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Antimicrobial Agents and Chemotherapy, January 2005, p. 358-365, Vol. 49, No. 1
0066-4804/05/$08.00+0 doi:10.1128/AAC.49.1.358-365.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
the Canadian Nosocomial Infection Surveillance Program,
Health Canada
Nosocomial Infections, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba,1 Division of Nosocomial and Occupational Infections, Centre for Infectious Disease Prevention and Control, Public Health Agency of Canada, Ottawa, Ontario,5 The Vancouver General Hospital, Vancouver, British Columbia,2 The University of Toronto,3 The Department of Microbiology, Sunnybrook and Women's College Health Sciences Centre, Toronto, Ontario, Canada4
Received 7 April 2004/ Returned for modification 4 August 2004/ Accepted 11 September 2004
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Plasmid-mediated ampC genes were first reported in 1988 (25, 31). The plasmid-mediated ampC genes are derived from inducible chromosomal genes that have become mobilized (11, 24, 25). The first genetically characterized plasmid-mediated AmpC was MIR-1, which was mobilized from an Enterobacter isolate (23). These plasmid-mediated genes are of special interest because their mobility allows them to emerge in one genus or species and spread to different organisms. The prevalence of plasmid-mediated AmpC-type resistance at the national level in most countries is unknown because studies have not examined the strains at the molecular level of detail required to elucidate the different mechanisms involved. A recent report from the United States, however, showed that among 752 Klebsiella spp. and E. coli strains from 70 sites in 25 states, 7 to 8.5% of the Klebsiella spp. and 4% of the E. coli strains contained plasmid-mediated AmpC-type enzymes (2). In this report, we present the first detailed characterization of cefoxitin-resistant strains of E. coli acquired from nosocomial sources at the national level in Canada. We used sequence analysis to determine the frequency of promoter or attenuator mutations and PCR to look for plasmid-mediated ampC genes. Molecular epidemiological methods were also used to determine the extent of clonal spread of cefoxitin-resistant strains.
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Study design. This was a prospective laboratory-based surveillance study (conducted from 1 October 1999 to 30 September 2000) in which all nonrepeat strains of E. coli determined to be clinically significant by the participating hospital laboratories were tested with the center's normal panel of beta-lactam antibiotics for extended-spectrum beta-lactamase (ESBL) production by use of the screening criteria described by NCCLS (17, 18, 19). Strains identified as possible ESBL producers were submitted to NML for further characterization. Denominator data, consisting of the total number of E. coli strains, were collected for the surveillance period to determine the rates of incidence of cefoxitin-resistant strains. Patient-specific information collected from the patients' charts included the service that the patient was on when the specimen was identified, date of birth, gender, date of specimen collection, and type of specimen.
Bacterial strains. All isolates were identified at the participating sites by the routine methods performed at each laboratory. Strains meeting the study criteria were submitted to NML, where, upon receipt, they were stored at 70°C in Microbank vials (Pro-Lab Diagnostics, Richmond Hill, Ontario, Canada). The identities of all isolates submitted were confirmed with Vitek GNI cards (bioMérieux, Hazelwood, Mo.). The control strains used in this study included Klebsiella pneumoniae ATCC 700603, Pseudomonas aeruginosa ATCC 27853, and E. coli ATCC 25922.
Antimicrobial susceptibility testing.
Potential ESBL-producing isolates were confirmed to be cefoxitin resistant (MICs
32 mg/liter) by the broth microdilution method, as described by NCCLS (17). The MICs of cephalosporins and aztreonam, with and without clavulanic acid, as well as the MICs of meropenem for all cefoxitin-resistant strains detected in this study were determined by broth microdilution (17). In addition, potential ESBLs were confirmed by the disk diffusion method as described by the NCCLS (18, 19) with disks containing ceftazidime (CAZ), ceftazidime-clavulanic acid, cefotaxime, and cefotaxime-clavulanic acid (Mast Diagnostics, Merseyside, United Kingdom). Susceptibilities to other classes of antimicrobials were determined with Vitek GNS-121 panels (bioMérieux).
