Rafiq Ahmed - Academia.edu (original) (raw)

Papers by Rafiq Ahmed

Virology Journal, 2009

Based upon whole genome and proteome analysis, Escherichia coli O157:H7-specific bacteriophage (p... more Based upon whole genome and proteome analysis, Escherichia coli O157:H7-specific bacteriophage (phage) wV8 belongs to the new myoviral genus, "the Felix O1-like viruses" along with Salmonella phage Felix O1 and Erwinia amylovora phage φEa21-4. The genome characteristics of phage wV8 (size 88.49 kb, mol%G+C 38.9, 138 ORFs, 23 tRNAs) are very similar to those of phage Felix O1 (86.16 kb, 39.0 mol%G+C, 131 ORFs and 22 tRNAs) and, indeed most of the proteins have their closest homologs within Felix O1. Approximately one-half of the Escherichia coli O157:H7 mutants resistant to phage wV8 still serotype as O157:H7 indicating that this phage may recognize, like coliphage T4, two different surface receptors: lipopolysaccharide and, perhaps, an outer membrane protein.

PLoS ONE, 2012

Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be respon... more Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be responsible for many food borne outbreaks in North America and elsewhere. Bacteriophage therapy may prove useful for controlling this pathogen in the host, their environment and food. Bacteriophage vB_EcoS_AKFV33 (AKFV33), a T5-like phage of Siphoviridae lysed common phage types of STEC O157:H7 and not non-O157 E. coli. Moreover, STEC O157:H7 isolated from the same feedlot pen from which the phage was obtained, were highly susceptible to AKFV33. Adsorption rate constant and burst size were estimated to be 9.31610 29 ml/min and 350 PFU/infected cell, respectively. The genome of AKVF33 was 108,853 bp (38.95% G+C), containing 160 open reading frames (ORFs), 22 tRNA genes and 32 strong promoters recognized by host RNA polymerase. Of 12 ORFs without homologues to T5-like phages, 7 predicted novel proteins while others exhibited low identity (,60%) to proteins in the National Centre for Biotechnology Information database. AKVF33 also lacked the Lshaped tail fiber protein typical of T5, but was predicted to have tail fibers comprised of 2 novel proteins with low identity (37-41%) to tail fibers of E. coli phage phiEco32 of Podoviridae, a putative side tail fiber protein of a prophage from E. coli IAI39 and a conserved domain protein of E. coli MS196-1. The receptor-binding tail protein (pb5) shared an overall identify of 29-72% to that of other T5-like phages, with no region coding for more than 6 amino acids in common. Proteomic analysis identified 4 structural proteins corresponding to the capsid, major tail, tail fiber and pore-forming tail tip (pb2). The genome of AKFV33 lacked regions coding for known virulence factors, integration-related proteins or antibiotic resistance determinants. Phage AKFV33 is a unique, highly lytic STEC O157:H7-specific T5-like phage that may have considerable potential as a pre-and post-harvest biocontrol agent.

Methods in Molecular Biology, 2009

Phage typing is a rapid, economical, reliable, and reproducible technique, requiring no specializ... more Phage typing is a rapid, economical, reliable, and reproducible technique, requiring no specialized equipment, for fingerprinting disease-causing agents for epidemiological investigation and surveillance.

2006 Fifth Mexican International Conference on Artificial Intelligence, 2006

... Regression and Neural Networks Simon X. Yang 1 , Lixu Qin 1 , Frank Pollari 2 , Kathryn Dore ... more ... Regression and Neural Networks Simon X. Yang 1 , Lixu Qin 1 , Frank Pollari 2 , Kathryn Dore 2 , Aamir Fazil 3 , Rafiq Ahmed 4 , Jane Buxton 5 , Karen Grimsrud 6 , Dean Middleton 7 1 School of Engineering, University of Guelph, Guelph, ON, {syang, lqin}@uoguelph.ca. ...

Soft Computing, 2008

A clear understanding of risk factors is important to develop appropriate prevention and control ... more A clear understanding of risk factors is important to develop appropriate prevention and control strategies for infection caused by such pathogens as Salmonella Typhimurium. In this study, there are 91 risk factors that nonlinearly contribute to the Salmonella Typhimurium infection and many of them are not of significance. It is very important to automatically extract a factor subset with those important risk factors. This paper proposes a genetic algorithm for factor subset extraction in conjunction with neural and statistical classifiers to classify case and control status in Salmonella Typhimurium infection. The results show that the proposed approach is able to find an appropriate factor subset and the proposed neural classifiers outperform the traditional statistical classifiers. A statistical analysis is conducted by varying the parameters in the genetic algorithm based neural classifier to minimise the prediction error and determine the optimal system configuration.

