Light tolerance of extended spectrum ß-lactamase producing Escherichia coli strains after repetitive exposure to far-UVC and blue LED light.

AIMS: The aim of this study was to investigate dual far-UVC (Ultraviolet-C) (222 nm) and blue LED (Light Emitting Diode) (405 nm) light on the inactivation of extended spectrum ß-lactamase-producing Escherichia coli (ESBL-Ec) and to determine if repetitive exposure to long pulses of light resulted in changes to light tolerance, and antibiotic susceptibility. METHODS AND RESULTS: Antimicrobial efficiency of dual and individual light wavelengths and development of light tolerance in E. coli was evaluated through a spread plate method after exposure to light at 25 cm. Dual light exposure for 30 min resulted in a 5-6 log10 CFU mL-1 reduction in two ESBL-Ec and two antibiotic-sensitive control E. coli strains. The overall inhibition achieved by dual light treatment was always greater than the combined reductions (log10 CFU) observed from exposure to individual light wavelengths (combined 222-405 nm), indicating a synergistic relationship between blue LED and far-UVC light when used together. Repetitive long pulses of dual and individual far-UVC light exposure resulted in light tolerance in two ESBL-Ec strains but not the antibiotic-sensitive E. coli strains. Subsequent passages of repetitive light-treated ESBL-Ec strains continued to exhibit light tolerance. Antibiotic susceptibility was determined through a standard disk diffusion method. No changes were observed in the antibiotic susceptibility profiles for any of the four strains after exposure to either dual or individual wavelengths. CONCLUSIONS: Dual light exposure was effective in the disinfection of ESBL-Ec in solution; however, antibiotic-resistant E. coli were able to develop light tolerance after repetitive exposure to light.

Fecal excretion of Campylobacter jejuni by young dairy calves and the relationship with neonatal immunity and personality traits.

AIMS: Zoonotic pathogens in bovine herds are major concerns for human and animal health, but their monitoring in animals can be challenging in the absence of clinical signs. Our objective was to determine the association between fecal excretion of Campylobacter jejuni, neonatal immunity, and personality traits of calves. METHODS AND RESULTS: Forty-eight dairy calves were reared in three indoor pens from birth to 4 weeks of life. Microbial analyses of the fecal samples collected weekly revealed that the proportion of calves naturally contaminated with C. jejuni in each pen reached 70% after 3 weeks of life. High (>16 g l-1) levels of IgG levels in the serum of neonatal calves were negatively (P = .04) associated with fecal detection of C. jejuni over the trial period. Calves that spent more time interacting with a novel object tended to be positive (P = .058) for C. jejuni. CONCLUSIONS: Overall, the findings indicate that the immunity of neonatal dairy animals and possibly the animal's behavior may contribute to the fecal shedding of C. jejuni.

Molecular detection and characterization of foodborne bacteria: Recent progresses and remaining challenges.

The global food demand is expected to increase in the coming years, along with challenges around climate change and food security. Concomitantly, food safety risks, particularly those related to bacterial pathogens, may also increase. Thus, the food sector needs to innovate to rise to this challenge. Here, we discuss recent advancements in molecular techniques that can be deployed within various foodborne bacteria surveillance systems across food settings. To start with, we provide updates on nucleic acid-based detection, with a focus on polymerase chain reaction (PCR)-based technologies and loop-mediated isothermal amplification (LAMP). These include descriptions of novel genetic markers for several foodborne bacteria and progresses in multiplex PCR and droplet digital PCR. The next section provides an overview of the development of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins systems, such as CRISPR-Cas9, CRISPR-Cas12a, and CRISPR-Cas13a, as tools for enhanced sensitive and specific detection of foodborne pathogens. The final section describes utilizations of whole genome sequencing for accurate characterization of foodborne bacteria, ranging from epidemiological surveillance to model-based predictions of bacterial phenotypic traits through genome-wide association studies or machine learning.

Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use.