Molecular subtyping by PFGE. Cefoxitin-resistant strains were subtyped by pulsed-field gel electrophoresis (PFGE) by the standardized protocol for E. coli (O157:H7) (30), and the fingerprints were analyzed with a BioNumerics software program (version 2.5; Applied Maths, Saint Martens-Latem, Belgium). Gels were normalized by using the molecular weight standard strain Salmonella enterica serovar Braenderup Universal Marker (kindly provided by B. Swaminathan, Centers for Disease Control and Prevention, Atlanta, Ga.). A 1.0% tolerance with 1.5% optimization was used during cluster analysis by the unweighted pair group method, and DNA relatedness was calculated on the basis of the Dice coefficient.
Molecular characterization of Ambler class C resistance determinants. In order to minimize the number of strains to be characterized, it was assumed that all strains that were identified at the same site and that had indistinguishable DNA fingerprints were identical.
PCR for amplification of the ampC promoter region of the E. coli strains was performed with the primer pairs and conditions described previously (4). Amplicons were purified with a Microcon PCR kit (Millipore) and were sequenced at the DNA Core Facility at NML. The resulting ampC promoter sequences were compared to the corresponding E. coli K-12 sequence (GenBank database accession number U00096) by using the DNASTAR MegAlign program (version 4.05).
To identify acquired AmpC-type resistance, individual PCRs were carried out with the cycling conditions described above and the following primers at 0.5 µM each: CIT-A (5'-ATGCAGGAGCAGGCTATTC-3') and CIT-B (5'-TGGAGCGTTTTCTCCTGAAC-3') for CMY-2-related genes, FOX-A (5'-TGTGGACGGCATTATCCAG-3' ) and FOX-B (5'-AAAGCGCGTAACCGGATTG-3') for FOX-related genes, and ENT-A (5'-AGTAAAACCTTCACCTTCACCG-3') and ENT-B (5'-ATGCGCCTCTTCCGCTTTC-3') for ACT-1/MIR-1-related genes.
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FIG. 1. Number of cefoxitin-resistant strains isolated by month and by site over the length of the study. Colors represent the total number of strains at a specific site.
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TABLE 1. Site of isolation of cefoxitin-resistant strains
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TABLE 2. Antimicrobial resistance patterns of study strainsa
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FIG. 2. Dendrogram depicting DNA macrorestriction patterns of cefoxitin-resistant E. coli strains generated with XbaI. The shaded region highlights the largest outbreak cluster described in the text.
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TABLE 3. Mutations at given positions in ampC promoter region for specific promoter typesa
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T at position 11, which changes the 10 box from TACAAT to TATAAT (the pertinent nucleotides are in boldface), and/or T
A at position 32, which changes the 35 box from TTGTCA to TTGACA, or an increase in the distance between the 35 and 10 boxes from 16 bp to either 17 or 18 bp by insertion of 1 or 2 bp between positions 13 and 14 (positions 13.1 and 13.2 in Table 3). Interestingly, the mutations in the 35 and 10 boxes and the insertions in the spacer region were mutually exclusive and were never found in the same promoter region.
Mutations that created an alternative displaced promoter also occurred in 11 sequence types (58 strains). Changes included G
A at position 18, which changed TGTCGT to TATCGT to create a 10 box, and/or C
T at position 42, which changed CTGACA to TTGACA to create a 35 box. The alternative 35 and 10 sequences were separated by 17 bp. Sequence type 15 (one strain) had, in addition to the G
A change at position 18, a G
A change at position 15, which created an alternate 10 box with the sequence TATCAT. Sequence type 48 (one strain) had the change at position 18 and the T
A change at position 32.
Changes at two other positions were found in the spacer region: a C
T change at position 29 in a single sequence type (type 28; one strain) and a G
A change at position 28 in 11 sequence types (35 strains). The sequence type 28 strain also had the change at position 32 and changes in the attenuator region and ampC-coding region. The change at position 28 was found to be associated with changes in the promoter region (positions 32, 13.1 and 13.2, and 11), the attenuator region, or other changes but never with the changes at position 42 and/or 18 that created the alternative 35 or 10 boxes. Due to their location in the spacer region, it is possible that nucleotides at these positions may interact with RNA polymerase. However, whether this has any affect on ampC expression awaits further evidence.
