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Applied and Environmental Microbiology, August 1999, p. 3373-3385, Vol. 65, No. 8
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Genetic Structure of Natural Populations of
Escherichia coli in Wild Hosts on Different
Continents
Valeria
Souza,*
Martha
Rocha,
Aldo
Valera, and
Luis E.
Eguiarte
Departmento de Ecología Evolutiva,
Instituto de Ecología, Universidad Nacional Autónoma
de México, México D.F. 04510, México
Received 10 March 1999/Accepted 4 June 1999
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ABSTRACT |
Current knowledge of genotypic and phenotypic diversity in the
species Escherichia coli is based almost entirely on
strains recovered from humans or zoo animals. In this study, we
analyzed a collection of 202 strains obtained from 81 mammalian species representing 39 families and 14 orders in Australia and the Americas, as well as several reference strains; we also included a strain from a
reptile and 10 from different families of birds collected in Mexico.
The strains were characterized genotypically by multilocus enzyme
electrophoresis (MLEE) and phenotypically by patterns of sugar
utilization, antibiotic resistance, and plasmid profile. MLEE analysis
yielded an estimated genetic diversity (H) of 0.682 for 11 loci. The
observed genetic diversity in this sample is the greatest yet reported
for E. coli. However, this genetic diversity is not
randomly distributed; geographic effects and host taxonomic group
accounted for most of the genetic differentiation. The genetic relationship among the strains showed that they are more associated by
origin and host order than is expected by chance. In a dendrogram, the
ancestral cluster includes primarily strains from Australia and ECOR
strains from groups B and C. The most differentiated E. coli in our analysis are strains from Mexican carnivores and strains from humans, including those in the ECOR group A. The kinds and
numbers of sugars utilized by the strains varied by host taxonomic
group and country of origin. Strains isolated from bats were found to
exploit the greatest range of sugars, while those from primates
utilized the fewest. Toxins are more frequent in strains from rodents
from both continents than in any other taxonomic group. Strains from
Mexican wild mammals were, on average, as resistant to antibiotics as
strains from humans in cities. On average, the Australian strains
presented a lower antibiotic resistance than the Mexican strains.
However, strains recovered from hosts in cities carried significantly
more plasmids than did strains isolated from wild mammals. Previous
studies have shown that natural populations of E. coli
harbor an extensive genetic diversity that is organized in a limited
number of clones. However, knowledge of this worldwide bacterium has
been limited. Here, we suggest that the strains from a wide range of
wild hosts from different regions of the world are organized in an
ecotypic structure where adaptation to the host plays an important role in the population structure.
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INTRODUCTION |
Escherichia coli is an
abundant and usually harmless commensal of the human digestive flora
(42). Nevertheless, pathogenic strains are an important
cause of sickness and mortality throughout the world, particularly for
children in underdeveloped countries (8). E. coli
is also a common member of the microbial commensal community of mammals
and birds. Surprisingly, little is known about the natural history and
genetic structure of E. coli in populations of wild animals
(42, 50). The standard reference collection of strains for
this species, the ECOR collection (32), contains a
number of strains isolated from five nonhuman mammalian orders, but
most of the strains were recovered from domestic or zoo animals
(32). The relevance of this limited sample has been questioned on the basis of possible cross-contamination from human host (42).
The first attempt to assess the genetic structure and diversity of
E. coli was made by Milkman, who analyzed 829 isolates obtained mainly from humans (26). Using multilocus enzyme
electrophoresis (MLEE) based on four loci, he determined that the
average genetic diversity (H) of this species was 0.23. Subsequent studies that extended the work of Milkman were primarily
concerned with the genotypic and phenotypic variation among strains
isolated from the commensal fecal flora of humans and those responsible
for neonatal septicemia, cystitis, pyelonephritis, and acute diarrhea (6, 38, 41, 47, 49, 50). Other studies have focused on
various aspects of this species' natural history, such as the turnover
of strains in a single host (5), the sharing of clones among
hosts (6), and the genetic structure and diversity of E. coli in its primary and secondary habitats (33, 46,
48). These and other studies have formed the basis of the clonal
paradigm for the genetic structure of bacterial populations (10,
15, 16, 19, 25, 45) and have been reviewed by Selander et al.
(42) and by Whittam (50).
Estimates of genetic diversity obtained by using strains isolated from
human fecal samples range from 0.45 to 0.54 (42, 50).
However, there is a caveat associated with this observation. The
majority of strains from humans were isolated from people living in the
developed countries of the West. Although some studies have included
strains from Tonga, even these are suspect, since Tonga was used as a
military base by both U.S. and New Zealand forces during World War II
(4). It is therefore possible that the diversity of E. coli from humans is also underestimated. A high degree of genetic
diversity (H = 0.61) has been found in E. coli isolated from sewage (33). These sewage samples
undoubtedly represent two quite distinct sources of strains: those from
the species' primary habitat, the lower intestinal tract, and those from its secondary habitat, the sewage environment. Whittam and collaborators (46-48) have shown that sympatric E. coli populations inhabiting primary and secondary habitats are
quite distinct from one another in terms of their clonal composition
(50).
The objective of this study was to extend our understanding of the
variation and genetic structure of E. coli by examining strains from a large variety of wild mammalian and avian hosts. We
assessed genotypic diversity, phenotypic diversity, and genetic relatedness of 202 E. coli strains by using 11 loci in MLEE,
plasmid profiles, resistance to six antibiotics, production of two
toxins, and the utilization of 12 sugars. In this study, we analyzed
how these genetic and phenotypic characteristics varied by host
taxonomic group and geographic origin. E. coli was sampled
mostly from wild mammals, and strains were taken from 81 species
representing 39 families and 14 orders of mammals (31) in
the Americas and Australia. We also included a sample from a reptile
and 10 strains from birds from Mexico. As a reference, we also studied
six strains from African baboons (35), 13 strains from the
ECOR collection (32), and strain K-12 (2).
