Previous Article | Next Article 
J Bacteriol, March 1998, p. 1159-1165, Vol. 180, No. 5
Department of Organismic and Evolutionary
Biology, Harvard University, Cambridge, Massachusetts 02138
Received 4 August 1997/Accepted 18 December 1997
We studied the ancestry of virulence-associated genes in
Escherichia coli by examining chromosomal regions specific
to pathogenic isolates. The four virulence determinants examined were
the alpha-hemolysin (hly) loci hlyI and
hlyII, the type II capsule gene cluster kps, and the P (pap) and S (sfa) fimbria gene
clusters. All four loci were shown previously to be associated with
pathogenicity islands of uropathogenic E. coli isolates.
The hly, kps, sfa, and
pap regions each have an unexpected clustered distribution
among the E. coli collection of reference (ECOR)
strains, but all these regions were absent from a collection of
diarrheagenic E. coli isolates. Strains in the ECOR
subgroup B2 typically had a combination of at least three of the four
loci, and all strains in subgroup D had a copy of the kps
and pap clusters. In contrast, only four strains in
subgroup A had either hly, kps,
sfa, or pap, and no subgroup A strains had all
four together. Strains of subgroup B1 were devoid of all four virulence
regions, with the exception of one isolate that had a copy of the
sfa gene cluster. This phylogenetic distribution
of strain-specific sequences corresponds to the ECOR groups with the
largest genome size, namely, B2 and D. We propose that the
pathogenicity islands are ancestral to subgroups B2 and D and were
acquired after speciation, with subsequent horizontal transfer into
some group A, B1, and E lineages. These results suggest that the
hly, kps, sfa, and pap
pathogenicity determinants may play a role in the evolution of enteric
bacteria quite apart from, and perhaps with precedence over, their
ability to cause disease.
Escherichia coli is a
genetically diverse species, the majority of isolates of which are
commensal organisms of the intestinal tract. However, some isolates are
opportunistic pathogens causing intestinal and extraintestinal
infections in a range of hosts. For example, the enteropathogenic
E. coli (EPEC) is the leading cause of severe infantile
diarrhea in the developing world, and enterohemorrhagic E. coli (EHEC) O157:H7 has recently emerged as the cause of bloody
diarrhea and hemolytic-uremic syndrome in major food-borne outbreaks in
the United States, Europe, and Asia (33, 34).
Pathogenicity islands (PAIs) encompass large segments of sometimes
unstable chromosomal DNA (5 to 200 kb) containing virulence gene
clusters (11, 14, 19) that are often flanked by insertion sequence elements or tRNA genes (2, 6, 14). Five such islands have previously been identified in pathogenic E. coli isolates (10, 14). PAIs I, II, IV, and V carry a
number of virulence gene clusters, among them the P (pap)
and P-related (prf) fimbria gene clusters and two
alpha-hemolysin loci, hlyI and hlyII (2, 3,
16, 21). The locus LEE (locus of enterocyte effacement) was identified in an EPEC strain (23);
LEE carries a different set of virulence genes than those
found in PAI I, II, IV, or V but is inserted in the same chromosomal
site as PAI I, at 82 min at the selenocysteine-specific tRNA (2,
23).
We examined the occurrence, phylogenetic distribution, and genetic
diversity of the four virulence determinants hly,
kps, pap, and sfa among E. coli natural isolates. The purpose was to test the conventional
view that chromosomal virulence determinants are temporary insertions
into the bacterial chromosome which come and go as the lineage
undergoes expansion and diversification (2, 3, 11, 14, 19).
The hly locus contains the gene for alpha-hemolysin
production, whereas the kps gene cluster contains genes for
type II capsule (4, 8, 21, 26). The pap and sfa gene clusters encode P and S fimbriae that are
associated mostly with uropathogenic E. coli strains
(3, 9, 12, 13, 17). The distribution of the four virulence
determinants was confined predominately to two lineages of the
E. coli reference collection (ECOR) strains, subgroups
B2 and D, with sporadic occurrences in subgroups A, B1, and E.
Does the observed phylogenetic clustering we have found reflect common
descent of the pathogenicity determinants in the subgroup B2 and D
lineages? If it does, then this would imply that these particular
pathogenicity determinants have a long-term persistence in the genomes
of these particular bacterial lineages. Did horizontal transfer of PAIs
play an important role during the evolution of E. coli,
and what role, if any, do PAIs play in genome size evolution? To
address these issues we also analyzed nucleotide sequence variation at
the three loci hlyA, kpsD, and papH to
determine levels of genetic diversity compared with the housekeeping
gene mdh for malate dehydrogenase. These data were analyzed
for evidence of horizontal transfer among ECOR subgroups and long-term
persistence within subgroups.
Bacterial strains.
Two E. coli reference
collections of natural isolates were examined: the ECOR collection and
the diarrheagenic E. coli (DEC) collection (25,
34). The ECOR collection consists of 72 strains, 62 of which were
recovered from healthy humans and animals, and 10 from women with
urinary tract infections. The ECOR collection encompasses much of the
total variation found within this species, and the major lineages are
divided into five groups: A, B1, B2, D, and E. The DEC collection
is made up of 15 strains recovered from patients infected with an
organism from one of three enteric diseae categories: EPEC, EHEC, and
enterotoxigenic E. coli (ETEC). Genomic DNA was
extracted with the G-Nome DNA isolation kit from Bio 101 (Vista,
Calif.).
PCR and DNA probe construction.
Nine sets of primers for
amplification of sequences of the hly, kps,
pap, and sfa gene clusters were used to obtain
probes to screen strains for the presence of these virulence
determinants (Table 1). In the 7.9-kb
sfa operon there are nine genes, and two probes were
designed for this region: sfa1 from the 5' end of the gene cluster and
sfa2 from the 3' region (Table 1 and Fig.