Generic Escherichia coli is commonly used as an indicator of fecal contamination to assess water quality and human health risk. Where measured E. coli exceedances occur, the presence of other pathogenic microorganisms, such as Shiga toxin-producing E. coli (STEC), is assumed, but confirmatory data are lacking. Putative E. coli isolates (n = 709) were isolated from water, sediment, soil, periphyton, and feces samples (n = 189) from five sites representing native forest and agricultural environments. Ten E. coli isolates (1.41%) were stx2 positive, 19 (2.7%) were eae positive, and stx1-positive isolates were absent. At the sample level, stx2-positive E. coli (5 of 189, 2.6%) and eae-positive isolates (16 of 189, 8.5%) were rare. Using real-time PCR, these STEC-associated virulence factors were determined to be more prevalent in sample enrichments (stx1, 23.9%; stx2, 31.4%; eae, 53.7%) and positively correlated with generic E. coli isolate numbers (P < 0.05) determined using culture-based methods. Whole-genome sequencing (WGS) was undertaken on a subset of 238 isolates with assemblies representing seven E. coli phylogroups (A, B1, B2, C, D, E, and F), 22 Escherichia marmotae isolates, and 1 Escherichia ruysiae isolate. Virulence factors, including those from extraintestinal pathogenic E. coli, were extremely diverse in isolates from the different locations and were more common in phylogroup B2. Analysis of the virulome from WGS data permitted the identification of gene repertoires that may be involved in environmental fitness and broadly align with phylogroup. Although recovery of STEC isolates was low, our molecular data indicate that they are likely to be widely present in environmental samples containing diverse E. coli phylogroups. IMPORTANCE This study takes a systematic sampling approach to assess the public health risk of Escherichia coli recovered from freshwater sites within forest and farmland. The New Zealand landscape is dominated by livestock farming, and previous work has demonstrated that "recreational exposure to water" is a risk factor for human infection by Shiga toxin-producing Escherichia coli (STEC). Though STEC isolates were rarely isolated from water samples, STEC-associated virulence factors were identified more commonly from water sample culture enrichments and were associated with increased generic E. coli concentrations. Whole-genome sequencing data from both E. coli and newly described Escherichia spp. demonstrated the presence of virulence factors from E. coli pathotypes, including extraintestinal pathogenic E. coli. This has significance for understanding and interpreting the potential health risk from E. coli where water quality is poor and suggests a role of virulence factors in survival and persistence of E. coli and Escherichia spp.

Growth medium- and strain-dependent bactericidal efficacy of blue light against Shiga toxin-producing Escherichia coli on food-grade stainless steel and plastic.

Shiga toxin-producing Escherichia coli (STEC) are a major group of human pathogens and may persist on both abiotic and biotic surfaces. In this report, two blue-light prototypes were used to evaluate the antimicrobial efficacy against STEC on food processing surfaces (stainless steel and polyoxymethylene plastic). Investigation using a light-bulb prototype (Prototype 1 at 405 nm, 26 mW/cm2) showed significant antimicrobial effects in nutrient deficient condition but not in nutrient rich condition, demonstrating that the presence of organic matters from rich nutrient medium was thought to be light-absorptive and reduce the bactericidal efficacy of blue light, as evident from the lack of bacterial reduction when suspended in cooked meat broth. An advanced (surface-mounted-diode) light panel, Prototype 2 with high light intensity (405 nm; 50 mW/cm2) was able to inactivate a cocktail of seven STEC strains (from seven major serotypes O26, O45, O103, O111, O121, O145 and O157) on type 304 stainless steel (1.66 log10 CFU) and polyoxymethylene plastic (4.25 log10 CFU) at light dosages of 720 and 45 J/cm2, respectively when cells were illuminated in a nutrient-deficient medium (M9 broth). Post-treatment, no STEC cells were recoverable from plastic, both when tested on plates (agar or petrifilms) and by polymerase chain reaction (PCR). In contrast, surviving colonies were identified on samples taken from stainless steel, albeit only four strains could be detected by PCR analysis - those belonging to serotypes O26, O45, O103 and O157 - which indicated that the susceptibility of STEC to blue light varied across the tested strains.

Hyperspectral imaging and machine learning in food microbiology: Developments and challenges in detection of bacterial, fungal, and viral contaminants.

