Previous Article | Next Article 
Applied and Environmental Microbiology, March 2007, p. 1976-1983, Vol. 73, No. 6
0099-2240/07/$08.00+0 doi:10.1128/AEM.02171-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
Plasmid Replicon Typing of Commensal and Pathogenic Escherichia coli Isolates
Timothy J. Johnson,1
Yvonne M. Wannemuehler,1
Sara J. Johnson,1
Catherine M. Logue,2
David G. White,3
Curt Doetkott,2 and
Lisa K. Nolan1*
Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, 1802 Elwood Drive, VMRI #2, Iowa State University, Ames, Iowa 50011,1
U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, 8401 Muirkirk Rd., Laurel, Maryland 20708,2
Information Technology Services, North Dakota State University, Fargo, North Dakota 581053
Received 15 September 2006/
Accepted 20 January 2007

ABSTRACT
Despite the critical role of plasmids in horizontal gene transfer,
few studies have characterized plasmid relatedness among different
bacterial populations. Recently, a multiplex PCR replicon typing
protocol was developed for classification of plasmids occurring
in members of the
Enterobacteriaceae. Here, a simplified version
of this replicon typing procedure which requires only three
multiplex panels to identify 18 plasmid replicons is described.
This method was used to screen 1,015
Escherichia coli isolates
of avian, human, and poultry meat origin for plasmid replicon
types. Additionally, the isolates were assessed for their content
of several colicin-associated genes. Overall, a high degree
of plasmid variability was observed, with 221 different profiles
occurring among the 1,015 isolates examined. IncFIB plasmids
were the most common type identified, regardless of the source
type of
E. coli. IncFIB plasmids occurred significantly more
often in avian pathogenic
E. coli (APEC) and retail poultry
E. coli (RPEC) than in uropathogenic
E. coli (UPEC) and avian
and human fecal commensal
E. coli isolates (AFEC and HFEC, respectively).
APEC and RPEC were also significantly more likely than UPEC,
HFEC, and AFEC to possess the colicin-associated genes
cvaC,
cbi, and/or
cma in conjunction with one or more plasmid replicons.
The results suggest that
E. coli isolates contaminating retail
poultry are notably similar to APEC with regard to plasmid profiles,
with both generally containing multiple plasmid replicon types
in conjunction with colicin-related genes. In contrast, UPEC
and human and avian commensal
E. coli isolates generally lack
the plasmid replicons and colicin-related genes seen in APEC
and RPEC, suggesting limited dissemination of such plasmids
among these bacterial populations.

INTRODUCTION
Naturally occurring bacterial plasmids are extremely diverse,
self-replicating extrachromosomal elements that encode a variety
of traits, including antibiotic and heavy metal resistance,
virulence, and environmental adaptability and persistence (
10,
14-
18). Plasmids are also important agents of horizontal gene
transfer (HGT), playing a major role in bacterial adaptation
to environmental change (
32). Additionally, plasmids contribute
to genome plasticity by their carriage of mobile genetic elements,
such as insertion sequences and transposons, that can interact
with the bacterial chromosome and contribute to homologous or
nonhomologous recombination (
10).
Due to their role in HGT, especially with regard to the emergence and dissemination of antimicrobial resistance (10, 12), much attention has been paid to the identification and classification of bacterial plasmids. Plasmids have historically been classified according to their incompatibility with other plasmids, a property that is related to their replication (5). Incompatibility (Inc) typing is based on the fact that two plasmids sharing common replication and partitioning elements are unable to proliferate stably in the same cell line (5). Since Inc typing is based on replication factors, the terms Inc and Rep to describe plasmid types have been used interchangeably (3, 5, 10). Currently, there are 26 known Inc groups occurring among the Enterobacteriaceae, a number which has remained static for several years (5, 10). Classification of plasmids into Inc groups is desirable because specific plasmid types have been associated with virulence and/or antimicrobial resistance (1, 2, 4, 11, 12, 14-18, 22, 23, 35, 36).
Unfortunately, physical Inc testing is tedious, particularly when applied to large bacterial populations. In 1988, Couturier and coworkers (5) developed a hybridization method for the comprehensive typing of bacterial plasmids according to replicon type. From this study, a bank of Rep probes corresponding to 19 different Inc groups in the Enterobacteriaceae was developed (5). Although this procedure represented a significant advance in plasmid typing, the method was time-consuming, labor-intensive, and incompatible with current high-throughput approaches. Recognizing a need for a streamlined procedure, Carattoli et al. (3) demonstrated that a PCR-based replicon typing protocol could be used to detect 18 plasmid replicons frequently found among the Enterobacteriaceae. Although their procedure is greatly simplified, it still requires several steps, including five multiplex and three simplex PCR procedures. Therefore, it would be tedious and costly to apply this procedure to large collections of isolates.