PLoS ONE, 2012

Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be respon... more Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be responsible for many food borne outbreaks in North America and elsewhere. Bacteriophage therapy may prove useful for controlling this pathogen in the host, their environment and food. Bacteriophage vB_EcoS_AKFV33 (AKFV33), a T5-like phage of Siphoviridae lysed common phage types of STEC O157:H7 and not non-O157 E. coli. Moreover, STEC O157:H7 isolated from the same feedlot pen from which the phage was obtained, were highly susceptible to AKFV33. Adsorption rate constant and burst size were estimated to be 9.31610 29 ml/min and 350 PFU/infected cell, respectively. The genome of AKVF33 was 108,853 bp (38.95% G+C), containing 160 open reading frames (ORFs), 22 tRNA genes and 32 strong promoters recognized by host RNA polymerase. Of 12 ORFs without homologues to T5-like phages, 7 predicted novel proteins while others exhibited low identity (,60%) to proteins in the National Centre for Biotechnology Information database. AKVF33 also lacked the Lshaped tail fiber protein typical of T5, but was predicted to have tail fibers comprised of 2 novel proteins with low identity (37-41%) to tail fibers of E. coli phage phiEco32 of Podoviridae, a putative side tail fiber protein of a prophage from E. coli IAI39 and a conserved domain protein of E. coli MS196-1. The receptor-binding tail protein (pb5) shared an overall identify of 29-72% to that of other T5-like phages, with no region coding for more than 6 amino acids in common. Proteomic analysis identified 4 structural proteins corresponding to the capsid, major tail, tail fiber and pore-forming tail tip (pb2). The genome of AKFV33 lacked regions coding for known virulence factors, integration-related proteins or antibiotic resistance determinants. Phage AKFV33 is a unique, highly lytic STEC O157:H7-specific T5-like phage that may have considerable potential as a pre-and post-harvest biocontrol agent.

Journal of Clinical Microbiology, 2014

Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar En... more Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar Enteritidis for over 2 decades. However, knowledge of the genetic and evolutionary relationships between phage types is very limited, making differences difficult to interpret. Here, single nucleotide polymorphisms (SNPs) identified from whole-genome comparisons were used to determine the relationships between some S. Enteritidis phage types (PTs) commonly associated with food-borne outbreaks in the United States. Emphasis was placed on the predominant phage types PT8, PT13a, and PT13 in North America. With >89,400 bp surveyed across 98 S. Enteritidis isolates representing 14 distinct phage types, 55 informative SNPs were discovered within 23 chromosomally anchored loci. To maximize the discriminatory and evolutionary partitioning of these highly homogeneous strains, sequences comprising informative SNPs were concatenated into a single combined data matrix and subjected to phylogenetic analysis. The resultant phylogeny allocated most S. Enteritidis isolates into two distinct clades (clades I and II) and four subclades. Synapomorphic (shared and derived) sets of SNPs capable of distinguishing individual clades/subclades were identified. However, individual phage types appeared to be evolutionarily disjunct when mapped to this phylogeny, suggesting that phage typing may not be valid for making phylogenetic inferences. Furthermore, the set of SNPs identified here represents useful genetic markers for strain differentiation of more clonal S. Enteritidis strains and provides core genotypic markers for future development of a SNP typing scheme with S. Enteritidis.

Expert Systems with Applications, 2008

... Yang a , Corresponding Author Contact Information , E-mail The Corresponding Author , Frank P... more ... Yang a , Corresponding Author Contact Information , E-mail The Corresponding Author , Frank Pollari b , Kathryn Dore b , Aamir Fazil c , Rafiq ... In addition, statistical models have difficulty in dealing with highly nonlinear functions (Hajmeer & Basheer, 2003), and can have only ...

Proceedings of the 12th International Conference on Interaction Design and Children, Jun 24, 2013

Bulletin of the American Astronomical Society, May 1, 1999

The morphology of galaxies is an important issue in the large scale study of the Universe. Recent... more The morphology of galaxies is an important issue in the large scale study of the Universe. Recent pictures from the Hubble Deep Field (HDF) project and initiation of several large scale sky surveys is producing an ever growing extra-galactic database. One of the challenges facing astronomers today is in the automated identification and classification of galaxies in these databases. Fortunately, recent advances in computer vision and artificial intelligence technology can now be put to practical use in solving this problem. In this poster we describe three variation of a computational scheme to build an automatic galaxy classifier. Our concentration is on the computational scheme that utilizes shape features extracted by using computer vision techniques and a classifier that is built upon artificial neural networks. This method of classification has not been fully explored in the past. We report here a prototype model and our effort to embark on a full scale study.

The Canadian journal of infectious diseases = Journal canadien des maladies infectieuses, 2002

Verotoxigenic Escherichia coli (VTEC) was first described in Canada during the 1980s as an emergi... more Verotoxigenic Escherichia coli (VTEC) was first described in Canada during the 1980s as an emerging foodborne disease in association with morbidity and mortality in outbreaks of hemorrhagic colitis caused by E coli O157:H7. To describe the surveillance activities and epidemiological laboratory markers of VTEC that are used at the National Laboratory for Enteric Pathogens (NLEP) to investigate sporadic cases and outbreaks of E coli O157:H7 and non-O157 VTEC in Canada. Passive surveillance was conducted by obtaining data on laboratory confirmed cases of VTEC from the Provincial Laboratories of Public Health across Canada. The laboratory epidemiological markers generated for isolates of VTEC included biotyping, serotyping, phage typing, toxin detection and characterization, and molecular typing using pulsed-field gel electrophoresis. Major outbreaks of VTEC O157:H7 disease have been associated with ground beef, unpasteurized apple juice, salami and untreated water. In 1999 and 2000, a ...