Hyperspectral imaging (HSI) is a robust and nondestructive method that can detect foreign particles such as microbial, chemical, and physical contamination in food. This review summarizes the work done in the last two decades in this field with a highlight on challenges, risks, and research gaps. Considering the challenges of using HSI on complex matrices like food (e.g., the confounding and masking effects of background signals), application of machine learning and modeling approaches that have been successful in achieving better accuracy as well as increasing the detection limit have also been discussed here. Foodborne microbial contaminants such as bacteria, fungi, viruses, yeast, and protozoa are of interest and concern to food manufacturers due to the potential risk of either food poisoning or food spoilage. Detection of these contaminants using fast and efficient methods would not only prevent outbreaks and recalls but will also increase consumer acceptance and demand for shelf-stable food products. The conventional culture-based methods for microbial detection are time and labor-intensive, whereas hyperspectral imaging (HSI) is robust, nondestructive with minimum sample preparation, and has gained significant attention due to its rapid approach to detection of microbial contaminants. This review is a comprehensive summary of the detection of bacterial, viral, and fungal contaminants in food with detailed emphasis on the specific modeling and datamining approaches used to overcome the specific challenges associated with background and data complexity.

Culture and genome-based analysis of four soil Clostridium isolates reveal their potential for antimicrobial production.

BACKGROUND: Soil bacteria are a major source of specialized metabolites including antimicrobial compounds. Yet, one of the most diverse genera of bacteria ubiquitously present in soil, Clostridium, has been largely overlooked in bioactive compound discovery. As Clostridium spp. thrive in extreme environments with their metabolic mechanisms adapted to the harsh conditions, they are likely to synthesize molecules with unknown structures, properties, and functions. Therefore, their potential to synthesize small molecules with biological activities should be of great interest in the search for novel antimicrobial compounds. The current study focused on investigating the antimicrobial potential of four soil Clostridium isolates, FS01, FS2.2 FS03, and FS04, using a genome-led approach, validated by culture-based methods. RESULTS: Conditioned/spent media from all four Clostridium isolates showed varying levels of antimicrobial activity against indicator microorganism; all four isolates significantly inhibited the growth of Pseudomonas aeruginosa. FS01, FS2.2, and FS04 were active against Bacillus mycoides and FS03 reduced the growth of Bacillus cereus. Phylogenetic analysis together with DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and functional genome distribution (FGD) analyses confirmed that FS01, FS2.2, and FS04 belong to the species Paraclostridium bifermentans, Clostridium cadaveris, and Clostridium senegalense respectively, while FS03 may represent a novel species of the genus Clostridium. Bioinformatics analysis using antiSMASH 5.0 predicted the presence of eight biosynthetic gene clusters (BGCs) encoding for the synthesis of ribosomally synthesized post-translationally modified peptides (RiPPs) and non-ribosomal peptides (NRPs) in four genomes. All predicted BGCs showed no similarity with any known BGCs suggesting novelty of the molecules from those predicted gene clusters. In addition, the analysis of genomes for putative virulence factors revealed the presence of four putative Clostridium toxin related genes in FS01 and FS2.2 genomes. No genes associated with the main Clostridium toxins were identified in the FS03 and FS04 genomes. CONCLUSIONS: The presence of BGCs encoding for uncharacterized RiPPs and NRPSs in the genomes of antagonistic Clostridium spp. isolated from farm soil indicated their potential to produce novel secondary metabolites. This study serves as a basis for the identification and characterization of potent antimicrobials from these soil Clostridium spp. and expands the current knowledge base, encouraging future research into bioactive compound production in members of the genus Clostridium.

An investigation of the environmental niches of blown pack spoilage causing Clostridium estertheticum and Clostridium gasigenes on New Zealand beef and sheep farms.

