Valeria Parreira

• PhD
• Adjunct Faculty at University of Guelph

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing threat to global health. Wastewater-based surveillance (WBS) has proven to be an important tool for tracking the dissemination of SARS-CoV-2 variants of concern (VOCs) in the community. In Canada, metagenomic analysis of aircraft wastewater was adopted at an early...

Avian necrotic enteritis due to the Gram-positive bacterium Clostridium perfringens has re-emerged following the ban on antibiotic growth promoters in many poultry producing countries. The limited number of previous studies has left important gaps in our understanding of the genetic diversity and virulence traits of the pathogen. To address these k...

Avian necrotic enteritis due to the Gram-positive bacterium Clostridium perfringens has re-emerged following the ban on antibiotic growth promoters in many poultry producing countries. The limited number of previous studies has left important gaps in our understanding of the genetic diversity and virulence traits of the pathogen. To address these k...

Aquatic ecosystems serve as crucial reservoirs for pathogens and antimicrobial resistance genes, thus presenting a significant global health risk. Here, we investigated the phylogenomics of Aeromonas veronii from Lake Wilcox in Ontario. Among the 11 bacterial isolates, nine were identified as A. veronii. Notably, 67% of A. veronii isolates were pot...

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown wastewater (WW) surveillance to be an effective means of tracking the emergence of viral lineages which arrive by many routes of transmission including via transportation hubs. In the Canadian province of Ontario, numerous municipal wastewater treatment plants (WWTP...

Nontyphoidal Salmonella enterica serovars are foodborne pathogens commonly transmitted through poultry products. Draft genome sequences of three Salmonella enterica subsp. enterica serovar Shamba isolates which were obtained from poultry house dust in South Africa are reported herein.

This study assessed the microbial dynamics of fresh and treated vegetable products during storage.

Aquatic ecosystems are important reservoirs for clinically relevant pathogens and antimicrobial resistance genes, thus presenting a significant risk to global health. Here, we assessed the phylogenomics of Aeromonas veronii (A. veronii) recovered from Lake Wilcox in Ontario using a combination of morphological, biochemical, and whole-genome sequenc...

The SARS-CoV-2 pandemic has shown that wastewater (WW) surveillance is an effective means of tracking the emergence of viral lineages in communities, arriving by many routes including via transportation hubs. In Ontario, numerous municipal WWTPs participate in WW surveillance of infectious disease targets such as SARS-CoV-2 by qPCR and whole genome...

Objective Vibrio cholerae is an enteric pathogen that poses a significant threat to global health. It causes severe dehydrating diarrheal disease cholera in humans. V. cholerae could be acquired either from consuming contaminated seafood or direct contact with polluted waters. As part of a larger program that assesses the microbial community profil...

Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity of RT-qPCR has...

Salmonella enterica is a zoonotic pathogen and a leading cause of foodborne gastroenteritis in humans. Here, we report the draft genome sequences of two Salmonella Uzaramo isolates, which were isolated from poultry organs during routine post-mortem examination in South Africa. Currently, whole-genome sequences on Salmonella Uzaramo are scanty.

Simple Summary Necrotic enteritis is a complex gastrointestinal disease of broiler chickens that imposes a substantial economic burden on poultry producers worldwide. The causative agent is pathogenic strains of Clostridium perfringens type G. While numerous efforts to develop an effective vaccine against the disease were unsuccessful, a previous s...

Proteus mirabilis is a Gram-negative bacterium that is frequently implicated in urinary tract infections in humans and companion animals and has also been associated with foodborne infections in several countries. Here, we report the draft genome sequences of two P. mirabilis isolates recovered from municipal wastewater.

Avian necrotic enteritis is an enteric disease of broiler chickens caused by certain pathogenic strains of Clostridium perfringens in combination with predisposing factors. A vaccine offering complete protection against the disease has not yet been commercialized. In a previous study, we produced five recombinant proteins predicted to be surface-ex...

