Characterization of MLST-99 Salmonella Typhimurium and the monophasic variant I:4,[5],12:i:- isolated from Canadian Atlantic coast shellfish

Salmonella enterica subsp. enterica Typhimurium and its monophasic variant I 1;4,[5],12:i:- (MVST) are responsible for thousands of reported cases of salmonellosis each year in Canada, and countries worldwide. We investigated S. Typhimurium and MVST isolates recovered from raw shellfish harvested in Atlantic Canada by the Canadian Food Inspection Agency (CFIA) over the past decade, to assess the potential impact of these isolates on human illness and to explore possible routes of shellfish contamination. Whole-genome sequence analysis was performed on 210 isolates of S. Typhimurium and MVST recovered from various food sources, including shellfish. The objective was to identify genetic markers linked to ST-99, a sequence type specifically associated with shellfish, which could explain their high prevalence in shellfish. We also investigated the genetic similarity amongst CFIA ST-99 isolates recovered in different years and geographical locations. Finally, the study aimed to enhance the molecular serotyping of ST-99 isolates, as they are serologically classified as MVST but are frequently misidentified as S. Typhimurium through sequence analysis. To ensure recovery of ST-99 from shellfish was not due to favourable growth kinetics, we measured the growth rates of these isolates relative to other Salmonella and determined that ST-99 did not have a faster growth rate and/or shorter lag phase than other Salmonella evaluated. The CFIA ST-99 isolates from shellfish were highly clonal, with up to 81 high-quality single nucleotide variants amongst isolates. ST-99 isolates both within the CFIA collection and those isolated globally carried numerous unique deletions, insertions and mutations in genes, including some considered important for virulence, such as gene deletions in the type VI secretion system. Interestingly, several of these genetic characteristics appear to be unique to North America. Most notably was a large genomic region showing a high prevalence in genomes from Canadian isolates compared to those from the USA. Although the functions of the majority of the proteins encoded within this region remain unknown, the genes umuC and umuD, known to be protective against UV light damage, were present. While this study did not specifically examine the effects of mutations and insertions, results indicate that these isolates may be adapted to survive in specific environments, such as ocean water, where wild birds and/or animals serve as the natural hosts. Our hypothesis is reinforced by a global phylogenetic analysis, which indicates that isolates obtained from North American shellfish and wild birds are infrequently connected to isolates from human sources. These findings suggest a distinct ecological niche for ST-99, potentially indicating their specialization and adaptation to non-human hosts and environments, such as oceanic habitats.

Identifying water quality and environmental factors that influence indicator and pathogen decay in natural surface waters

Biphasic decay has been observed for indicators and pathogens in bench-scale and in-situ water experiments for decades, however, first-order decay kinetics continue to be applied to persistence data because of their simplicity and ease of application. Model uncertainty introduced by broadly applying first-order decay kinetics to persistence data may lead to erroneous decision making in the fields of water management and protection. As surface waters are exposed to highly variable environmental and water quality factors that influence microbial and viral persistence, it is expected that first-order decay kinetics are not representative of most of the persistence literature for indicators and pathogens in surface water matrices. This review compiled the methods and results of 61 studies that conducted experiments evaluating the persistence of fecal indicator bacteria (FIB), bacteriophages, pathogenic bacteria, viruses, and protozoa in natural surface water matrices. The goals of this review were trifold: (1) collate studies in the literature with data available for future persistence modeling, (2) present the current state of knowledge with regards to the environmental and water quality factors affecting persistence in natural surface waters, and (3) identify recurrent evidence for interactions between the frequently studied factors to inform future factor analyses. Comparing the methods and results across the 61 studies suggest potential interactions between sunlight and water type; sunlight and method of detection; predation and water type; predation and temperature; and water type and method of detection. The majority of the identified literature evaluated FIB or bacteria persistence; future experiments are needed that focus on protozoa, brackish or marine water types, and molecular-based methods of detection.

Fate of Salmonella in Central Florida Surface Waters and Evaluation of EPA Worst Case Water as a Standard Medium

HIGHLIGHTS

Survival of Salmonella was studied in surface waters. Salmonella stayed alive in nonsterile microcosms for 168 days. Limited decline was seen in sterile surface, deionized, and EPA Worst Case water. EPA Worst Case water offers potential as a standardized medium.

The Effect of Previous Life Cycle Phase on the Growth Kinetics, Morphology, and Antibiotic Resistance of Salmonella Typhimurium DT104 in Brain Heart Infusion and Ground Chicken Extract

Growth models are predominately used in the food industry to estimate the potential growth of selected microorganisms under environmental conditions. The growth kinetics, cellular morphology, and antibiotic resistance were studied throughout the life cycle of Salmonella Typhimurium. The effect of the previous life cycle phase [late log phase (LLP), early stationary phase (ESP), late stationary phase (LSP), and early death phase (EDP)] of Salmonella after reinoculation in brain heart infusion broth (BHI), ground chicken extract (GCE), and BHI at pH 5, 7, and 9 and salt concentrations 2, 3, and 4% was investigated. The growth media and previous life cycle phase had significant effects on the lag time (λ), specific growth rate (μ max), and maximum population density (Y max). At 2 and 4% salt concentration, the LLP had the significantly (p < 0.05) fastest μ max (1.07 and 0.69 log CFU/ml/h, respectively). As the cells transitioned from the late log phase (LLP) to the early death phase (EDP), the λ significantly (p < 0.05) increased. At pH 5 and 9, the EDP had a significantly (p < 0.05) lower Y max than the LLP, ESP, and LSP. As the cells transitioned from a rod shape to a coccoid shape in the EDP, the cells were more susceptible to antibiotics. The cells regained their resistance as they transitioned back to a rod shape from the EDP to the log and stationary phase. Our results revealed that growth kinetics, cell's length, shape, and antibiotic resistance were significantly affected by the previous life cycle phase. The results of this study also demonstrate that the previous life cycle should be considered when developing growth models of foodborne pathogens to better ensure the safety of poultry and poultry products.

What's the risk? Identifying potential human pathogens within grey-headed flying foxes faeces

Pteropus poliocephalus (grey-headed flying foxes) are recognised vectors for a range of potentially fatal human pathogens. However, to date research has primarily focused on viral disease carriage, overlooking bacterial pathogens, which also represent a significant human disease risk. The current study applied 16S rRNA amplicon sequencing, community analysis and a multi-tiered database OTU picking approach to identify faecal-derived zoonotic bacteria within two colonies of P. poliocephalus from Victoria, Australia. Our data show that sequences associated with Enterobacteriaceae (62.8% ± 24.7%), Pasteurellaceae (19.9% ± 25.7%) and Moraxellaceae (9.4% ± 11.8%) dominate flying fox faeces. Further colony specific differences in bacterial faecal colonisation patterns were also identified. In total, 34 potential pathogens, representing 15 genera, were identified. However, species level definition was only possible for Clostridium perfringens, which likely represents a low infectious risk due to the low proportion observed within the faeces and high infectious dose required for transmission. In contrast, sequences associated with other pathogenic species clusters such as Haemophilus haemolyticus-H. influenzae and Salmonella bongori-S. enterica, were present at high proportions in the faeces, and due to their relatively low infectious doses and modes of transmissions, represent a greater potential human disease risk. These analyses of the microbial community composition of Pteropus poliocephalus have significantly advanced our understanding of the potential bacterial disease risk associated with flying foxes and should direct future epidemiological and quantitative microbial risk assessments to further define the health risks presented by these animals.