Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil

Dried and Tested: Inoculation Method Impacts Low-Moisture Food Persistent Bacterial Populations

Pathogen contamination and harborage in low-moisture food (LMF) processing environments have resulted in outbreaks and recalls, but researchers are limited in their abilities to investigate solutions. Methods used in most laboratory studies do not accurately reflect the route of contamination or harborage of pathogens in LMF environments, which complicates studying of sanitation methods. Inoculation methods were compared to establish low-moisture food persistent bacterial populations (LMF PBPs) that realistically reflect populations found in LMF environments. Culture-preparation techniques, food matrices, and ratios of nutrient to moisture were compared for their impacts on Salmonella Tennessee survival. A slurry method with 0.5 mL of culture to 0.4 g (NFDM) was easiest to form, inoculate, and process for further investigation, as was more consistent than other methods. With the chosen technique, LMF PBPs of Salmonella Tennessee (0.5: 0.4 [mL Salmonella Tennessee to g Powder]) with different powders (NFDM, peanut butter powder [PB], chicken powder [CP] and silicon dioxide [SiO2]) were made using lawn-based and broth-based cultures and distributed evenly on sterilized stainless-steel coupons to compare the impacts of preparation and food matrix on survival. Coupons stored at 22-25 °C and 50% relative humidity (RH) were assessed on 0, 1, 3, 5, and 7 days. Matrices and culture preparation showed significant differences (p ≤ 0.05). Salmonella LMF PBP derived from bacterial lawns demonstrated higher initial populations (10.1 ± 0.0 log CFU/cm2) compared to the broth cultures (8.2 ± 0.2 log CFU/cm2). Salmonella LMF PBP reductions were lower for the lawn-prepared cultures (0.3-2.7 log CFU/cm2) compared to broth-based cultures (1.0-5.1 log CFU/cm2) for all food matrices. Salmonella in LMF PBP with SiO2 (2.7-5.1 log CFU/cm2) reduced significantly more than in other food matrices (0.7-2.2 log CFU/cm2) and Sal without a matrix (0.3-1.5 log CFU/cm2) for both culturing methods.

Quantification of Viable Salmonella by Propidium Monoazide Real-Time PCR After Long-Term Storage of Peanut Products

In this study, the performance of quantitative PCR, combined or not with propidium monoazide (PMA), to recover Salmonella from peanut products after different storage times was evaluated. The samples were inoculated with 5-6 log cfu g-1 of Salmonella Typhimurium ATCC 14028 and stored at 28 °C for up to 540 d. The correlation between the threshold cycle number (Ct) and the colony-forming units (cfu) was obtained by a standard curve, which showed a linear correlation (R2 = 0.97). The highest counts were recovered by qPCR (p < 0.05); however, it quantified both viable and non-viable cells. For roasted peanuts, a significant difference (p < 0.05) between qPCR-PMA and the culture method was verified only for samples stored for 30 d, i.e., 2.8 versus 4.0 log cfu g-1. Further, there was no VBNC status in the roasted peanuts, even after long-term exposure to desiccation stress. For peanut-based products, after 540 d, only paçoca showed a significant difference (p < 0.05) among the three methods evaluated. In peanut brittle, qPCR-PMA detected 1.5 log cfu g-1, while, in the culture method, Salmonella was recovered in 1 g. The pathogen was below the detection limit in pé-de-moça either by plate count or qPCR-PMA. Therefore, qPCR-PMA shows potential for use in quantifying Salmonella in peanut products.

Type I toxin-antitoxin systems in bacteria: from regulation to biological functions

Toxin-antitoxin systems are ubiquitous in the prokaryotic world and widely distributed among chromosomes and mobile genetic elements. Several different toxin-antitoxin system types exist, but what they all have in common is that toxin activity is prevented by the cognate antitoxin. In type I toxin-antitoxin systems, toxin production is controlled by an RNA antitoxin and by structural features inherent to the toxin messenger RNA. Most type I toxins are small membrane proteins that display a variety of cellular effects. While originally discovered as modules that stabilize plasmids, chromosomal type I toxin-antitoxin systems may also stabilize prophages, or serve important functions upon certain stress conditions and contribute to population-wide survival strategies. Here, we will describe the intricate RNA-based regulation of type I toxin-antitoxin systems and discuss their potential biological functions.

Salmonella dry surface biofilm: morphology, single-cell landscape, and sanitization

In this study, Salmonella Typhimurium dry surface biofilm (DSB) formation was investigated in comparison with wet surface biofilm (WSB) development. Confocal laser scanning microscopic analysis revealed a prominent green cell signal during WSB formation, whereas a red signal predominated during DSB formation. Electron microscopy was also used to compare the features of DSB and WSB. Overall, WSB was unevenly scattered over the surface, whereas DSB was evenly dispersed. In contrast to WSB cells, which have a distinct plasma membrane and outer membrane layer, DSB cells are contained in large capsules and compressed. Next, microbiome single-cell transcriptomics was used to investigate the functional heterogeneity of the Salmonella DSB microbiome, with nine clusters successfully identified. Although over 60% of the dried cells were metabolically inactive, the rest of the Salmonella cells still demonstrated specific antioxidative and virulence capabilities, suggesting a possible concern for low-moisture food (LMF) safety. Finally, because sanitization in LMF industries must be conducted without water, a list of 39 flavonoids was tested for their combined effect with 70% isopropyl alcohol (IPA) against DSB, and morin induced the greatest reduction in the green:red ratio from 3.67 to 0.43. Significantly higher reductions of Salmonella viability in DSB were achieved by 10-, 100-, 1,000-, and 10,000-µg/mL morin (1.69 ± 0.25, 3.21 ± 0.23, 4.32 ± 0.24, and 5.18 ± 0.16 log CFU/sample reductions) than 70% IPA alone (1.55 ± 0.20 log CFU/sample reduction) (P < 0.05), indicating the potential to be formulated as a dry sanitizer for the LMF industry.IMPORTANCEDSB growth of foodborne pathogens in LMF processing environments is associated with food safety, financial loss, and compromised consumer trust. This work is the first comprehensive examination of the characteristics of Salmonella DSB while exploring its underlying survival mechanisms. Furthermore, morin dissolved in 70% IPA was proposed as an efficient dry sanitizer against DSB to provide insights into biofilm control during LMF processing.

Comparative Gene Expression Analysis of Salmonella Typhimurium DT104 in Ground Chicken Extract and Brain Heart Infusion Broth

Salmonella enterica Typhimurium DT104 (S. Typhimurium DT104) is an important foodborne pathogen that is associated with poultry and poultry products. Currently, there is very little information on the underlying molecular mechanisms that allow DT104 to survive and propagate in poultry meat and the poultry processing environment. The current study assessed the global gene expression of DT104 in ground chicken extract (GCE) compared to brain heart infusion (BHI) medium using RNA-Seq technology. DT104 was grown to the early stationary phase (ESP), inoculated into GCE or BHI, and then re-grown to the log phase before RNA was extracted and transcripts were quantified by RNA-Seq. Gene expression for DT104 grown in GCE was then compared to that of DT104 grown in BHI for samples grown to the ESP. Growth in GCE resulted in the up-regulated expression of genes related to translation, carnitine metabolism (23-283-fold change), and cobalamin (vitamin B12) biosynthesis (14-fold change). In particular, the presence of carnitine in chicken meat, and thus, in GCE, which lacks carbohydrates, may allow Salmonella to utilize this compound as a carbon and nitrogen source. This study demonstrates that RNA-Seq data can provide a comprehensive analysis of DT104 gene expression in a food model for poultry products. This study also provides additional evidence for the importance of metabolic adaptation in the ability of S. enterica to successfully adapt to and occupy niches outside of its host and provides potential targets that could be used to develop intervention strategies to control Salmonella in poultry.