Human fecal biomarkers (HFBs) have a longstanding history in the field of microbial source tracking (MST) serving as indicators of human fecal contamination in drinking and recreational water. Further, HFBs have aided in recent efforts to monitor human pathogen transmission within communities. The dilution of wastewater from various sources through...

Listeria monocytogenes is an opportunistic foodborne pathogen which has been implicated in many outbreaks of foodborne diseases. This study evaluated the effects of gastric acidity and gastric digestion time of adults, L. monocytogenes strain and food type on the survival of L. monocytogenes under simulated stomach conditions of adults in in vitro...

Bacillus anthracis is widespread in soil and a causative agent of anthrax, primarily in herbivores. Here, we report the draft genome sequence of Bacillus anthracis strain N1, which was isolated from a recreational freshwater lake and found to carry multiple antibiotic resistance genes and biosynthetic gene clusters.

Exiguobacterium spp. are facultative anaerobic, Gram-positive, non-spore-forming bacilli, reported to tolerate extreme environments. Here, we report the draft genome sequence of Exiguobacterium sp. strain N5, isolated from a recreational freshwater lake.

Big data is and will continue to be a major disruptor in the area of food safety. Although “big data” can provide valuable and significant contributions to many areas of food safety, it also raises important questions about security, privacy, data control, data governance, transparency, de-identification, and anonymization that must be carefully co...

Powdered infant formula (PIF) can be contaminated with Cronobacter sakazakii , which can cause severe illnesses in infants. Synbiotics, a combination of probiotics and prebiotics, could act as an alternative control measure for C. sakazakii contamination in PIF and within the infant gut, but synbiotics have not been well studied for their ability t...

We report metagenomic sequencing analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in composite wastewater influent from 10 regions in Ontario, Canada, during the transition between Delta and Omicron variants of concern. The Delta and Omicron BA.1/BA.1.1 and BA.2-defining mutations occurring in various frequencies were re...

Cronobacter sakazakii is an opportunistic foodborne pathogen that can be fatal to infants; it is commonly associated with powdered infant formula due to contamination during manufacturing processes or during preparation in hospitals or homes. This project aimed to select a potential synbiotic, a combination of probiotic strains with a prebiotic pro...

Escherichia coli is a commensal of the gastrointestinal tract of humans and animals, and a leading cause of gastroenteritis, bloodstream, and urinary tract infection, among others. Pathogenic E. coli causing diarrhea is delineated into six different types (pathotypes) based on the type of infection they cause. While these pathotypes have similar me...

Cronobacter species, in particular C. sakazakii , is an opportunistic bacterial pathogen implicated in the development of potentially debilitating illnesses in infants (<12months old). The combination of a poorly developed immune system and gut microbiota put infants at a higher risk of infection compared to other age groups. Probiotics and prebiot...

Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-anal...

The survival of Listeria monocytogenes was assessed during long-term storage on three dried fruits: dried apples, raisins and dried strawberries. Using sand as a carrier, the dried fruits were dry-inoculated with a four-strain cocktail of L. monocytogenes to achieve numbers of 4.0 to 4.6 log CFU/g. The inoculated foods were stored at 4°C, 25–81% re...

The COVID-19 pandemic has brought about a consideration of our understanding of transmission of the causal agent, SARS-CoV-2 to humans and its potential effect on food safety and food security. The main routes of transmission are reported to be person-to-person, by respiratory droplets and to a lesser degree, by fomites. Concerns have been raised o...

The survival and virulence of Listeria monocytogenes was assessed during storage on three low-moisture foods (LMFs): chocolate liquor, corn flakes, and shelled, dry-roasted pistachios (water activity [aw] of 0.18, 0.27, and 0.20, respectively). The LMFs were inoculated with a four-strain cocktail of L. monocytogenes at 8 log CFU/g, dried, held unti...

The ecology of Listeria monocytogenes has been previously investigated in various whole and minimally processed raw vegetables, but not in turnips. A 2018 national Canadian recall for packaged fresh-cut turnips contaminated with L. monocytogenes raised concerns about turnips being able to support the growth of this microorganism. Thus, this study e...

