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author:("conll, John M")
1.  An assessment of the efficacy of searching in biomedical databases beyond MEDLINE in identifying studies for a systematic review on ward closures as an infection control intervention to control outbreaks 
Systematic Reviews  2014;3:135.
Background
The purpose of our study is to determine the value and efficacy of searching biomedical databases beyond MEDLINE for systematic reviews.
Methods
We analyzed the results from a systematic review conducted by the authors and others on ward closure as an infection control practice. Ovid MEDLINE including In-Process & Other Non-Indexed Citations, Ovid Embase, CINAHL Plus, LILACS, and IndMED were systematically searched for articles of any study type discussing ward closure, as were bibliographies of selected articles and recent infection control conference abstracts. Search results were tracked, recorded, and analyzed using a relative recall method. The sensitivity of searching in each database was calculated.
Results
Two thousand ninety-five unique citations were identified and screened for inclusion in the systematic review: 2,060 from database searching and 35 from hand searching and other sources. Ninety-seven citations were included in the final review. MEDLINE and Embase searches each retrieved 80 of the 97 articles included, only 4 articles from each database were unique. The CINAHL search retrieved 35 included articles, and 4 were unique. The IndMED and LILACS searches did not retrieve any included articles, although 75 of the included articles were indexed in LILACS. The true value of using regional databases, particularly LILACS, may lie with the ability to search in the language spoken in the region. Eight articles were found only through hand searching.
Conclusions
Identifying studies for a systematic review where the research is observational is complex. The value each individual study contributes to the review cannot be accurately measured. Consequently, we could not determine the value of results found from searching beyond MEDLINE, Embase, and CINAHL with accuracy. However, hand searching for serendipitous retrieval remains an important aspect due to indexing and keyword challenges inherent in this literature.
doi:10.1186/2046-4053-3-135
PMCID: PMC4231196  PMID: 25387523
Bibliographic databases; MEDLINE; Embase; Information retrieval; Bibliometrics; Sensitivity; Specificity; Systematic review
3.  Antimicrobial resistance programs in Canada 1995-2010: a critical evaluation 
Background
In Canada, systematic efforts for controlling antibiotic resistance began in 1997 following a national Consensus Conference. The Canadian strategy produced 27 recommendations, one of which was the formation of the Canadian Committee on Antibiotic Resistance (CCAR). In addition several other organizations began working on a national or provincial basis over the ensuing years on one or more of the 3 identified core areas of the strategy. Critical evaluation of the major programs within Canada which focused on antimicrobial resistance and the identified core components has not been previously conducted.
Findings
Data was collected from multiple sources to determine the components of four major AMR programs that were considered national based on their scope or in the delivery of their mandates. Assessment of program components was adapted from the report from the International Forum on Antibiotic Resistance colloquium. Most of the programs used similar tools but only the Do Bugs Need Drugs Program (DBND) had components directed towards day cares and schools. Surveillance programs for antimicrobial resistant pathogens have limitations and/or significant sources of bias. Overall, there has been a 25.3% decrease in oral antimicrobial prescriptions in Canada since 1995, mainly due to decreases in β lactams, sulphonamides and tetracyclines in temporal association with multiple programs with the most comprehensive and sustained national programs being CCAR and DBND.
Conclusions
Although there has been a substantial decrease in oral antimicrobial prescriptions in Canada since 1995, there remains a lack of leadership and co-ordination of antimicrobial resistance activities.
doi:10.1186/2047-2994-1-10
PMCID: PMC3436608  PMID: 22958783
antimicrobial resistance; stewardship; antibiotic; scripts; prescribing; population; program components
8.  Novel Staphylococcal Cassette Chromosome mec Type, Tentatively Designated Type VIII, Harboring Class A mec and Type 4 ccr Gene Complexes in a Canadian Epidemic Strain of Methicillin-Resistant Staphylococcus aureus▿  
Staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic element characterized by flanking terminal direct and, in most cases, inverted repeat sequences, the mec and ccr gene complexes, and their surrounding DNA regions. Unique combinations of the mec and ccr gene complexes generate various SCCmec types. Six SCCmec types have been reported to date. We describe here a novel SCCmec type identified in a Canadian methicillin-resistant Staphylococcus aureus (MRSA) epidemic strain. MRSA clinical isolates were screened for known SCCmec types by multiplex and conventional PCR methods. Three phenotypically and genotypically identical MRSA clinical isolates with a pulsotype identical to CMRSA9 were identified locally and found to be nontypeable by available SCCmec typing schemes. Complete sequencing of the SCCmec element revealed a nucleotide fragment of 32,168 bp integrated at an identical chromosomal integration site (attBscc) at the 3′ end of the orfX gene. The nucleotide sequences at the chromosome-SCCmec junction regions were typical of other SCCmec types, but the element harbored a unique combination of class A mec and type 4 ccr gene complexes. Sequence recombination analysis suggested that this unique SCCmec type may be derived from homologous recombination between the previously described SCCRP62A of S. epidermidis strain RP62A and SCC composite island of S. epidermidis ATCC 12228, respectively, or via recombination of other staphylococcal strains that carry the same or similar mobile cassettes. We identified a previously undescribed type of SCCmec from isolate C10682, tentatively designated type VIII, and we provide compelling evidence supporting the ability of SCC elements to transfer horizontally or undergo recombination to generate new SCCmec types.
