Catherine D Carrillo

Canadian Food Inspection Agency · Science Branch

The timely identification and characterization of foodborne bacteria for risk assessment purposes is a key operation in outbreak investigations. Current methods require several days and/or provide low-resolution characterization. Here we describe a whole-genome-sequencing (WGS) approach (GeneSippr) enabling same-day identification of colony isolate...

Bacterial pathogens, such as Shiga toxin-producing Escherichia coli (STEC) and Shigella spp., are important causes of foodborne illness internationally. Recovery of these organisms from foods is critical for food safety investigations to support attribution of illnesses to specific food commodities; however, isolation of bacterial cultures can be c...

Shiga toxin (Stx) is the definitive virulence factor of Shiga toxin-producing Escherichia coli (STEC). Stx variants are currently organised into a taxonomic system of three Stx1 (a,c,d) and seven Stx2 (a,b,c,d,e,f,g) subtypes. In this study, seven STEC isolates from food and clinical samples possessing stx2 sequences that do not fit current Shiga t...

Shiga toxin–producing Escherichia coli (STEC) O157:H7/nonmotile and some non-O157 STEC strains are foodborne pathogens. In response to pork-associated O157 STEC outbreaks in Canada, we investigated the occurrence of STEC in Canadian retail raw ground pork during the period of 1 November 2014 to 31 March 2016. Isolated STEC strains were characterize...

Bacterial carbapenem resistance is a major public health concern since these antimicrobials are often the last resort to treat serious human infections. To evaluate methodologies for detection of carbapenem resistance, carbapenem-tolerant bacteria were isolated from wastewater treatment plants in Toronto, Ottawa, and Arnprior, Ontario. A total of 1...

Background Despite the potential for dissemination of antimicrobial resistance (AMR) through food and food production, there are few studies of the prevalence of AMR organisms (AROs) in various agri-food products. Sequencing technologies are increasingly being used to track the spread of AMR genes (ARGs) in bacteria, and metagenomics has the potent...

Metagenomics analysis of foods has the potential to provide comprehensive data on the presence and prevalence of antimicrobial resistance (AMR) genes in the microbiome of foods. However, AMR genes are generally present in low abundance compared to other bacterial genes in the food microbiome and consequently require multiple rounds of in-depth sequ...

Background With the escalating risk of antimicrobial resistance (AMR), there are limited analytical options available that can comprehensively assess the burden of AMR carried by clinical/environmental samples. Food can be a potential source of AMR bacteria for humans, but its significance in driving the clinical spread of AMR remains unclear, larg...

This study was to assess the gene diversity and characterize a large set of plasmids harboring extended β-lactamase (ESBL) genes from raw and digested dairy manure. A total of eighty-four plasmids that were captured in this E. coli recipient were sequenced using Illumina MiSeq sequencing technology. Twenty-four plasmids of interest were subsequentl...

Shiga toxigenic Escherichia coli (STEC) have been implicated in major foodborne outbreaks worldwide. The STEC family of pathogens is biochemically diverse, and current microbiological methods for detecting STEC are limited by the lack of a universal selective enrichment approach and prone to interference by high levels of background microbiota asso...

Healthy poultry can be a reservoir for extraintestinal pathogenic Escherichia coli (ExPEC), some of which could be multidrug resistant to antimicrobials. These ExPEC strains could contaminate the environment and/or food chain representing thus, food safety and human health risk. However, few studies have shown the virulence of poultry-source antimi...

Antimicrobial resistance (AMR) has become a critical threat to public health worldwide. The use of antimicrobials in food and livestock agriculture, including the production of poultry, is thought to contribute to the dissemination of antibiotic resistant bacteria (ARB) and the genes and plasmids that confer the resistant phenotype (ARG). However,...

Background Sequence-based methods for the detection of bacteria such as 16S rRNA amplicon sequencing and metagenomics can provide a comprehensive view of the bacterial microbiome of food. These methods rely on the detection of gene sequences to indicate the presence of viable bacteria. This indirect form of detection can be prone to experimental ar...

Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data,...

Whole-genome sequencing (WGS) technologies are rapidly being adopted for routine use in food microbiology laboratories worldwide. Examples of how WGS is used to support food safety testing include gene marker discovery (e.g., virulence and anti-microbial resistance gene determination) and high-resolution typing (e.g., cg/wgMLST analysis). This has...

The increasing prevalence of antimicrobial resistance (AMR) in Campylobacter spp. is a global concern. This study evaluated the use of whole-genome sequencing (WGS) to predict AMR in Campylobact er jejuni and C. coli . A panel of 271 isolates recovered from Canadian poultry was used to compare AMR genotype to antimicrobial susceptibility testing (A...