The effect of emulsifier type and oil inclusion on stress-related gene expression of Salmonella typhimurium in oil-in-water emulsion

Salmonella has been associated with numerous outbreaks from contaminated food products, including emulsions. Emulsions are influenced by emulsifier type and oil presence, which can have varying degrees of stress or protection on bacteria. Although our previous research has shown that emulsifier solutions, rather than emulsions, provide a protective effect on Salmonella typhimurium after thermal treatment, the underlying mechanism remains unclear. This study selected S. typhimurium as the model microorganism and utilized the same emulsifiers (Tween 20, Tween 80, Triton X-100) to create emulsifier solutions and emulsions with the same oil fraction (60% (v/v)) to examine their effect on the expression of nine selected genes (rpoE, rpoH, otsB, proV, fadA, fabA, dnaK, ibpA, ompC) associated with stress response. Specifically, the study observed variations in gene expression under normal and thermal stress at 55°C. After 20-h incubation, Triton X-100 emulsion caused an upregulation of stress-related genes, rpoE, otsB, and fabA, suggesting stressful environment. After thermal treatment, S. typhimurium in Triton X-100 solution showed a longer 5-log reduction time with increased proV and decreased fabA and ompC expression, suggesting enhanced thermal protection compared to its emulsion. Conversely, Tween 80 solution increased fabA and ompC expression, indicating greater membrane fluidity and passive diffusion, potentially reducing thermal resistance. However, according to the upregulation of ibpA, this effect was likely mitigated by the overproduction of heat shock proteins. Notably, Triton X-100 environments exhibited the most significant gene expression changes after heat treatment, whereas Tween 80 without oil was the most inhospitable for bacterial survival. These findings inform bacterial responses under various conditions, aiding food safety strategies.

Heat Resistance, Virulence, and Gene Expression of Desiccation-Adapted Salmonella Enteritidis During Long-Term Storage in Low-Water Activity Foods

Desiccation stress could induce crossprotection and even affect virulence of Salmonella enterica. However, the influence of food matrices with low-water activity on desiccation adaptation of Salmonella still remains unclear. This study investigated the survival and adaptation of Salmonella Enteritidis in skim milk powder, ginger powder, and chocolate powder under desiccation storage conditions for a total of 12 weeks. High survival rates of Salmonella Enteritidis in all food matrices maintained over the long-term desiccation storage. Desiccation-adapted Salmonella Enteritidis enhanced heat resistance (p < 0.05) with the increase of storage time. Food composition plays an important role in the induction of crossresistance of desiccation-adapted Salmonella. After desiccation storage, Salmonella Enteritidis in ginger powder was most tolerant to heat treatment. Salmonella Enteritidis in skim milk powder was most resistant to the gastrointestinal simulation environment, and had strongest adhesion to Caco-2 cells. The effects of food composition on gene expression (rpoS, proV, otsA, otsB, grpE, dnaK, rpoH, and sigDE) in desiccation-adapted Salmonella Enteritidis were not significant (p > 0.05). At initial desiccation storage, osmotic protection-related genes (fadA, proV, otsA, and otsB), stress response regulator (rpoS), and heat-resistance-related genes (grpE, dnaK, and rpoH) were all significantly upregulated (p < 0.05). However, after 4-week storage, the expression level of desiccation-related genes, proV, otsA, otsB, grpE, dnaK, and rpoH, significantly decreased (p < 0.05). This study enables a better understanding of Salmonella's responses to long-term desiccation stress in different kinds of low-water activity foods.

Adaptive laboratory evolution of Salmonella enterica in acid stress

Introduction

Adaptive laboratory evolution (ALE) studies play a crucial role in understanding the adaptation and evolution of different bacterial species. In this study, we have investigated the adaptation and evolution of Salmonella enterica serovar Enteritidis to acetic acid using ALE.

Materials and methods

Acetic acid concentrations below the minimum inhibitory concentration (sub-MIC) were used. Four evolutionary lineages (EL), namely, EL1, EL2, EL3, and EL4, of S. Enteritidis were developed, each demonstrating varying levels of resistance to acetic acid.

Results

The acetic acid MIC of EL1 remained constant at 27 mM throughout 70 days, while the MIC of EL2, EL3, and EL4 increased throughout the 70 days. EL4 was adapted to the highest concentration of acetic acid (30 mM) and demonstrated the highest increase in its MIC against acetic acid throughout the study, reaching an MIC of 35 mM on day 70. The growth rates of the evolved lineages increased over time and were dependent on the concentration of acetic acid used during the evolutionary process. EL4 had the greatest increase in growth rate, reaching 0.33 (h-1) after 70 days in the presence of 30 mM acetic acid as compared to EL1, which had a growth rate of 0.2 (h-1) after 70 days with no exposure to acetic acid. Long-term exposure to acetic acid led to an increased MIC of human antibiotics such as ciprofloxacin and meropenem against the S. enterica evolutionary lineages. The MIC of ciprofloxacin for EL1 stayed constant at 0.016 throughout the 70 days while that of EL4 increased to 0.047. Bacterial whole genome sequencing revealed single-nucleotide polymorphisms in the ELs in various genes known to be involved in S. enterica virulence, pathogenesis, and stress response including phoP, phoQ, and fhuA. We also observed genome deletions in some of the ELs as compared to the wild-type S. Enteritidis which may have contributed to the bacterial acid adaptation.

Discussion

This study highlights the potential for bacterial adaptation and evolution under environmental stress and underscores the importance of understanding the development of cross resistance to antibiotics in S. enterica populations. This study serves to enhance our understanding of the pathogenicity and survival strategies of S. enterica under acetic acid stress.

Synergistic effects of sequential light treatment with 222-nm/405-nm and 280-nm/405-nm wavelengths on inactivation of foodborne pathogens

Light-based technologies of different wavelengths can inactivate pathogenic microorganisms, but each wavelength has its limitations. This work explores the potential of sequential treatments with different wavelengths for enhancing the disinfection performance of individual treatments by employing various bactericidal mechanisms. The effectiveness, inactivation kinetics, and bactericidal mechanisms of treatments with 222/405, 280/405, and 405 nm alone against Escherichia coli O157:H7, Listeria monocytogenes, Staphylococcus aureus, Salmonella Typhimurium, and Pseudomonas aeruginosa were evaluated. Inactivation experiments were performed in thin liquid bacterial suspensions that were treated either individually with 48 h of 405-nm light or sequentially with (i) 30 s of 222-nm far-UV-C light, followed by 48 h of 405-nm light, or (ii) 30 s of 280-nm far-UV-C light, followed by 48 h of 405-nm light. Survivors were recovered and enumerated by standard plate counting. All inactivation curves were non-linear and followed the Weibull model (0.99 ≥ R2 ≥ 0.70). Synergistic effects were found for E. coli, L. monocytogenes, and S. Typhimurium, with maximum inactivation level increases of 2.9, 3.3, and 1.1 log CFU after the sequential treatments, respectively. Marginal synergy was found for S. aureus, and an antagonistic effect was found for P. aeruginosa after sequential treatments. Significant differences in reactive oxygen species accumulation were found (P < 0.05) after various treatment combinations, and the performance of sequential treatments was correlated with cellular oxidative damage. The sequential wavelength treatments proposed demonstrate the potential for enhanced disinfection of multiple foodborne pathogens compared with individual wavelength treatments, which can have significant food safety benefits. IMPORTANCE Nonthermal light-based technologies offer a chemical-free method to mitigate microbial contamination in the food and healthcare industries. However, each individual wavelength has different limitations in terms of efficacy and operating conditions, which limits their practical applicability. In this study, bactericidal synergism of sequential treatments with different wavelengths was identified. Pre-treatments with 280 and 222 nm enhanced the disinfection performance of follow-up 405-nm treatments for multiple foodborne pathogens by inducing higher levels of cellular membrane damage and oxidative stress. These findings deliver useful information for light equipment manufacturers, food processors, and healthcare users, who can design and optimize effective light-based systems to realize the full potential of germicidal light technologies. The results from the sequential treatments offer practical solutions to improve the germicidal efficacy of visible light systems, as well as provide inspiration for future hurdle disinfection systems design, with a positive impact on food safety and public health.