The transfer of blown pack spoilage causing Clostridium spores from the farm to the meat plant is of growing concern to the meat industry. This study investigated the environmental niches of these Clostridium spp., specifically Clostridium estertheticum and Clostridium gasigenes in the beef and sheep farm environments in New Zealand. Faecal, soil, grass, drinking water, puddle water and feed (fodder beet, hay, bailage and silage, where available) samples were collected on five beef and sheep farms during Winter and Spring in 2018, in North and South Island, respectively. Beef and sheep farm samples were tested for C. estertheticum and C. gasigenes using enrichment plus PCR, qPCR and direct plating. C. estertheticum was detected in bovine faecal (4%), soil (2-18%) and grass (0-12%) samples at concentration of up to 2.0 log10 cfu/g. C. gasigenes were found in 18-46% of faecal, 16-82% of soil, 12-44% of grass, 0-44.4% of drinking water and 0-58.3% of puddle water samples tested and the direct counts ranged from 2.4 log10 cfu/ml in puddle water to 3.4 log10 cfu/g in soil. C. estertheticum were detected by qPCR in sheep farms in ovine feces (2.3%), soil (2.3%) and fodder beet (10%). All other sample types (grass, drinking water, puddle water, baleage, hay, silage and fodder beet) were negative using direct and enrichment plus PCR methods. In contrast C. gasigenes was detected in of faecal (22.7-38.6%), soil (22.7-84.1%), grass (17.5-34.1%) drinking water (35.7-78.6%), puddle water (33.3-40%), hay baleage (57%), silage (2%) and fodder beet (10%) at concentrations of up to 3.7 log10 cfu/g/ml. It was concluded that C. estertheticum and C. gasigenes were common on beef and sheep farms with the latter having higher incidence and mean concentration.

Comparative genomics of Clostridium species associated with vacuum-packed meat spoilage.

Bacterial species belonging to the genus Clostridium have been recognized as causative agents of blown pack spoilage (BPS) in vacuum packed meat products. Whole-genome sequencing of six New Zealand psychrotolerant clostridia isolates derived from three meat production animal types and their environments was performed to examine their roles in BPS. Comparative genome analyses have provided insight into the genomic diversity and physiology of these bacteria and divides clostridia into two separate species clusters. BPS-associated clostridia encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) that enable them to utilize the intramuscular carbohydrate stores and facilitate sporulation. In total, 516 glycoside hydrolases (GHs), 93 carbohydrate esterases (CEs), 21 polysaccharide lyases (PLs), 434 glycosyl transferases (GTs) and 211 carbohydrate-binding protein modules (CBM) with predicted activities involved in the breakdown and transport of carbohydrates were identified. Clostridia genomes have different patterns of CAZyme families and vary greatly in the number of genes within each CAZy category, suggesting some level of functional redundancy. These results suggest that BPS-associated clostridia occupy similar environmental niches but apply different carbohydrate metabolism strategies to be able to co-exist and cause meat spoilage.

Genetic Factors Affect the Survival and Behaviors of Selected Bacteria during Antimicrobial Blue Light Treatment.

Antimicrobial resistance is a global, mounting and dynamic issue that poses an immediate threat to human, animal, and environmental health. Among the alternative antimicrobial treatments proposed to reduce the external use of antibiotics is electromagnetic radiation, such as blue light. The prevailing mechanistic model is that blue light can be absorbed by endogenous porphyrins within the bacterial cell, inducing the production of reactive oxygen species, which subsequently inflict oxidative damages upon different cellular components. Nevertheless, it is unclear whether other mechanisms are involved, particularly those that can affect the efficacy of antimicrobial blue light treatments. In this review, we summarize evidence of inherent factors that may confer protection to a selected group of bacteria against blue light-induced oxidative damages or modulate the physiological characteristics of the treated bacteria, such as virulence and motility. These include descriptions of three major photoreceptors in bacteria, chemoreceptors, SOS-dependent DNA repair and non-SOS protective mechanisms. Future directions are also provided to assist with research efforts to increase the efficacy of antimicrobial blue light and to minimize the development of blue light-tolerant phenotypes.

Effect of novel and conventional food processing technologies on Bacillus cereus spores.