doi:10.1128/AAC.01118-08
PMCID: PMC2630601  PMID: 19064897
9.  Embracing ecology to limit antimicrobial resistance 
doi:10.1503/cmaj.081587
PMCID: PMC2638035  PMID: 19221342
11.  The emerging epidemoiology of VRE in Canada: Results of the CNISP Passive Reporting Network, 1994 to 1998 
OBJECTIVE:
To provide a rapid and efficient means of collecting descriptive epidemiological data on occurrences of vancomycin-resistant enterococcus (VRE) in Canada.
DESIGN AND METHODS:
Passive reporting of data on individual or cluster occurrences of VRE using a one-page surveillance form.
SETTING:
The surveillance form was periodically distributed to all Canadian Hospital Epidemiology Committee members, Community and Hospital Infection Control Association members, L'Association des professionnels pour la prevention des infections members and provincial laboratories, representing 650 health care facilities across Canada.
PATIENTS:
Patients colonized or infected with VRE within Canadian health care facilities.
RESULTS:
Until the end of 1998, 263 reports of VRE were received from 113 health care facilities in 10 provinces, comprising a total of 1315 cases of VRE, with 1246 cases colonized (94.7%), 61 infected (4.6%)and eight of unknown status. (0.6%). VRE occurrences were reported in 56% of acute care teaching facilities and 38% of acute care community facilities. All facilities of more than 800 beds reported VRE occurences compared with only 10% of facilities with less than 200 beds (r2=0.86). Medical and surgical wards accounted for 51.4% of the reported VRE occurences. Sixty-five (24.7%) reports indicated an index case was from a foreign country, with 85.2% from the United States and 14.8% from other countries. Some type of screening was conducted in 50% of the sites.
CONCLUSIONS:
A VRE passive reporting network provided a rapid and efficient means of providing data on the evolving epidemiology of VRE in Canada.
PMCID: PMC2094843  PMID: 18159364
Epidemiology; Surveillance; Vancomycin-resistant enterococcus
12.  Novel Multiplex PCR Assay for Simultaneous Identification of Community-Associated Methicillin-Resistant Staphylococcus aureus Strains USA300 and USA400 and Detection of mecA and Panton-Valentine Leukocidin Genes, with Discrimination of Staphylococcus aureus from Coagulase-Negative Staphylococci▿  
Journal of Clinical Microbiology  2007;46(3):1118-1122.
We developed a novel multiplex PCR assay for rapid identification and discrimination of the USA300 and USA400 strains and concomitant detection of Panton-Valentine leukocidin genes, with simultaneous discrimination of methicillin-resistant Staphylococcus aureus strains from methicillin-susceptible S. aureus strains, S. aureus strains from coagulase-negative staphylococci, and staphylococci from other bacteria.
doi:10.1128/JCM.01309-07
PMCID: PMC2268379  PMID: 18160447
15.  Novel Multiplex PCR Assay for Detection of the Staphylococcal Virulence Marker Panton-Valentine Leukocidin Genes and Simultaneous Discrimination of Methicillin-Susceptible from -Resistant Staphylococci 
Journal of Clinical Microbiology  2006;44(3):1141-1144.
We developed a new multiplex PCR assay for detection of Panton-Valentine leukocidin virulence genes and simultaneous discrimination of methicillin-susceptible from -resistant staphylococci. This assay is simple, rapid, and accurate and offers the potential for prompt detection of newly emerging community-associated methicillin-resistant Staphylococcus aureus.
doi:10.1128/JCM.44.3.1141-1144.2006
PMCID: PMC1393128  PMID: 16517915
17.  Novel Multiplex PCR Assay for Characterization and Concomitant Subtyping of Staphylococcal Cassette Chromosome mec Types I to V in Methicillin-Resistant Staphylococcus aureus 
Journal of Clinical Microbiology  2005;43(10):5026-5033.