1A). We applied long-range PCR
(7) to obtain three probes, pap1, pap2, and pap3, from the
9-kb pap gene cluster (Table 1 and Fig. 1B). Probe kps1
represents kps region 1, and probe kps2 represents
kps region 3 (Table 1 and Fig. 1C). Two alpha-hemolysin gene
probes, hly1 and hly2, were made from a hemolysin gene cluster in an
EHEC strain and a uropathogenic E. coli strain, J96,
respectively (Table 1 and Fig. 1D). Following amplification, the PCR
products were purified with the Qiaquick PCR purification kit (Qiagen, Inc., Chatsworth, Calif.). All probes were prepared with DNA from ECOR
52 as a template. The probes were labeled with fluorescein-conjugated nucleotides according to the manufacturer's instructions
(Amersham, Arlington Heights, Ill.).
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
Chromosomal Regions Specific to Pathogenic Isolates
of Escherichia coli Have a Phylogenetically
Clustered Distribution
ABSTRACT
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
INTRODUCTION
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
MATERIALS AND METHODS
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
TABLE 1.
Forward and reverse primers used in construction
of probes
View larger version (17K):
[in a new window]
FIG. 1.
Gene organization of kps, sfa,
pap, and hly gene clusters. (A and B)
Organization of pap and sfa gene clusters. Boxes
indicate genes, and uppercase letters indicate gene designation(s). (C)
The kps genes in region 1 (five genes
[kpsSCUDE]) and region 3 (two genes [kpsMT])
are conserved among E. coli isolates that synthesize
serologically distinct capsules. The number of genes in the central
region 2 (kpsDBACES) reflects the size and complexity of the
polysaccharide repeating unit. (D) The alpha-hemolysin determinant from
E. coli J96 is represented; it consists of four genes.
Black bars below gene clusters indicate the position of DNA fragments
used as probes.
DNA hybridization. Bacterial genomic DNA was digested with EcoRI, and the digests were separated by electrophoresis in 0.6% agarose gels in 1× Tris-borate-EDTA. DNA fragments were transferred by alkaline blotting to Hybond-N+ membranes (Amersham). Membranes were prehybridized for 30 min at 65°C in a solution of 5× SSC (1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate, and 5% dextran sulfate. Hybridizations to labeled probes were carried out overnight at 65°C. Hybridized fragments were detected with the enhanced chemiluminescence system (Amersham).
Nucleotide sequencing. PCR products from three genes, hlyA, kpsD, and papH, were sequenced with an Applied Biosystems model 373A automated DNA sequencing system with a DyeDeoxy terminator cycle sequencing kit. For all strains, both strands were sequenced. From eight ECOR isolates, representing three ECOR subgroups, A, B2, and D, 570 bp of the hlyA gene was sequenced. A 729-bp region of the kpsD gene was sequenced from each of nine ECOR strains from subgroups A, B2, and D. A 462-bp portion of the papH gene was sequenced from six ECOR isolates.
Statistical analysis. To assay possible intragenic recombination events the Stephens test was used (31). The Stephens test identifies nonrandom clustering of polymorphic sites that may reflect the results of recombination events. The Stephens method examines the distribution of polymorphic sites relative to the phylogenetic partitions they support. Polymorphic sites supporting a particular phylogenetic partition are expected to be randomly distributed along the sequence if there is no recombination. Nucleotide sequences were analyzed by use of the computer program MEGA (20). Phylogenetic trees were constructed from synonymous site variation by the neighbor-joining method (28).
Nucleotide sequence accession numbers. The nucleotide sequences of the genes described in this paper have been deposited in the GenBank database under the accession no. AF037572 to AF037588.
| |
RESULTS |
|---|
|
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
|
|---|
Distribution of virulence determinants associated with PAIs. We determined the distribution of four virulence-associated regions in the 72 isolates of the ECOR reference collection and the 15 isolates of the DEC reference collection. The loci assayed were the two adhesin gene clusters sfa and pap; the kps capsule operon; and the alpha-hemolysin loci hlyI and hlyII. The distribution of the four virulence determinants was confined predominately to two lineages of the ECOR strains, subgroup B2 and D (Fig. 2).
|
Nucleotide sequence variation. The single genes hlyA (hlyII), kpsD (kps), and papH (pap) from each of the three virulence gene clusters were sequenced from representative isolates of the ECOR collection.
Within the hlyA alleles from nine E. coli strains, there were only six polymorphic sites in the 570-bp segment sequenced. ECOR 24 and ECOR 43 had virtually identical sequences and are distinct at five of the six polymorphic sites detected in the other ECOR strains examined (Fig. 3). The hlyA locus has a GC content of 40%, which is atypical for genes of E. coli, and a codon adaptation index (CAI) of 0.228.
|
|
Rates of synonymous and nonsynonymous substitution. For hlyA we estimated the numbers of synonymous (silent) substitutions per 100 synonymous sites (kS) and nonsynonymous (replacement) substitutions per 100 nonsynonymous sites (kN) (24). There were reduced levels of synonymous and nonsynonymous site variation at the hlyA locus relative to the gene mdh, coding for malate dehydrogenase; however, the kN/kS ratio was high because three of six polymorphic sites encoded amino acid replacements. The kN/kS ratio indicates the relative degree of functional constraints experienced by an evolving protein. Examination of the genes in Table 2 indicates that both mdh and kpsD have an increased level of functional constraint relative to hlyA and papH. At the kps and papH loci, the levels of variation at synonymous sites were similar to that of the housekeeping gene mdh (Table 2). However, at both of these loci there were elevated levels of nonsynonymous site variation; in the case of papH, most of the variation was accounted for by polymorphism contributed by the ECOR 49 papH sequence (Fig. 2).
|
Distribution of polymorphic nucleotide sites. To test for nonrandom clustering of polymorphic nucleotide sites, a pattern that may be indicative of intragenic recombination, we used the Stephens test (31). Among the six papH sequences, there were 22 polymorphic sites in the 462 bp sequenced, and the Stephens test identified two statistically significant partitions. The first identified a 177-bp segment of invariant sites (P < 0.006) in ECOR 49, and the second identified a 156-bp region of invariant sites shared between ECOR 49 and ECOR 50.