Extraintestinal pathogenic E. coli (ExPEC) is a pathotype causing a wide variety of diseases of humans and animals. This group has been found to commonly possess plasmids associated with virulence and antimicrobial resistance (6, 14-18, 26, 34). This is particularly true within the commercial poultry environment, where ExPEC isolates causing colibacillosisreferred to as avian pathogenic E. coli [APEC]have abundant plasmids (7, 14-18). In fact, we have recently reported that ColV and ColBM virulence plasmids are a defining trait of the APEC pathotype (16, 17, 26). These plasmids have been shown to belong to the IncFIB incompatibility group and contain a highly conserved region harboring the FIB replicon, the ColV and/or ColBM operons, and several known virulence genes and iron acquisition and transport operons (16, 17). Additionally, these and other plasmids encoding multiple drug resistances have been isolated from APEC and uropathogenic E. coli (UPEC) (14-18).
Recent work has also focused on the possibility of APEC as a food-borne source of virulent clones with the capacity to cause human extraintestinal diseases, such as urinary tract infections (UTIs) and neonatal meningitis (27, 28). However, while some ExPEC isolates of humans and birds are similar, most appear to have distinct differences (27). Therefore, a more likely scenario would be that APEC serves as a reservoir of plasmid-linked virulence and/or resistance genes for other ExPEC isolates via contaminated poultry meat. However, definitive statements about this cannot be made without a better understanding of the plasmid content of E. coli within these environments. Thus, the aim of this study was to employ a simplified replicon typing procedure to determine the plasmid replicon profiles of 1,015 E. coli isolates. These isolates, which included commensal and pathogenic E. coli isolates obtained from avian and human hosts and isolates from retail poultry meat, were analyzed to determine if these groups share similar plasmid profiles.

MATERIALS AND METHODS
Bacterial strains and plasmids.
Isolates used for the plasmid replicon typing studies were obtained
from a variety of sources within the United States (Table
1).
Of the 1,015 isolates in this study, 422 originated from sites
of infection in birds clinically diagnosed with colibacillosis
(APEC), and 92 were commensal strains obtained from fecal swabs
of apparently healthy chickens and turkeys (avian fecal
E. coli [AFEC]). These originated from a variety of locations, including
California, Georgia, Minnesota, Nebraska, North Dakota, and
Iowa (
26,
27). Two hundred strains were isolated from retail
chicken breasts (retail poultry
E. coli [RPEC]) obtained from
three FoodNet laboratories (Maryland, Georgia, and Oregon) participating
in the National Antimicrobial Resistance Monitoring System (
http://www.fda.gov/cvm/narms_pg.html).
One hundred one strains were isolated from the feces of healthy,
antibiotic-free humans (human fecal
E. coli [HFEC]) from Iowa,
Minnesota, and North Dakota, and 200 isolates originated from
cases of human UTI (UPEC) from a hospital in North Dakota (
27).
Positive controls used in the replicon typing procedure were
kindly provided by Alessandra Carattoli (Istituto Superiore
di Sanità, Rome, Italy). These were originally created
within the laboratory of Werner K. Maas and have been described
elsewhere (
3,
5).
E. coli DH5

was used as a negative control
for all of the genes studied (
29). Additionally APEC O1, known
to possess plasmids containing the IncFIB and IncHI2 replicons
and to harbor
cma and
cbi (
17,
18), and APEC O2, known to possess
plasmids containing the IncFIB and IncFIIA replicons and to
harbor
cvaC (
15,
16), were used as positive wild-type control
strains. All bacterial strains were stored promptly at 70°C
in brain heart infusion broth (Difco Laboratories, Detroit,
MI) with 10% glycerol until use (
30).
Multiplex PCR for plasmid replicon typing and colicin-associated genes.