Performance and transcriptome analysis of Salmonella enterica serovar Enteritidis PT 30 under persistent desiccation stress: Cultured by lawn and broth methods

Lawn-harvest method uses a solid medium (e.g., tryptic soy agar, TSA) to produce bacterial lawns and is widely accepted for the culture of microorganisms in microbial studies of low-moisture foods (LMFs, foods with water activity less than 0.85). It produces desiccation-tolerant cells with higher D-values in LMFs; however, little is known about the molecular mechanisms underlying bacterial resistance. Salmonella enterica Enteritidis PT 30 (S. Enteritidis), the most pertinent pathogen in LMFs, was cultured in TSA and tryptic soy broth (TSB). Cells were harvested and inoculated on filter papers to assess their performance under a relative humidity of 32 ± 2%. Transcriptome analysis of cultured cells during long-term desiccation (24, 72, and 168 h) was conducted in TruSeq PE Cluster Kit (Illumina) by paired-end methods. Lawn-cultured S. Enteritidis cells have stronger survivability (only decreased by 0.78 ± 0.12 log after 130 d of storage) and heat tolerance (higher D/β value) than those from the broth method. More desiccation genes of lawn-cultured cells were significantly upregulated from growth to long-term desiccation. Differentially expressed genes were the most enriched in the ribosome and sulfur metabolism pathways in the lawn- and broth-cultured groups. This study tracked the transcriptomic differences between two cultured groups in response to long-term desiccation stress and revealed some molecular mechanisms underlying their different suitability in microbial studies of LMFs.

Effect of oil exposure stages on the heat resistance of Salmonella enterica serovar Enteritidis phage type 30 in peanut flour

The oil in low-moisture foods (LMFs) shows protective effects on bacteria during thermal processing. However, the circumstances under which this protective effect strengthens remain unclear. This study aimed to understand which step of the oil exposure to bacterial cells (inoculation, isothermal inactivation, or recovery and enumeration step) in LMFs can enhance their heat resistance. Peanut flour (PF) and defatted PF (DPF) were selected as the oil-rich and oil-free LMF models. Salmonella enterica Enteritidis Phage Type 30 (S. Enteritidis) was inoculated into four designated PF groups representing different oil exposure stages. It was isothermally treated to obtain heat resistance parameters. At a constant moisture content (a_w,25°C = 0.32 ± 0.02) and controlled a_w,85°C (0.32 ± 0.02), S. Enteritidis exhibited significantly high (p < 0.05) D values in oil-rich sample groups. For instance, the heat resistance values of S. Enteritidis in the PF-DPF and DPF-PF groups were D_80°C of 138.22 ± 7.45 min and 101.89 ± 7.82 min; however, the D_80°C in the DPF-DPF group was 34.54 ± 2.07 min. The oil addition after the thermal treatment also helped injured bacterial recovery in the enumeration. For instance, the D_80°C, D_85°C, and D_90°C values in the DFF-DPF oil groups were 36.86 ± 2.30, 20.65 ± 1.23, and 7.91 ± 0.52 min, respectively, which were higher than those in the DPF-DPF group at 34.54 ± 2.07, 17.87 ± 0.78, and 7.10 ± 0.52 min. We confirmed that the oil protected S. Enteritidis in PF in all three stages: desiccation process, heat treatment, and recovery of bacterial cells in plates.

The genetic response of Salmonella Typhimurium during trans-cinnamaldehyde assisted heat treatment and its correlation with bacterial resistance in different low moisture food components

Our previous study found that water activity (a_w)- and matrix-dependent bacterial resistance wasdeveloped in Salmonella Typhimurium during antimicrobial-assisted heat treatment in low moisture foods (LMFs) matrices. To better understand the molecular mechanism behind the observed bacterial resistance, gene expression analysis was conducted on S. Typhimurium adapted to different conditions with or without the trans-cinnamaldehyde (CA)-assisted heat treatment via quantitative polymerase chain reaction (qPCR). Expression profiles of nine stress-related genes were analyzed. The upregulation of rpoH and dnaK and downregulation of ompC were observed during bacterial adaptation in LMF matrices and the combined heat treatment, which likely contributed to the bacterial resistance during the combined treatment. Their expression profiles were partially consistent with the previously-observed effect of a_w or matrix on bacterial resistance. The upregulation of rpoE, otsB, proV, and fadA was also observed during adaptation in LMF matrices and might contribute to desiccation resistance, but likely did not contribute to bacterial resistance during the combined heat treatment. The observed upregulation of fabA and downregulation of ibpA could not be directly linked to bacterial resistance to either desiccation or the combined heat treatment. The results may assist the development of more efficient processing methods against S. Typhimurium in LMFs.

Increased heat tolerance and transcriptome analysis of Salmonella enterica Enteritidis PT 30 heat-shocked at 42 ℃

In this study, we compared the heat tolerance parameter (D_65℃) values of Salmonella enterica serovar Enteritidis PT 30 (S. Enteritidis ) heat adapted at different degrees (at 42 ℃ for 20-180 min) and cultivated using two methods. The treated group with the highest D_65℃ value (LP-42 ℃-60 min) and the untreated groups (Control-TSB and Control-TSA) were subjected to transcriptome analysis. Heat-adaptation increased the D_65℃ values of S. Enteritidis by 24.5-60.8%. The D_65℃ values of the LP-42 ℃-60 min group (1.85 ± 0.13 min, 7.7% higher) was comparable to that of the Control-TSA. A total of 483 up- and 443 downregulated genes of S. enteritidis were identified in the LP-42 ℃-60 min group (log₂fold change > 1, adjusted p-value < 0.05). Among these genes, 5 co-expressed and 15 differentially expressed genes in the LP-42 ℃-60 min and Control-TSA grops possibly contributed to the high D_65℃ values of S. Enteritidis . The Rpo regulon was involved in the heat adaptation of S. Enteritidis , as evidenced by the significant upregulation of rpoS, rpoN, and rpoE. KEGG enrichment pathways, such as biosynthesis of secondary metabolites, tricarboxylic acid, and ribosomes were identified and mapped to reveal the molecular mechanisms of S. enteritidis during heat adaptation. This study quantified the enhanced heat tolerance of S. Enteritidis heat adapted at different degrees of heat-adaptation. The results of this study may serve as a basis for elucidating the molecular mechanisms underlying the enhanced heat tolerance at the transcriptome level.