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MATERIALS AND METHODS |
Bacterial strains.
The complete list of hosts sampled by
diet and geographic origin as well as their taxonomic classification by
order and proximity to human environment is presented in Table A1 in
the Appendix.
Strain isolation.
Strains collected in Mexico, Costa Rica,
and Venezuela were recovered from captive or wild mammals and birds.
Fecal samples were transported in swab-transport system containing
Aimes media (Difco). Mexican samples were suspended in 1 ml of Luria
broth and incubated; an aliquot was then streaked for single colonies on a minimal lactose plate. More than one isolate was sometimes taken
from a single host individual. The Mexican samples were processed as
follows. After incubation, the Lac+ colonies were tested
for growth on minimal citrate plates. The Lac+
Cit
colonies were then tested to confirm that they
matched the biochemical characteristics of E. coli: gas
production positive, H2S negative, urea negative, methyl
red positive, Voges-Proskauer negative (13). The Australian
strains were collected and cultured by David Gordon. These strains were
isolated from anal or cloacal samples or from fecal samples from wild
mammals. A primary isolation of the strains was carried out by
streaking the sample on a MacConkey plate to obtain single colonies.
Only one isolate was taken from each individual host. Subsequently,
single colonies from each plate were restreaked twice onto MacConkey
plates. Colonies morphologically consistent with E. coli
were then tested for growth on minimal lactose and minimal citrate
plates. All Lac+ Cit colonies were tested to
confirm that they matched the biochemical characteristics of E. coli: phenylalanine negative, H2S negative, urea
negative, indole positive, methyl red positive, Voges-Proskauer negative (13). In Australia and Mexico, all incubations were carried out overnight at 37°C. Following isolation, all strains were
immediately stored at 
80°C. All the strains classified by us as
E. coli were confirmed as E. coli by serotyping
in the Faculty of Medicine, Universidad Nacional Autónoma de Mexico.
In addition to the newly isolated strains, 13 strains from the E. coli reference collection ECOR (32), the sequenced K-12 strain MG1655 (2), and 6 strains from yellow baboons
(Papio cynocephalus) were included in the analysis
(35).
MLEE analysis.
MLEE using cellulose acetate membranes was
carried out in Tris-glycine buffer (pH 8.5) (17). Ten
enzymes were selected based on previous studies (40): ADH
(alcohol dehydrogenase), ARK (arginine kinase), G6PDH
(glucose-6-phosphate dehydrogenase), IDH (isocitrate dehydrogenase),
MDH (malate dehydrogenase), ME (malic enzyme), MPI (mannose-6-phosphate
isomerase), PEP (peptidase), PGM (phosphoglucomutase), and XDH
(xanthine dehydrogenase). Eleven loci were resolved with those enzymes
because ME exhibited two loci. All of the strains were examined at
least twice to confirm their electrophoretic types (Table
1).
Biotype analysis.
All strains were taken from freezer
cultures and grown on MacConkey plates. A single colony of each strain
was tested for growth on minimal plates containing a 0.4%
concentration (27) of one of the following sugars: adonitol,
arabinose, dulcitol, inositol, maltose, mannitol, raffinose, rhamnose,
salicin, sucrose, sorbitol, trehalose, and xylose.
Antibiotic resistance and toxin production.
Resistance to
each of six antibiotics was tested by using Luria broth plates
supplemented with one of the following antibiotics: ampicillin (50 µg/ml), chloramphenicol (12 µg/ml), kanamycin (50 µg/ml),
neomycin (50 µg/ml), streptomycin (50 µg/ml), and tetracycline (25 µg/ml). The concentrations were based on previous studies of E. coli (27, 35).
Strains were also tested for hemolysin production with heart infusion
agar supplemented with blood (5%) and were tested for
verotoxin (VT)
production with Rainbow Agar O157 (Biolog, Inc.).
However, Rainbow Agar
O157 is not a direct test for VT production;
rather, it detects a trait
that has been found to be highly correlated
with VT production in
clinically pathogenic strains such as O157:H7
(
44). This
pathogenic strain is
-glucuronidase negative (black
colonies); other
VT-producing strains typically overproduce
-galactosidase
relative
to
-glucuronidase (blue, purple, or violet colonies),
and it is the
production of these two compounds that Rainbow Agar
has the ability to
detect. We took dark and bluish colonies to
represent VT-positive
strains. To determine the average number
of colonies per host group, we
scored for dark colonies as follows:
2 for black colonies; 1 for dark
blue, violet, and purple; and
0 for red and white
colonies.
Plasmid analysis.
Isolated colonies were grown in
Tris-borate medium and plasmids were extracted by the alkaline lysis
procedure (12). Plasmid profiles were run in 0.7% agarose
gel and stained with ethidium bromide. Megaplasmids were extracted
directly in horizontal agarose gels by a modification of the procedure
of Eckhardt (12). For purposes of statistical analysis, the
observed plasmid bands were assigned to categories according to their size.
Statistical analysis.
The isolates were grouped on the basis
of the taxonomic order of the host from which they were isolated, host
diet, and host geographic origin. Some of these groups are
naturally confounded (most carnivora eat meat and most rodents are
granivores), and it is not possible to separate their contribution to
phenotypic or genetic diversity. For example, Australia lacks native
primates and Mexico lacks monotremes. To partially compensate for these confounding effects, various subsets of the data were used in the analyses.
Average genetic diversity per locus was estimated as
H =
hj/
m, where
m equals the number of loci
scored and
hj = [
n/(
n 1)] (1
pij2), where
pij
is the frequency of allele
i at locus
j, and
n is
the number of multilocus genotypes (
30,
40).