E. coli isolates were examined for the presence of 18 plasmid replicons using three multiplex panels (Table 2). Isolates were also surveyed for their possession of cvaC, the structural gene of the ColV operon, cma, the colicin M activity gene, and cbi, the colicin B immunity gene, as previously described (16, 17). All primers, annealing temperatures, and expected amplicon sizes are listed in Table 2. Primers were obtained from Integrated DNA Technologies (Coralville, IA). Template DNA for PCR was prepared using a boiling lysis procedure as previously described (13). Targeted genes were amplified in a multiplex panel using a simplified version of the multiplex PCR technique described by Carattoli et al. (3). That is, the eight panels previously used for PCR were reduced to three (Table 2). PCR was performed using AmpliTaq polymerase Gold (Applied Biosystems, Foster City, CA) according to the manufacturer's instructions. Conditions used for PCR were as follows: 5 min at 94°C; 30 cycles of 30 s at 94°C, 30 s at 60°C, and 90 s at 72°C; and a final extension of 5 min at 72°C. Amplicons were visualized on 1.5% Tris-acetate-EDTA agarose gels alongside a 1-kb ladder (Promega Corp.), and if an amplicon of the expected size was observed, then an isolate was considered positive for that particular gene. To validate the multiplex panels, amplicons from the positive controls were excised from agarose, purified, and bidirectionally sequenced using their respective primers. The amplicon sequences were compared to the National Center for Biotechnology Information database using BLAST.
Biostatistics.
Two-way frequency tables of source population (AFEC, APEC, RPEC,
HFEC, and UPEC) versus trait (plasmid replicon type,
cvaC,
cma,
and
cbi) were generated to allow comparisons of the frequency
of occurrence of the plasmid replicons and colicin-associated
genes across populations (
33). Because there were a number of
traits being assessed simultaneously in this study, a resampling-based
multiplicity adjustment to the Fisher's exact test results was
applied using the MULTTEST procedure in SAS (
38). Comparisons
of the proportions of isolates from systemic disease and cellulitis
for each plasmid replicon were also made using Fisher's exact
test with a resampling-based multiplicity adjustment to control
type I error (
38). Utilizing the principle of small multiples
in graphical display (
37), a color-coded matrix icon was created
for each trait to summarize all possible pairwise comparisons
among the five populations in two ways.
Plasmid profiles were obtained by concatenating the presence or absence of each trait in a prespecified order into a character string variable using SAS. A one-way frequency table of this new variable allowed easy assessment of the most commonly occurring profiles. A two-way frequency table of this plasmid profile variable versus source population enabled comparisons of unique plasmid profiles across the populations (38).
Average linkage cluster analysis based upon Jaccard distances calculated from the presence or absence of the various virulence factors among the isolates was used to look for groups or clusters of isolates among the five populations. A composite graphic combining the dendrogram from this cluster analysis, color-coded bands for each source population, and a modified heat map illustrating the presence or absence of each trait for each isolate was generated to allow assessment of all data elements for all isolates simultaneously (27).

RESULTS
Validation of the simplified plasmid replicon typing procedure.
The replicon typing procedure used in this study was a modified
version of that described by Carattoli et al. (
3). Changes in
this procedure included (i) a reduction in the number of overall
PCRs per isolate from eight to three; (ii) use of a boiling
lysis preparation rather than a commercial genomic DNA purification
kit; and (iii) use of a universal cycling procedure for all
three panels. These changes resulted in an overall decrease
in the time, materials, and costs to type these isolates. To
validate the simplified procedure, we tested the three multiplex
panels against the following: known positive controls, containing
cloned plasmid replicons; the negative control
E. coli DH5

,
containing no plasmid replicons; and APEC strains O1 and O2,
containing multiple plasmids which were previously sequenced
and analyzed (
5,
14-
18). The cloned replicons produced bands
of expected sizes for their respective replicon types. Also
as expected, APEC strains O1 and O2 were positive for the IncFIB
and Frep amplicons, and APEC O1 was also positive for the IncHI2
plasmid. No amplicons were observed in the negative control,
E. coli DH5

. Sequencing and BLAST analysis verified that amplicons
of expected sizes were specific for their respective replicons.
Prevalence of plasmid replicons and colicin-associated genes among APEC, UPEC, RPEC, HFEC, and AFEC.
A total of 1,015 E. coli isolates were examined for the presence of the 18 plasmid replicon types using the simplified three-panel multiplex PCR protocol. The most commonly occurring amplicons in each of the five groups examined were Frep and IncFIB (Table 3). IncFIB was the most common replicon type found among APEC isolates, followed by IncI1, IncFIIA, IncP, IncB/O, IncN, and IncFIC. The IncFIB plasmid replicon was also the most common type occurring among AFEC isolates, followed by IncI1 and IncN. The E. coli isolates from retail poultry (RPEC) closely mirrored APEC with regard to the presence of IncFIB and IncI1 plasmid replicons (see the figures). Among the UPEC, IncFIB, and IncB/O plasmid replicons were most often identified, with other replicon types being much less frequently observed. Results for the human commensal isolates examined (HFEC) mirrored the UPEC results.