Metabolomics-based response of Salmonella to desiccation stress and skimmed milk powder storage

The strong survival ability of Salmonella in low-moisture foods (LMFs) has been of public concern, and is considered a threat to people's health. Recently, the development of omics technology has promoted research on the molecular mechanisms of the desiccation stress response of pathogenic bacteria. However, multiple analytical aspects related to their physiological characteristics remain unclear. We explored the physiological metabolism changes of S. enterica Enteritidis exposed to a 24 h-desiccation treatment and a subsequent 3-month desiccation storage in skimmed milk powder (SMP) with an approach of gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-Q Exactive-mass spectrometry (UPLC-QE-MS). A total of 8,292 peaks were extracted, of which 381 were detected by GC-MS and 7,911 peaks were identified by LC-MS/MS, respectively. Through analyses of differentially expressed metabolites (DEMs) and key pathways, a total of 58 DEMs emerged from the 24 h-desiccation treatment, which exhibited the highest relevance for five metabolic pathways, involving glycine, serine, and threonine metabolism, pyrimidine metabolism, purine metabolism, vitamin B6 metabolism, and pentose phosphate pathway. After 3-month SMP storage, 120 DEMs were identified, which were related to several regulatory pathways including arginine and proline metabolism, serine and threonine metabolism, β-alanine metabolism, glycerolipid metabolism, and glycolysis. The analyses of key enzyme activities of XOD, PK, and G6PDH and ATP content provided further evidence that supported the metabolic responses such as nucleic acid degradation, glycolysis, and ATP production played an important role in Salmonella's adaptation to desiccation stress. This study enables a better understanding of metabolomics-based responses of Salmonella at the initial stage of desiccation stress and the following long-term adaptive stage. Meanwhile, the identified discriminative metabolic pathways may serve as potentially useful targets in developing strategies for the control and prevention of desiccation-adapted Salmonella in LMFs.

Practice and Progress: Updates on Outbreaks, Advances in Research, and Processing Technologies for Low-moisture Food Safety

Large, renowned outbreaks associated with low-moisture foods (LMFs) bring to light some of the potential, inherent risks that accompany foods with long shelf lives if pathogen contamination occurs. Subsequently, in 2013, Beuchat et al. (2013) noted the increased concern regarding these foods, specifically noting examples of persistence and resistance of pathogens in low-water activity foods (LWAFs), prevalence of pathogens in LWAF processing environments, and sources of and preventive measures for contamination of LWAFs. For the last decade, the body of knowledge related to LMF safety has exponentially expanded. This growing field and interest in LMF safety have led researchers to delve into survival and persistence studies, revealing that some foodborne pathogens can survive in LWAFs for months to years. Research has also uncovered many complications of working with foodborne pathogens in desiccated states, such as inoculation methods and molecular mechanisms that can impact pathogen survival and persistence. Moreover, outbreaks, recalls, and developments in LMF safety research have created a cascading feedback loop of pushing the field forward, which has also led to increased attention on how industry can improve LMF safety and raise safety standards. Scientists across academia, government agencies, and industry have partnered to develop and evaluate innovate thermal and nonthermal technologies to use on LMFs, which are described in the presented review. The objective of this review was to describe aspects of the extensive progress made by researchers and industry members in LMF safety, including lessons-learned about outbreaks and recalls, expansion of knowledge base about pathogens that contaminate LMFs, and mitigation strategies currently employed or in development to reduce food safety risks associated with LMFs.

Salmonella enterica Outbreaks Linked to the Consumption of Tahini and Tahini-Based Products

Salmonella is a leading cause of bacterial foodborne illness in the world. Although typically associated with foods of animal origin, low-moisture foods, such as tahini, are quickly gaining recognition as an important vehicle of Salmonella exposure. This review offers the Canadian perspective on the issue of Salmonella in tahini and tahini-based products. A summary of several recent food product recalls and foodborne outbreaks related to the presence of Salmonella in tahini and tahini-based products such as halva are presented. The properties of the food vehicles, their production practices, and potential routes of contamination are discussed. Particular focus is placed on the ecology of Salmonella in the tahini production continuum, including its survival characteristics and response to intervention technologies.

Changes in the genomes and methylomes of three Salmonella enterica serovars after long-term storage in ground black pepper

Low moisture foods (LMFs) have traditionally been recognized as safe for consumption, as most bacteria require higher water content to grow. However, outbreaks due to LMF foods are increasing, and the microbial pathogen Salmonella enterica is frequently implicated. S. enterica can survive in LMFs for years, but few serovars have been studied, and the mechanisms which underlie this longevity are not well understood. Here, we determine that S. enterica serovars S. Tennessee, S. Anatum, and S. Reading but not S. Oranienburg can survive in the ground black pepper for 6 years. S. Reading was not previously associated with any LMF. Using both Illumina and Pacific Biosciences sequencing technologies, we also document changes in the genomes and methylomes of the surviving serovars over this 6-year period. The three serovars acquired a small number of single nucleotide polymorphisms (SNPs) including seven substitutions (four synonymous, two non-synonymous, and one substitution in a non-coding region), and two insertion-deletions. Nine distinct N6-methyladenine (m6A) methylated motifs across the three serovars were identified including five which were previously known, G^m6ATC, CAG^m6AG, BATGC^m6AT, CRT^m6AYN⁶CTC, and CC^m6AN⁷TGAG, and four novel serovar-specific motifs, GRT^m6AN⁸TTYG, GA^m6ACN⁷GTA, GAA m^6ACY, and CAA^m6ANCC. Interestingly, the BATGCAT motif was incompletely methylated (35–64% sites across the genome methylated), suggesting a possible role in gene regulation. Furthermore, the number of methylated BATGC^m6AT motifs increased after storage in ground black pepper for 6 years from 475 to 657 (S. Tennessee), 366 to 608 (S. Anatum), and 525 to 570 (S. Reading), thus warranting further study as an adaptive mechanism. This is the first long-term assessment of genomic changes in S. enterica in a low moisture environment, and the first study to examine the methylome of any bacteria over a period of years, to our knowledge. These data contribute to our understanding of S. enterica survival in LMFs, and coupled with further studies, will provide the information necessary to design effective interventions which reduce S. enterica in LMFs and maintain a healthy, safe food supply.

Salmonella enterica in soybean production chain: Occurrence, characterization, and survival during soybean storage

This study aimed to determine Salmonella enterica occurrence along the soybean meal production chain (raw material, in-processing samples, final products, and in the environment of five processing plants), characterize the isolates, and assess the survival of Salmonella Senftenberg 775W in soybeans stored under different temperature conditions. Among 713 samples analyzed, 12.9% (n = 92) were positive for Salmonella enterica. Dust collected inside and outside processing plants (n = 148) comprised the samples with the highest positivity for Salmonella enterica, 47.3%. The occurrence of Salmonella enterica varied among the different processing plants. Twenty-nine (n = 29) Salmonella serotypes were isolated, with S. Mbandaka as the most frequent serotype, whereas S. Typhimurium was mainly linked to final product samples (soybean meal). S. Senftenberg 775W did not survive for a long time in soybean stored at 20-37 °C, but at 20 °C, cells were viable for more than 60 days. This study suggests that soybean meal may harbor Salmonella serotypes related to foodborne disease outbreaks in humans and can be responsible for Salmonella introduction into livestock and, consequently, in foods of animal origin. This study provides crucial data on contamination pathways of Salmonella in the soybean production chain, contributing to the understanding of Salmonella epidemiology which is strategic for the development of preventive and control measures to reduce the burden of salmonellosis linked to products of animal origin.