The Canadian journal of infectious diseases = Journal canadien des maladies infectieuses, 2003

Salmonella infections cause gastrointestinal and systemic diseases worldwide and are the leading ... more Salmonella infections cause gastrointestinal and systemic diseases worldwide and are the leading causes of food-borne illnesses in North America (1-4). Salmonella serotype typhimurium (ST), in particular, is increasingly becoming a major public health concern because of its ability to acquire multiple resistant genes (5,6). To describe demographic, temporal and geographical distributions, and reported risk factors of nonoutbreak cases of ST reported to a surveillance system in Ontario. Descriptive analyses were performed on data on salmonellosis cases reported in Ontario between 1990 and 1998. Direct age- and sex-standardized rates were computed, and temporal trend analyses were performed using simple linear regression and a general additive model with a locally weighted regression (LOESS) smoother. The mean annual rates of infections with all Salmonella serotypes and with ST were 27 cases per 100,000 persons and 3.7 cases per 100,000 persons, respectively. Males and children under ...

The Journal of Infectious Diseases, 2004

This study investigated the burden of illness associated with 440 cases of Salmonella enterica se... more This study investigated the burden of illness associated with 440 cases of Salmonella enterica serotype Typhimurium infection identified in Canada between December 1999 and November 2000. We categorized case subjects' infections by definitive phage type 104 (DT104) and antimicrobial-resistance patterns. These variables were then investigated as risk factors for hospitalization. Hospitalization was more likely to occur among case subjects whose infections were resistant to at least ampicillin, chloramphenicol and/or kanamycin, streptomycin, sulphamethoxazole, and tetracycline (R-type AK/CSSuT; odds ratio [OR], 2.3; P=.003), compared with case subjects with AK/CSSuT-susceptible infections, and among case subjects with non-DT104 R-type AKSSuT infections (OR, 3.6; P=.005), compared with case subjects with non-DT104 AKSSuT-susceptible infections. In contrast, hospitalization rates did not differ between case subjects with DT104 infections and case subjects with non-DT104 infections or between case subjects with DT104 R-type ACSSuT infections and case subjects with DT104 ACSSuT-susceptible infections. We estimated that 57% of the hospitalizations among AK/CSSuT case subjects and 72% of the hospitalizations among non-DT104 AKSSuT case subjects were attributable to the resistance patterns of the infections.

Journal of Clinical Microbiology, 2001

In the summer of 1999, the incidence of Salmonella enterica serotype Infantis infections in Alber... more In the summer of 1999, the incidence of Salmonella enterica serotype Infantis infections in Alberta rose dramatically. Subsequent laboratory and epidemiological investigations established that an outbreak of human disease caused by this organism was occurring across Canada and was associated with pet treats for dogs produced from processed pig ears. Laboratory investigations using phage typing and pulsed-field gel electrophoresis (PFGE) established that isolates of Salmonella serotype Infantis from pig ear pet treats and humans exposed to pig ear pet treats comprised a well-defined subset of all isolates analyzed. Of the 53 subtypes of Salmonella serotype Infantis obtained around the time of the outbreak as defined by PFGE and phage typing, only 6 subtypes were associated with both human infection and isolation from pig ears. Together with information from epidemiological studies, these investigations established pig ear pet treats as the cause of the Salmonella serotype Infantis outbreak. The results are consistent with a model in which contaminated pig ear pet treats constitute a long-term, continuing vehicle for infection of the human population rather than causing temporally delimited point-source outbreaks. During the course of this outbreak, several other Salmonella serotypes were also isolated from pet treats, suggesting these products may be an important source of enteric infection in both humans and dogs. Though isolates of Salmonella serotypes other than Salmonella serotype Infantis from pet treats were also subjected to PFGE and phage typing, no link with human disease could be definitively established, and the contribution of pig ear pet treats to human disease remains unclear. Elimination of bacterial contamination from pet treats is required to reduce the risk of infection from these products.

Journal of Clinical Microbiology, 2003

Resistance to the extended-spectrum cephalosporins can occur in Salmonella species via the produc... more Resistance to the extended-spectrum cephalosporins can occur in Salmonella species via the production of extended-spectrum and AmpC ␤-lactamases. We describe human infections with Salmonella enterica serotype Newport phage type 14 strains resistant to ceftazidime (CAZ) and cefoxitin (FOX) related to the handling of pet treats containing dried beef. These strains were isolated from five patients in Calgary, Alberta, Canada, during 2002 and were compared to a strain cultured from a commercial pet treat present at the property of one of the patients. The strains were resistant to FOX, CAZ, cefpodoxime, ampicillin, and chloramphenicol; intermediate resistant to ceftriaxone and cefotaxime; and sensitive to the aminoglycosides, ciprofloxacin, cefepime, and imipenem. Isoelectric focusing, multiplex PCR, and sequencing of the amplicons showed that all strains produced the plasmid-encoded AmpC ␤-lactamase, CMY-2. Restriction analysis of plasmid DNA following transformation demonstrated that bla CMY-2 was encoded on an approximately 140-kb plasmid. Pulsed-field gel electrophoresis showed the human and pet treat Salmonella strains to be highly related. This study is the first to implicate the transfer of multidrug-resistant Salmonella species through the handling of commercial pet treats containing animal products. In addition to documenting the first cases of human infection caused by CMY-2-producing S. enterica serotype Newport strains in Canada, this study illustrates the necessity of rapid and accurate laboratory-based surveillance in the identification of novel types of antimicrobial resistance.