Standard error
of
H was obtained with the ETDIV program
(
46). We used modified
Gst statistics
to analyze the data. For example, the proportion
of genetic variation
attributable to geographic effects is (
HT HG)/
HT, where
HG is the arithmetic average of the
H's calculated
separately for electrotypes (ETs) from each
locality, and
HT is
the diversity of all strains
regardless of locality (
29,
30,
40). Standard error of
Gst was also obtained with the ETDIV
program
(
46). The statistical significance of
Gst was analyzed
with a
2 test of
independence, using the formula
2 =
nGst(
a 1), where
n is the
number of individuals and
a is
the total number of alleles;
degrees of freedom are (
k 1)(
a 1), where
k is the number of subdivisions (
16).
The frequencies of different biotype traits were compared using
2 tests or Fisher's exact test when appropriate
(
37). To test
for the association of phenotypic traits, a
concordance analysis
was done by using contingency coefficients
(
37). As contingency
coefficients do not range from
1 to
1, as is the case for parametric
measures of association, the absolute
values of the coefficients
are not
presented.
A dendrogram was constructed using Nei's genetic distances
(
30) and the neighbor-joining (NJ) method, using the
Phylogeny
Inference Package (PHYLIP, version 3.5c by Joseph
Felsenstein,
University of
Washington).
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RESULTS |
Allozyme analysis.
The 202 strains examined yielded 187 genotypes (i.e., ETs). The number of alleles per locus averaged 6.8 (Table 2; range, 4 to 9). Null alleles
were detected at all loci except MDH. The locus with the greatest
allelic diversity was ME2 (0.80) and G6PD was the least variable
(0.441). The average allelic diversity (H ± standard
error [SE]) for the 11 loci was 0.682 ± 0.034 for the 187 ETs,
and for the 202 isolates, we obtained an H of 0.673 ± 0.034 (Table 2).
In Table
3, we present genetic diversity
and genetic differentiation results at different levels of analysis. At
the geographic
level, the diversity (
H) ranges from 0.489 in
the human-related
strains of the ECOR collection to 0.705 in the
strains isolated
from Mexican mammals. The genetic differentiation ± SE among those
data sets (
Gst = 0.047 ± 0.014;
2 = 630.9) is significantly different
from zero (
P < 0.0001).
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TABLE 3.
Genetic diversity and genetic differentiation in E. coli from different geographical origins and with different
host taxonomies and diets
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If we take into account the host order, the genetic diversity ranges
from 0.511 in artiodactyls to 0.665 in bats; the genetic
differentiation among the strains from different hosts
(
Gst =
0.075 ± 0.017;
2 = 898.56) is also significantly different from 0 (
P < 0.0001;
Table
3).
Considering host diet, the genetic diversity ranges from 0.672 in the
strains associated with insectivores of different countries
to 0.566 in
the Australian strains with different diets. There
is no genetic
differentiation according to host diet (
Gst = 0.025
± 0.007;
2 = 323.64,
P = 0.126). If we analyze only the host diet in Australia
(
Gst = 0.01 ± 0.01;
2 = 28.68,
P = 0.999), we also do
not find a significant difference.
However, diet is significant in
Mexico (
Gst = 0.044 ± 0.012;
2 = 296,
P = 0.005).
The genetic differentiation between rodents from Australia and Mexico
(
Gst = 0.098 ± 0.03;
2 = 234.85,
P < 0.0001) was
significantly different from zero (Table
3), with more diversity in the
Mexican isolates (
H = 0.639) than
the isolates from
Australian rodents (
H = 0.515). However, partitioning
the strains of Australia showed a nonsignificant differentiation
(
Gst = 0.036 = 0.011;
2 = 48.95,
P = 0.184), because
the genetic diversity is very similar
in marsupials (
H = 0.552) and rodents (
H = 0.515).
The genetic relationship among 202 strains was analyzed with Nei
genetic distances, and we constructed an NJ dendrogram (Fig.
1). We also performed other phylogenetic
analyses using UPGMA
(using both the number of mismatches and Nei
distances as genetic
distances) distance method and constructed a PAUP
tree using parsimony
(figures not shown). All the analyzed trees showed
results analogous
to those of the NJ dendrogram. Based on biochemical
tests and
the UPGMA dendrograms, we decided to root the NJ dendrogram
with
the reptile strain, which shows a long branch. If this root is
correct, in the dendrogram we can define an ancestral group from
which
all the other strains are derived. In this supposedly ancestral
group,
we found several strains (
10) from marsupials and rodents
from Australia as well as 11 strains from a diverse group of mammals
from Mexico and three strains from the cosmopolitan house mouse
Mus musculus. In this clade, we also observed the strains
from
groups B1 and C of the ECOR collection, as well as one strain
from
the group A (ECOR8). The majority of the human-associated
ECOR group A
isolates are present in the most differentiated cluster
(G), along with
strain K-12 (MG1655, identical in our analysis
to ECOR11) and a group
of strains from Mexican carnivores, several
from rodents, and all the
nonpathogenic strains from humans. The
rest of the ECOR isolates (no. 5 and 41) are in cluster C along
with most of the bird strains and
isolates from the old world
and new world monkeys. In cluster B, we
observed a diverse group
of strains mostly from
Lagomorpha
and carnivores. Cluster D has
a tight group of Australian strains from
marsupials and rodents.
Strains from Mexican rodents and bats are
mostly in clusters E
and F. Cluster F also contains strains from
domestic carnivores
and wild dolphins. It is evident in this tree that
most of the
strains from wild animals are grouped by host order. It is
also
interesting that most of the Australian strains are in two
clusters
(A and G) while Mexican strains are dispersed along the tree.
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FIG. 1.