Global transcriptomic analysis of ethanol tolerance response in Salmonella Enteritidis

Adaptation to sublethal amounts of ethanol enables Salmonella Enteritidis to survive under normally lethal ethanol conditions, which is referred to as the ethanol tolerance response (ETR). To uncover mechanisms underlying this adaptative response, RNA-seq and RT-qPCR techniques were employed to reveal global gene expression patterns in S. Enteritidis after sublethal ethanol treatment. It was observed that 811 genes were significantly differentially expressed in ethanol-treated cells compared with control cells, among which 328 were up-regulated and 483 were down-regulated. Functional analysis revealed that these genes were enriched in different pathways, including signal transduction, membrane transport, metabolism, transcription, translation, and cell motility. Specifically, a couple of genes encoding histidine kinases and response regulators in two-component systems were up-regulated to activate sensing and signaling pathways. Membrane function was also influenced by ethanol treatment since ABC transporter genes for transport of glutamate, phosphate, 2-aminoethylphosphonate, and osmoprotectant were up-regulated, while those for transport of iron complex, manganese, and ribose were down-regulated. Accompanied with this, diverse gene expression alterations related to the metabolism of amino acids, carbohydrates, vitamins, and nucleotides were observed, which suggested nutritional requirements for S. Enteritidis to mount the ETR. Furthermore, genes associated with ribosomal units, bacterial chemotaxis, and flagellar assembly were generally repressed as a possible energy conservation strategy. Taken together, this transcriptomic study indicates that S. Enteritidis employs multiple genes and adaptation pathways to develop the ETR.

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A total of 811 genes were involved in ethanol tolerance of Salmonella Enteritidis.

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Certain genes encoding two-component signaling systems were upregulated.

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Differential expression of many metabolism-related genes was observed.

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Bacterial chemotaxis and flagellar assembly were repressed by ethanol stress.

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Diverse membrane transport functions were influenced by ethanol stress.

Survivability and thermal resistance of Salmonella and Escherichia coli O121 in wheat flour during extended storage of 360 days

Foodborne pathogens like Salmonella and Escherichia coli O121 can endure the harsh low water activity (a_w) environment of wheat flour for elongated periods of time and can proliferate when hydrated for baking or other purposes. This study determined the survivability and thermal tolerance (D- and z-values) of Salmonella and Escherichia coli O121 in wheat flour and muffin batter (prepared from inoculated flour on the days of analyses) during the storage period of 360 days. The Salmonella and E. coli O121 studies were conducted as two independent experiments. Both studies were designed as randomized complete block with three replications as blocks. All experimental data were analyzed using one-way ANOVA and Tukey's test in Minitab® software, and P ≤ 0.05 was considered significant. The wheat flour was spray inoculated individually with 7-isolate Salmonella or 3-isolate E. coli O121 cocktail and then dried back to the original a_w levels. On each analysis day, inoculated wheat flour (~5 g) or muffin batter (~2.5 g) was placed inside the TDT disks, heat treated at set temperatures in hot water baths, and sampled at predetermined time intervals for determining the survival microbial population. The population of E. coli O121 and Salmonella cocktails in wheat flour at day 1 were 7.6 ± 0.18 and 7.8 ± 0.07 log CFU/g, respectively, which decreased to 2.0 ± 0.40 and 2.8 ± 0.59 log CFU/g on day 360, respectively. The D-values of Salmonella and E. coli O121 cocktails in inoculated flour and muffin batter prepared from inoculated flour (on the day of analysis) were determined on days 1, 30, 90, 180, 270, and 360 [given enough surviving bacterial population (~3 to 4 log CFU/g) was present in the flour]. The population of Salmonella and E. coli O121 in wheat flour decreased by 5.0 and 5.6 log CFU/g, respectively, during the storage period of 360 days. The D_70°C, D_75°C, and D_80°C values of Salmonella in wheat flour remained similar during the storage period. Whereas, for E. coli O157:H7 in wheat flour, the D_70°C value decreased from 20.3 ± 2.82 to 7.1 ± 2.82 min, and D_75°C decreased from 10.2 ± 2.14 to 2.7 ± 0.27 min, during the storage period of 180 days. The z-values of Salmonella or E. coli O157:H7 remained similar during the storage period. The D- and z-values from this research can be employed for validation of thermal process to ensure safety of wheat flour.

Water sorption characteristics of freeze-dried bacteria in low-moisture foods

Water sorption isotherms of bacteria reflect the water activity with the change of moisture content of bacteria at a specific temperature. The temperature-dependency of water activity change can help to understand the thermal resistance of bacteria during a thermal process. Thermal resistance of bacteria in low-moisture foods may differ significantly depending on the physiological characteristics of microorganisms, including cell structure, existence of biofilms, and growth state. Previous studies demonstrated that the incremental change of a_w in bacterial cells during thermal treatments resulted in changes in their thermotolerance. In this study, a pathogen associated with low-moisture foods outbreaks, Salmonella Enteritidis PT30 (in planktonic and biofilm forms), and its validated surrogate, Enterococcus faecium, were lyophilized and their water sorption isotherms (WSI) at 20, 40, and 60 °C were determined by using a vapor sorption analyzer and simulated by the Guggenheim, Anderson and De Boer model (GAB). The published thermal death times at 80 °C (D_{80 °C}-values) of these bacteria in low-moisture environments were related with their WSI-derived a_w changes. The results showed that planktonic E. faecium and biofilms of Salmonella, exhibiting higher thermal resistance compared to the planktonic cultures of Salmonella, had a smaller increase in a_w when thermally treated from 20 to 60 °C in sealed test cells. The computational modeling also showed that when temperature increased from 20 to 60 °C, with an increase in relative humidity from 10% to 60%, freeze-dried planktonic E. faecium and Salmonella cells would equilibrate to their surrounding environments in 0.15 s and 0.25 s, respectively, suggesting a rapid equilibration of bacterial cells to their microenvironment. However, control of bacteria with different cell structure and growth state would require further attentions on process design adjustment because of their different water sorption characteristics.

Characterization of Basal Transcriptomes Identifies Potential Metabolic and Virulence-Associated Adaptations Among Diverse Nontyphoidal Salmonella enterica Serovars

The zoonotic pathogen Salmonella enterica includes >2,600 serovars, which differ in the range of hosts they infect and the severity of disease they cause. To further elucidate the mechanisms behind these differences, we performed transcriptomic comparisons of nontyphoidal Salmonella (NTS) serovars with the model for NTS pathogenesis, S. Typhimurium. Specifically, we used RNA-seq to characterize the understudied NTS serovars S. Javiana and S. Cerro, representing a serovar frequently attributed to human infection via contact with amphibians and reptiles, and a serovar primarily associated with cattle, respectively. Whole-genome sequence (WGS) data were utilized to ensure that strains characterized with RNA-seq were representative of their respective serovars. RNA extracted from representative strains of each serovar grown to late exponential phase in Luria-Bertani (LB) broth showed that transcript abundances of core genes were significantly higher (p<0.001) than those of accessory genes for all three serovars. Inter-serovar comparisons identified that transcript abundances of genes in Salmonella Pathogenicity Island (SPI) 1 were significantly higher in both S. Javiana and S. Typhimurium compared to S. Cerro. Together, our data highlight potential transcriptional mechanisms that may facilitate S. Cerro and S. Javiana survival in and adaptation to their respective hosts and impact their ability to cause disease in others. Furthermore, our analyses demonstrate the utility of omics approaches in advancing our understanding of the diversity of metabolic and virulence mechanisms of different NTS serovars.