Mutations in the attenuator region are assumed to destabilize the stem-loop structure and allow increased levels of ampC transcription. Direct proof of this, by use of site-directed mutagenesis, for example, has not been obtained because of the difficulty of introducing mutations in the region due to the stem-loop structure (5). Mutations in the attenuator region (positions +17 to + 37) were found in 27 sequence types (63 strains). Most commonly, four changes were found together: C
T at position +22, T
G at position +26, A
T at position +27, and G
A at position +32. These changes occurred in nine sequence types (34 strains). The changes at positions +26 and +27 always occurred together and with the changes at positions +22 and +32, although the reverse was not true. Three sequence types (four strains) had single-base-pair deletions in the attenuator region, and in two types these occurred with the four most common changes to the attenuator region mentioned above. All 17 other variants with changes in the attenuator region (29 strains) had single-base-pair mutations. We note that changes in the attenuator region were often found in conjunction with changes in the promoter region, with this occurring in 25 sequence types.
Changes at three positions were found outside of the promoter and attenuator regions: at positions 1, +6, and +58. Two of these were the two most commonly found changes; the C
T change at position +58 was found in 19 sequence types (85 strains), and the C
T change at position 1 was found in 11 sequence types (59 strains). These two changes were most often found together (nine sequence types; 57 strains) and may represent strain-specific polymorphisms.
As mentioned above, changes were found at three positions in the ampC-coding region, and all led to changes in the amino acid sequence. A T
C change at position +63 causes a Phe
Leu change, a C
T change at position +70 causes a Thr
Met change, and a G
A change at position +81 causes a Ala
Thr change. In fact, changes at these three positions were very common, being found in 84% (42 of 49) of the sequence types (107 strains). Interestingly, the change at position +70 was never found with changes at position +63 or +81. The change at position +63 was always found with the change at position +81, although the reverse was not the case. The contribution, if any, of these three amino acid changes to increased AmpC activity is unknown, as all occurred within the first 8 residues of the AmpC enzyme in the leader peptide region. It could be that changes here lead to the more efficient transfer of the enzyme precursor into the periplasmic space. Previous evidence (27) indicated that in the SHV-7 beta-lactamase an Ile8Phe change could lead to a more mature enzyme in the periplasmic space and hence increased MICs of some beta-lactams.
In the collection of strains that we analyzed, the most common sequence type was 03, and 36 strains were of this type. Type 03 contained the strong alternate promoter caused by the changes at positions 42 and 18 and also included the changes at positions 1 and +58. Interestingly, the third most common sequence type, type 18 (n = 19 strains), differed from type 03 only in that it did not contain the mutation at position 42. The second most common sequence type, type 04, contained the four changes most often found in the attenuator region, as well as the change at position +70 in the ampC-coding region. As mentioned above, the effect of changes in the attenuator on transcription efficiency is not directly known, but we note that type 04 contains no changes in the promoter region.
PCR promoter amplification from three isolates yielded amplicons of approximately 1.5 kb, which was significantly larger than the expected 191-bp amplicon. Sequence analysis of these amplicons revealed the presence of IS elements in the ampC promoter regions in these strains (Fig. 3). In one strain an IS911 variant was inserted 11 bp upstream of the wild-type 10 box, which, as a result, was located 17 bp downstream of the IS911-specific sequence TTGACC, which is expected to act as a 35 box. Thus, in this strain the resulting hybrid promoter most likely drives the expression of ampC. IS911 is flanked by the trimer ATT; thus, insertion appears to have caused duplication at positions 22 to 24. In two strains IS10 was inserted between the ampC attenuator region and the start codon. It is likely that the strong pOUT promoter of IS10 drives the expression of ampC in these strains (28). As well, the effect of the attenuator would be negated by the location of IS10. In both strains IS10 is flanked by the 9-bp direct repeat CGTTTTGTA; thus, insertion appears to have caused a duplication of positions +38 to +46. Interestingly, the two strains with the IS10 insertion had very different macrorestriction profiles (more than seven band differences).
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FIG. 3. Schematic diagram showing the insertion of the IS10 (two strains) and IS911-like (one strain) elements in the ampC promoter region, as found in this study.