For the 48 polymorphic sites among the nine kpsD sequences (shown in Fig. 3), six partitions were found for which there were statistically significant P values for either clustered polymorphic sites or segments composed of invariant sites. The first partition grouped ECOR 8 and ECOR 46 kpsD sequences and was based on only three polymorphic sites (sites 2, 9, and 25) and a 159-bp segment of consecutive nonpolymorphic sites (P < 0.006). The second partition identified a cluster of nine polymorphic sites (P < 0.002) in ECOR 14, eight of which were found at the 5' end of the kpsD gene. The third partition involved only three clustered sites in ECOR 8 with a 324-bp segment of consecutive nonpolymorphic sites (P < 0.006). The fourth partition identified 15 clustered polymorphic sites (P < 0.000), the majority of which were in the 3' end of the kps gene and separated ECOR 48 from the rest. Two sites grouped strains ECOR 14 and ECOR 49, and the probability of two polymorphic sites as close as or closer than 2 bp is 0.009. The final statistically significant kps partition identified grouped kps sequences from ECOR 11 and ECOR 49 and is based on a run of 275 bp of consecutive nonpolymorphic sites (P < 0.006).Evolutionary trees for the kpsD and papH sequences. For purposes of comparison, the housekeeping gene mdh from eight ECOR strains (5) analyzed at the kpsD and papH loci was used to construct an mdh gene tree (Fig. 4). Previous analysis has shown that the mdh gene tree is congruent with phylogenetic relationships based on multilocus enzyme electrophoresis and DNA hybridization analysis (5), thus providing a reliable measure of overall chromosomal relationships. No phylogenetic tree was constructed for hlyA, as there was not sufficient nucleotide sequence polymorphism to determine relationships among strains. Among all trees there are three isolates in common: ECOR 46, ECOR 49, and ECOR 52. Relationships among the ECOR strains were not congruent among the kpsD, papH, and mdh trees, particularly at the kps locus, at which phylogenetic comparisons with the mdh gene tree indicate several possible horizontal transfer events. The long branch length found in the ECOR 14 and ECOR 48 kpsD sequences can be accounted for by possible intragenic recombination events from an unknown source, identified by the Stephens test, involving the 5' region in ECOR 14 and the 3' region in ECOR 48.
| |
DISCUSSION |
|---|
|
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
|
|---|
Pathogenic isolates of E. coli are known to carry large chromosomal regions required for virulence, which are termed PAIs. Natural isolates are polymorphic for the presence and copy number of these DNA sequences. For example, the pathogenicity islands PAI I and PAI II of uropathogenic strains (2, 3), which are 70 and 190 kb in length, as well as the class II capsule synthesis operon (kps), are absent from E. coli K-12 (4). The prevailing view of E. coli as a relatively benign organism obtaining novel sequences from an outside source and thereby becoming pathogenic or switching disease syndrome or host has been supported by many authors (2, 3, 11, 14, 19). For example, Whittam and colleagues have proposed that the O157:H7 clone emerged when an EPEC O55:H7-like progenitor was lysogenized by a bacteriophage containing Shiga-like toxin genes (34).
Recently, Pupo and colleagues (27) have described the relationship between pathogenic and nonpathogenic isolates of E. coli. The pathogenic isolates included EPEC, EHEC, ETEC, enteroinvasive E. coli, and urinary tract infection strains, and the nonpathogenic isolates were represented by the ECOR strains. The authors concluded that pathogenic strains arising from E. coli do not have a single evolutionary origin within E. coli but have arisen many times, with the exception of Shigella and the EHEC clones. The Shigella isolates examined were all closely related to each other, clustering within ECOR subgroup A strains, confirming earlier conclusions that Shigella species are a clonal lineage of E. coli (35). Further, the results verified earlier findings of Whittam et al. (34) that strains causing the same disease do not form a monophyletic group. Wieler et al. (36) recently examined the insertion sites of the LEE locus in DEC strains and showed that the LEE insertion site differs in relation to the clonal lineage of the strains, which they conclude is due to multiple insertions during the evolution of these pathogens.
As shown by the phylogenetic distribution in Fig. 2, the majority of ECOR B2 and D isolates contain at least two of the four regions examined. Most isolates of subgroup B2 and all isolates of subgroup D have a copy of kps and pap; in addition, subgroup B2 strains have a copy of sfa. Among the other ECOR lineages there is only a sporadic occurrence of these sequences. In particular, among subgroup A strains (which is the largest set of lineages represented in the ECOR collection [25 of 72]), only five strains show hybridization to the probes for hly, kps, and pap, and only two strains (ECOR 11 and ECOR 24) contain sequences with homology to both the kps and pap regions.