Listeria monocytogenes, a resilient and ubiquitous foodborne pathogen, is associated with a high case-fatality rate in humans. This study investigated the culturable microbiota of low-moisture foods (LMFs) imported into Canada to see how well bacteria isolated from these foods could inhibit or inactivate the growth of L. monocytogenes. Imported LMF...

Microbial community assembly is a complex process shaped by multiple factors, including habitat filtering, species assortment and stochasticity. Understanding the relative importance of these drivers would enable scientists to design strategies initiating a desired reassembly for e.g., remediating low diversity ecosystems. Here, we aimed to examine...

Listeria monocytogenes is an important foodborne pathogen that has caused many outbreaks, mainly related to foods that can support its growth. However, due to the emergence of low-moisture foods (LMFs) as potential sources of foodborne outbreaks, concerns exist about the potential public health implications of finding L. monocytogenes in LMFs, espe...

Microbial community assembly is a complex process shaped by multiple factors, including habitat filtering, species assortment and stochasticity. Understanding the relative importance of these drivers would enable scientists to design strategies initiating a desired reassembly for e.g., remediating low diversity ecosystems. Here, we aimed to examine...

Necrotic enteritis (NE) caused by netB-positive strains of Clostridium perfringens is an important disease of intensively-reared broiler chickens. It is widely controlled by antibiotic use, but this practice that has come under increasing scrutiny and alternative approaches are required. As part of the search for alternative approaches over the las...

Clostridium perfringens is an important cause of foal necrotizing enteritis and canine acute hemorrhagic diarrhea. A major virulence determinant of the strains associated with these diseases appears to be a beta-sheet pore-forming toxin, NetF, encoded within a pathogenicity locus (NetF locus) on a large tcp-conjugative plasmid. Strains producing Ne...

Background Necrotic enteritis (NE) caused by netB-positive type A Clostridium perfringens is an important bacterial disease of poultry. Through its complex regulatory system, C. perfringens orchestrates the expression of a collection of toxins and extracellular enzymes that are crucial for the development of the disease; environmental conditions pl...

NetF-producing Clostridium perfringens have recently been identified as a cause of necrotizing enteritis in neonatal foals, but little is known about its prevalence in clinically normal foals. Foals (n = 88) ranging in age from < 1 wk to 2 to 4 mo (median age 2 to 4 wk) on 8 horse-breeding farms in Ontario were examined on 1 or 2 occasions for the...

Clostridium perfringens type A-associated diarrhea and enteric disease in dogs and foals is not well characterized, since the association of disease is complicated by the common presence of type A organisms in the bowel and feces of healthy animals. The recent description of a novel pore-forming toxin, NetF, which is strongly associated with these...

A role for type A Clostridium perfringens in acute hemorrhagic and necrotizing gastroenteri-tis in dogs and in necrotizing enterocolitis of neonatal foals has long been suspected but incompletely characterized. The supernatants of an isolate made from a dog and from a foal that died from these diseases were both found to be highly cytotoxic for an...

The recent discovery of a novel beta-pore-forming toxin, NetF, which is strongly associated with canine and foal necrotizing enteritis should improve our understanding of the role of type A Clostridium perfringens associated disease in these animals. The current study presents the complete genome sequence of two netF-positive strains, JFP55 and JFP...

Summary of predicted genes identified by MyRast software in pJFP838E. (XLSX)

Summary of predicted genes identified by MyRast software in pJFP55K. (XLSX)

Summary of predicted genes identified by MyRast software in pJFP55H. (XLSX)

Shared unique chromosomal nucleotide sequences by two netF-positive C. perfringens. (XLSX)

Summary of predicted genes identified by MyRast software in pJFP55G. (XLSX)

Summary of predicted genes identified by MyRast software in pJFP838D. (XLSX)

Summary of predicted genes identified by MyRast software in pJFP55J. (XLSX)

Unique chromosomal nucleotide sequences of JFP838 identified by PanSeq. (XLSX)

Unique chromosomal nucleotide sequences of JFP55 identified by PanSeq. (XLSX)

This review summarizes advances in understanding the pathogenesis of necrotic enteritis (NE) of chickens caused by netB-positive Clostridium perfringens. The discovery of NetB as the essential toxin trigger for the disease was followed by recognition that it forms part of a large plasmid-encoded 42 kb pathogenicity locus (NELoc-1). While the locus...