Influence of drying conditions, food composition, and water activity on the thermal resistance of Salmonella enterica

Salmonella contamination of low-water activity (a_w) foods poses a serious concern worldwide. The present study was conducted to assess the effects of drying conditions, food composition, and water activity on the desiccation tolerance and thermal resistance of S. Enteritidis FUA1946, S. Senftenberg ATCC43845 and S. Typhimurium ATCC13311 in pet food, binder formulation, and skim milk powder. The samples were wet inoculated with the individual Salmonella strains and were equilibrated to a_w 0.33 and 0.75, followed by an isothermal treatment at 70 °C. The thermal inactivation data was fitted to the Weibull model. Irrespective of the a_w, food composition and physical structure of the selected foods, strain S. Enteritidis FUA1946 displayed the highest desiccation and thermal resistance, followed by S. Senftenberg ATCC43845 and S. Typhimurium ATCC13311. The food matrix and strain type significantly (p < 0.05) influenced the thermal resistance of microorganisms in foods along with a_w change during thermal treatments. To further study the effect of food composition, an additional set of experiments using dry inoculation of the resistant Salmonella strain in the low-a_w foods was designed. Significant (p < 0.05) matrix-dependent interaction on Salmonella reduction was observed. The water adsorption isotherms of selected low-a_w foods were measured at 20 and 70 °C to relate the thermal inactivation kinetics with the change in the a_w. The characterization of thermal resistance of the Salmonella serovars in low-a_w products with different compositions and a_w in this study may be used for the validation of thermal challenge studies.

Microbial anhydrobiosis

The loss of cellular water (desiccation) and the resulting low cytosolic water activity are major stress factors for life. Numerous prokaryotic and eukaryotic taxa have evolved molecular and physiological adaptions to periods of low water availability or water-limited environments that occur across the terrestrial Earth. The changes within cells during the processes of desiccation and rehydration, from the activation (and inactivation) of biosynthetic pathways to the accumulation of compatible solutes, have been studied in considerable detail. However, relatively little is known on the metabolic status of organisms in the desiccated state; that is, in the sometimes extended periods between the drying and rewetting phases. During these periods, which can extend beyond decades and which we term 'anhydrobiosis', organismal survival could be dependent on a continued supply of energy to maintain the basal metabolic processes necessary for critical functions such as macromolecular repair. Here, we review the state of knowledge relating to the function of microorganisms during the anhydrobiotic state, highlighting substantial gaps in our understanding of qualitative and quantitative aspects of molecular and biochemical processes in desiccated cells.

Induction of a Viable but Nonculturable State, Thermal and Sanitizer Tolerance, and Gene Expression Correlation with Desiccation-Adapted Biofilm and Planktonic Salmonella in Powdered Infant Formula

ABSTRACT

This study was conducted to investigate the effects of the physiological state, desiccation adaptation, and storage of powdered infant formula on Salmonella cell survival and expression of desiccation stress-related genes. Powdered infant formula was inoculated with Salmonella Typhimurium in the biofilm state on beads and in the planktonic state on nitrocellulose filters and stored at 25°C for up to 270 days. Both 5-cyano-2,3-ditoyl tetrazolium chloride flow cytometry and xylose lysine deoxycholate agar plate counts revealed that biofilm-forming Salmonella cells tended to enter the viable but nonculturable (VBNC) state (P < 0.05). The population reduction of all desiccation-adapted Salmonella Typhimurium decreased significantly in both physiological states after exposure to mild heat (60°C) compared with nonadapted control cells (P < 0.05). Salmonella cells were cross-protected from heat in both physiological states, but cross-protection against hydrogen peroxide was induced for only planktonic Salmonella cells. The reverse transcription quantitative PCR results revealed that the rpoS gene in biofilm Salmonella cells on all desiccation adaption days and in planktonic Salmonella cells on day 7 of dry storage was significantly upregulated (P < 0.05). The rpoE, grpE, and invA genes in Salmonella cells in both physiological states were significantly down-regulated (P < 0.05). Physiological state and storage time might affect expression of these genes. Prior exposure to adverse conditions, including low water activity, and the physiological state impacted Salmonella survival, and its ability to enter the VBNC state and gene expression.

HIGHLIGHTS

Gene expression profile analysis and target gene discovery of Mycobacterium tuberculosis biofilm

Tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tuberculosis) is a fatal infectious disease to human health, and the drug tolerance and immune evasion of M. tuberculosis were reported to be related to its biofilm formation; however, the difficulty of M. tuberculosis biofilm culture and its unknown global mechanism impede its further research. Here, we developed a modified in vitro M. tuberculosis biofilm model with shorter culture time. Then we used Illumina RNA-seq technology to determine the global gene expression profile of M. tuberculosis H37Rv biofilms. Over 437 genes are expressed at significantly different levels in biofilm cells than in planktonic cells; among them, 153 were downregulated and 284 were upregulated. Go enrichment analysis and KEGG pathway analysis showed that genes involved in biosynthesis and metabolism of sulfur metabolism, steroid degradation, atrazine degradation, mammalian cell entry protein complex, etc. are involved in M. tuberculosis biofilm cells. Especially, ATP-binding cassette (ABC) transporters Rv1217c and Rv1218c were significantly upregulated in biofilm, whereas efflux pump inhibitors (EPIs) piperine and 1-(1-naphthylmethyl)-piperazine (NMP) inhibited biofilm formation and the expression of the Rv1217c and Rv1218c genes in a concentration-dependent manner, respectively, indicating Rv1217c and Rv1218c are potential target genes of M. tuberculosis biofilm. This study is the first RNA-Seq-based transcriptome profiling of M. tuberculosis biofilms and provides insights into a potential strategy for M. tuberculosis biofilm inhibition. KEY POINTS: • Characterize M. tuberculosis transcriptomes in biofilm cells by RNA-seq. • Inhibit the expression of Rv1217c and Rv1218c repressed biofilm formation.

Trehalose and α-glucan mediate distinct abiotic stress responses in Pseudomonas aeruginosa

An important prelude to bacterial infection is the ability of a pathogen to survive independently of the host and to withstand environmental stress. The compatible solute trehalose has previously been connected with diverse abiotic stress tolerances, particularly osmotic shock. In this study, we combine molecular biology and biochemistry to dissect the trehalose metabolic network in the opportunistic human pathogen Pseudomonas aeruginosa PAO1 and define its role in abiotic stress protection. We show that trehalose metabolism in PAO1 is integrated with the biosynthesis of branched α-glucan (glycogen), with mutants in either biosynthetic pathway significantly compromised for survival on abiotic surfaces. While both trehalose and α-glucan are important for abiotic stress tolerance, we show they counter distinct stresses. Trehalose is important for the PAO1 osmotic stress response, with trehalose synthesis mutants displaying severely compromised growth in elevated salt conditions. However, trehalose does not contribute directly to the PAO1 desiccation response. Rather, desiccation tolerance is mediated directly by GlgE-derived α-glucan, with deletion of the glgE synthase gene compromising PAO1 survival in low humidity but having little effect on osmotic sensitivity. Desiccation tolerance is independent of trehalose concentration, marking a clear distinction between the roles of these two molecules in mediating responses to abiotic stress.

Author summary

To survive outside their host, pathogenic bacteria must withstand various environmental stresses. The sugar molecule trehalose is associated with a range of abiotic stress tolerances, particularly osmotic shock. In this study, we analyse the trehalose metabolic network in the human pathogen Pseudomonas aeruginosa PAO1 and define its role in abiotic stress protection. We show that trehalose metabolism in PAO1 is intimately connected to the biosynthesis of branched α-glucan, or glycogen. Disruption of either trehalose or glycogen biosynthesis significantly reduces the ability of PAO1 to survive on steel work surfaces. While both trehalose and glycogen are important for stress tolerance, they counter very different stresses. Trehalose is important for the osmotic stress response, and survival in conditions of elevated salt. On the other hand, glycogen is responsible for desiccation tolerance and survival in low humidity environments. Trehalose does not apparently contribute to desiccation tolerance, marking a clear distinction between the roles of trehalose and glycogen in mediating abiotic stress responses in P. aeruginosa.