The sporadic occurrence of hly, kps, pap, and sfa among ECOR group A isolates could have resulted from either widespread loss from strains within this group, which is unlikely, or transfer from perhaps a group B2 or D strain. The hlyA locus has been detected on an E. coli plasmid (8), which suggests a mechanism of horizontal transfer. Given the low GC content of the hlyA gene, 40% (compared to an average of 52% for most E. coli genes), and the limited nucleotide sequence polymorphism, this region may have been recently acquired from an unknown source. Alternatively, the highly conserved nucleotide sequence at hlyA may be due to selective constraints at the protein level. These conflicting views may be addressed with additional nucleotide sequence information from this gene cluster. Among the kpsD sequences examined, those of subgroup A strains ECOR 8 and ECOR 11 showed identity with those of subgroup B2, which is most easily explained by recent horizontal transfer between these subgroups. Marklund and coworkers (22) have proposed that E. coli acquired the pap locus after the speciation of E. coli and suggest that the different pap genes could have been acquired by horizontal gene transfer. Moreover, they proposed that the recent genetic exchanges involving the entire pilin gene clusters have occurred in response to selection pressures exerted by the host. Among the papH sequences studied, only that of ECOR 49 is radically different, and all of the amino acid substitutions are encoded in the first hundred bases of this gene; based on additional nucleotide sequence analysis, it appears that this diversity resulted from horizontal transfer at the papA locus, 63 bp upstream of papH, and that the variation in ECOR 49 is a result of hitchhiking (5a).
The stratification in the distribution of these virulence regions may be a consequence of the fact that the majority of the isolates of groups B2 and D were recovered from primates. For example, among isolates with sequences that show hybridization to the kps probe, all but two were isolated from primates; likewise all pap- and sfa-positive strains, with one exception, are all from primates. In contrast, ECOR isolates of subgroup B1 were predominantly isolated from nonprimate hosts (Table 3).
|
Natural isolates of E. coli may vary in genome size by up to 1 Mb (1, 25a). The mechanism(s) of chromosome size variation in natural isolates of E. coli remains largely unknown. It may be relevant to these observations that isolates belonging to ECOR subgroup A have a significantly smaller genome size than those of either subgroup B2 or D, which have the largest genome size among natural isolates of E. coli (1). Comparisons of genome size with the presence of regions of interest in ECOR strains indicate that ECOR 14, which has a putative PAI present, has a genome size of 5,000 kb and differs in size by more than 300 kb from a closely related lineage, ECOR 13, where we found none of the four regions present. Isolates of group B2 and D (ECOR 51, 62, 63, 38, and 40) for which genome size is available range in size from 4,952 to 5,302 kb, and all isolates have two or more of the regions under study associated with them.
To determine the relationship between uropathogenic E. coli and DEC, isolates from the DEC collection were examined (34). The DEC collection comprises 15 clones representing E. coli isolates recovered from patients with enteric disease in one of three disease categories, EPEC, EHEC, and ETEC. Among the 15 DEC isolates examined, none had sequences which hybridized with the hlyII, pap, sfa, and kps probes. This result confirms earlier findings that DEC strains require a very different set of virulence determinants (the LEE locus) than those of uropathogenic E. coli isolates. The result also suggests that isolates may not typically carry PAIs for multiple disease categories. Further, our data support the view of long-term persistence of PAIs within E. coli lineages and indicate that whereas some pathogenicity determinants may be genetically labile, others are maintained for long periods of evolutionary time. Currently we are investigating whether hly, kps, pap, and sfa are confined to a single PAI. Future studies will include analysis of the insertion sites of putative PAIs in subgroup B2 and D strains.
| |
ACKNOWLEDGMENT |
|---|
This research was supported by grant GM322 from the National Institutes of Health.
| |
FOOTNOTES |
|---|
* Corresponding author. Mailing address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138. Phone: (617) 496-3917. Fax: (617) 496-5854. E-mail: dhartl{at}oeb.harvard.edu.
| |
REFERENCES |
|---|
|
Top
Abstract
Introduction
Materials & Methods
Results
Discussion
References
|
|---|
| 1. |
Bergthorsson, U., and H. Ochman.
1995.
Heterogeneity of genome sizes among natural isolates of Escherichia coli.
J. Bacteriol.
177:5784-5789 |
| 2. |
Blum, G.,
M. Ott,
A. Lischewski,
A. Ritter,
H. Imrich,
H. Tschape, and J. Hacker.
1994.
Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen.
Infect. Immun.
62:606-614 |
| 3. | Blum, G., V. Falbo, A. Caprioli, and J. Hacker. 1995. Gene clusters encoding the cytotoxic necrotizing factor type 1, Prs-fimbriae and alpha-hemolysin form the pathogenicity island II of the uropathogenic Escherichia coli strain J96. FEMS Microbiol. Lett. 126:189-195[Medline]. |
| 4. | Boulnois, G. J., and I. S. Roberts. 1990. Genetics of capsular polysaccharide production in bacteria. Curr. Top. Microbiol. Immunol. 150:1-18[Medline]. |
| 5. |
Boyd, E. F.,
K. Nelson,
F.-S. Wang,
T. S. Whittam, and R. K. Selander.
1994.
Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica.
Proc. Natl. Acad. Sci. USA
91:1280-1284 |
| 5a. | Boyd, E. F., and D. L. Hartl. Unpublished data. |
| 6. | Cheetham, B. F., and M. E. Katz. 1995. A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol. Microbiol. 18:201-208[Medline]. |
| 7. |
Cheng, S.,
C. Fockler,
W. M. Barnes, and R. Higuchi.
1994.
Effective amplification of long targets from cloned inserts and human genomic DNA.
Proc. Natl. Acad. Sci. USA
91:5695-5699 |
| 8. |
Felmlee, T.,
S. Pellett, and R. A. Welch.
1985.
Nucleotide sequence of an Escherichia coli chromosomal hemolysin.