This chapter provides a summary of the effect of thermal and non-thermal processing technologies on Bacillus cereus spores, a well-known pathogenic bacterium associated with foodborne illnesses. B. cereus has been frequently detected in rice, milk products, infant food, liquid eggs products and meat products all over the world. This Gram positive, rod-shaped, facultative anaerobe can produce endospores that can withstand pasteurization, UV radiation, and chemical reagents commonly used for sanitization. B. cereus spores can germinate into vegetative cells that can produce toxins. The conventional regime for eliminating spores from food is retorting which uses the application of high temperature (121 °C). However, at this temperature, there could be a significant amount of loss in the organoleptic and functional qualities of the food components, especially proteins. This leads to the research on the preventive measures against germination and if possible, to reduce the resistance before using a non-thermal technology (temperatures less than retorting-121 °C) for inactivation. This chapter reviews the development and success of several food processing technologies in their ability to inactivate B. cereus spores in food.

Multiple genome sequences of lactic acid bacteria, Carnobacterium divergens and Carnobacterium maltaromaticum strains, isolated from vacuum-packaged lamb meat.

Here, we report the whole-genome sequences of 11 Carnobacterium divergens and 2 Carnobacterium maltaromaticum bacteria isolated from vacuum-packed chill-stored lamb meat in New Zealand. Examination of these lactic acid bacteria (LAB) genomes will improve our knowledge of their potential antimicrobial activities and spoilage mechanisms of importance to the meat industry.

Impact of systemic antimicrobial therapy on the faecal microbiome in symptomatic dairy cows.

Antimicrobial resistance is a global threat to human and animal health, with the misuse and overuse of antimicrobials suggested as the main drivers of resistance. Antimicrobial therapy can alter the bacterial community composition and the faecal resistome in cattle. Little is known about the impact of systemic antimicrobial therapy on the faecal microbiome in dairy cows in the presence of disease. Therefore, this study aimed to assess the impact of systemic antimicrobial therapy on the faecal microbiome in dairy cows in the pastoral farm environment, by analysing faecal samples from cattle impacted by several different clinically-defined conditions and corresponding antimicrobial treatments. Analysis at the individual animal level showed a decrease in bacterial diversity and richness during antimicrobial treatment but, in many cases, the microbiome diversity recovered post-treatment when the cow re-entered the milking herd. Perturbations in the microbiome composition and the ability of the microbiome to recover were specific at the individual animal level, highlighting that the animal is the main driver of variation. Other factors such as disease severity, the type and duration of antimicrobial treatment and changes in environmental factors may also impact the bovine faecal microbiome. AmpC-producing Escherichia coli were isolated from faeces collected during and post-treatment with ceftiofur from one cow while no third-generation cephalosporin resistant E. coli were isolated from the untreated cow samples. This isolation of genetically similar plasmid-mediated AmpC-producing E. coli has implications for the development and dissemination of antibiotic resistant bacteria and supports the reduction in the use of critically important antimicrobials.

Medium-term storage of calf beddings affects bacterial community and effectiveness to inactivate zoonotic bacteria.

Land-spreading of animal faecal wastes -such as animal beddings- can introduce zoonotic enteropathogens into the food system environment. The study evaluated the effectiveness of animal beddings naturally contaminated by calf manure to reduce E. coli O157:H7 or Salmonella enterica. The two pathogens were introduced separately as a four strains-cocktail and at high (>6.5 Log10 g-1) concentration into bedding materials, and their inactivation over a 10 weeks-period was monitored by using a Most Probable Number (MPN) enumeration method. Inactivation of E. coli O157:H7 was more effective in the bedding inoculated immediately after collection from calf pens than in the beddings inoculated after a 2 months-pre-storage period: E. coli O157:H7 levels were reduced by 6.6 Log10 g-1 in unstored bedding (0.5 Log10 g-1 recovered; 95%CI: 0.0-1.2), and by 4.9 Log10 g-1 in pre-stored bedding (2.2 Log10 g-1 recovered; 95%CI: 1.5-2.8) with a significant (p<0.05) difference between unstored and pre-stored. S. enterica was inactivated less effectively as counts were reduced by one order of magnitude, with no significant difference in inactivation between unstored and pre-stored beddings. Low levels of naturally occurring E. coli O157 and Salmonella spp. were detected in the non-inoculated beddings, as well as in the straw prior to use in the animal facility. To better understand the possible biological processes involved, the bacterial community present in the beddings was characterised by short-read 16S rRNA sequencing. Pre-storage of the bedding affected the composition but not the diversity of the bacterial community. Analyses of the key bacterial phyla suggested that the presence of a diverse and stable bacterial community might facilitate inactivation of the introduced pathogens, and a possible role of bacterial orders associated with lignocellulolytic resources. Overall, the study contributed to the understanding of the fate of zoonotic bacteria introduced in animal beddings during storage and identified bedding storage practices pre-and post-use in animal facilities that could be important to prevent the risk of zoonosis dissemination to the environment or to the dairy herds.