Dendrogram depicting the strain similarities for the 202 strains of E. coli. The NJ tree was obtained from a Nei's
distance matrix derived from the multilocus electrophoresis data using
the PHYLIP 3.5 program. For each strain, the name of the host along
with the strain reference number is printed. Australian strains are in
bold, bird strains are in italics, and ECOR strains are underlined.
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Biotype analyses.
A minority of the strains could utilize
adonitol, arabinose, dulcitol, inositol, or salicin, while most strains
could ferment maltose, mannose, rhamnose, sorbose, trehalose, and
xylose (Table 4). For 10 of the 12 substrates tested, the proportion of strains able to exploit a
substrate varied significantly depending on the taxonomic group of the
host from which they were isolated (Table 4). The ability of the
strains to ferment maltose, rhamnose, and xylose was independent of
host taxonomic group. Overall, strains isolated from hosts with
diversified diets such as rodents, birds, and marsupials could ferment
the greatest number of substrates, while strains from hosts with very
specialized diets such as Monotremata, Cetacea,
Xenarthra, and Sirenia could exploit fewer
sugars.
Geographic effects on the frequency of sugar utilization could also be
detected. A comparison of strains isolated from rodents
in Australia
and Mexico revealed that for mannitol only 32% (
n = 16) of the strains from Australia could ferment this sugar,
compared to 85% (
n = 30) of the strains from Mexico
(
P < 0.001).
Similarly, 32% of strains from
Australian rodents can ferment
raffinose compared to 64% of the
strains from Mexican rodents
(
P < 0.02).
Antibiotic resistance, toxin production, and plasmid profiles.
Of the antibiotics tested, resistance to streptomycin was most frequent
while resistance to chloramphenicol was rare (Table 5). Resistance to antibiotics was more
frequent among strains from Mexico than among strains from Australia
(9.6% of strains from Australia were resistant to one or more
antibiotics compared to 41% of strains from Mexico). There was an
insufficient number of strains with resistance to permit a detailed
analysis of the distribution of antibiotic resistance as a function of
host taxonomic group. However, considering the Mexican isolates alone,
strains isolated from bats tended to have a much higher frequency of
antibiotic resistance than other mammals. For example, 46% of strains
from bats were ampicillin resistant, 100% were streptomycin resistant, and 15% presented neomycin resistance; none of those strains was resistant to the other antibiotics.
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TABLE 5.
Overall frequency of antibiotic resistance in E. coli and comparison of frequencies between strains isolated from
Australia and México
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Overall, 44% of the strains produced more
-galactosidase than
-glucuronidase (i.e., were VT positive), and 2% of strains
produced
hemolysin. No difference in the overall frequency of
hemolysins or VT
production between strains from Australia and
Mexico could be detected
(Table
6; the average for Mexico was
0.64 ± 0.06 and the average for Australia was 0.57 ± 0.10 [not
significant by Student's
t test]). The frequency of
the marker
for VT production varied with the host taxonomic group from
which
the strains were isolated (Table
6). Among the Mexican isolates,
the frequency of positive strains ranged from 0.28 for strains
isolated
from
Lagomorpha to 0.69 in strains isolated from rodents.
Isolates from Australian rodents also showed a higher than average
frequency of VT production compared to strains from marsupials.
However, none of these differences are significant from zero.
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TABLE 6.
Average and frequency of dark colonies in rainbow agar in
E. coli strains isolated from various wild hosts
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Concordance analysis (
40) of the phenotypic traits using the
strains isolated from Mexico revealed that the presence or
absence of
these traits is not independent (Table
7). Three major
forms of association were
detected: (i) the concurrence of the
ability to utilize the less
frequently fermented sugars, such
as dulcitol and inositol; (ii) the
concurrence of the inability
to exploit sugars utilized by most
strains, such as xylose and
trehalose; and (iii) the negative
association of two traits, such
as where the ability to exploit one
sugar (e.g., salicin) results
in a lower-than-expected frequency of
strains able to exploit
a second sugar (e.g., sucrose). Resistance to
various antibiotics
was also found to be concurrent in a strain more
often than would
be expected by chance. Resistance to ampicillin was
associated
with the ability to utilize arabitol, adonitol, dulcitol,
and
salicin. Also the ability to exploit salicin was found to be more
frequently associated with streptomycin resistance than expected.
Similar kinds of association were seen in the strains from Australia
(results not shown).
We divided the samples by the distance of the host to the human
environment (Table
8). We observed in the
Mexican isolates
and in the ECOR isolates a significantly higher amount
of plasmids
among isolates collected in cities and places close to
humans
than in those collected at isolated sites (
2 = 28.98,
P < 0.001) (Table
8). The effect of possible
human
contact on the number of plasmids was also observed on a larger
geographical scale. In Mexican strains, we observed an average
of 1.7 plasmids per strain, while in the less-populated Australia,
the strains
presented a significantly lower average (0.45 plasmids
per strain;
2 = 322.8,
P < 0.001).
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TABLE 8.
Antibiotic resistance and plasmid numbers in E. coli isolated from different sources in relation to their
proximity to human environment
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On the other hand,
E. coli associated with wild animals in
isolated places in Mexico is, on average, resistant to as many
antibiotics (average ± SE = 0.58 ± 0.06; Table
8) as
E. coli in the other human-related sources from Mexico
(weighted average
± SE of all the other sources = 0.43 ± 0.01). Our sample of the
ECOR collection had the highest antibiotic
resistance (average
± SE = 0.68 ± 0.02; data not shown
in table), while Australian
isolates had the lowest antibiotic
resistance (average ± SE =
0.19 ± 0.01). In our
sample, we did not observe that the antibiotic
resistance is correlated
with the mean number of plasmids. Most
of the multidrug-resistant
strains from wild mammals did not have
any plasmids, suggesting that
the genes for antibiotic resistance
are chromosomal in some of the wild
animal
strains.