J. Bacteriol.
163:94-105 |
| 9. | Gaastra, W., and A. M. Svennerholm. 1996. Colonization factors of human enterotoxigenic Escherichia coli (ETEC). Trends Microbiol. 4:444-452[Medline]. |
| 10. | Groisman, E. A., and H. Ochman. 1996. Pathogenicity islands: bacterial evolution in quantum leaps. Cell 87:791-794[Medline]. |
| 11. | Hacker, J., L. Bender, M. Ott, J. Wiingender, B. Lund, R. Marre, and W. Goebel. 1990. Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates. Microb. Pathog. 8:213-225[Medline]. |
| 12. | Hacker, J. 1992. Role of fimbrial in the pathogenesis of Escherichia coli infections. Can. J. Microbiol. 38:720-727[Medline]. |
| 13. |
Hacker, J.,
H. Kestler,
H. Hoschützky,
K. Jann,
F. Lottspeich, and T. K. Korhonen.
1993.
Cloning and characterization of the S fimbrial adhesin II complex of an Escherichia coli O18:K1 meningitis isolate.
Infect. Immun.
61:544-550 |
| 14. | Hacker, J., G. Oehler-Blum, I. Mühlodorfer, and H. Tschäpe. 1997. Pathogenicity islands of virulent bacteria: structure, function, and impact on microbial evolution. Mol. Microbiol. 23:1089-1097[Medline]. |
| 15. |
Herzer, P. J.,
S. Inouye,
M. Inouye, and T. S. Whittam.
1990.
Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli.
J. Bacteriol.
172:6175-6181 |
| 16. |
Hull, S. I.,
R. A. Hull,
B. H. Minshew, and S. Falkow.
1982.
Genetics of hemolysin of Escherichia coli.
J. Bacteriol.
151:1006-1012 |
| 17. | Hultgren, S. J., C. H. Jones, and S. Normark. 1996. Bacterial adhesins and their assembly, p. 2730-2756. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2. ASM Press, Washington, D.C. |
| 18. | Jukes, T. H., and C. R. Cantor. 1969. . Evolution of protein molecules. Academic Press, New York, N.Y. |
| 19. |
Knapp, S.,
J. Hacker,
T. Jarchau, and W. Goebel.
1986.
Large, unstable inserts in the chromosome affect virulence properties of uropathogenic Escherichia coli O6 strain 536.
J. Bacteriol.
168:22-30 |
| 20. | Kumar, S., K. Tamura, and M. Nei. 1993. MEGA: molecular evolutionary genetics analysis, version 1. The Pennsylvania State University, University Park. |
| 21. |
Low, D.,
V. David,
D. Lark,
G. Schoolnik, and S. Falkow.
1984.
Gene clusters governing the production of hemolysin and mannose-resistant hemagglutination are closely linked in Escherichia coli serotype O4 and O6 isolates from urinary tract infections.
Infect. Immun.
43:353-358 |
| 22. | Marklund, B. I., J. M. Tennent, E. Garcia, A. Hamers, M. Baga, F. Lindberg, W. Gaastra, and S. Normark. 1992. Horizontal gene transfer of the Escherichia coli pap and prs pili operons as a mechanism for the development of tissue-specific adhesive properties. Mol. Microbiol. 6:2225-2242[Medline]. |
| 23. |
McDaniel, T. K.,
K. G. Jarvis,
M. S. Donnenberg, and J. B. Kaper.
1995.
A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens.
Proc. Natl. Acad. Sci. USA
92:1664-1668 |
| 24. | Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426[Abstract]. |
| 25. |
Ochman, H., and R. K. Selander.
1984.
Standard reference strains of Escherichia coli from natural populations.
J. Bacteriol.
157:690-693 |
| 25a. | Ochman, H. Personal communication. |
| 26. |
Pazzani, C.,
C. Rosenow,
G. J. Boulnois,
D. Bronner,
K. Jann, and I. S. Roberts.
1993.
Molecular analysis of region 1 of the Escherichia coli K5 antigen gene cluster: a region encoding proteins involved in cell surface expression of capsular polysaccharide.
J. Bacteriol.
175:5978-5983 |
| 27. | Pupo, G. M., D. K. R. Karaolis, R. Lan, and P. R. Reeves. 1997. Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies. Infect. Immun. 65:2685-2692[Abstract]. |
| 28. | Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425[Abstract]. |
| 29. | Schmoll, T., H. Hoschutzky, J. Morschhauser, F. Lottspeich, K. Jann, and J. Hacker. 1989. Analysis of genes coding for the sialic acid-binding adhesin and two other minor fimbrial subunits of the S-fimbrial adhesin determinant of Escherichia coli. Mol. Microbiol. 3:1735-1744[Medline]. |
| 30. |
Sharp, P., and W. H. Li.
1987.
The codon Adaptation Index a measure of directional synonymous codon usage bias, and its potential applications.
Nucleic Acids Res.
15:1281-1295 |
| 31. | Stephens, J. C. 1985. Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Mol. Biol. Evol. 2:539-556[Abstract]. |
| 32. | van Die, I., B. Geffen, W. Hoekstra, and H. E. N. Bergmans. 1984. Type 1C fimbriae of a uropathogenic Escherichia coli strain: cloning and characterization of the gene involved in the expression of the 1C antigen and nucleotide sequence of the subunit gene. Gene 34:187-196. |
| 33. | Whittam, T. S. 1996. Genetic variation and evolutionary processes in natural populations of Escherichia coli, p. 2708-2720. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2. ASM Press, Washington, D.C. |
| 34. |
Whittam, T. S.,
M. L. Wolfe,
I. K. Wachsmuth,
F. Ørskov,
I. Ørskov, and R. A. Wilson.
1993.
Clonal relationships among Escherichia coli strains that cause hemorrhagic colitis and infantile diarrhea.
Infect. Immun.
61:1619-1629 |
| 35. |
Whittam, T. S.,
H. Ochman, and R. K. Selander.
1983.