A role for type A Clostridium perfringens in acute hemorrhagic and necrotizing gastroenteritis in dogs and in necrotizing enterocolitis of neonatal foals has long been suspected but incompletely characterized. The supernatants of an isolate made from a dog and from a foal that died from these diseases were both found to be highly cytotoxic for an e...

Necrotic enteritis in broiler chickens is associated with netB positive Clostridium perfringens type A strains. It is known that C. perfringens strains isolated from outbreaks of necrotic enteritis are more capable of secreting factors inhibiting growth of other C. perfringens strains than strains isolated from the gut of healthy chickens. This cha...

Up to 60% of cases of equine colitis have no known cause. To improve understanding of the causes of acute colitis in horses, we hypothesized that Clostridium perfringens producing enterotoxin (CPE) and/or beta2 toxin (CPB2) are common and important causes of severe colitis in horses and/or that C. perfringens producing an as-yet-undescribed cytotox...

Salmonella hold considerable promise as vaccine delivery vectors for heterologous antigens in chickens. Such vaccines have the potential additional benefit of also controlling Salmonella infection in immunized birds. As a way of selecting attenuated strains with optimal immunogenic potential as antigen delivery vectors, this study screened 20 novel...

Necrotic enteritis (NE) is an economically important disease of poultry caused by certain Clostridium perfringens type A strains. NE pathogenesis involves the NetB toxin, which is encoded on a large conjugative plasmid within a 42-kb pathogenicity locus. Recent multilocus sequence type (MLST) studies have identified two predominant NE-associated cl...

Twenty-six isolates of Clostridium perfringens of different MLST types from chickens with necrotic enteritis (NE) (15 netB-positive) or from healthy chickens (6 netB-positive, 5 netB-negative) were found to contain 1-4 large plasmids, with most netB-positive isolates containing 3 large and variably sized plasmids which were more numerous and larger...

Amino acid alignments of proteins encoded by different C. perfringens plasmids. Plasmid names and their respective orf number (plasmid name orf#) are described for each protein. Identical residues (*), conservative amino acid substitutions (:), and semi-conservative amino acid substitutions (.) are shown below the aligned sequences. (MUSCLE −3.7)....

PFGE analyses of plasmids from transconjugants C. perfringens strains. Agarose plugs containing DNA from each specified isolate were digested with NotI and subjected to PFGE and staining with ethidium bromide. Lines indicate: CW504 recipient strain (plasmid free); T98 (transconjugant carrying the plasmid pCpb2); T117 (transconjugant carrying three...

List of primers. (A) Primers used for PCR DIG labelling and mutation (B) Primers used for overlapping PCR reactions of the three Pathogenicity loci characteristic of necrotic enteritis C. perfringens isolates. (DOCX)

Comparison of NE C. perfringens plasmids. (A) Comparison of coding sequences pNetB-NE10 and pJIR3535 NE C. perfringens plasmids by means of BLASTn analyses. Open reading frames are labeled according to the annotation of plasmid pNetB-NE10 (B) Comparison of open reading frames pCpb2-CP1 and pJIR3844 NE C. perfringens plasmids by means of BLASTn anal...

Overlapping PCR analysis of NE locus in C. perfringens. PCR reactions were performed using DNA from C. perfringens strains described on Table 1. Healthy and NE C. perfringens isolates H26, H34, NE04, NE09, NE10, NE14, NE20, NE23, NE28, NE30, NE42, respectively. Genetic organization of NE loci. (A) Overlapping PCR analysis of NE locus 1. (B) Overlap...