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TABLE 4. Promoter sequence types of strains containing CMY-2 gene
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This report describes the first national study of cefoxitin-resistant strains in Canadian hospitals. The number of cefoxitin-resistant E. coli strains did not dramatically increase over the study, which is in contrast to the findings for the classical Ambler class A ESBLs, a steady increase in the numbers of which occurred during the same study period in Canada (16). We note that these strains were a subgroup (cefoxitin resistant) of a collection of E. coli isolates selected as having reduced susceptibilities to extended-spectrum cephalosporins (NCCLS ESBL screen test) and so produced data for only a minimum number of cefoxitin-resistant E. coli strains in Canadian hospitals. Interestingly, although the strains were potential ESBL producers by screen tests, only a low percentage of the AmpC producers were clinically resistant to extended-spectrum cephalosporins (Table 2). As well, although cefotetan is a cephamycin, no strain was resistant to this drug, and hence, it is inadequate to use MICs of cefotetan as an indicator of possible AmpC activity. Although intrahospital outbreaks occurred at almost half of the sites, the sizes of the outbreaks remained small (2 to 4 strains), with the exception of one large outbreak (17 strains), which occurred at a site in western Canada. The lack of clonal strain dissemination, the high numbers of mutations in the promoter and attenuator regions, and the small number of acquired AmpC resistance genes suggests that antimicrobial selective pressure may be playing a large role in the potential emergence of cefoxitin resistance in a patient.
An analysis of 168 promoter regions in E. coli clearly showed the presence of two conserved regions, the 35 box and the 10 box, also called the Pribnow box (12). For most promoters the degree of homology to the 35 box consensus sequence, TTGACA, and the 10 box consensus sequence, TATAAT, is directly related to promoter strength. Furthermore, the spacing between these two regions plays a role in promoter strength, with the optimal distance being 17 bp. Numerous studies have reported that variations in the promoter and attenuator regions of ampC are a mechanism of hyperproduction of the AmpC protein that results in resistance to cefoxitin (3, 4, 5, 7, 10, 14, 20, 21, 22, 29). While some of the mutations described in this report may be polymorphisms that do not alter ampC expression, some of the changes observed have been shown to increase gene expression in previous studies. Changes at position 42 (C
T) in the ampC promoter were shown to increase transcription by 43-fold (5) or 18-fold (20), depending on the type of transcriptional reporter system used. The C
T transition at position 42 results in a consensus TTGACA box upstream of the native 35 sequence and in modification of the transcriptional initiation site up to 5 bp upstream from the original site (20). Interestingly, almost all of the promoters harboring this change (five of six) also had a corresponding T
A transversion at position 18. This change resulted in a new 10 box separated by 17 bp from the new 42 box, resulting in the formation of a strong promoter, as has been described in other clinical cefoxitin-resistant E. coli strains (5, 10, 20). These mutations (those at both positions 42 and 18 or position 18 only) were the most common promoter-region variations found in this study (32%; 59 of 183 isolates), suggesting that these changes may be favored in situ over other promoter-region mutations which may effect ampC expression.
Changes in the 35 and 10 boxes or in the spacer region that result in ampC promoter sequences more closely resembling the E. coli consensus promoter sequence have been described previously (4, 7, 10, 13, 29). A T
A transversion at position 32 resulted in the formation of a 35 consensus box and increased the level of ampC expression in two independent studies (4, 13). This mutation was the second most common promoter alteration observed in the present study, with 19% (33 of 183) of promoters sequenced containing this change. By use of a reporter system, only a single strain that had the C
T transition at the 11 position has been characterized, and the results showed a sixfold increase in promoter strength (7). In the present study only two strains were observed to have this mutation. Insertions of nucleotides between the 10 and 35 regions of the ampC promoter which produce 17 or 18 bp of separation between these regions have been reported previously and are thought to result in a more efficient promoter (10, 13, 29). In addition to the previously reported changes in the spacer region, this report describes two promoter variants with a doublet of T-A inserted between nucleotides 14 and 13, creating a novel 18-bp spacer region.