Multilocus genetic structure in natural populations of Escherichia coli.
Proc. Natl. Acad. Sci. USA
80:1751-1755 |
| 36. | Wieler, L. H., T. K. McDaniel, T. S. Whittam, and J. B. Kaper. 1997. Insertion site of the locus of enterocyte effacement in enteropathogenic and enterohemorrhagic Escherichia coli differs in relation to the clonal phylogeny of the strains. FEMS Microbiol. Lett. 156:49-53[Medline]. |
J Bacteriol, March 1998, p. 1159-1165, Vol. 180, No. 5
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
This article has been cited by other articles:
-
Bonnet, C., Diarrassouba, F., Brousseau, R., Masson, L., Topp, E., Diarra, M. S.
(2009). Pathotype and Antibiotic Resistance Gene Distributions of Escherichia coli Isolates from Broiler Chickens Raised on Antimicrobial-Supplemented Diets. Appl. Environ. Microbiol.
75: 6955-6962
[Abstract] [Full Text] -
Unno, T., Han, D., Jang, J., Lee, S.-N., Ko, G., Choi, H. Y., Kim, J. H., Sadowsky, M. J., Hur, H.-G.
(2009). Absence of Escherichia coli Phylogenetic Group B2 Strains in Humans and Domesticated Animals from Jeonnam Province, Republic of Korea. Appl. Environ. Microbiol.
75: 5659-5666
[Abstract] [Full Text] -
Ghenghesh, K. S., Elkateb, E., Berbash, N., Abdel Nada, R., Ahmed, S. F., Rahouma, A., Seif-Enasser, N., Elkhabroun, M.-A., Belresh, T., Klena, J. D.
(2009). Uropathogens from diabetic patients in Libya: virulence factors and phylogenetic groups of Escherichia coli isolates. J Med Microbiol
58: 1006-1014
[Abstract] [Full Text] -
Regua-Mangia, A. H., Gomes, T. A. T., Vieira, M. A. M., Irino, K., Teixeira, L. M.
(2009). Molecular typing and virulence of enteroaggregative Escherichia coli strains isolated from children with and without diarrhoea in Rio de Janeiro city, Brazil. J Med Microbiol
58: 414-422
[Abstract] [Full Text] -
Ewers, C., Antao, E.-M., Diehl, I., Philipp, H.-C., Wieler, L. H.
(2009). Intestine and Environment of the Chicken as Reservoirs for Extraintestinal Pathogenic Escherichia coli Strains with Zoonotic Potential. Appl. Environ. Microbiol.
75: 184-192
[Abstract] [Full Text] -
Le Gall, T., Clermont, O., Gouriou, S., Picard, B., Nassif, X., Denamur, E., Tenaillon, O.
(2007). Extraintestinal Virulence Is a Coincidental By-Product of Commensalism in B2 Phylogenetic Group Escherichia coli Strains. Mol Biol Evol
24: 2373-2384
[Abstract] [Full Text] -
Lloyd, A. L., Rasko, D. A., Mobley, H. L. T.
(2007). Defining Genomic Islands and Uropathogen-Specific Genes in Uropathogenic Escherichia coli. J. Bacteriol.
189: 3532-3546
[Abstract] [Full Text] -
Germon, P., Roche, D., Melo, S., Mignon-Grasteau, S., Dobrindt, U., Hacker, J., Schouler, C., Moulin-Schouleur, M.
(2007). tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains. Microbiology
153: 826-837
[Abstract] [Full Text] -
Girardeau, J. P., Dalmasso, A., Bertin, Y., Ducrot, C., Bord, S., Livrelli, V., Vernozy-Rozand, C., Martin, C.
(2005). Association of Virulence Genotype with Phylogenetic Background in Comparison to Different Seropathotypes of Shiga Toxin-Producing Escherichia coli Isolates. J. Clin. Microbiol.
43: 6098-6107
[Abstract] [Full Text] -
Wooldridge, K. G., Kizil, M., Wells, D. B., Ala'Aldeen, D. A. A.
(2005). Unusual Genetic Organization of a Functional Type I Protein Secretion System in Neisseria meningitidis. Infect. Immun.
73: 5554-5567
[Abstract] [Full Text] -
Hommais, F., Pereira, S., Acquaviva, C., Escobar-Paramo, P., Denamur, E.
(2005). Single-Nucleotide Polymorphism Phylotyping of Escherichia coli. Appl. Environ. Microbiol.
71: 4784-4792
[Abstract] [Full Text] -
Gamage, S. D., Patton, A. K., Hanson, J. F., Weiss, A. A.
(2004). Diversity and Host Range of Shiga Toxin-Encoding Phage. Infect. Immun.
72: 7131-7139
[Abstract] [Full Text] -
Schouler, C., Koffmann, F., Amory, C., Leroy-Setrin, S., Moulin-Schouleur, M.
(2004). Genomic subtraction for the identification of putative new virulence factors of an avian pathogenic Escherichia coli strain of O2 serogroup. Microbiology
150: 2973-2984
[Abstract] [Full Text] -
Grozdanov, L., Raasch, C., Schulze, J., Sonnenborn, U., Gottschalk, G., Hacker, J., Dobrindt, U.
(2004). Analysis of the Genome Structure of the Nonpathogenic Probiotic Escherichia coli Strain Nissle 1917. J. Bacteriol.
186: 5432-5441
[Abstract] [Full Text] -
Escobar-Paramo, P., Clermont, O., Blanc-Potard, A.-B., Bui, H., Le Bouguenec, C., Denamur, E.
(2004). A Specific Genetic Background Is Required for Acquisition and Expression of Virulence Factors in Escherichia coli. Mol Biol Evol
21: 1085-1094
[Abstract] [Full Text] -
Hoffmann, H., Roggenkamp, A.