Repeats found on the upstream region of parM gene. Possible tandem repeats found on the upstream region of parM gene next to rep gene from C. perfringens plasmids using etandem (http://emboss.bioinformatics.nl/cgi-bin/emboss/etandem). (DOCX)

PFGE and Southern blot analyses of plasmids from healthy C. perfringens poultry strains. (A) PFGE analyses of plasmids from healthy C. perfringens poultry strains. Agarose plugs containing DNA from each specified isolate were digested with NotI and subjected to PFGE and staining with ethidium bromide. See Table1 and 2 for isolate features. Line num...

This study examined known or possible virulence-associated genes in type A Clostridium perfringens from cases of both bovine clostridial abomasitis (BCA) and jejunal hemorrhage syndrome (JHS) and compared these to isolates from calves that were healthy or had undifferentiated diarrheal illness. A real-time polymerase chain reaction (PCR) assay was...

An enzyme-linked immunosorbent assay (ELISA) was developed for detection and quantitation of beta2-toxin in neonatal piglet intestinal contents. Polystyrene plates were coated with polyclonal capture antibodies prepared against consensus recombinant beta2-toxin. The ELISA was developed using consensus recombinant beta2-toxin, atypical recombinant b...

This study examined the prevalence and expression of the "consensus" and the "atypical"cpb2 genes in Clostridium perfringens isolates from cattle, chickens, dogs, goats, horses, pigs and sheep using polymerase chain reaction (PCR), sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by Western blotting. Almost all porcine isolates (1...

Clostridium perfringens is a common inhabitant of the avian and mammalian gastrointestinal tracts and can behave commensally or pathogenically. Some enteric diseases caused by type A C. perfringens, including bovine clostridial abomasitis, remain poorly understood. To investigate the potential basis of virulence in strains causing this disease, we...

Contig alignments on C. perfringens F262 NcoI optical map. Footnote: Optical mapping assembled approximately 3.1 Mbp of the estimated 3.46 Mbp chromosome. Contigs are designated as placed “in silico” based on comparison of optically mapped restriction sites to the contigs by use of the MapSolver™ software. (TIF)

PanSeq results for the orphan contigs. (DOC)

Virulence genes (Shimizu et al. , 2002) present in Clostridium perfringens F262. (DOC)

PanSeq results for Cfrag. (DOC)

PanSeq results for the Clostridium perfringens F262 pseudochromosome. (DOC)

Pneumonia caused by Rhodococcus equi remains a significant problem in foals. The objective of this study was to develop a safe and efficacious attenuated strain of R. equi for eventual use in oral immunization of foals. The approach involved expression of vapA in a live, virulence plasmid-negative, strain of R. equi (strain 103-). PCR-amplified fra...

Rhodococcus equi is a soil bacterium and, like Mycobacterium tuberculosis, a member of the mycolata. Through possession of a virulence plasmid, it has the ability to infect the alveolar macrophages of foals, resulting in pyogranulomatous bronchopneumonia. The virulence plasmid has an orphan two-component system (TCS) regulatory gene, orf8, mutation...

This study assessed the protective efficacy of oral vaccination with 2 experimental attenuated Salmonella Typhimurium-vectored vaccines for necrotic enteritis in protecting chickens against intestinal colonization by common serovars of Salmonella belonging to the 4 major serogroups affecting chickens. Birds were vaccinated orally with 1 × 10⁸ colon...

[This corrects the article on p. e10795 in vol. 5.].

Optical mapping of CP4 chromosome. Optical mapping of NcoI-digested genomic DNA isolated from strain CP4 was performed by OpGen, Inc. This technique is limited to the mapping of chromosomal fragments. The lower bar represents the optical map and the upper bar the in silico NcoI-digested pseudomolecule generated from the CP4 draft genome sequence. L...

Mapping of CP4 Solexa reads to plasmid sequences. CP4 Solexa reads were mapped to C. perfringens virulence plasmids A) pCPF5603, B) pCPF4969 and C) pCP8533etx using Maq, and the depth of coverage along the plasmid visualized with Circos. From inner to outer: ring 1, plasmid sequence with the conserved backbone region in red, variable region in blue...