Journal of Clinical Microbiology, 2003

Salmonella enterica subsp. enterica serotype Enteritidis is not readily subtyped beyond the level... more Salmonella enterica subsp. enterica serotype Enteritidis is not readily subtyped beyond the level of phage type (PT). A recently developed method for ribotyping of this organism, which uses a mixture of PstI and SphI (PS) for restriction of DNA (PS ribotyping), has proved useful for further subtyping of a number of PTs of this organism, including PT 4. However, it has not been extensively tested with PT 8. In the present study the PS ribotyping method was used to investigate outbreaks of both S. enterica serotype Enteritidis PT 4 and PT 8 and provided subtyping data that were consistent with information obtained from epidemiologic investigations. The method proved to be more discriminatory than phage typing and pulsed-field gel electrophoresis (PFGE) combined and was useful for investigating a pseudo-outbreak involving isolates that had identical PTs and PFGE types but that could not be linked epidemiologically. Several PS ribotypes were found within the cluster of isolates indistinguishable by other subtyping methods, confirming the epidemiologic findings. Although the PS ribotyping method proved to have a superior discriminatory ability in resolving clusters, it did not have high enough throughput for use in outbreak investigations. This method has therefore been adapted for use in automated ribotyping with a RiboPrinter, and the results were compared with those obtained by manual ribotyping. Both methods produce equivalent results and are useful for obtaining epidemiologically relevant subtyping data for S. enterica serotype Enteritidis, including PT 8 strains not extensively tested previously.

Journal of Clinical Microbiology, 2011

Due to a highly homogeneous genetic composition, the subtyping of Salmonella enterica serovar Ent... more Due to a highly homogeneous genetic composition, the subtyping of Salmonella enterica serovar Enteritidis strains to an epidemiologically relevant level remains intangible for pulsed-field gel electrophoresis (PFGE). We reported previously on a highly discriminatory PFGE-based subtyping scheme for S. enterica serovar Enteritidis that relies on a single combined cluster analysis of multiple restriction enzymes. However, the ability of a subtyping method to correctly infer genetic relatedness among outbreak strains is also essential for effective molecular epidemiological traceback. In this study, genetic and phylogenetic analyses were performed to assess whether concatenated enzyme methods can cluster closely related salmonellae into epidemiologically relevant hierarchies. PFGE profiles were generated by use of six restriction enzymes (XbaI, BlnI, SpeI, SfiI, PacI, and NotI) for 74 strains each of S. enterica serovar Enteritidis and S. enterica serovar Typhimurium. Correlation analysis of Dice similarity coefficients for all pairwise strain comparisons underscored the importance of combining multiple enzymes for the accurate assignment of genetic relatedness among Salmonella strains. The mean correlation increased from 81% and 41% for single-enzyme PFGE up to 99% and 96% for five-enzyme combined PFGE for S. enterica serovar Enteritidis and S. enterica serovar Typhimurium strains, respectively. Data regressions approached 100% correlation among Dice similarities for S. enterica serovar Enteritidis and S. enterica serovar Typhimurium strains when a minimum of six enzymes were concatenated. Phylogenetic congruence measures singled out XbaI, BlnI, SfiI, and PacI as most concordant for S. enterica serovar Enteritidis, while XbaI, BlnI, and SpeI were most concordant among S. enterica serovar Typhimurium strains. Together, these data indicate that PFGE coupled with sufficient enzyme numbers and combinations is capable of discerning accurate genetic relationships among Salmonella serovars comprising highly homogeneous strain complexes.

Applied and Environmental Microbiology, 2014

The development and implementation of effective antimicrobial interventions by the beef processin... more The development and implementation of effective antimicrobial interventions by the beef processing industry in the United States have dramatically reduced the incidence of beef trim contamination by Escherichia coli O157:H7. However, individual processing plants still experience sporadic peaks in contamination rates where multiple E. coli O157:H7-positive lots are clustered in a short time frame. These peaks have been referred to as "high event periods" (HEP) of contamination. The results reported here detail the characterization of E. coli O157:H7 isolates from 21 HEP across multiple companies and processing plants to gain insight regarding the mechanisms causing these incidents. Strain genotypes were determined by pulsed-field gel electrophoresis, and isolates were investigated for characteristics linking them to human illness. Through these analyses, it was determined that individual HEP show little to no diversity in strain genotypes. Hence, each HEP has one strain type that makes up most, if not all, of the contamination. This is shown to differ from the genotypic diversity of E. coli O157:H7 found on the hides of cattle entering processing plants. In addition, it was found that a large proportion (81%) of HEP are caused by strain types associated with human illness. These results pose a potential challenge to the current model for finished product contamination during beef processing.

Journal of Clinical Microbiology, Jun 1, 2000

A major Canada-wide outbreak of gastroenteritis due to Salmonella enterica serotype Enteritidis p... more A major Canada-wide outbreak of gastroenteritis due to Salmonella enterica serotype Enteritidis phage type (PT) 8 occurred in 1998, and this was traced to contaminated cheese in a commercial lunch pack product. Phage typing and pulsed-field gel electrophoresis linked the clinical and cheese isolates of serotype Enteritidis but failed to differentiate outbreak from nonoutbreak PT 8 strains. Further differentiation was made by biotyping based on melibiose fermentation.