Extraintestinal pathogenic Escherichia coli (ExPEC) include several serotypes that have been associated with colibacillosis in poultry and with urinary tract infections (UTIs) and newborn meningitis in humans. In this study, 57 antimicrobial-resistant E. coli from apparently healthy broiler chickens were characterized for their health and safety ri...

This study investigated virulence potential of poultry antimicrobial resistant extraintestinal pathogenic E. coli (ExPEC). A total of 46 E. coli isolates from poultry meat, feces, or humans were sequenced and identified as ExPEC. Based on their characteristics, eight of these ExPEC isolates were evaluated for their potentials using a Caenorhabditis...

This study investigated effects of in-feed encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination (CIN+CIT) on antimicrobial resistance (AMR) phenotypes and genotypes of E. coli isolated from feces of 6-, 16-, 23- and 27-days old broiler chickens. Five dietary treatments included the basal diet (NC), the basal diet supplemented...

Campylobacter fetus is currently classified into three main subspecies, but only two of these, C. fetus subspecies fetus and C. fetus subsp. venerealis originate principally from ruminants where they inhabit different niches and cause distinct pathogenicity. Their importance as pathogens in international trade and reporting is also different yet th...

Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data,...

Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. Cefotaxime-resistant bacteria were quantified and isolated from...

Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data,...

Following two O121 Shiga toxin–producing Escherichia coli (STEC) outbreaks linked to wheat flour, this study was conducted to gain baseline information on the occurrence of bacterial pathogens and levels of indicator organisms in wheat flour in Canada. A total of 347 prepackaged wheat flour samples were analyzed for Salmonella species, STEC, Lister...

Persistent contamination of food manufacturing environments by Listeria monocytogenes is an important public health risk, because such contamination events defy standard sanitization protocols, for example, the application of quaternary ammonium compounds such as benzalkonium chloride (BC), providing a source for prolonged dissemination of the bact...

The Deputy Heads of the Canadian federal food safety partner agencies (Public Health Agency of Canada, Health Canada and Canadian Food Inspection Agency) have identified the application of emerging science to support the management of food safety issues as a key priority for the modernization of regulatory food safety. One example of an emerging sc...

Microbiological surveillance of the food chain plays a critical role in improving our understanding of the distribution and circulation of food-borne pathogens along the farm to fork continuum toward the development of interventions to reduce the burden of illness. The application of molecular subtyping to bacterial isolates collected through surve...

Whole-genome sequencing (WGS) is used increasingly in public-health laboratories for typing and characterizing foodborne pathogens. To evaluate the performance of existing bioinformatic tools for in silico prediction of antimicrobial resistance (AMR) and serotypes of Salmonella enterica, WGS-based genotype predictions were compared with the results...

A previous soil metagenomics study recovered a novel cephalosporin resistance determinant, pbpTET A6, for which the exact resistance mechanism was unclear. Here, using a three-dimensional structure-guided mutagenesis approach, it is demonstrated that PBPTET A6 is a probable member of the Class-A penicillin binding proteins and that its ability to c...

Due to the public health importance of flagellar genes for typing, it is important to understand mechanisms that could alter their expression or presence. Phenotypic novelty in flagellar genes arise predominately through accumulation of mutations but horizontal transfer is known to occur. A linear plasmid termed pBSSB1 previously identified in Salm...

Heidelberg is among the top three Salmonella enterica serovars associated with human foodborne illness in Canada. Traditional culture and antimicrobial susceptibility testing techniques can be time-consuming to identify Salmonella Heidelberg resistant to cephalosporins and fosfomycin. Rapid and accurate detection of such antibiotic-resistant Salmon...

A 2016/2017 outbreak of Shiga toxin-producing Escherichia coli (STEC) O121 in Canada, was linked to wheat flour, milled at a single facility on three consecutive days in October 2016. Most Probable Number (MPN) estimates of the concentration of STEC O121 in the recalled flour were made using the results of qualitative testing conducted during the o...

Antimicrobial resistance (AMR) represents an existential threat to the function of modern medicine. Genomics and machine learning methods are being increasingly used to analyze and predict AMR. This type of surveillance is very important to try to reduce the impact of AMR. Machine learning models are typically trained using genomic data, but the as...

Citrobacter braakii and Citrobacter freundii are Gram-negative opportunistic pathogens associated with many infectious diseases, including septicemia, in humans and animals. Here, we report the draft genome sequences of seven C. braakii strains and one C. freundii strain isolated from Canadian wastewater treatment facilities.

Due to the public health importance of flagellar genes for typing, it is important to understand mechanisms that could alter their expression or presence. Phenotypic novelty in flagellar genes arise predominately through accumulation of mutations but horizontal transfer is known to occur. A linear plasmid termed pBSSB1 previously identified in Salm...

Whole-genome sequencing (WGS) of bacterial pathogens is currently widely used to support public-health investigations. The ability to assess WGS data quality is critical to underpin the reliability of downstream analyses. Sequence contamination is a quality issue that could potentially impact WGS-based findings; however, existing tools do not readi...