Overlapping PCR analysis of NE locus 1. PCR products spanning the entire locus are represented by black bars and the PCR results for each strain tested are given below as follows: +.PCR product was of expected size; −, no PCR product produced. Where the PCR product did not match the expected size, the actual size is given. (0.08 MB PDF)

Overlapping PCR analysis of NE locus 2. PCR products spanning the entire locus are represented by black bars and the PCR results for each strain tested are given below as follows: +.PCR product was of expected size; −, no PCR product produced. (0.07 MB PDF)

Overlapping PCR analysis of NE locus 3. PCR products spanning the entire locus are represented by black bars and the PCR results for each strain tested are given below as follows: +.PCR product was of expected size; −, no PCR product produced. (0.02 MB PDF)

Primers used for PCR DIG labeling and sequencing. (0.04 MB PDF)

Primers used for overlapping PCR analysis of NELoc-1, -2 and -3. (0.05 MB PDF)

F5/8 Type C Domain Protein Alignment and Peptide ID Matching. Multiple alignment of protein sequences from three paralogous F5/8 Type C domain proteins, two chromosomal (B and C) and one located in NELoc-1 (A), was used to generate a phylogenetic tree. Peptide sequences obtained from Kulkarni et al. [19] were compared against each of the three para...

Polymorphism maps of NE loci. Green vertical lines indicate approximate position of polymorphisms between the seven NE strains. The shortest green line represents a single nucleotide polymorphism (SNP) in one strain and the longest green line indicates a SNP in three strains. (0.17 MB PDF)

Phylogenetic analysis of sequenced C. perfringens strains. The phylogenetic relationship among our eight sequenced isolates was assessed by (A) PFGE analysis of SmaI-digested genomic DNA and (B) sequence alignment of the whole proteome from each strain using CVtree. Additional eight publicly available C. perfringens genomes were also included for c...

Type A Clostridium perfringens causes poultry necrotic enteritis (NE), an enteric disease of considerable economic importance, yet can also exist as a member of the normal intestinal microbiota. A recently discovered pore-forming toxin, NetB, is associated with pathogenesis in most, but not all, NE isolates. This finding suggested that NE-causing s...

Clostridium perfringens isolates were recovered by enrichment from retail grocery chicken samples (n = 88) in Ontario, Canada, with one sample per site. The gene associated with necrotic enteritis in chickens, netB, was found in 21% of the isolates. The tpeL gene was found in 2% and the cpb2 gene in 68% (95% "atypical" genes) of isolates. This stud...

Necrotic enteritis (NE) in broiler chickens is caused by Clostridium perfringens, and there is currently no effective vaccine for NE. We previously showed that in broiler chickens protection against NE can be achieved through intramuscular immunization with alpha toxin (AT) and hypothetical protein (HP), and we subsequently identified B-cell epitop...

This study identified and assessed secreted proteins of Clostridium perfringens additional to those previously described for their ability to protect broiler chickens against necrotic enteritis (NE). Secreted proteins of virulent and avirulent C. perfringens were electrophoretically separated and reacted with serum of chickens immune to NE. Three i...

Clostridium perfringens is an important pathogen of animals and humans and is the causative agent of necrotic enteritis (NE) in poultry. This study focuses on the typing of intestinal C. perfringens isolates (n = 61) from outbreaks of NE collected from several areas of Southern Ontario, using a recently developed multilocus sequence typing (MLST) t...

The prevalence of persistent bacteremic Bartonella spp. and hemoplasma infections was determined in healthy pet cats in Ontario. Blood samples from healthy cats sent to a diagnostic laboratory for routine health assessment over the course of 1 y were tested for Bartonella spp. using both polymerase chain reaction (PCR) and blood culture, and for th...

Necrotic enteritis (NE) in broiler chickens is caused by Clostridium perfringens but currently no effective vaccine is available. Our previous study showed that certain C. perfringens secreted proteins when administered intramuscularly protected chickens against experimental infection. In the current study, genes encoding three C. perfringens prote...