Canadian Journal of Infectious Diseases, 2002

Virology Journal, 2009

Based upon whole genome and proteome analysis, Escherichia coli O157:H7-specific bacteriophage (p... more Based upon whole genome and proteome analysis, Escherichia coli O157:H7-specific bacteriophage (phage) wV8 belongs to the new myoviral genus, "the Felix O1-like viruses" along with Salmonella phage Felix O1 and Erwinia amylovora phage φEa21-4. The genome characteristics of phage wV8 (size 88.49 kb, mol%G+C 38.9, 138 ORFs, 23 tRNAs) are very similar to those of phage Felix O1 (86.16 kb, 39.0 mol%G+C, 131 ORFs and 22 tRNAs) and, indeed most of the proteins have their closest homologs within Felix O1. Approximately one-half of the Escherichia coli O157:H7 mutants resistant to phage wV8 still serotype as O157:H7 indicating that this phage may recognize, like coliphage T4, two different surface receptors: lipopolysaccharide and, perhaps, an outer membrane protein.

PLoS ONE, 2012

Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be respon... more Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be responsible for many food borne outbreaks in North America and elsewhere. Bacteriophage therapy may prove useful for controlling this pathogen in the host, their environment and food. Bacteriophage vB_EcoS_AKFV33 (AKFV33), a T5-like phage of Siphoviridae lysed common phage types of STEC O157:H7 and not non-O157 E. coli. Moreover, STEC O157:H7 isolated from the same feedlot pen from which the phage was obtained, were highly susceptible to AKFV33. Adsorption rate constant and burst size were estimated to be 9.31610 29 ml/min and 350 PFU/infected cell, respectively. The genome of AKVF33 was 108,853 bp (38.95% G+C), containing 160 open reading frames (ORFs), 22 tRNA genes and 32 strong promoters recognized by host RNA polymerase. Of 12 ORFs without homologues to T5-like phages, 7 predicted novel proteins while others exhibited low identity (,60%) to proteins in the National Centre for Biotechnology Information database. AKVF33 also lacked the Lshaped tail fiber protein typical of T5, but was predicted to have tail fibers comprised of 2 novel proteins with low identity (37-41%) to tail fibers of E. coli phage phiEco32 of Podoviridae, a putative side tail fiber protein of a prophage from E. coli IAI39 and a conserved domain protein of E. coli MS196-1. The receptor-binding tail protein (pb5) shared an overall identify of 29-72% to that of other T5-like phages, with no region coding for more than 6 amino acids in common. Proteomic analysis identified 4 structural proteins corresponding to the capsid, major tail, tail fiber and pore-forming tail tip (pb2). The genome of AKFV33 lacked regions coding for known virulence factors, integration-related proteins or antibiotic resistance determinants. Phage AKFV33 is a unique, highly lytic STEC O157:H7-specific T5-like phage that may have considerable potential as a pre-and post-harvest biocontrol agent.

Methods in Molecular Biology, 2009

Phage typing is a rapid, economical, reliable, and reproducible technique, requiring no specializ... more Phage typing is a rapid, economical, reliable, and reproducible technique, requiring no specialized equipment, for fingerprinting disease-causing agents for epidemiological investigation and surveillance.

2006 Fifth Mexican International Conference on Artificial Intelligence, 2006

... Regression and Neural Networks Simon X. Yang 1 , Lixu Qin 1 , Frank Pollari 2 , Kathryn Dore ... more ... Regression and Neural Networks Simon X. Yang 1 , Lixu Qin 1 , Frank Pollari 2 , Kathryn Dore 2 , Aamir Fazil 3 , Rafiq Ahmed 4 , Jane Buxton 5 , Karen Grimsrud 6 , Dean Middleton 7 1 School of Engineering, University of Guelph, Guelph, ON, {syang, lqin}@uoguelph.ca. ...

Soft Computing, 2008

A clear understanding of risk factors is important to develop appropriate prevention and control ... more A clear understanding of risk factors is important to develop appropriate prevention and control strategies for infection caused by such pathogens as Salmonella Typhimurium. In this study, there are 91 risk factors that nonlinearly contribute to the Salmonella Typhimurium infection and many of them are not of significance. It is very important to automatically extract a factor subset with those important risk factors. This paper proposes a genetic algorithm for factor subset extraction in conjunction with neural and statistical classifiers to classify case and control status in Salmonella Typhimurium infection. The results show that the proposed approach is able to find an appropriate factor subset and the proposed neural classifiers outperform the traditional statistical classifiers. A statistical analysis is conducted by varying the parameters in the genetic algorithm based neural classifier to minimise the prediction error and determine the optimal system configuration.