Jaurin et al. (13) first reported on a transcriptional attenuator region in the E. coli ampC promoter region. It was hypothesized that mutations in this region contribute to AmpC overproduction by causing destabilization of the hairpin structure, resulting in increased transcription. Of the 27 attenuator-region variants observed in the present study, 9 involved changes at 4 positions, and 2 of these also had 1-bp deletions. All of the 19 remaining variants had single-base-pair changes or a 1-bp deletion, which was detected in a single variant. All the changes resulted in a reduction of the thermodynamic strength of formation of the stem-loop structure to some extent (data not shown), providing further evidence that these mutations may be associated with increased transcription. We note, however, that 85% (23 of 27) of sequence types with attenuator mutations also had changes that create a stronger promoter (Table 3). Nonetheless, the only changes that we detected in type 14 strains (two strains) were the mutations at positions +22, +26, +27, and +32; hence, these strains may prove useful for quantification of the contributions of these attenuator mutations to cefoxitin resistance.
The insertion of IS elements in promoter regions that cause the up-regulation of gene expression by producing an alternate promoter has been described. A previous report (15) has described a laboratory mutant of E. coli that overproduced AmpC by the insertion of an IS2 element. Additionally, a recent study identified a possible IS element inserted upstream of the ampC gene in Acinetobacter baumannii, although the nucleotide sequence of the element was never elucidated (8). To our knowledge, the present report is the first to describe clinical isolates of E. coli with the AmpC phenotype as a result of the insertion of mobile elements. We provide sequence-based evidence that the insertion of IS elements creates new promoters which may be responsible for the up-regulation of ampC gene expression (Fig. 3). Insertion of IS911 in the promoter spacer region resulted in the possible generation of a stronger 35 sequence and a 17-bp spacer region, thereby creating a hybrid promoter sequence that more closely resembles the E. coli consensus promoter sequence. Insertion of the IS10 element between the attenuator and the start codon presumably allows ampC to be transcribed via the strong pOUT promoter of IS10 and also negates any effect from the attenuator region (28). Interestingly, the two AmpC strains identified as harboring identical IS10 sequences had unique DNA fingerprints, suggesting that the insertion site for IS10 may not be a random event.
In the present study, 13.5% of the isolates harbored a gene that correlated with acquired AmpC-type resistance, and in all strains the gene was identified as CMY-2. Although this gene was identified in 25 strains, only 7 of these strains were found to contain the wild-type ampC promoter sequence (Table 4). In two strains with sequence types containing only two changes, the change at position 28 and the change at either position +70 (type 17) or position +81 (type 52), CMY-2 is likely the major factor contributing to cefoxitin resistance. All other CMY-2-containing strains have sequence types with changes in the promoter and/or attenuator region. CMY-2-mediated resistance has been documented in Canadian isolates of Salmonella serovars (1, 26). In addition, a dramatic increase in a multidrug-resistant S. enterica serovar Newport containing the CMY-2 gene on a plasmid has been observed in the United States (6, 9, 32, 34). Furthermore, it has been shown that plasmidic CMY-2 can be transferred between Salmonella and E. coli strains isolated from food animals and humans (33). It will be important to examine the plasmids carrying the CMY-2 genes in the E. coli strains identified in this study and compare them to the CMY-2-harboring Salmonella strains to determine if similar genetic vectors are responsible for the resistance observed. That work is under way.
To our knowledge, this report describes the largest study to date on the contribution of ampC promoter mutations to cefoxitin resistance in E. coli, and the report also provides evidence that supports previous work involving mutations which affect ampC expression. However, as described above, this report describes additional mutations that affect promoter strength and that possibly result in increased gene expression. To substantiate these claims, further work is under way to examine gene expression in the strains containing the altered promoters.
As has been observed in previous studies related to nosocomial AmpC-type resistance, most strains remain genetically distinct, have resistance phenotypes that coincide with mutations in the promoter and the attenuator regions, and do not harbor acquired AmpC-type resistance (10, 20). This study supports this general observation for nosocomial E. coli isolates. Taken together, these findings suggest that E. coli AmpC-type resistance in the hospital setting is not primarily due to the dissemination of clonal strains or the spread of resistant plasmids but is due to the emergence of resistant strains in patients, possibly through antimicrobial selective pressure. Further studies focusing on antimicrobial use and resistance in patient populations will be required to substantiate this claim.
This project was partially funded by Astra Zeneca Canada.