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DISCUSSION |
The estimated genetic diversity (H = 0.682) from
our collection of E. coli is higher than the diversity
reported for any collection of E. coli (5, 26, 33, 34,
38, 42, 46-48) and higher than most studied bacteria (7, 9,
10, 14, 28, 29, 39, 43, 45). This high diversity could be due in
part to the fact that we intentionally selected a wide range of "good and informative characters" based on the analysis done by Selander and collaborators (40, 42). On the other hand, the observed genetic diversity would change if other loci were selected or if MLEE
were performed with starch and a discontinuous buffer with a different
pH (17). For example, based on 11 loci, the H was
originally determined to be 0.42 for the ECOR collection (32). Subsequently, the number of loci examined was
increased to 35, resulting in an H of 0.34 (41).
However, the high genetic diversity we observed in our study could also
be the result of the high diversity of hosts represented in our
collection; the sample we studied includes isolates from all of the
major mammalian orders (98.3% of the species are within those orders
[31]). Even though isolates from some minor orders are
lacking, when we add 10 isolates from 10 different birds the genetic
diversity increased only 0.2%. The geographic scope of the sample is
also patchy, with only a few strains from Africa or Asia and none from either polar region. The results suggest, however, that filling these
gaps may not significantly increase estimates of the genetic diversity
of E. coli. For example, in the Mexican mammalian samples alone, the genetic diversity (H) was estimated as 0.698 ± 0.048 (data not shown). But inclusion of the Australian samples,
which represent an isolated continent with a unique mammalian fauna, lowered the estimate of the genetic diversity by 1%.
Previous studies of E. coli suggest that much of the
observed allelic variation is selectively neutral and this, coupled
with a large effective population size, can explain much of this
species' genetic diversity (42, 50). Population structure
has been thought to account for little of the observed diversity
(5, 11, 20, 42). However, genetic diversity in our
collection of E. coli is probably ecologically
(ecotypically) structured and as such, adaptation to the host plays an
important role in population structure. We observed that host order and
geographic origin are the most important factors to differentiate
E. coli. Overall, 7.5% of the diversity can be explained by
the order of the host, while nearly 10% of the genetic diversity of
strains from rodents (Australia versus America) can be explained by
geography alone. This contrasts with the observation that spatial
structure accounts for only 2% of the genetic diversity among strains
isolated from humans living in North America and Europe
(27). That spatial structure accounts for so little of the
genetic diversity of E. coli from humans probably reflects
the fact that the samples are derived from a single, highly mobile host
species. The larger geographic component of diversity observed in the
strains from rodents can be attributed both to Australia's long
isolation and to the distinct rodent communities of the two continents.
In Mexico, the diet of the host accounts for 4.4% of the diversity of
E. coli. However, in Australia or in the total collection,
the diet of the host was not an important factor differentiating populations.
The observed differentiation by host could be due in part to the
presence of different ecological niches in the different orders. We
observed that the type and range of sugars that can be exploited by
E. coli strains are associated with the taxonomic group of
the host from which the strains were isolated. Significant heterogeneity in sugar utilization also resulted when strains were
grouped on the basis of host diet. Nevertheless, these results are
somewhat ambiguous. This may reflect the joint problem of sample size
for the diet grouping (for example, four dietary modes among the 14 bat
hosts) and the inevitable interactions between host taxonomy and diet.
Overall, E. coli from the less-represented hosts with
specialized diets (monotremes, dolphins, Xenarthra, and
Sirenia) exploited the fewest sugars. The strains from
hoofed mammals also used few sugars, while bacteria from birds,
marsupials, and rodents could utilize a larger number of sugars. The
frequency with which strains can exploit some sugars was also
found to vary with the geographic origin of the strains. For example, a
greater proportion of strains from Mexican rodents can utilize
raffinose and mannitol than strains from Australian rodents.
In previous studies, the majority of strains (69%) in the ECOR
collection that were isolated from strictly herbivorous mammals could
exploit raffinose, whereas in this study, less than half the strains
recovered from the herbivorous groups could utilize raffinose (27,
32, 42). Only 30% of ECOR strains can ferment sorbose, compared
to the 82% frequency of utilization observed in this study (27,
32, 42). No ECOR strains could use salicin, while in this
study, 9% of the strains did so, in contrast with 41% in a population
of strains from yellow baboons (35). Host digestive
physiology and anatomy clearly vary among mammal species and reflect
the interaction of phylogeny and diet. Host diet will in turn influence
the kinds of growth substrates available to E. coli. As a
result, E. coli strains will be confronted with very
different biotic and abiotic environments in different host species.
Our study suggests that these different environments result in E. coli that exhibit some degree of host specificity. Further work is
required to determine the mechanisms responsible for this specificity
and the role that such specificity plays in E. coli's evolution.
The dendrogram depicted in Fig. 1 provides additional support for the
observation that host and geographic effects contribute to the genetic
structure of E. coli populations. For example, strains
isolated from birds, rodents, and carnivores seem to cluster more often
than other hosts, as do Australian strains. Strains from ungulates are
in many clusters. In our tree, the ancestral cluster corresponds to
some of the Australian strains along with the ECOR strains from groups
B1 and C, while the most differentiated cluster presents strains from
the ECOR group A along with carnivores from Mexico and other humans.
Using the sequence data of 13 gene phylogenies, Lecointre et al.
(23) observed that the ECOR strains had a different
organization than previously reported. In their study the most
pathogenic strains from group B2 were the ancestral group, while A and
B1 were the most evolved sister groups. In their scenario, the
capability of E. coli to invade other niches (extraintestinal virulence) is an ancestral trait that has evolved to
the more benign intestinal strains in the other groups (23). We do not have strains from group B2 in our study, but preliminary data
from our laboratory (data not shown) suggest a similar scenario for the
evolution of diarrheic E. coli. We observed that four of the
Mexican strains from our ancestral group present genes from the
pathogenic island LEE (eae and espB) associated
with an intestinal lesion in the EPEC and EHEC strains. We also
observed in this ancestral clade six strains with ETEC serotypes.