(2003). Population Genetics of the Nomenspecies Enterobacter cloacae. Appl. Environ. Microbiol.
69: 5306-5318
[Abstract] [Full Text] -
Sorsa, L. J., Dufke, S., Heesemann, J., Schubert, S.
(2003). Characterization of an iroBCDEN Gene Cluster on a Transmissible Plasmid of Uropathogenic Escherichia coli: Evidence for Horizontal Transfer of a Chromosomal Virulence Factor. Infect. Immun.
71: 3285-3293
[Abstract] [Full Text] -
Bekal, S., Brousseau, R., Masson, L., Prefontaine, G., Fairbrother, J., Harel, J.
(2003). Rapid Identification of Escherichia coli Pathotypes by Virulence Gene Detection with DNA Microarrays. J. Clin. Microbiol.
41: 2113-2125
[Abstract] [Full Text] -
Dezfulian, H., Batisson, I., Fairbrother, J. M., Lau, P. C. K., Nassar, A., Szatmari, G., Harel, J.
(2003). Presence and Characterization of Extraintestinal Pathogenic Escherichia coli Virulence Genes in F165-Positive E. coli Strains Isolated from Diseased Calves and Pigs. J. Clin. Microbiol.
41: 1375-1385
[Abstract] [Full Text] -
Dobrindt, U., Agerer, F., Michaelis, K., Janka, A., Buchrieser, C., Samuelson, M., Svanborg, C., Gottschalk, G., Karch, H., Hacker, J.
(2003). Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays. J. Bacteriol.
185: 1831-1840
[Abstract] [Full Text] -
Zhang, L., Foxman, B., Marrs, C.
(2002). Both Urinary and Rectal Escherichia coli Isolates Are Dominated by Strains of Phylogenetic Group B2. J. Clin. Microbiol.
40: 3951-3955
[Abstract] [Full Text] -
Blanc-Potard, A.-B., Tinsley, C., Scaletsky, I., Le Bouguenec, C., Guignot, J., Servin, A. L., Nassif, X., Bernet-Camard, M.-F.
(2002). Representational Difference Analysis between Afa/Dr Diffusely Adhering Escherichia coli and Nonpathogenic E. coli K-12. Infect. Immun.
70: 5503-5511
[Abstract] [Full Text] -
Schubert, S., Picard, B., Gouriou, S., Heesemann, J., Denamur, E.
(2002). Yersinia High-Pathogenicity Island Contributes to Virulence in Escherichia coli Causing Extraintestinal Infections. Infect. Immun.
70: 5335-5337
[Abstract] [Full Text] -
Bingen-Bidois, M., Clermont, O., Bonacorsi, S., Terki, M., Brahimi, N., Loukil, C., Barraud, D., Bingen, E.
(2002). Phylogenetic Analysis and Prevalence of Urosepsis Strains of Escherichia coli Bearing Pathogenicity Island-Like Domains. Infect. Immun.
70: 3216-3226
[Abstract] [Full Text] -
Johnson, J. R., Stell, A. L., O'Bryan, T. T., Kuskowski, M., Nowicki, B., Johnson, C., Maslow, J. N., Kaul, A., Kavle, J., Prats, G.
(2002). Global Molecular Epidemiology of the O15:K52:H1 Extraintestinal Pathogenic Escherichia coli Clonal Group: Evidence of Distribution beyond Europe. J. Clin. Microbiol.
40: 1913-1923
[Abstract] [Full Text] -
Clermont, O., Cordevant, C., Bonacorsi, S., Marecat, A., Lange, M., Bingen, E.
(2001). Automated Ribotyping Provides Rapid Phylogenetic Subgroup Affiliation of Clinical Extraintestinal Pathogenic Escherichia coli Strains. J. Clin. Microbiol.
39: 4549-4553
[Abstract] [Full Text] -
Johnson, J. R., O'Bryan, T. T., Kuskowski, M., Maslow, J. N.
(2001). Ongoing Horizontal and Vertical Transmission of Virulence Genes and papA Alleles among Escherichia coli Blood Isolates from Patients with Diverse-Source Bacteremia. Infect. Immun.
69: 5363-5374
[Abstract] [Full Text] -
Dobrindt, U., Blum-Oehler, G., Hartsch, T., Gottschalk, G., Ron, E. Z., Funfstuck, R., Hacker, J.
(2001). S-Fimbria-Encoding Determinant sfaI Is Located on Pathogenicity Island III536 of Uropathogenic Escherichia coli Strain 536. Infect. Immun.
69: 4248-4256
[Abstract] [Full Text] -
Johnson, J. R., Stell, A. L., Kaster, N., Fasching, C., O'Bryan, T. T.
(2001). Novel Molecular Variants of Allele I of the Escherichia coli P Fimbrial Adhesin Gene papG. Infect. Immun.
69: 2318-2327
[Abstract] [Full Text] -
Brown, E. W., LeClerc, J. E., Li, B., Payne, W. L., Cebula, T. A.
(2001). Phylogenetic Evidence for Horizontal Transfer of mutS Alleles among Naturally Occurring Escherichia coli Strains. J. Bacteriol.
183: 1631-1644
[Abstract] [Full Text] -
Picard, B., Duriez, P., Gouriou, S., Matic, I., Denamur, E., Taddei, F.
(2001). Mutator Natural Escherichia coli Isolates Have an Unusual Virulence Phenotype. Infect. Immun.
69: 9-14
[Abstract] [Full Text] -
Guignot, J., Breard, J., Bernet-Camard, M.-F., Peiffer, I., Nowicki, B. J., Servin, A. L., Blanc-Potard, A.-B.