Matrix icons were used to better visualize differences among
populations for the various traits examined (Fig.
1). These
icons tell the viewer if the incidences of replicon types for
the groups being compared are statistically different from one
another (red or pink in the top half) and also how great the
differences are between the groups (light blue, dark blue, or
pink in the bottom half). In general, most of the significant
differences observed were found among the IncN, IncFIB, IncI1,
IncFIIA, and IncP replicons and in the distribution of
cvaC,
cbi, and
cma genes. For these replicons, significant differences
in prevalence were usually seen between APEC or RPEC and UPEC,
HFEC, or AFEC, indicating distinct differences between these
groups in terms of plasmid profiles.
cvaC,
cbi, and
cmagenes
of the ColV, ColB, and ColM colicin operons, respectively (
16,
17)were included to better discriminate among the different
types of IncFIB-containing isolates. The
cvaC gene occurred
significantly more often among APEC isolates than all other
E. coli isolates examined (Table
3 and Fig.
1). With the exception
of APEC,
cvaC occurred significantly more often in the RPEC
isolates than it did in all the other groups.
cma and
cbi also
occurred significantly more often among APEC and RPEC isolates
than in the other groups of
E. coli isolates (Table
3 and Fig.
1).
Prevalence of plasmid replicons and colicin-associated genes among APEC isolates associated with cellulitis or systemic disease.
Because of expected differences in genotype between APEC isolates
causing systemic disease and those causing cellulitis, these
groups were also compared for plasmid replicon types and colicin-associated
genes. Significant differences in plasmid replicon content were
observed between APEC isolates recovered from systemic disease
and those from cases of cellulitis (Table
4). In particular,
the IncA/C, IncFIB, IncFIC, IncI1, and IncHI2 replicons occurred
significantly more often among cellulitis strains, whereas the
IncB/O replicon was observed significantly more often among
APEC strains recovered from systemic disease. Additionally,
cvaC,
cbi, and
cma prevalences were significantly different
between groups, with
cvaC occurring more often among the systemic
disease isolates and
cbi and
cma occurring more often among
the cellulitis isolates. The IncT, IncW, and IncX replicons
were not detected in any of these isolates.
Most frequently identified plasmid profiles among E. coli isolates.
Overall, a high degree of variability in plasmid profiles was
observed among the 1,015
E. coli isolates, with 221 different
combinations identified. Only 13% of the
E. coli isolates failed
to yield any of the tested replicons or colicin-associated genes
(Table
5). Among the replicon profiles identified, IncFIB occurring
alone was the most common. Several other common replicon combinations
involving IncFIB were found: IncFIB plus
cvaC, IncFIB plus IncI1
plus
cvaC, and IncFIB plus IncI1. Among APEC isolates, the most
common replicon profiles identified were IncFIB plus
cvaC and
IncFIB plus
cvaC plus IncI1, and among RPEC isolates, the most
common profile was IncFIB plus
cvaC. The IncFIB replicon was
also the most commonly identified type among HFEC and UPEC isolates
tested, although these populations did not tend to contain colicin-associated
genes or additional replicon types (Table
5).
A two-way clustering heat map was produced to better illustrate
the similarities and differences in the occurrence of plasmid
replicon profiles between the groups examined (Fig.
2). This
map used trait prevalence to cluster groups (
y axis) and traits
(
x axis) based upon their similarities in trait prevalence.
From this analysis, APEC and RPEC were found to be more closely
related to each other, in terms of plasmid trait profile, than
they were to UPEC, HFEC, and AFEC. Also,
cvaC (ColV),
cbi (ColB),
cma (ColM), IncFIB, IncI1, and IncP clustered together based
upon their similarities in occurrence among the five groups
examined.
Additionally, an average linkage cluster analysis was performed
on the data in an effort to better discern patterns of replicon
types among the different
E. coli groups. This analysis grouped
organisms according to plasmid/gene profile and allowed an illustration
of an isolate's source relative to its profile. These results
are combined with a heat map display of the presence or absence
of each gene to help understand the basis of the clusters (Fig.
3). The isolates clustered into five distinct groups, illustrated
in the column immediately to the right of the dendrogram. One
cluster (light blue) contained most of the UPEC, HFEC, and AFEC
but also a mix of isolates from other sources. Isolates of this
cluster generally contained an F-type plasmid but lacked other
plasmid types and/or colicin-associated genes. The next two
clusters (gold and red) contained mostly APEC and RPEC, which
were characterized by possession of an F-type plasmid, colicin-associated
genes, and/or additional plasmid replicons. The fourth cluster
(dark blue) contained mostly UPEC, HFEC, and AFEC and generally
lacked the traits examined. The fifth cluster (purple) contained
almost exclusively APEC and RPEC, and these isolates possessed
an F-type plasmid replicon type along with colicin-associated
genes and additional plasmid replicons.