Preliminary analysis (data not shown) indicates that pathogenic
chromosomal genes are common and diverse along the tree, suggesting an
ancestral origin.
We also observed both that the VT marker is widespread in the tree and
that VTs are more frequent in strains from rodents from both
continents. The latter observation is consistent with the idea that
rodents act as a reservoir of many diseases (1). On the
other hand, artiodactyls have strains with the lower percentage of
-galactosidase production, contrary to the belief that domestic cattle naturally harbor -galactosidase-producing E. coli
(i.e., O157:H7) (36, 44). However, none of the levels of VT
production per host are significantly different from the average for
their country of origin. Another characteristic that is widespread in the collection is antibiotic resistance. With the exception of strains
from Australian mammals, most of the E. coli strains present some antibiotic resistance, and multidrug resistance is frequent in
Mexico. This could be in part the result of the widespread use of
antibiotics and to the lack of real isolation from human environment in
a country like Mexico. However, since antibiotic resistance is not
randomly distributed in the wild E. coli strains (bats and
rodents host strains with higher multidrug resistance), we believe that
at least some of the antibiotic resistance may be related to additional
nonhuman environmental pressures.
On the other hand, the number and size of plasmids are highly variable
in E. coli, ranging from hundreds of base pairs to several
hundred kilobase pairs. Their G+C contents can vary widely and are
often different from that of their usual bacterial host, indicating a
variety of sources from which plasmids (or part of them) are derived
(3, 18, 21, 22, 24). No pattern has been observed in the
number of plasmids in these bacteria, and this may be due in part to
their possible heterogeneous origin (3, 21, 22).
Nevertheless, we observed that with human proximity, the number of
plasmids per strain increases. This could be a reflection of the
acquisition of accessory elements due to increased densities of both
hosts and bacteria in cities. Increased density could facilitate the
movement of plasmids among strains of E. coli as well as
other related bacteria. Such an exchange was observed by Boyd et al.
(3), who analyzed the structure of F group-related plasmids
in the ECOR collection. They found different phylogenetic relationships
between plasmids and bacterial strains, suggesting that horizontal
transfer of plasmids occurs at high rates within the ECOR collection.
| |
APPENDIX |
| |
ACKNOWLEDGMENTS |
We thank the numerous colleagues who assisted us in
obtaining samples. David Gordon collected all the Australian samples, helped with some statistical analysis, and reviewed many previous versions of the manuscript. Blanca Hernández, Jordan Goluvov, Meli Mandrujano, Rodrigo Medellin, Saul Aguilar, Osiris Gaona, Angeles
Mendoza, Gabriel Pérez, Luis Medrano, Adolfo Navarro, Juan
Castillo, Alejandro Zavala, Benjamin Morales, Ricardo Frias, Alejandro
Velázques, Hector Arita, Carlos Alvarez, José Charles, Hilary Charles, Alvaro Miranda, David Valenzuela, Luisa Sandner, René Cerritos, and Jorge Ortega collected the Mexican
samples. We also thank Antonio Cruz for valuable technical assistance
and Armando Navarro, who performed the serotype analysis in the Faculty of Medicine, Universidad Nacional Autónoma de México. We
thank Pilar Beltrán, Robert K. Selander, Brandon Gaut, Andrew
Peek, and Juan Nuñez, who read the manuscript and gave useful
comments. Richard Goldstein kindly provided the MG1655 strain of
E. coli K-12, and Dan Dykhuizen sent us the yellow baboon strains.
This research was supported by DGAPA-UNAM IN208995 grant to V.S. and
CONACyT 3675-N grant to L.E.E. and V.S., and M.R. was supported by a
graduate student scholarship from CONACyT.
| |
FOOTNOTES |
*
Corresponding author. Mailing address: Departmento de
Ecología Evolutiva, Instituto de Ecología, Universidad
Nacional Autónoma de México, Apartado Postal 70-275, México D.F. 04510, México. Phone: 525 622 9006. Fax: 525 622 8995. E-mail: souza{at}servidor.unam.mx.
| |
REFERENCES |
| 1.
|
Baquero, F., and J. Blazquez.
1998.
Evolution of antibiotic resistance.
Trends Ecol. Evol.
12:482-488.
|
| 2.
|
Blattner, F. R.,
I. G. Plunkett,
C. A. Bloch,
N. T. Perna,
V. Burland,
M. Riley,
J. Collado-Vides,
J. D. Glasner,
C. K. Rode,
G. F. Mayhew,
J. Gregor,
N. W. Davis,
H. A. Kirkpatrick,
M. A. Goeden,
D. J. Rose,
B. Mau, and Y. Shao.
1997.
The complete genome sequence of Escherichia coli K-12.
Science
277:1453-1462[Abstract/Free Full Text].
|
| 3.
|
Boyd, E. F.,
C. W. Hill,
S. M. Rich, and D. L. Hartl.
1996.
Mosaic structure of plasmids from natural populations of Escherichia coli.
Genetics
143:1091-1100[Abstract].
|
| 4.
|
Campbell, I. C.
1992.
Island kingdom: Tonga ancient and modern.
Canterbury University Press, Christchurch, New Zealand.
|
| 5.
|
Caugant, D. A.,
B. R. Levin, and R. K. Selander.
1981.
Genetic diversity and temporal variation in the E. coli population of a human host.
Genetics
98:467-490[Abstract/Free Full Text].
|
| 6.
|
Caugant, D. A.,
B. R. Levin,
G. Lidin-Janson,
T. S. Whittam,
C. Svanborg Eden, and R. K. Selander.
1983.