Control of Salmonella in low-moisture foods: Enterococcus faecium NRRL B-2354 as a surrogate for thermal and non-thermal validation

Salmonella has been implicated in multiple foodborne outbreaks and recalls associated with low water activity foods (La_wF). To verify the effectiveness of a process against Salmonella in La_wF, validation using a nonpathogenic surrogate strain is essential. Enterococcus faecium NRRL B-2354 strain has been used as a potential surrogate of Salmonella in different processing of La_wF. However, the survival of Salmonella and E. faecium in La_wF during food processing is a dynamic function of a_w, food composition and structure, processing techniques, and other factors. This review assessed pertinent literature on the thermal and non-thermal inactivation of Salmonella and its presumable surrogate E. faecium in various La_wF and provided an overview of its suitibility in different La_wF. Overall, based on the D-values, survival/reduction, temperature/time to obtain 4 or 5-log reductions, most studies concluded that E. faecium is a suitable surrogate of Salmonella during La_wF processing as its magnitude of resistance was slightly greater or equal (i.e., statistical similar) as compared to Salmonella. Studies also showed its unsuitability which either does not provide a proper margin of safety or being overly resistant and may compromise the quality and organoleptic properties of food. This review provides useful information and guidance for future validation studies of La_wF.

Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-Starved Salmonella enterica Serovar Typhimurium

An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression during environmental stress. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers of Salmonella stress survival. Generally thought to be 50-500 nucleotides in length and to occur in intergenic regions, sRNAs typically regulate protein expression through base pairing with mRNA targets. In this work, through employing a refined definition of sRNAs allowing for shorter sequences and sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs, and our computational analyses find the majority to be highly conserved and structurally related to known sRNAs. Importantly, we show that deletion of one of the sRNAs dynamically expressed during C-starvation, sRNA4130247, significantly impairs the Salmonella C-starvation response (CSR), confirming its involvement in the Salmonella CSR. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs in Salmonella, experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and more than doubles the Salmonella enterica sRNAs described to date.

Impact of the Resistance Responses to Stress Conditions Encountered in Food and Food Processing Environments on the Virulence and Growth Fitness of Non-Typhoidal Salmonellae

The success of Salmonella as a foodborne pathogen can probably be attributed to two major features: its remarkable genetic diversity and its extraordinary ability to adapt. Salmonella cells can survive in harsh environments, successfully compete for nutrients, and cause disease once inside the host. Furthermore, they are capable of rapidly reprogramming their metabolism, evolving in a short time from a stress-resistance mode to a growth or virulent mode, or even to express stress resistance and virulence factors at the same time if needed, thanks to a complex and fine-tuned regulatory network. It is nevertheless generally acknowledged that the development of stress resistance usually has a fitness cost for bacterial cells and that induction of stress resistance responses to certain agents can trigger changes in Salmonella virulence. In this review, we summarize and discuss current knowledge concerning the effects that the development of resistance responses to stress conditions encountered in food and food processing environments (including acid, osmotic and oxidative stress, starvation, modified atmospheres, detergents and disinfectants, chilling, heat, and non-thermal technologies) exerts on different aspects of the physiology of non-typhoidal Salmonellae, with special emphasis on virulence and growth fitness.

Taxonomic and Functional Shifts in the Sprout Spent Irrigation Water Microbiome in Response to Salmonella Contamination of Alfalfa Seeds

Despite recent advances in Salmonella-sprout research, little is known about the relationship between Salmonella and the sprout microbiome during sprouting. Sprout spent irrigation water (SSIW) provides an informative representation of the total microbiome of this primarily aquaponic crop. This study was designed to characterize the function and taxonomy of the most actively transcribed genes in SSIW from Salmonella enterica serovar Cubana-contaminated alfalfa seeds throughout the sprouting process. Genomic DNA and total RNA from SSIW was collected at regular intervals and sequenced using Illumina MiSeq and NextSeq platforms. Nucleic acid data were annotated using four different pipelines. Both metagenomic and metatranscriptomic analyses revealed a diverse and highly dynamic SSIW microbiome. A "core" SSIW microbiome comprised Klebsiella, Enterobacter, Pantoea, and Cronobacter The impact, however, of Salmonella contamination on alfalfa seeds influenced SSIW microbial community dynamics not only structurally but also functionally. Changes in genes associated with metabolism, genetic information processing, environmental information processing, and cellular processes were abundant and time dependent. At time points of 24 h, 48 h, and 96 h, totals of 541, 723, and 424 S Cubana genes, respectively, were transcribed at either higher or lower levels than at 0 h in SSIW during sprouting. An array of S Cubana genes (107) were induced at all three time points, including genes involved in biofilm formation and modulation, stress responses, and virulence and tolerance to antimicrobials. Taken together, these findings expand our understanding of the effect of Salmonella seed contamination on the sprout crop microbiome and metabolome.IMPORTANCE Interactions of human enteric pathogens like Salmonella with plants and plant microbiomes remain to be elucidated. The rapid development of next-generation sequencing technologies provides powerful tools enabling investigation of such interactions from broader and deeper perspectives. Using metagenomic and metatranscriptomic approaches, this study identified not only changes in microbiome structure of SSIW associated with sprouting but also changes in the gene expression patterns related to the sprouting process in response to Salmonella contamination of alfalfa seeds. This study advances our knowledge on Salmonella-plant (i.e., sprout) interaction.

Mechanisms of Salmonella Attachment and Survival on In-Shell Black Peppercorns, Almonds, and Hazelnuts

Salmonella enterica subspecies I (ssp 1) is the leading cause of hospitalizations and deaths due to known bacterial foodborne pathogens in the United States and is frequently implicated in foodborne disease outbreaks associated with spices and nuts. However, the underlying mechanisms of this association have not been fully elucidated. In this study, we evaluated the influence of storage temperature (4 or 25°C), relative humidity (20 or 60%), and food surface characteristics on the attachment and survival of five individual strains representing S. enterica ssp 1 serovars Typhimurium, Montevideo, Braenderup, Mbandaka, and Enteritidis on raw in-shell black peppercorns, almonds, and hazelnuts. We observed a direct correlation between the food surface roughness and S. enterica ssp 1 attachment, and detected significant inter-strain difference in survival on the shell surface under various storage conditions. A combination of low relative humidity (20%) and ambient storage temperature (25°C) resulted in the most significant reduction of S. enterica on shell surfaces (p < 0.05). To identify genes potentially associated with S. enterica attachment and survival on shell surfaces, we inoculated a library of 120,000 random transposon insertion mutants of an S. Enteritidis strain on almond shells, and screened for mutant survival after 1, 3, 7, and 14 days of storage at 20% relative humidity and 25°C. Mutants in 155 S. Enteritidis genes which are involved in carbohydrate metabolic pathways, aerobic and anaerobic respiration, inner membrane transport, and glutamine synthesis displayed significant selection on almond shells (p < 0.05). Findings of this study suggest that various food attributes, environmental factors, and an unexpectedly complex metabolic and regulatory network in S. enterica ssp 1 collectively contribute to the bacterial attachment and survival on low moisture shell surface, providing new data for the future development of knowledge-based intervention strategies.