The following individuals are members of CNISP: E. Bryce, Vancouver General Hospital, Vancouver, British Columbia; J. Conly, University of Calgary, Calgary, Alberta; J. Embil, Health Sciences Centre, Winnipeg, Manitoba; J. Embree, Health Sciences Centre, Winnipeg, Manitoba; M. Gardam, University Health Network, Toronto, Ontario; M. Gourdeau, Hôpital de l'Enfant-Jésus, Quebec City, Quebec; K. Green, Community and Hospital Infection Control Association-Canada; M. John, St. Joseph's Health Centre, London, Ontario; B. A. Henderson, Peter Lougheed Centre, Calgary, Alberta; J. Hutchinson, Health Sciences Centre, St. John's, Newfoundland; M. Ishak, Centre Hospitalier Angrignon, Verdun, Quebec; V. Roth, The Ottawa Hospital, Ottawa, Ontario; L. Johnston, Queen Elizabeth II Health Sciences Centre, Halifax, Nova Scotia; J. Langley, I.W.K. Grace Health Science Centre, Halifax, Nova Scotia; M. Loeb, Hamilton Health Sciences Corp., Hamilton, Ontario; A. Matlow, Hospital for Sick Children, Toronto, Ontario; A. McGeer, Mount Sinai Hospital, Toronto, Ontario; M. Miller, Jewish General Hospital, Montreal, Quebec; D. Moore, Montreal Children's Hospital, Montreal, Quebec; M. Mulvey, Canadian Science Centre for Human and Animal Health, Health Canada; M. Ofner-Agostini, Centre for Infectious Disease Prevention and Control, Health Canada; S. Paton, Centre for Infectious Disease Prevention and Control, Health Canada; A. Simor, Sunnybrook and Women's College Health Sciences Centre, Toronto, Ontario; G. Taylor, University of Alberta, Edmonton, Alberta; A. Khan, The Moncton Hospital, Moncton, New Brunswick; M. Vearncombe, Sunnybrook and Women's College Health Sciences Centre, Toronto, Ontario; K. Weiss, Hôpital Maisonneuve-Rosemont, Montreal, Quebec; A. Wong, Royal University Hospital, Saskatoon, Saskatchewan; and D. Zoutman, Kingston General Hospital, Kingston, Ontario.
The members of the Canadian Hospital Epidemiology Committee (CHEC) are Elizabeth Bryce, Vancouver General Hospital, Vancouver, British Columbia; John Conly, Foothills Medical Centre, Calgary, Alberta; John Embil, Health Sciences Centre, Winnipeg, Manitoba; Joanne Embree, Health Sciences Centre, Winnipeg; Michael Gardam, University Health Network, Toronto, Ontario; Gordon Dow, The Moncton Hospital, Moncton, New Brunswick; Elizabeth Henderson, Peter Lougheed Centre, Calgary; James Hutchinson, Health Sciences Centre, St. Johns, Newfoundland; Michael John, London Health Sciences Centre, London, Ontario; Lynn Johnston, Queen Elizabeth II Health Sciences Centre, Halifax, Nova Scotia; Pamela Kibsey, Victoria General Hospital, Victoria, British Columbia; Joanne Langley, I. W. K. Grace Health Science Centre, Halifax; Mark Loeb, Hamilton Health Sciences Corporation, Hamilton, Ontario; Anne Matlow, Hospital for Sick Children, Toronto; Allison McGeer, Mount Sinai Hospital, Toronto; Sophie Michaud, CHUS-Hôpital Fleurimont, Sherbrooke, Quebec; Mark Miller, SMBD-Jewish General Hospital, Montreal, Quebec; Dorothy Moore, Montreal Childrens Hospital, Montreal; Virginia Roth, The Ottawa Hospital, Ottawa, Ontario; Andrew Simor, Sunnybrook and Womens College Health Sciences Centre, Toronto; Geoffrey Taylor, University of Alberta Hospital, Edmonton, Alberta; Mary Vearncombe, Sunnybrook and Womens College Health Sciences Centre, Toronto; Alice Wong, Royal University Hospital, Saskatoon, Saskatchewan; and Dick Zoutman, Kingston General Hospital, Kingston, Ontario.
Members of the Canadian Hospital Epidemiology Committee are listed in Acknowledgments. ![]()
Members of the Canadian Nosocomial Infection Surveillance Program are listed in Acknowledgments. ![]()
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