DISCUSSION
The purpose of this study was to create and use a simplified
plasmid replicon typing procedure to examine five populations
of
E. coli from avian hosts, human hosts, and retail poultry
meat. These populations included APEC, human UPEC, AFEC, HFEC,
and RPEC. This study focused on the plasmid profiles for each
of the five groups to determine if there were overlaps in profiles
among
E. coli isolates originating from poultry, poultry products,
or humans.
This study revealed that APEC and RPEC isolates shared similar plasmid profiles. That is, these groups could be distinguished from UPEC, HFEC, and AFEC based upon their possession of multiple plasmid replicons (i.e., replicons in addition to IncFIB) and the presence of one or more of the three colicin-related genes examined (Fig. 1 to 3). While definitive statements cannot be made about these observations without further study, the results presented here show that E. coli isolates contaminating retail poultry are more similar to APEC than AFEC in terms of their plasmid profiles. This finding would appear to be counterintuitive, as one might expect that the primary source of RPEC is the feces of apparently healthy poultry at slaughter (8). Further studies will be needed to confirm our observation, but the results presented here are intriguing and warrant further attention.
Recent attention has been given to the notion that APEC might be a food-borne source of ExPEC causing human UTIs or act as a reservoir of plasmid-linked virulence and resistance genes for human UPEC. However, the plasmid replicon profiles of the APEC and UPEC strains examined here were very different from one another. In fact, the plasmid profiles of UPEC showed more similarities to those of commensals than they did to APEC profiles. These findings are in congruence with a previous study comparing APEC and UPEC (27), which showed that there were significant differences in the distribution of plasmid-associated traits between the two groups of isolates. Thus, if APEC isolates are involved in human UTIs, either as a causative agent or as a reservoir of plasmid-linked resistance and virulence traits for UPEC, they are unlikely to be involved in many of these infections.
APEC plasmids have received recent attention for their role in virulence and antimicrobial resistance. Indeed, a conserved portion of APEC virulence plasmids may be the defining trait of the pathotype, and the virulence and antimicrobial resistance genes associated with these plasmids are widespread among APEC isolates (16, 17, 26, 39). Since it appears that virulence and R plasmids commonly cotransfer during conjugation, as is the case with several well-studied APEC isolates (14-18, 31), the impact that these plasmids may have on the proliferation of multidrug-resistant, highly virulent strains in the environment cannot be overemphasized. Results presented in this study suggest that this may be the case, as the most commonly occurring plasmid profiles among APEC and RPEC involve the presence of multiple plasmid replicons which have been associated with both virulence and multidrug resistance (1, 2, 4, 11, 12, 14-18, 22, 23, 35, 36).
There has also been recent interest in commensals as a source of antimicrobial resistance genes for pathogenic strains. The transfer of R plasmids from animal to human E. coli strains is well-documented (20, 21, 24, 25). Our results indicate that commensal E. coli isolates from humans and poultry birds do harbor plasmid types which have been shown to carry mobile genetic elements encoding drug resistance, albeit at a low frequency compared to that of APEC and RPEC. Therefore, the results of this study lend credibility to the idea that commensal E. coli isolates are reservoirs of plasmids harboring genes for multidrug resistance and/or virulence.
Previously, it has been difficult to characterize large populations of E. coli strains by their plasmid replicon types. However, in the present study, a simplified multiplex PCR protocol for replicon typing was validated and used to characterize over 1,000 E. coli isolates, which are representative of the types and numbers of plasmids they possess. However, pitfalls in this screening method do exist. While the presence of a plasmid replicon in an isolate likely indicates the presence of a particular plasmid type, it is possible that such a replicon type might have integrated into the bacterial chromosome or exist on cointegrate plasmids with multiple replicons (9, 19). However, BLAST analysis of the plasmid replicons sought in this study suggests that while this phenomenon does occur, it is rare. Another potential pitfall with this technique is that unknown plasmid replicons will be missed with this screening procedure. This is also a possibility, as observed with the control strain APEC O1, which possesses four plasmids, of which only two are typeable. Nevertheless, the total number of Inc groups appears to have plateaued in recent years, indicating that there may be a finite number of plasmid types in the environment (5). Still, the best method to ultimately verify the presence of a particular plasmid type is still gentle isolation and careful visualization. However, the techniques presented here are an extremely useful way to analyze large populations for the potential presence of plasmids.