PLoS ONE, 2012

Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be respon... more Despite multiple control measures, Escherichia coli O157:H7 (STEC O157:H7) continues to be responsible for many food borne outbreaks in North America and elsewhere. Bacteriophage therapy may prove useful for controlling this pathogen in the host, their environment and food. Bacteriophage vB_EcoS_AKFV33 (AKFV33), a T5-like phage of Siphoviridae lysed common phage types of STEC O157:H7 and not non-O157 E. coli. Moreover, STEC O157:H7 isolated from the same feedlot pen from which the phage was obtained, were highly susceptible to AKFV33. Adsorption rate constant and burst size were estimated to be 9.31610 29 ml/min and 350 PFU/infected cell, respectively. The genome of AKVF33 was 108,853 bp (38.95% G+C), containing 160 open reading frames (ORFs), 22 tRNA genes and 32 strong promoters recognized by host RNA polymerase. Of 12 ORFs without homologues to T5-like phages, 7 predicted novel proteins while others exhibited low identity (,60%) to proteins in the National Centre for Biotechnology Information database. AKVF33 also lacked the Lshaped tail fiber protein typical of T5, but was predicted to have tail fibers comprised of 2 novel proteins with low identity (37-41%) to tail fibers of E. coli phage phiEco32 of Podoviridae, a putative side tail fiber protein of a prophage from E. coli IAI39 and a conserved domain protein of E. coli MS196-1. The receptor-binding tail protein (pb5) shared an overall identify of 29-72% to that of other T5-like phages, with no region coding for more than 6 amino acids in common. Proteomic analysis identified 4 structural proteins corresponding to the capsid, major tail, tail fiber and pore-forming tail tip (pb2). The genome of AKFV33 lacked regions coding for known virulence factors, integration-related proteins or antibiotic resistance determinants. Phage AKFV33 is a unique, highly lytic STEC O157:H7-specific T5-like phage that may have considerable potential as a pre-and post-harvest biocontrol agent.

Journal of Clinical Microbiology, 2014

Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar En... more Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar Enteritidis for over 2 decades. However, knowledge of the genetic and evolutionary relationships between phage types is very limited, making differences difficult to interpret. Here, single nucleotide polymorphisms (SNPs) identified from whole-genome comparisons were used to determine the relationships between some S. Enteritidis phage types (PTs) commonly associated with food-borne outbreaks in the United States. Emphasis was placed on the predominant phage types PT8, PT13a, and PT13 in North America. With >89,400 bp surveyed across 98 S. Enteritidis isolates representing 14 distinct phage types, 55 informative SNPs were discovered within 23 chromosomally anchored loci. To maximize the discriminatory and evolutionary partitioning of these highly homogeneous strains, sequences comprising informative SNPs were concatenated into a single combined data matrix and subjected to phylogenetic analysis. The resultant phylogeny allocated most S. Enteritidis isolates into two distinct clades (clades I and II) and four subclades. Synapomorphic (shared and derived) sets of SNPs capable of distinguishing individual clades/subclades were identified. However, individual phage types appeared to be evolutionarily disjunct when mapped to this phylogeny, suggesting that phage typing may not be valid for making phylogenetic inferences. Furthermore, the set of SNPs identified here represents useful genetic markers for strain differentiation of more clonal S. Enteritidis strains and provides core genotypic markers for future development of a SNP typing scheme with S. Enteritidis.

Expert Systems with Applications, 2008

... Yang a , Corresponding Author Contact Information , E-mail The Corresponding Author , Frank P... more ... Yang a , Corresponding Author Contact Information , E-mail The Corresponding Author , Frank Pollari b , Kathryn Dore b , Aamir Fazil c , Rafiq ... In addition, statistical models have difficulty in dealing with highly nonlinear functions (Hajmeer & Basheer, 2003), and can have only ...

Proceedings of the 12th International Conference on Interaction Design and Children, Jun 24, 2013

Bulletin of the American Astronomical Society, May 1, 1999

The morphology of galaxies is an important issue in the large scale study of the Universe. Recent... more The morphology of galaxies is an important issue in the large scale study of the Universe. Recent pictures from the Hubble Deep Field (HDF) project and initiation of several large scale sky surveys is producing an ever growing extra-galactic database. One of the challenges facing astronomers today is in the automated identification and classification of galaxies in these databases. Fortunately, recent advances in computer vision and artificial intelligence technology can now be put to practical use in solving this problem. In this poster we describe three variation of a computational scheme to build an automatic galaxy classifier. Our concentration is on the computational scheme that utilizes shape features extracted by using computer vision techniques and a classifier that is built upon artificial neural networks. This method of classification has not been fully explored in the past. We report here a prototype model and our effort to embark on a full scale study.

The Canadian journal of infectious diseases = Journal canadien des maladies infectieuses, 2002

Verotoxigenic Escherichia coli (VTEC) was first described in Canada during the 1980s as an emergi... more Verotoxigenic Escherichia coli (VTEC) was first described in Canada during the 1980s as an emerging foodborne disease in association with morbidity and mortality in outbreaks of hemorrhagic colitis caused by E coli O157:H7. To describe the surveillance activities and epidemiological laboratory markers of VTEC that are used at the National Laboratory for Enteric Pathogens (NLEP) to investigate sporadic cases and outbreaks of E coli O157:H7 and non-O157 VTEC in Canada. Passive surveillance was conducted by obtaining data on laboratory confirmed cases of VTEC from the Provincial Laboratories of Public Health across Canada. The laboratory epidemiological markers generated for isolates of VTEC included biotyping, serotyping, phage typing, toxin detection and characterization, and molecular typing using pulsed-field gel electrophoresis. Major outbreaks of VTEC O157:H7 disease have been associated with ground beef, unpasteurized apple juice, salami and untreated water. In 1999 and 2000, a ...