(2000). Pyelonephritogenic Diffusely Adhering Escherichia coli EC7372 Harboring Dr-II Adhesin Carries Classical Uropathogenic Virulence Genes and Promotes Cell Lysis and Apoptosis in Polarized Epithelial Caco-2/TC7 Cells. Infect. Immun.
68: 7018-7027
[Abstract] [Full Text] -
Culham, D. E., Wood, J. M.
(2000). An Escherichia coli Reference Collection Group B2- and Uropathogen-Associated Polymorphism in the rpoS-mutS Region of the E. coli Chromosome. J. Bacteriol.
182: 6272-6276
[Abstract] [Full Text] -
Mundy, L. M., Sahm, D. F., Gilmore, M.
(2000). Relationships between Enterococcal Virulence and Antimicrobial Resistance. Clin. Microbiol. Rev.
13: 513-522
[Abstract] [Full Text] -
Clermont, O., Bonacorsi, S., Bingen, E.
(2000). Rapid and Simple Determination of the Escherichia coli Phylogenetic Group. Appl. Environ. Microbiol.
66: 4555-4558
[Abstract] [Full Text] -
Hilali, F., Ruimy, R., Saulnier, P., Barnabe, C., Lebouguenec, C., Tibayrenc, M., Andremont, A.
(2000). Prevalence of Virulence Genes and Clonality in Escherichia coli Strains That Cause Bacteremia in Cancer Patients. Infect. Immun.
68: 3983-3989
[Abstract] [Full Text] -
Mazel, D., Dychinco, B., Webb, V. A., Davies, J.
(2000). Antibiotic Resistance in the ECOR Collection: Integrons and Identification of a Novel aad Gene. Antimicrob. Agents Chemother.
44: 1568-1574
[Abstract] [Full Text] -
Wada, A., Mikkola, R., Kurland, C. G., Ishihama, A.
(2000). Growth Phase-Coupled Changes of the Ribosome Profile in Natural Isolates and Laboratory Strains of Escherichia coli. J. Bacteriol.
182: 2893-2899
[Abstract] [Full Text] -
Johnson, J. R., Russo, T. A., Tarr, P. I., Carlino, U., Bilge, S. S., Vary, J. C. Jr., Stell, A. L.
(2000). Molecular Epidemiological and Phylogenetic Associations of Two Novel Putative Virulence Genes, iha and iroNE. coli, among Escherichia coli Isolates from Patients with Urosepsis. Infect. Immun.
68: 3040-3047
[Abstract] [Full Text] -
Bonacorsi, S. P. P., Clermont, O., Tinsley, C., Le Gall, I., Beaudoin, J.-C., Elion, J., Nassif, X., Bingen, E.
(2000). Identification of Regions of the Escherichia coli Chromosome Specific for Neonatal Meningitis-Associated Strains. Infect. Immun.
68: 2096-2101
[Abstract] [Full Text] -
Johnson, J. R., O'Bryan, T. T.
(2000). Improved Repetitive-Element PCR Fingerprinting for Resolving Pathogenic and Nonpathogenic Phylogenetic Groups within Escherichia coli. CVI
7: 265-273
[Abstract] [Full Text] -
Amor, K., Heinrichs, D. E., Frirdich, E., Ziebell, K., Johnson, R. P., Whitfield, C.
(2000). Distribution of Core Oligosaccharide Types in Lipopolysaccharides from Escherichia coli. Infect. Immun.
68: 1116-1124
[Abstract] [Full Text] -
Johnson, J. R., Kuskowski;, M., Denamur, E., Elion, J., Picard, B.
(2000). Clonal Origin, Virulence Factors, and Virulence. Infect. Immun.
68: 424-425
[Full Text] -
Prats, G., Navarro, F., Mirelis, B., Dalmau, D., Margall, N., Coll, P., Stell, A., Johnson, J. R.
(2000). Escherichia coli Serotype O15:K52:H1 as a Uropathogenic Clone. J. Clin. Microbiol.
38: 201-209
[Abstract] [Full Text] -
Fidelma Boyd, E., Waldor, M. K.
(1999). Alternative Mechanism of Cholera Toxin Acquisition by Vibrio cholerae: Generalized Transduction of CTXPhi by Bacteriophage CP-T1. Infect. Immun.
67: 5898-5905
[Abstract] [Full Text] -
Liu, S.-L., Schryvers, A. B., Sanderson, K. E., Johnston, R. N.
(1999). Bacterial Phylogenetic Clusters Revealed by Genome Structure. J. Bacteriol.
181: 6747-6755
[Abstract] [Full Text] -
Lai, X.-H., Wang, S.-Y., Uhlin, B. E.
(1999). Expression of cytotoxicity by potential pathogens in the standard Escherichia coli collection of reference (ECOR) strains. Microbiology
145: 3295-3303
[Abstract] [Full Text] -
Hurtado, A., Rodríguez-Valera, F.
(1999). Accessory DNA in the Genomes of Representatives of the Escherichia coli Reference Collection. J. Bacteriol.
181: 2548-2554
[Abstract] [Full Text] -
Picard, B., Garcia, J. S., Gouriou, S., Duriez, P., Brahimi, N., Bingen, E., Elion, J., Denamur, E.
(1999). The Link between Phylogeny and Virulence in Escherichia coli Extraintestinal Infection. Infect. Immun.
67: 546-553
[Abstract] [Full Text] -
Rode, C. K., Melkerson-Watson, L. J., Johnson, A. T., Bloch, C. A.
(1999). Type-Specific Contributions to Chromosome Size Differences in Escherichia coli. Infect. Immun.
67: 230-236
[Abstract] [Full Text]
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Copyright © 2009 by the American Society for Microbiology. For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»