Non-Targeted Metabolomic Profiling Identifies Metabolites with Potential Antimicrobial Activity from an Anaerobic Bacterium Closely Related to Terrisporobacter Species.

This work focused on the metabolomic profiling of the conditioned medium (FS03CM) produced by an anaerobic bacterium closely related to Terrisporobacter spp. to identify potential antimicrobial metabolites. The metabolome of the conditioned medium was profiled by two-channel Chemical Isotope Labelling (CIL) LC-MS. The detected metabolites were identified or matched by conducting a library search using different confidence levels. Forty-eight significantly changed metabolites were identified with high confidence after the growth of isolate FS03 in cooked meat glucose starch (CMGS) medium. Some of the secondary metabolites identified with known antimicrobial activities were 4-hydroxyphenyllactate, 3-hydroxyphenylacetic acid, acetic acid, isobutyric acid, valeric acid, and tryptamine. Our findings revealed the presence of different secondary metabolites with previously reported antimicrobial activities and suggested the capability of producing antimicrobial metabolites by the anaerobic bacterium FS03.

Effect of Hurdle Approaches Using Conventional and Moderate Thermal Processing Technologies for Microbial Inactivation in Fruit and Vegetable Products.

Thermal processing of packaged fruit and vegetable products is targeted at eliminating microbial contaminants (related to spoilage or pathogenicity) and extending shelf life using microbial inactivation or/and by reducing enzymatic activity in the food. The conventional process of thermal processing involves sterilization (canning and retorting) and pasteurization. The parameters used to design the thermal processing regime depend on the time (minutes) required to eliminate a known population of bacteria in a given food matrix under specified conditions. However, due to the effect of thermal exposure on the sensitive nutrients such as vitamins or bioactive compounds present in fruits and vegetables, alternative technologies and their combinations are required to minimize nutrient loss. The novel moderate thermal regimes aim to eliminate bacterial contaminants while retaining nutritional quality. This review focuses on the "thermal" processing regimes for fruit and vegetable products, including conventional sterilization and pasteurization as well as mild to moderate thermal techniques such as pressure-assisted thermal sterilization (PATS), microwave-assisted thermal sterilization (MATS) and pulsed electric field (PEF) in combination with thermal treatment as a hurdle approach or a combined regime.

Nature-Inspired Antimicrobial Surfaces and Their Potential Applications in Food Industries.

Antimicrobial resistance (AMR) is a growing global concern and has called for the integration of different areas of expertise for designing robust solutions. One such approach is the development of antimicrobial surfaces to combat the emerging resistance in microbes against drugs and disinfectants. This review is a compressive summary of the work done in the field of material science, chemistry, and microbiology in the development of antimicrobial materials and surfaces that are inspired by examples in nature. The focus includes examples of natural antimicrobial surfaces, such as cicada wings or nanopillars, dragonfly wings, shrimp shells, taro leaves, lotus leaves, sharkskin, gecko skin, and butterfly wings, along with their mechanism of action. Techniques, compositions, and combinations that have been developed to synthetically mimic these surfaces against bacterial/viral and fungal growth in food-processing areas have also been discussed. The applications of synthetic mimics of natural antimicrobial surfaces in food-processing environments is still a naïve area of research. However, this review highlights the potential applications of natural antimicrobial surfaces in the food-processing environment as well as outlines the challenges that need mitigations.

A Comprehensive Review of Variability in the Thermal Resistance (D-Values) of Food-Borne Pathogens-A Challenge for Thermal Validation Trials.