The Canadian journal of infectious diseases = Journal canadien des maladies infectieuses, 2003

Salmonella infections cause gastrointestinal and systemic diseases worldwide and are the leading ... more Salmonella infections cause gastrointestinal and systemic diseases worldwide and are the leading causes of food-borne illnesses in North America (1-4). Salmonella serotype typhimurium (ST), in particular, is increasingly becoming a major public health concern because of its ability to acquire multiple resistant genes (5,6). To describe demographic, temporal and geographical distributions, and reported risk factors of nonoutbreak cases of ST reported to a surveillance system in Ontario. Descriptive analyses were performed on data on salmonellosis cases reported in Ontario between 1990 and 1998. Direct age- and sex-standardized rates were computed, and temporal trend analyses were performed using simple linear regression and a general additive model with a locally weighted regression (LOESS) smoother. The mean annual rates of infections with all Salmonella serotypes and with ST were 27 cases per 100,000 persons and 3.7 cases per 100,000 persons, respectively. Males and children under ...

The Journal of Infectious Diseases, 2004

This study investigated the burden of illness associated with 440 cases of Salmonella enterica se... more This study investigated the burden of illness associated with 440 cases of Salmonella enterica serotype Typhimurium infection identified in Canada between December 1999 and November 2000. We categorized case subjects' infections by definitive phage type 104 (DT104) and antimicrobial-resistance patterns. These variables were then investigated as risk factors for hospitalization. Hospitalization was more likely to occur among case subjects whose infections were resistant to at least ampicillin, chloramphenicol and/or kanamycin, streptomycin, sulphamethoxazole, and tetracycline (R-type AK/CSSuT; odds ratio [OR], 2.3; P=.003), compared with case subjects with AK/CSSuT-susceptible infections, and among case subjects with non-DT104 R-type AKSSuT infections (OR, 3.6; P=.005), compared with case subjects with non-DT104 AKSSuT-susceptible infections. In contrast, hospitalization rates did not differ between case subjects with DT104 infections and case subjects with non-DT104 infections or between case subjects with DT104 R-type ACSSuT infections and case subjects with DT104 ACSSuT-susceptible infections. We estimated that 57% of the hospitalizations among AK/CSSuT case subjects and 72% of the hospitalizations among non-DT104 AKSSuT case subjects were attributable to the resistance patterns of the infections.

Journal of Clinical Microbiology, 2001

In the summer of 1999, the incidence of Salmonella enterica serotype Infantis infections in Alber... more In the summer of 1999, the incidence of Salmonella enterica serotype Infantis infections in Alberta rose dramatically. Subsequent laboratory and epidemiological investigations established that an outbreak of human disease caused by this organism was occurring across Canada and was associated with pet treats for dogs produced from processed pig ears. Laboratory investigations using phage typing and pulsed-field gel electrophoresis (PFGE) established that isolates of Salmonella serotype Infantis from pig ear pet treats and humans exposed to pig ear pet treats comprised a well-defined subset of all isolates analyzed. Of the 53 subtypes of Salmonella serotype Infantis obtained around the time of the outbreak as defined by PFGE and phage typing, only 6 subtypes were associated with both human infection and isolation from pig ears. Together with information from epidemiological studies, these investigations established pig ear pet treats as the cause of the Salmonella serotype Infantis outbreak. The results are consistent with a model in which contaminated pig ear pet treats constitute a long-term, continuing vehicle for infection of the human population rather than causing temporally delimited point-source outbreaks. During the course of this outbreak, several other Salmonella serotypes were also isolated from pet treats, suggesting these products may be an important source of enteric infection in both humans and dogs. Though isolates of Salmonella serotypes other than Salmonella serotype Infantis from pet treats were also subjected to PFGE and phage typing, no link with human disease could be definitively established, and the contribution of pig ear pet treats to human disease remains unclear. Elimination of bacterial contamination from pet treats is required to reduce the risk of infection from these products.

Journal of Clinical Microbiology, 2003

Resistance to the extended-spectrum cephalosporins can occur in Salmonella species via the produc... more Resistance to the extended-spectrum cephalosporins can occur in Salmonella species via the production of extended-spectrum and AmpC ␤-lactamases. We describe human infections with Salmonella enterica serotype Newport phage type 14 strains resistant to ceftazidime (CAZ) and cefoxitin (FOX) related to the handling of pet treats containing dried beef. These strains were isolated from five patients in Calgary, Alberta, Canada, during 2002 and were compared to a strain cultured from a commercial pet treat present at the property of one of the patients. The strains were resistant to FOX, CAZ, cefpodoxime, ampicillin, and chloramphenicol; intermediate resistant to ceftriaxone and cefotaxime; and sensitive to the aminoglycosides, ciprofloxacin, cefepime, and imipenem. Isoelectric focusing, multiplex PCR, and sequencing of the amplicons showed that all strains produced the plasmid-encoded AmpC ␤-lactamase, CMY-2. Restriction analysis of plasmid DNA following transformation demonstrated that bla CMY-2 was encoded on an approximately 140-kb plasmid. Pulsed-field gel electrophoresis showed the human and pet treat Salmonella strains to be highly related. This study is the first to implicate the transfer of multidrug-resistant Salmonella species through the handling of commercial pet treats containing animal products. In addition to documenting the first cases of human infection caused by CMY-2-producing S. enterica serotype Newport strains in Canada, this study illustrates the necessity of rapid and accurate laboratory-based surveillance in the identification of novel types of antimicrobial resistance.