ACKNOWLEDGMENTS
This project was funded, in part, by the Alliance for the Prudent
Use of Antibiotics and the Iowa State University Biotechnology
Council, Provost's Office, and College of Veterinary Medicine.

FOOTNOTES
* Corresponding author. Mailing address: Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, 1802 Elwood Drive, VMRI #2, Iowa State University, Ames, IA 50011. Phone: (515) 294-3470. Fax: (515) 294-3839. E-mail:
lknolan{at}iastate.edu.

Published ahead of print on 2 February 2007. 

REFERENCES
1 - Boyd, D., A. Cloeckaert, E. Chaslus-Dancla, and M. R. Mulvey. 2002. Characterization of variant Salmonella genomic island 1 multidrug resistance regions from serovars Typhimurium DT104 and Agona. Antimicrob. Agents Chemother. 46:1714-1722.[Abstract/Free Full Text]
2 - Carattoli, A., V. Miraqou, A. Bertini, A. Loli, C. Colinon, L. Villa, J. M. Whichard, and G. M. Rossolini. 2006. Replicon typing of plasmids encoding resistance to newer beta-lactams. Emerg. Infect. Dis. 12:1145-1148.[Medline]
3 - Carattoli, A., A. Bertini, L. Villa, V. Falbo, K. L. Hopkins, and E. J. Threlfall. 2005. Identification of plasmids by PCR-based replicon typing. J. Microbiol. Methods 63:219-228.[CrossRef][Medline]
4 - Carattoli, A., L. Villa, C. Pezzella, E. Bordi, and P. Visca. 2001. Expanding drug resistance through integron acquisition by IncFI plasmids of Salmonella enterica Typhimurium. Emerg. Infect. Dis. 7:444-447.[Medline]
5 - Couturier, M., F. Bex, P. L. Bergquist, and W. K. Maas. 1988. Identification and classification of bacterial plasmids. Microbiol. Rev. 52:375-395.[Free Full Text]
6 - Dobrindt, U. 2005. (Patho-)genomics of Escherichia coli. Int. J. Med. Microbiol. 295:357-371.[CrossRef][Medline]
7 - Doetkott, D. M., L. K. Nolan, C. W. Giddings, and D. L. Berryhill. 1996. Large plasmids of avian Escherichia coli isolates. Avian Dis. 40:927-930.[CrossRef][Medline]
8 - Doyle, M. P., and M. C. Erickson. 2006. Reducing the carriage of foodborne pathogens in livestock and poultry. Poult. Sci. 85:960-973.[Abstract/Free Full Text]
9 - Froehlich, B., J. Parkhill, M. Sanders, M. A. Quail, and J. R. Scott. 2005. The pCoo plasmid of enterotoxigenic Escherichia coli is a mosaic cointegrate. J. Bacteriol. 187:6509-6516.[Abstract/Free Full Text]
10 - Frost, L. S., R. Leplae, A. O. Summers, and A. Toussaint. 2005. Mobile genetic elements: the agents of open source evolution. Nat. Rev. Microbiol. 3:722-732.[CrossRef][Medline]
11 - Gilmour, M. W., N. R. Thomson, M. Sanders, J. Parkhill, and D. E. Taylor. 2004. The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics. Plasmid 52:182-202.[CrossRef][Medline]
12 - Hopkins, K. L., E. Liebana, L. Villa, M. Batchelor, E. J. Threlfall, and A. Carattoli. 2006. Replicon typing of plasmids carrying CTX-M or CMY ß-lactamases circulating among Salmonella and Escherichia coli isolates. Antimicrob. Agents Chemother. 50:3203-3206.[Abstract/Free Full Text]
13 - Johnson, J. R., and A. L. Stell. 2000. Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise. J. Infect. Dis. 181:261-272.[CrossRef][Medline]
14 - Johnson, T. J., C. W. Giddings, S. M. Horne, P. S. Gibbs, R. E. Wooley, J. Skyberg, P. Olah, R. Kercher, J. S. Sherwood, S. L. Foley, and L. K. Nolan. 2002. Location of increased serum survival gene and selected virulence traits on a conjugative R plasmid in an avian Escherichia coli isolate. Avian Dis. 46:342-352.[CrossRef][Medline]
15 - Johnson, T. J., K. E. Siek, S. J. Johnson, and L. K. Nolan. 2005. DNA sequence and comparative genomics of pAPEC-O2-R, an avian pathogenic Escherichia coli transmissible R plasmid. Antimicrob. Agents Chemother. 49:4681-4688.[Abstract/Free Full Text]