Staphylococcal cassette chromosome mec (SCCmec) typing is essential for understanding the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA). SCCmec elements are currently classified into types I to V based on the nature of the mec and ccr gene complexes, and are further classified into subtypes according to their junkyard region DNA segments. Previously described traditional SCCmec PCR typing schemes require multiple primer sets and PCR experiments, while a previously published multiplex PCR assay is limited in its ability to detect recently discovered types and subtypes such as SCCmec type V and subtypes IVa, b, c, and d. We designed new sets of SCCmec type- and subtype-unique and specific primers and developed a novel multiplex PCR assay allowing for concomitant detection of the methicillin resistance (mecA gene) (also serving as an internal control) to facilitate detection and classification of all currently described SCCmec types and subtypes I, II, III, IVa, b, c, d, and V. Our assay demonstrated 100% sensitivity and specificity in accurately characterizing 54 MRSA strains belonging to the various known SCCmec types and subtypes, when compared with previously described typing methods. Further application of our assay in 453 randomly selected local clinical isolates confirmed its feasibility and practicality. This novel assay offers a rapid, simple, and feasible method for SCCmec typing of MRSA, and may serve as a useful tool for clinicians and epidemiologists in their efforts to prevent and control infections caused by this organism.
doi:10.1128/JCM.43.10.5026-5033.2005
PMCID: PMC1248471  PMID: 16207957
21.  The costs and consequences of methicillin-resistant Staphylococcus aureus infection treatments in Canada 
BACKGROUND:
A multinational randomized controlled trial has shown a trend toward early discharge of patients taking oral linezolid versus intravenous vancomycin (IV) in the treatment of methicillinresistant Staphylococcus aureus (MRSA) infections. Infection treatments resulting in shorter hospitalization durations are associated with cost savings from the hospital perspective.
OBJECTIVE:
To determine whether similar economic advantages are associated with oral linezolid, the costs and consequences of linezolid use following vancomycin IV versus the existing practice in the treatment of infections caused by MRSA were compared.
METHODS:
The charts of all patients admitted to one of three tertiary care teaching hospitals between January 1, 1997 and August 31, 2000 and treated with vancomycin IV for an active MRSA infection (skin and soft tissue only) were reviewed. Based on the vancomycin IV chart review data set and a simulated linezolid data set, the clinical consequences and the associated costs of MRSA treatment with vancomycin IV, and oral and IV forms of linezolid were quantified and compared within the framework of a cost-consequence analysis.
RESULTS:
Patients treated with oral and IV forms of linezolid compared with the existing practice had a shorter length of stay and required fewer home IV care services, which resulted in a cost savings of $750 (2001 values) to the Canadian health care perspective.
CONCLUSIONS:
The estimated cost savings associated with linezolid use not only offset the higher acquisition cost of the anti-infective, but may be substantial to health care systems across Canada, especially as the incidence of MRSA continues to rise.
PMCID: PMC2094976  PMID: 18159495
Consequences; Costs; Linezolid; Methicillin-resistant Staphylococcus aureus; MRSA; Vancomycin
24.  New Quadriplex PCR Assay for Detection of Methicillin and Mupirocin Resistance and Simultaneous Discrimination of Staphylococcus aureus from Coagulase-Negative Staphylococci 
Journal of Clinical Microbiology  2004;42(11):4947-4955.
Major challenges in diagnostic molecular microbiology are to develop a simple assay to distinguish Staphylococcus aureus from the less virulent but clinically important coagulase-negative staphylococci (CoNS) and to simultaneously determine their antibiotic resistance profiles. Multiplex PCR assays have been developed for the detection of methicillin- and mupirocin-resistant S. aureus and CoNS but not for the simultaneous discrimination of S. aureus from CoNS. We designed a new set of Staphylococcus genus-specific primers and developed a novel quadriplex PCR assay targeting the 16S rRNA (Staphylococcus genus specific), nuc (S. aureus species specific), mecA (a determinant of methicillin resistance), and mupA (a determinant of mupirocin resistance) genes to identify most staphylococci, to discriminate S. aureus from CoNS and other bacteria, and to simultaneously detect methicillin and mupirocin resistance. Validation of the assay with 96 ATCC control strains and 323 previously characterized clinical isolates, including methicillin- and mupirocin-sensitive and -resistant S. aureus and CoNS isolates and other bacteria, demonstrated 100% sensitivity, specificity, and accuracy. This assay represents a simple, rapid, accurate, and reliable approach for the detection of methicillin- and mupirocin-resistant staphylococci and offers the hope of preventing their widespread dissemination through early and reliable detection.
doi:10.1128/JCM.42.11.4947-4955.2004
PMCID: PMC525205  PMID: 15528678

Results 1-25 (48)