Journal of Clinical Microbiology, 2003

Salmonella enterica subsp. enterica serotype Enteritidis is not readily subtyped beyond the level... more Salmonella enterica subsp. enterica serotype Enteritidis is not readily subtyped beyond the level of phage type (PT). A recently developed method for ribotyping of this organism, which uses a mixture of PstI and SphI (PS) for restriction of DNA (PS ribotyping), has proved useful for further subtyping of a number of PTs of this organism, including PT 4. However, it has not been extensively tested with PT 8. In the present study the PS ribotyping method was used to investigate outbreaks of both S. enterica serotype Enteritidis PT 4 and PT 8 and provided subtyping data that were consistent with information obtained from epidemiologic investigations. The method proved to be more discriminatory than phage typing and pulsed-field gel electrophoresis (PFGE) combined and was useful for investigating a pseudo-outbreak involving isolates that had identical PTs and PFGE types but that could not be linked epidemiologically. Several PS ribotypes were found within the cluster of isolates indistinguishable by other subtyping methods, confirming the epidemiologic findings. Although the PS ribotyping method proved to have a superior discriminatory ability in resolving clusters, it did not have high enough throughput for use in outbreak investigations. This method has therefore been adapted for use in automated ribotyping with a RiboPrinter, and the results were compared with those obtained by manual ribotyping. Both methods produce equivalent results and are useful for obtaining epidemiologically relevant subtyping data for S. enterica serotype Enteritidis, including PT 8 strains not extensively tested previously.

Journal of Clinical Microbiology, 2011

Due to a highly homogeneous genetic composition, the subtyping of Salmonella enterica serovar Ent... more Due to a highly homogeneous genetic composition, the subtyping of Salmonella enterica serovar Enteritidis strains to an epidemiologically relevant level remains intangible for pulsed-field gel electrophoresis (PFGE). We reported previously on a highly discriminatory PFGE-based subtyping scheme for S. enterica serovar Enteritidis that relies on a single combined cluster analysis of multiple restriction enzymes. However, the ability of a subtyping method to correctly infer genetic relatedness among outbreak strains is also essential for effective molecular epidemiological traceback. In this study, genetic and phylogenetic analyses were performed to assess whether concatenated enzyme methods can cluster closely related salmonellae into epidemiologically relevant hierarchies. PFGE profiles were generated by use of six restriction enzymes (XbaI, BlnI, SpeI, SfiI, PacI, and NotI) for 74 strains each of S. enterica serovar Enteritidis and S. enterica serovar Typhimurium. Correlation analysis of Dice similarity coefficients for all pairwise strain comparisons underscored the importance of combining multiple enzymes for the accurate assignment of genetic relatedness among Salmonella strains. The mean correlation increased from 81% and 41% for single-enzyme PFGE up to 99% and 96% for five-enzyme combined PFGE for S. enterica serovar Enteritidis and S. enterica serovar Typhimurium strains, respectively. Data regressions approached 100% correlation among Dice similarities for S. enterica serovar Enteritidis and S. enterica serovar Typhimurium strains when a minimum of six enzymes were concatenated. Phylogenetic congruence measures singled out XbaI, BlnI, SfiI, and PacI as most concordant for S. enterica serovar Enteritidis, while XbaI, BlnI, and SpeI were most concordant among S. enterica serovar Typhimurium strains. Together, these data indicate that PFGE coupled with sufficient enzyme numbers and combinations is capable of discerning accurate genetic relationships among Salmonella serovars comprising highly homogeneous strain complexes.

Applied and Environmental Microbiology, 2014

The development and implementation of effective antimicrobial interventions by the beef processin... more The development and implementation of effective antimicrobial interventions by the beef processing industry in the United States have dramatically reduced the incidence of beef trim contamination by Escherichia coli O157:H7. However, individual processing plants still experience sporadic peaks in contamination rates where multiple E. coli O157:H7-positive lots are clustered in a short time frame. These peaks have been referred to as "high event periods" (HEP) of contamination. The results reported here detail the characterization of E. coli O157:H7 isolates from 21 HEP across multiple companies and processing plants to gain insight regarding the mechanisms causing these incidents. Strain genotypes were determined by pulsed-field gel electrophoresis, and isolates were investigated for characteristics linking them to human illness. Through these analyses, it was determined that individual HEP show little to no diversity in strain genotypes. Hence, each HEP has one strain type that makes up most, if not all, of the contamination. This is shown to differ from the genotypic diversity of E. coli O157:H7 found on the hides of cattle entering processing plants. In addition, it was found that a large proportion (81%) of HEP are caused by strain types associated with human illness. These results pose a potential challenge to the current model for finished product contamination during beef processing.

Journal of Clinical Microbiology, Jun 1, 2000

A major Canada-wide outbreak of gastroenteritis due to Salmonella enterica serotype Enteritidis p... more A major Canada-wide outbreak of gastroenteritis due to Salmonella enterica serotype Enteritidis phage type (PT) 8 occurred in 1998, and this was traced to contaminated cheese in a commercial lunch pack product. Phage typing and pulsed-field gel electrophoresis linked the clinical and cheese isolates of serotype Enteritidis but failed to differentiate outbreak from nonoutbreak PT 8 strains. Further differentiation was made by biotyping based on melibiose fermentation.

Canadian Journal of Infectious Diseases, 2002