Genetic diversity and relationships among strains of Escherichia coli in the intestine and those causing urinary tract infections.
Prog. Allergy
33:203-227[Medline].
|
| 7.
|
Caugant, D. A.,
L. F. Mocca,
C. E. Frasch,
L. O. Frøholm,
W. D. Zollinger, and R. K. Selander.
1987.
Genetic structure of Neisseria meningitidis populations in relation to serogroup, serotype, and outer membrane protein pattern.
J. Bacteriol.
169:2781-2792[Abstract/Free Full Text].
|
| 8.
|
Cravioto, A.,
A. Tello,
A. Navarro,
J. Ruiz,
H. Villafán,
F. Uribe, and C. Eslava.
1991.
Association of Escherichia coli Hep-2 adherence patterns with type and duration of diarrhoea.
Lancet
337:262-264[Medline].
|
| 9.
|
Denny, T. P.,
M. N. Gilmour, and R. K. Selander.
1988.
Genetic diversity and relationships of two pathovars of Pseudomonas syringae.
J. Gen. Microbiol.
134:1949-1960[Abstract/Free Full Text].
|
| 10.
|
Duncan, K. E.,
N. Ferguson,
K. Kimura,
X. Zhou, and C. A. Istock.
1994.
Fine-scale genetic and phenotypic structure in natural populations of Bacillus subtilis and Bacillus licheniformis: implications for bacterial evolution and speciation.
Evolution
48:2002-2025.
|
| 11.
|
Dykhuizen, D. E., and L. Green.
1991.
Recombination in Escherichia coli and the definition of biological species.
J. Bacteriol.
173:7257-7268[Abstract/Free Full Text].
|
| 12.
|
Eckhardt, T.
1978.
A rapid method for the identification of plasmid deoxyribonucleic acid in bacteria.
Plasmid
1:584-588[Medline].
|
| 13.
|
Ewing, W. H.
1986.
Edwards and Ewing's identification of Enterobacteriaceae; 4th ed.
Elsevier Science Publishing Co., New York, N.Y.
|
| 14.
|
Gordon, D. M.,
M. Wexler,
T. B. Reardon, and P. J. Murphy.
1995.
The genetic structure of Rhizobium populations.
Soil Biol. Biochem.
27:491-499.
|
| 15.
|
Guttman, D. S., and D. E. Dykhuizen.
1994.
Clonal divergence in Escherichia coli as a result of recombination, not mutation.
Science
266:1380-1383[Abstract/Free Full Text].
|
| 16.
|
Hagen, M. J., and J. L. Hamrick.
1996.
Population level processes in Rhizobium leguminosarum bv. trifolii: the role of founder effects.
Mol. Ecol.
5:707-714.
|
| 17.
|
Hebert, P. D. N., and M. J. Beaton.
1993.
Methodologies for allozyme analysis using cellulose acetate electrophoresis.
Helena Laboratories, Beaumont, Tex.
|
| 18.
|
Hughes, V. M., and N. Datta.
1983.
Conjugative plasmids in bacteria of the "pre-antibiotic era".
Nature (London)
302:725-726[Medline].
|
| 19.
|
Istock, C. A.,
K. E. Duncan,
N. Ferguson, and X. Zhou.
1992.
Sexuality in a natural population of bacteria: Bacillus subtilis challenges the clonal paradigm.
Mol. Ecol.
1:95-103[Medline].
|
| 20.
|
Jensen, R. A.
1985.
Biochemical pathways can be traced backward through evolutionary time.
Mol. Biol. Evol.
2:92-108[Abstract].
|
| 21.
|
Jones, C., and J. Stanley.
1992.
Salmonella plasmids of the pre-antibiotic era.
J. Gen. Microbiol.
138:189-197[Abstract/Free Full Text].
|
| 22.
|
Joset, F., and J. Guespin-Michel.
1993.
Procaryotic genetics.
Blackwell Science, Cambridge, Mass.
|
| 23.
|
Lecointre, G.,
L. Rachdi,
P. Darlu, and E. Denamur.
1998.
Escherichia coli molecular phylogeny using the incongruence length difference test.
Mol. Biol. Evol.
15:1685-1695[Abstract].
|
| 24.
|
Maloy, S. R.,
J. E. Cronan, and D. Freifelder.
1994.
Microbial genetics, 2nd ed.
Jones and Bartlett Publishers, Boston, Mass.
|
| 25.
|
Maynard Smith, J.,
N. H. Smith,
M. O'Rourke, and B. G. Spratt.
1993.
How clonal are bacteria?
Proc. Natl. Acad. Sci. USA
90:4384-4388[Abstract/Free Full Text].
|
| 26.
|
Milkman, R.
1973.
Electrophoretic variation in Escherichia coli from natural sources.
Science
182:1024-1026[Abstract/Free Full Text].
|
| 27.
|
Miller, R. D., and D. L. Hartl.
1986.
Biotyping confirms a nearly clonal population structure in Escherichia coli.
Evolution
40:1-12.
|
| 28.
|
Musser, J. M.,
S. J. Barenkamp,
D. M. Granoff, and R. K. Selander.
1986.
Genetic relationships of serologically nontypable and serotype b strains of Haemophilus influenzae.
Infect. Immun.
52:183-191[Abstract/Free Full Text].
|
| 29.
|
Nei, M.
1977.
F-statistics and analysis of gene diversity in subdivided populations.
Ann. Hum. Genet. Lond.
41:225-233.
|
| 30.
|
Nei, M.
1972.
Genetic distance between populations.
Amer. Nat.
106:283-292.
|
| 31.
|
Nowak, R. M.
1991.
Walker's mammals of the world, 5th ed.