16 - Johnson, T. J., K. E. Siek, S. J. Johnson, and L. K. Nolan. 2006. DNA sequence of a ColV plasmid and prevalence of selected plasmid-encoded virulence genes among avian Escherichia coli strains. J. Bacteriol. 188:745-758.[Abstract/Free Full Text]
17 - Johnson, T. J., S. J. Johnson, and L. K. Nolan. 2006. Complete DNA sequence of a ColBM plasmid from an avian pathogenic Escherichia coli suggests that it evolved from closely related ColV virulence plasmids. J. Bacteriol. 188:5975-5983.[Abstract/Free Full Text]
18 - Johnson, T. J., Y. Wannemeuhler, J. Scaccianoce, S. J. Johnson, and L. K. Nolan. 2006. Complete DNA sequence, comparative genomics, and prevalence of an IncHI2 plasmid occurring among extraintestinal pathogenic Escherichia coli. Antimicrob. Agents Chemother. 50:3929-3933.[Abstract/Free Full Text]
19 - Kahn, P. L., and M. Clermont. 1975. Characterization of V-prime factors in Escherichia coli K-12. J. Bacteriol. 124:589-592.[Abstract/Free Full Text]
20 - Levy, S. B., G. B. Fitzgerald, and A. B. Macone. 1976. Spread of antibiotic-resistant plasmids from chicken to chicken and from chicken to man. Nature 260:40-42.[CrossRef][Medline]
21 - Linton, A. H., K. Howe, P. M. Bennett, and M. H. Richmond. 1977. The colonization of the human gut by antibiotic resistant Escherichia coli from chickens. J. Appl. Bacteriol. 43:465-469.[Medline]
22 - Llanes, C., M. Couturier, L. Asfeld, F. Grimont, and Y. Michel-Briand. 1994. Replicon typing of 71 multiresistant Serratia marcescens strains. Res. Microbiol. 145:17-25.[Medline]
23 - Novais, A., R. Canton, A. Valverde, E. Machado, J. C. Galan, L. Peixe, A. Carattoli, F. Baquero, and T. M. Coque. 2006. Dissemination and persistence of blaCTX-M-9 are linked to class 1 integrons containing CR1 associated with defective transposon derivatives from Tn402 located in early antibiotic resistance plasmids of IncHI2, IncP1-alpha, and IncFI groups. Antimicrob. Agents Chemother. 50:2741-2750.[Abstract/Free Full Text]
24 - Ojeniyi, A. A. 1989. Direct transmission of Escherichia coli from poultry to humans. Epidemiol. Infect. 103:513-522.[Medline]
25 - Ramchandani, M., A. R. Manges, C. DebRoy, S. P. Smith, J. R. Johnson, and L. W. Riley. 2005. Possible animal origin of human-associated, multidrug-resistant, uropathogenic Escherichia coli. Clin. Infect. Dis. 40:251-257.[CrossRef][Medline]
26 - Rodriguez-Siek, K. E., C. W. Giddings, C. Doetkott, T. J. Johnson, and L. K. Nolan. 2005. Characterizing the APEC pathotype. Vet. Res. 36:241-256.[CrossRef][Medline]
27 - Rodriguez-Siek, K. E., C. W. Giddings, C. Doetkott, T. J. Johnson, M. K. Fakhr, and L. K. Nolan. 2005. Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis. Microbiology 151:2097-2110.[Abstract/Free Full Text]
28 - Ron, E. Z. 2006. Host specificity of septicemic Escherichia coli: human and avian pathogens. Curr. Opin. Microbiol. 9:28-32.[CrossRef][Medline]
29 - Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
30 - Sanderson, K. E., and D. R. Zeigler. 1991. Storing, shipping, and maintaining records on bacterial strains. Methods Enzymol. 204:248-264.[CrossRef][Medline]
31 - Skyberg, J. A., T. J. Johnson, J. R. Johnson, C. Clabots, C. M. Logue, and L. K. Nolan. 2006. Acquisition of avian pathogenic Escherichia coli plasmids by a commensal E. coli isolate enhances its abilities to kill chicken embryos, grow in human urine, and colonize the murine kidney. Infect. Immun. 74:6287-6292.[Abstract/Free Full Text]
32 - Smets, B. F., and T. Barkay. 2005. Horizontal gene transfer: perspectives at a crossroads of scientific disciplines. Nat. Rev. Microbiol. 3:675-678.[CrossRef][Medline]
33 - Snedecor, G. W., and W. G. Cochran. 1980. Statistical methods, 7th ed. Iowa State University Press, Ames, IA.