The Small Toxic Salmonella Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR

Next-generation sequencing (NGS) has enabled the revelation of a vast number of genomes from organisms spanning all domains of life. To reduce complexity when new genome sequences are annotated, open reading frames (ORFs) shorter than 50 codons in length are generally omitted. However, it has recently become evident that this procedure sorts away ORFs encoding small proteins of high biological significance. For instance, tailored small protein identification approaches have shown that bacteria encode numerous small proteins with important physiological functions. As the number of predicted small ORFs increase, it becomes important to characterize the corresponding proteins. In this study, we discovered a conserved but previously overlooked small enterobacterial protein. We show that this protein, which we dubbed TimP, is a potent toxin that inhibits bacterial growth by targeting the cell membrane. Toxicity is relieved by a small regulatory RNA, which binds the toxin mRNA to inhibit toxin synthesis.

Small proteins are gaining increased attention due to their important functions in major biological processes throughout the domains of life. However, their small size and low sequence conservation make them difficult to identify. It is therefore not surprising that enterobacterial ryfA has escaped identification as a small protein coding gene for nearly 2 decades. Since its identification in 2001, ryfA has been thought to encode a noncoding RNA and has been implicated in biofilm formation in Escherichia coli and pathogenesis in Shigella dysenteriae. Although a recent ribosome profiling study suggested ryfA to be translated, the corresponding protein product was not detected. In this study, we provide evidence that ryfA encodes a small toxic inner membrane protein, TimP, overexpression of which causes cytoplasmic membrane leakage. TimP carries an N-terminal signal sequence, indicating that its membrane localization is Sec-dependent. Expression of TimP is repressed by the small RNA (sRNA) TimR, which base pairs with the timP mRNA to inhibit its translation. In contrast to overexpression, endogenous expression of TimP upon timR deletion permits cell growth, possibly indicating a toxicity-independent function in the bacterial membrane.

Survival and thermal resistance of Salmonella in dry and hydrated nonfat dry milk and whole milk powder during extended storage

Foodborne pathogens such as Salmonella can endure dry environments of milk powders for extended periods due to the increased adaptability at a low water activity (a_w) and proliferate when powders are hydrated. This study compared the survivability and the thermal resistance of a 5-serovar Salmonella cocktail in dry and hydrated nonfat dry milk (NFDM) and whole milk powder (WMP) stored for 180 days at ambient temperature (~20 °C). This study was designed as two factorial (storage days and milk powder type) randomized complete block design with three replications as blocks. The milk powders were spray inoculated with 5-serovar Salmonella cocktail and dried back to the original pre-inoculation a_w. The D-values of Salmonella in inoculated NFDM and WMP were determined periodically (every 30 days, starting from day one). The milk powders were also individually hydrated on each analysis day to determine D- and z-values of Salmonella in hydrated powders. The D-values were determined using thermal-death-time disks and hot-water baths at 80, 85 and 90 °C for milk powders, and 59, 62 and 65 °C for hydrated powders. The D- and z-values of Salmonella at specific temperatures within dry or hydrated powders during the storage period were compared at P ≤ 0.05 using two-way ANOVA and Tukey's Test. The D-values of Salmonella in WMP on day 1 were 18.9, 9.9 and 4.4 min at 80, 85 and 90 °C, respectively, which increased to 29.4, 13.6 and 6.5 min at 80, 85 and 90 °C, respectively, on day 180. Whereas, D-values of Salmonella in NFDM on day 1 were 17.9, 9.2 and 4.4 min at 80, 85 and 90 °C, respectively, and stayed similar during the storage. The D-values of Salmonella in milk powder remained similar throughout the storage once hydrated. The overall z-value of Salmonella in NFDM and WMP was 16.3 °C, whereas in hydrated NFDM and WMP, the overall z-value was 6.4 °C.

Microbial safety of oily, low water activity food products: A review

Oily, low water activity (OL a_w) products including tahini (sesame seed paste), halva (tahini halva), peanut butter, and chocolate, have been recently linked to numerous foodborne illness outbreaks and recalls. This review discusses the ingredients used and processing of OL a_w products with a view to provide greater understanding of the routes of their contamination with foodborne pathogens and factors influencing pathogen persistence in these foods. Adequate heat treatment during processing may eliminate bacterial pathogens from OL a_w foods; however, post-processing contamination commonly occurs. Once these products are contaminated, their high fat and sugar content can enhance pathogen survival for long periods. The physiological basis and survival mechanisms used by pathogens in these products are comprehensively discussed here. Foodborne outbreaks and recalls linked to OL a_w foods are summarized and it was observed that serotypes of Salmonella enterica were the predominant pathogens causing illnesses. Further, intervention strategies available to control foodborne pathogens such as thermal inactivation, use of natural antimicrobials, irradiation and hydrostatic pressure are assessed for their usefulness to achieve pathogen control and enhance the safety of OL a_w foods. Sanitation, hygienic design of manufacturing facilities, good hygienic practices, and environmental monitoring of OL a_w food industries were also discussed.

Survival and thermal resistance among four Salmonella serovars inoculated onto flaxseeds

Thermal resistance among Salmonella serovars has been shown to vary, however, such data are minimal for Salmonella inoculated onto low moisture foods. We evaluated survival and subsequent thermal resistance for 32 strains of Salmonella from four serovars (Agona, Enteritidis, Montevideo, and Tennessee) on flaxseed over 24 weeks. After inoculation, flaxseeds were adjusted to a_w = 0.5 and stored at 22 °C. After 24 weeks at 22 °C, strains of serovar Agona had a significantly slower rate of reduction compared to those of Enteritidis and Montevideo (adj. p < 0.05). Inoculated flaxseeds were processed at 71 °C with vacuum steam pasteurization at 4 time points during storage. Average initial D_71°C values ranging from 1.0 to 1.5 min were similar across serovars. Over 24 weeks, D_71°C varied in a serovar-dependent manner. D_71°C at 8, 16, and 24 weeks did not change significantly for Enteritidis and Montevideo but did for Tennessee and Agona. While significant, the differences in D_71°C over time were less than 1 min, indicating that storage time prior to heat treatment would have a minimal effect on the processing time required to inactivate Salmonella on flaxseed.

Changes in cellular structure of heat-treated Salmonella in low-moisture environments

AIMS

Salmonella cells desiccated in an environment with low-water activity (a_w ) show longer survival times and enhanced resistance to heat. However, little is known about the cellular ultrastructure of Salmonella in low-a_w environment in relation to the survival and persistence during desiccation.

MATERIALS AND RESULTS

In this study, Salmonella Enteritidis strain PT30 was dehydrated by exposure to air or by mixing with wheat flour (a_w 0·30 at room temperature) for 7 days followed by heat treatment at 80°C for 10, 20, 60 min respectively. Transmission electron microscopy (TEM) was employed to examine and compare the ultrastructure of heat-treated S. Enteritidis cells after desiccation with the cells suspended in trypticase soy broth (TSB). Cells suspended in TSB broth showed disrupted ribosomes, congregated proteins and denatured DNA. However, no significant alterations were observed in the ultrastructure of the desiccated cells after heat treatment. The number of desiccated S. Enteritidis cells decreased by <1·5 log CFU per gram after 80°C treatment for 60 min, however, cells suspended in TSB declined more than 5 log₁₀ CFU per mL at 80°C within 5 min.

CONCLUSIONS

A drastic difference in the number of survivors and cellular ultrastructure was observed between vegetative and air or food-dried S. Enteritidis cells after subjecting to heat treatment at 80°C. No significant ultrastructure changes were observed in desiccated cells after heat treatment except for roughening and corrugating surfaces.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides a direct comparison to illustrate how desiccation influences the cell ultrastructure before/after heat treatment, which will aid in better understanding of the fundamental mechanism underlying the increased thermal resistance of Salmonella cells in low-a_w environment.