Johns Hopkins University Press, Baltimore, Md.
|
| 32.
|
Ochman, H., and R. K. Selander.
1984.
Standard reference strains of Escherichia coli from natural populations.
J. Bacteriol.
157:690-693[Abstract/Free Full Text].
|
| 33.
|
Pupo, G. M., and B. J. Richardson.
1995.
Biochemical genetics of a natural population of Escherichia coli: seasonal changes in alleles and haplotypes.
Microbiology
141:1037-1044[Abstract/Free Full Text].
|
| 34.
|
Rocha, M.
1996.
Undergraduate dissertation.
Universidad Nacional Autónoma de México, México D.F..
|
| 35.
|
Routman, E.,
R. D. Miller,
J. Philips-Conroy, and D. L. Hartl.
1985.
Antibiotic resistance and population structure in Escherichia coli from free-ranging African yellow baboons.
Appl. Environ. Microbiol.
50:749-754[Abstract/Free Full Text].
|
| 36.
|
Schaechter, M.,
R. Curtis,
J. Ingraham,
E. Lin,
K. Brooks,
B. Magasanik,
D. Neidhardt,
W. Reznikoff,
M. Riley, and E. Umbarger.
1996.
The view from here, p. 1625-1648.
In
F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, D.C.
|
| 37.
|
Seigel, S.
1956.
Nonparametric statistics for the behavioral sciences.
McGraw-Hill, Inc., London, England.
|
| 38.
|
Selander, R. K., and B. R. Levin.
1980.
Genetic diversity and structure in Escherichia coli.
Science
210:545-547[Abstract/Free Full Text].
|
| 39.
|
Selander, R. K.,
R. M. McKinney,
T. S. Whittam,
W. F. Bibb,
D. J. Brenner,
F. S. Nolte, and P. E. Pattison.
1985.
Genetic structure of populations of Legionella pneumophilia.
J. Bacteriol.
163:1021-1037[Abstract/Free Full Text].
|
| 40.
|
Selander, R. K.,
D. A. Caugant,
H. Ochman,
J. M. Musser, and T. S. Whittam.
1986.
Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics.
Appl. Environ. Microbiol.
51:873-884[Free Full Text].
|
| 41.
|
Selander, R. K.,
T. K. Korhonen,
V. Väisänen-Rhen,
P. H. Williams,
P. E. Pattison, and D. A. Caugant.
1986.
Genetic relationships and clonal structure of strains of Escherichia coli causing neonatal septicemia and meningitis.
Infect. Immun.
52:213-222[Abstract/Free Full Text].
|
| 42.
|
Selander, R. K.,
D. A. Caugant, and T. S. Whittam.
1987.
Genetic structure and variation in natural populations of Escherichia coli, p. 1625-1648.
In
F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, D.C.
|
| 43.
|
Selander, R. K.,
P. Beltran,
N. H. Smith,
R. Helmuth,
F. A. Rubin,
D. J. Kopecko,
K. Ferris,
B. D. Tall,
A. Cravioto, and J. M. Musser.
1990.
Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers.
Infect. Immun.
58:2262-2275[Abstract/Free Full Text].
|
| 44.
|
Smith, H. R., and S. M. Scotland.
1988.
Vero cytotoxin-producing strains of Escherichia coli.
J. Med. Microbiol.
26:77-85[Free Full Text].
|
| 45.
|
Souza, V.,
L. Eguiarte,
G. Avila,
R. Cappello,
C. Gallardo,
J. Montoya, and D. Piñero.
1994.
Genetic structure of Rhizobium etli biovar phaseoli associated with wild and cultivated bean plants (Phaseolus vulgaris and Phaseolus coccineus) in Morelos, Mexico.
Appl. Environ. Microbiol.
60:1260-1268[Abstract/Free Full Text].
|
| 46.
|
Whittam, T. S.,
H. Ochman, and R. K. Selander.
1983.
Geographic components of linkage disequilibrium in natural populations of Escherichia coli.
Mol. Biol. Evol.
1:67-83[Abstract].
|
| 47.
|
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[Abstract/Free Full Text].
|
| 48.
|
Whittam, T. S.
1989.
Clonal dynamics of Escherichia coli in its natural habitat.
Antonie Leeuwenhoek
55:23-32.
|
| 49.
|
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[Abstract/Free Full Text].
|
| 50.
|
Whittam, T. S.
1996.
Genetic variation and evolutionary processes in natural populations of Escherichia coli, p. 2708-2728.
In
F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, D.C.
|
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147: 1671-1676
[Abstract]
[Full Text]
-
Gordon, D. M.
(2001). Geographical structure and host specificity in bacteria and the implications for tracing the source of coliform contamination. Microbiology
147: 1079-1085
[Full Text]
-
Gándara, B., Merino, A. L., Rogel, M. A., Martínez-Romero, E.
(2001). Limited Genetic Diversity of Brucella spp.. J. Clin. Microbiol.
39: 235-240
[Abstract]
[Full Text]
-
Johnson, J. R., Souza, V., Rocha, M., Valera, A., Eguiarte, L. E.
(2000). Genetic Diversity within E. coli. Appl. Environ. Microbiol.
66: 5104-5105
[Full Text]
-
Anderson, T. J. C., Haubold, B., Williams, J. T., Estrada-Franco{section}, J. G., Richardson, L., Mollinedo, R., Bockarie, M., Mokili, J., Mharakurwa, S., French, N., Whitworth, J., Velez, I. D., Brockman, A. H., Nosten, F., Ferreira, M. U., Day, K. P.
(2000). Microsatellite Markers Reveal a Spectrum of Population Structures in the Malaria Parasite Plasmodium falciparum. Mol Biol Evol
17: 1467-1482
[Abstract]
[Full Text]
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Abstract
Introduction