Campylobacter is the leading cause of food-borne bacterial disease in Canada and many developed countries. One of the most common sources of human campylobacteriosis is considered to be the consumption or handling of raw or undercooked poultry. To date, few Canadian studies have investigated both the prevalence of Campylobacter on retail poultry an...

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Enteritidis and Typhimurium are among the top Salmonella enterica serovars implicated in human salmonellosis worldwide. This study examined the individual and combined roles of catecholate-iron and hydroxamate-iron transporters in the survival in meat of Salmonella Enteritidis and Typhimurium. Catecholate-iron-III (Fe 3þ) and hydroxamate-Fe 3þ tran...

Exposure to antimicrobial resistant (AMR) bacteria is a major public health issue which may, in part, have roots in food production practices that are conducive to the selection of AMR bacteria ultimately impacting the human microbiome through food consumption. Of particular concern is the prophylactic use of antibiotics in animal husbandry, such a...

Whole-genome sequencing (WGS) of bacterial pathogens is currently widely used to support public-health investigations. The ability to assess WGS data quality is critical to underpin the reliability of downstream analyses. Sequence contamination is a quality issue that could potentially impact WGS-based findings; however, existing tools do not readi...

Whole-genome sequencing (WGS) of bacterial pathogens is currently widely used to support public-health investigations. The ability to assess WGS data quality is critical to underpin the reliability of downstream analyses. Sequence contamination is a quality issue that could potentially impact WGS-based findings; however, existing tools do not readi...

Next-generation sequencing plays an important role in the characterization of clinical bacterial isolates for source attribution purposes during investigations of foodborne illness outbreaks. Once an illness cluster and a suspect food vehicle have been identified, food testing is initiated for confirmation and to determine the scope of a contaminat...

Background The aim of this study was to characterize the genomes of 30 Listeria monocytogenes isolates collected at a pig slaughterhouse to determine the molecular basis for their persistence. Results Comparison of the 30 L. monocytogenes genomes showed that successive isolates (i.e., persistent types) recovered from thew sampling site could be li...

Using a combination of Illumina paired-end sequencing, Pacific Biosciences RS II sequencing, and OpGen Argus whole-genome optical mapping, we report here the first complete genome sequence of Yersinia massiliensis . The completed genome consists of a 4.99-Mb chromosome, a 121-kb megaplasmid, and a 57-kb plasmid.

The recovery of Campylobacter species from food and environmental sources is challenging due to the slow growth of these bacteria and the need to suppress competing organisms during the isolation procedures. The addition of multiple selective antimicrobials to growth media can negatively impact recovery of some Campylobacter spp. Here, we describe...

Listeria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium which is an important foodborne bacterial pathogen for humans worldwide with high mortality rates. Here, we report a 2,964,284-bp draft genome sequence of Listeria monocytogenes strain ATCC 7644 (American Type Culture Collection).

The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance wi...

The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance wi...

The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance wi...

Enterohemorrhagic Escherichia coli serotype O157:H7 is a major cause of foodborne outbreaks and hemolytic-uremic syndrome. Here, we report the draft genome sequences of three antibiotic-resistant E. coli O157:H7 strains isolated from feedlot cattle. These draft genome sequences will aid in the development of sequence-based tools for the detection o...

Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characterist...

Campylobacter jejuni and C. coli are the bacterial species most commonly associated with foodborne illness worldwide. Methods for isolation of these organisms from complex food matrices rely on conditions that allow for the growth of these organisms while inhibiting competitors. This chapter reviews the methodologies developed to isolate, identify,...

The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distances and genetic distances, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance...

The determination of Shiga toxin (ST) subtypes can be an important element in the risk characterization of foodborne ST-producing Escherichia coli (STEC) isolates for making risk management decisions. ST subtyping methods include PCR techniques based on electrophoretic or pyrosequencing analysis of amplicons and in silico techniques based on whole...

Genomic antimicrobial resistance (AMR) prediction tools have the potential to support foodborne illness outbreak investigations through their application in the analysis of bacterial genomes from causative strains. The AMR marker profile of a strain of interest, initially identified in outbreak-Associated clinical samples, may serve as the basis fo...

Salmonella enterica subspecies enterica serovar Berta has been isolated in multiple animal species and has been implicated in human disease. Here, we report a 4.7-Mbp draft genome sequence of S. enterica serovar Berta (ATCC strain 8392) and a nalidixic acid-resistant isolate derived from this strain.

Escherichia fergusonii is a Gram-negative, rod-shaped, non-spore-forming member of the Enterobacteriaceae family and is a bacterium with both biotechnological applications and implication in human clinical disease. Here, we report the draft genome sequences of three isolates of E. fergusonii from beef trim (GTA-EF02), ground beef (GTA-EF03), and ch...