathogenicity-associated islands (PAIs). We constructed and characterized several mutants of the ExPEC 536 strain with either (i) deletions of each single PAI or (ii) a complete deletion of all seven PAIs. In vitro phenotypic characterization of 536 mutants showed that the seven PAIs were dispensable for growth in the absence of external stress, as well as under a range of biologically relevant stressors, i.e., serum, bile, and oxidative, nitrosative, hyperosmotic, and acidic stress. However, challenge against the wild-type (WT) strain in a murine model shows that the deletion of all seven PAIs drastically reduces the fitness of 536 during persistent intestinal colonization. This defect seems to be linked to the hypermotility observed for mutants devoid of all seven PAIs. In addition, we show that PAIs diminish fitness of their carrier during growth in urine, suggesting that urinary tract infections are unlikely to provide selective pressure for the maintenance of ExPEC PAIs. Our results are in accordance with the coincidental-evolution hypothesis postulating that extraintestinal E. coli virulence is a by-product of commensalism.Journal of bacteriology 10/2010; 192(19):4885-93. · 3.94 Impact Factor
JOURNAL OF CLINICAL MICROBIOLOGY, Aug. 2011, p. 3105–3106
Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Vol. 49, No. 8
Unusual Genotype of a Uropathogenic Escherichia coli Strain
Assigned to the B2 Phylogenetic Group?
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 phylo-
group is good (4).
As part of a project investigating antimicrobial resistance,
virulence, and phylogeny, we used this method (1) to deter-
mine 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 Vi-
tek 2 Advanced Expert System (AES) (bioMe ´rieux, France).
Eight PAIs were screened by a multiplex PCR (6). The ampli-
fication products were sequenced (Macrogen). MLST was used
to determine the sequence type (7).
E. coli HUC270 was resistant only to ampicillin and ceph-
alothin, being susceptible to amoxicillin-clavulanic acid, pip-
eracillin-tazobactam, cefotaxime, ceftazidime, levofloxacin,
ciprofloxacin, gentamicin, trimethoprim-sulfamethoxazole,
and nitrofurantoin. An inverted relationship between the
presence of virulence factors and susceptibility to quino-
lones 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 con-
tain three or more PAIs (6). Indeed, E. coli HUC270 en-
coded 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 IICFT073, P-fimbriae and iron-regulated genes. How-
ever, 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 A0or A1(3) and B1 phylogroups. Accord-
ing to the MLST scheme (MLST databases at the Environ-
mental 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 se-
quences shared by group A ECOR strains and some show
sequences from B1 ECOR strains (1).
To our knowledge, the combination of yjaA and DNA
fragment tspE4.C2 genes reported here has not been de-
scribed 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-Pa ´ramo et al. (3). On the basis of the
results of PAI determination, MLST profile, and suscepti-
bility 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 consid-
ered potentially pathogenic.
N. Mendonc ¸a is supported by grant SFRH/BPD/45815/2008 from
Fundac ¸a ˜o para a Cie ˆncia e a Tecnologia, Lisboa, Portugal. This
work was supported financially by the ESCMID 2010 Research
Grant from the European Society of Clinical Microbiology and
Infectious Diseases and by the Center for Pharmaceutical Studies,
University of Coimbra.
The authors of this letter declare they have no conflicts of inter-
1. Clermont, O., S. Bonacorsi, and E. Bingen. 2000. Rapid and simple determi-
nation of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol.
2. Diard, M., et al. 2010. Pathogenicity-associated islands in extraintestinal
pathogenic Escherichia coli are fitness elements involved in intestinal coloni-
zation. J. Bacteriol. 192:4885–4893.
3. Escobar-Pa ´ramo, P., et al. 2004. Large-scale population structure of hu-
man commensal Escherichia coli isolates. Appl. Environ. Microbiol. 70:
4. Gordon, D. M., O. Clermont, H. Tolley, and E. Denamur. 2008. Assigning
Escherichia coli strains to phylogenetic groups: multi-locus sequence typing
versus the PCR triplex method. Environ. Microbiol. 10:2484–2496.
5. Moreno, E., et al. 2006. Quinolone, fluoroquinolone and trimethoprim/sulfa-
methoxazole resistance in relation to virulence determinants and phylogenetic
background among uropathogenic Escherichia coli. J. Antimicrob. Che-
6. Sabate ´, M., E. Moreno, T. Pe ´rez, A. Andreu, and G. Prats. 2006. Pathogenicity
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.
island markers in commensal and uropathogenic Escherichia coli isolates.
Clin. Microbiol. Infect. 12:880–886.
7. Wirth, T., et al. 2006. Sex and virulence in Escherichia coli: an evolutionary
perspective. Mol. Microbiol. 60:1136–1151.
Nuno Mendonc ¸a
Center of Pharmaceutical Sciences
Faculty of Pharmacy
University of Coimbra
College of Pharmacy
University of Michigan
Ann Arbor, Michigan
Grac ¸a Ribeiro
Clinical Pathology Service
University Hospitals of Coimbra
Gabriela Jorge Da Silva*
Laboratory of Microbiology
Center of Pharmaceutical Sciences
Faculty of Pharmacy
University of Coimbra
Health Sciences Campus
Azinhaga de Santa Comba
3000-548 Coimbra, Portugal
*Phone: 351 239488460
?Published ahead of print on 1 June 2011.
3106LETTERS TO THE EDITORJ. CLIN. MICROBIOL.