34 - Sorsa, L. J., S. Dufke, J. Heesemann, and S. Schubert. 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/Free Full Text]
35 - Tennstedt, T., R. Szczepanowski, I. Krahn, A. Puhler, and A. Schluter. 2005. Sequence of the 68,869 bp IncP-1
plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402-like integron and other transposable elements. Plasmid 53:218-238.[CrossRef][Medline] 36 - Tosini, F., P. Visca, I. Luzzi, A. M. Dionisi, C. Pezzella, A. Petrucca, and A. Carattoli. 1998. Class 1 integron-borne multiple-antibiotic resistance carried by IncFI and IncL/M plasmids in Salmonella enterica serotype Typhimurium. Antimicrob. Agents Chemother. 42:3053-3058.[Abstract/Free Full Text]
37 - Tufte, E. R. 1983. The visual display of quantitative information. Graphics Press, Cheshire, CT.
38 - Westfall, P. H., R. D. Tobias, D. Rom, R. D. Wolfinger, and Y. Hochberg. 1999. Multiple comparisons and multiple tests using the SAS system. SAS Institute, Inc., Cary, NC.
39 - Yang, H., S. Chen, D. G. White, S. Zhao, P. McDermott, R. Walker, and J. Meng. 2004. Characterization of multiple-antibiotic-resistant Escherichia coli isolates from diseased chickens and swine in China. J. Clin. Microbiol. 42:3843-3849.
Applied and Environmental Microbiology, March 2007, p. 1976-1983, Vol. 73, No. 6
0099-2240/07/$08.00+0 doi:10.1128/AEM.02171-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
This article has been cited by other articles:
-
Carattoli, A.
(2009). Resistance Plasmid Families in Enterobacteriaceae. Antimicrob. Agents Chemother.
53: 2227-2238
[Full Text]
-
Deschamps, C., Clermont, O., Hipeaux, M. C., Arlet, G., Denamur, E., Branger, C.
(2009). Multiple acquisitions of CTX-M plasmids in the rare D2 genotype of Escherichia coli provide evidence for convergent evolution. Microbiology
155: 1656-1668
[Abstract]
[Full Text]
-
Lindsey, R. L., Fedorka-Cray, P. J., Frye, J. G., Meinersmann, R. J.
(2009). Inc A/C Plasmids Are Prevalent in Multidrug-Resistant Salmonella enterica Isolates. Appl. Environ. Microbiol.
75: 1908-1915
[Abstract]
[Full Text]
-
Bean, D. C., Livermore, D. M., Hall, L. M. C.
(2009). Plasmids Imparting Sulfonamide Resistance in Escherichia coli: Implications for Persistence. Antimicrob. Agents Chemother.
53: 1088-1093
[Abstract]
[Full Text]
-
Garcia-Fernandez, A., Fortini, D., Veldman, K., Mevius, D., Carattoli, A.
(2009). Characterization of plasmids harbouring qnrS1, qnrB2 and qnrB19 genes in Salmonella. J Antimicrob Chemother
63: 274-281
[Abstract]
[Full Text]
-
Marcade, G., Deschamps, C., Boyd, A., Gautier, V., Picard, B., Branger, C., Denamur, E., Arlet, G.
(2009). Replicon typing of plasmids in Escherichia coli producing extended-spectrum {beta}-lactamases. J Antimicrob Chemother
63: 67-71
[Abstract]
[Full Text]
-
Johnson, T. J., Wannemuehler, Y., Johnson, S. J., Stell, A. L., Doetkott, C., Johnson, J. R., Kim, K. S., Spanjaard, L., Nolan, L. K.
(2008). Comparison of Extraintestinal Pathogenic Escherichia coli Strains from Human and Avian Sources Reveals a Mixed Subset Representing Potential Zoonotic Pathogens. Appl. Environ. Microbiol.
74: 7043-7050
[Abstract]
[Full Text]
-
Garcia-Fernandez, A., Chiaretto, G., Bertini, A., Villa, L., Fortini, D., Ricci, A., Carattoli, A.
(2008). Multilocus sequence typing of IncI1 plasmids carrying extended-spectrum {beta}-lactamases in Escherichia coli and Salmonella of human and animal origin. J Antimicrob Chemother
61: 1229-1233
[Abstract]
[Full Text]