The thermal processing of food relies heavily on determining the right time and temperature regime required to inactivate bacterial contaminants to an acceptable limit. To design a thermal processing regime with an accurate time and temperature combination, the D-values of targeted microorganisms are either referred to or estimated. The D-value is the time required at a given temperature to reduce the bacterial population by 90%. The D-value can vary depending on various factors such as the food matrix, the bacterial strain, and the conditions it has previously been exposed to; the intrinsic properties of the food (moisture, water activity, fat content, and pH); the method used to expose the microorganism to the thermal treatment either at the laboratory or commercial scale; the approach used to estimate the number of survivors; and the statistical model used for the analysis of the data. This review focused on Bacillus cereus, Cronobacter sakazakii, Escherichia coli, Listeria monocytogenes, and Clostridium perfringens owing to their pathogenicity and the availability of publications on their thermal resistance. The literature indicates a significant variation in D-values reported for the same strain, and it is concluded that when designing thermal processing regimes, the impact of multiple factors on the D-values of a specific microorganism needs to be considered. Further, owing to the complexity of the interactions involved, the effectiveness of regimes derived laboratory data must be confirmed within industrial food processing settings.

Genome collection of Shewanella spp. isolated from spoiled lamb.

The diversity of the genus Shewanella and their roles across a variety of ecological niches is largely unknown highlighting the phylogenetic diversity of these bacteria. From a food safety perspective, Shewanella species have been recognized as causative spoilage agents of vacuum-packed meat products. However, the genetic basis and metabolic pathways for the spoilage mechanism are yet to be explored due to the unavailability of relevant Shewanella strains and genomic resources. In this study, whole-genome sequencing of 32 Shewanella strains isolated from vacuum-packaged refrigerated spoiled lamb was performed to examine their roles in meat spoilage. Phylogenomic reconstruction revealed their genomic diversity with 28 Shewanella spp. strains belonging to the same putative novel species, two Shewanella glacialipiscicola strains (SM77 and SM91), Shewanella xiamenensis NZRM825, and Shewanella putrefaciens DSM 50426 (ATCC 8072) isolated from butter. Genome-wide clustering of orthologous gene families revealed functional groupings within the major Shewanella cluster but also considerable plasticity across the different species. Pan-genome analysis revealed conserved occurrence of spoilage genes associated with sulfur and putrescine metabolism, while the complete set of trimethylamine metabolism genes was observed in only Shewanella sp. SM74, S. glacialipiscicola SM77 and SM91 strains. Through comparative genomics, some variations were also identified pertaining to genes associated with adaptation to environmental cues such as temperature, osmotic, salt, oxidative, antimicrobial peptide, and drug resistance stresses. Here we provide a reference collection of draft Shewanella genomes for subsequent species descriptions and future investigations into the molecular spoilage mechanisms for further applications in the meat industry.

Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites.

Extended-spectrum beta lactamase (ESBL)-producing Escherichia coli are often isolated from humans with urinary tract infections and may display a multidrug-resistant phenotype. These pathogens represent a target for a One Health surveillance approach to investigate transmission between humans, animals and the environment. This study examines the multidrug-resistant phenotype and whole genome sequence data of four ESBL-producing E. coli isolated from freshwater in New Zealand. All four isolates were obtained from a catchment with a mixed urban and pastoral farming land-use. Three isolates were sequence type (ST) 131 (CTX-M-27-positive) and the other ST69 (CTX-M-15-positive); a phylogenetic comparison with other locally isolated strains demonstrated a close relationship with New Zealand clinical isolates. Genes associated with resistance to antifolates, tetracyclines, aminoglycosides and macrolides were identified in all four isolates, together with fluoroquinolone resistance in two isolates. The ST69 isolate harboured the bla CTX-M-15 gene on a IncHI2A plasmid, and two of the three ST131 isolates harboured the bla CTX-M-27 genes on IncF plasmids. The last ST131 isolate harboured bla CTX-M-27 on the chromosome in a unique site between gspC and gspD. These data highlight a probable human origin of the isolates with subsequent transmission from urban centres through wastewater to the wider environment.