Food and Water-Borne Pathogens: Epidemiology, Genomics, Virulence and Resistance Profiles

Determining the microbial quality and safety of meat is crucial because of its high potential to harbor pathogens. To address the critical knowledge gap and shed light on potential contamination risk in the meat supply chain, this study aimed to assess the underexplored microbial quality and safety of marketed beef meat in Oman. Thirty-three beef meat samples from six hypermarkets were analyzed for Aerobic Plate Count (APC), Psychrotrophic Bacteria Count (PBC), and coliform and Escherichia coli counts. Prevalences were 93% and 94% (means: 2.8 ± 1.1 and 2.6 ± 0.8 log CFU/g, respectively) for coliform, and 80% and 83% (means: 1.8 ± 1.4 and 1.7 ± 0.9 log CFU/g, respectively) for E. coli in imported and local samples, respectively. The mean counts of APC (6.3 ± 0.1 log CFU/g) and PBC (6.2 ± 0.2 log CFU/g) were statistically similar but different from those of coliform and E. coli. Bacterial identification using VITEK 2 compact revealed spoilage bacteria (Pseudomonas luteola, Pseudomonas fluorescens, and Shewanella putrefaciens) and pathogenic bacteria (Acinetobacter bumannii complex, Aerococcus viridans, Enterococcus faecalis, and Oligella ureolytica), which demonstrates a potential for both spoilage and pathogen-related risks. It is concluded that the APC counts of all samples exceeded acceptable standards set by the G.C.C. Standardization Organization (GSO), which was established to protect food safety and public health in Oman and other Gulf countries. This suggests an increased risk of spoilage and pathogen contamination. This study provides one of the earliest reports of microbial contamination levels in meat, serving as an eye-opener for policymakers and stakeholders. It highlights a need for stricter hygiene protocols and improved meat handling and processing practices to enhance meat safety and protect public health in Oman and the Gulf region. Full article

Cronobacter sakazakii, an opportunistic foodborne pathogen, has a strong resistance to osmotic stress and desiccation stress, but the current studies cannot elucidate this resistance mechanism absolutely. A mechanosensitive channel MscM was suspected of involving to desiccation resistance mechanism of C. sakazakii. To investigate the specific molecular mechanism, the mscM mutant strain (ΔmscM) was constructed using the homologous recombination method, and the cpmscM complementary strain was obtained by gene complementation, followed by the analysis of the difference between the wild-type (WT), mutant, and complementary strains. Compared to the wild-type bacteria (WT), the inactivation rate of the ΔmscM strain decreased by 15.83% (p < 0.01) after desiccation stress. The absence of the mscM gene led to an increase in the membrane permeability of mutant strains. Through turbidity assay, it was found that the intracellular content of potassium ion (K⁺) of the ΔmscM strain increased by 2.2-fold (p < 0.05) compared to the WT strain, while other metal ion contents, including sodium ion (Na⁺), calcium ion (Ca²⁺), and magnesium ion (Mg²⁺), decreased by 48.45% (p < 0.001), 24.29% (p < 0.001), and 26.11% (p < 0.0001), respectively. These findings indicate that the MscM channel primarily regulates cell membrane permeability by controlling K⁺ efflux to maintain the homeostasis of intracellular osmotic pressure and affect the desiccation tolerance of bacteria. Additionally, the deletion of the mscM gene did not affect bacterial growth and motility but impaired surface hydrophobicity (reduced 20.52% compared to the WT strain, p < 0.001), adhesion/invasion capability (reduced 26.03% compared to the WT strain, p < 0.001), and biofilm formation ability (reduced 30.19% compared to the WT strain, p < 0.05) of the bacteria. This study provides a reference for the role of the mscM gene in the desiccation resistance and biofilm formation of C. sakazakii. Full article

Avian pathogenic E. coli (APEC), a widespread bacterium, results in serious economic losses to the poultry industry annually, and it poses a threat to human health due to the contaminated retail poultry meat and eggs. Recently, it has been demonstrated that long non-coding RNAs played important roles in regulating gene expression and the animal immune response. This study aimed to systematically explore the function of the novel long intergenic non-coding transcript, lincRNA-73240, upon APEC infection. A bioinformatics analysis indicated that lincRNA-73240 had no coding ability and a relative stable secondary structure with multiple hairpin rings. Moreover, the RT-qPCR results showed that lincRNA-73240 was highly expressed in lungs, heart, liver, spleen, cecum tonsils, thymus, ileum, bursa of Fabricius, harderian gland, and muscles in comparison to the cerebrum. Additionally, overexpression of lincRNA-73240 can promote the expression levels of inflammation, apoptosis, autophagy, and oxidative stress-related genes, as well as the production of reactive oxygen species (ROS), malondialdehyde (MDA), and nitric oxide (NO) upon APEC infection, which lead to cellular injury and apoptosis. These findings collectively establish a foundation for the study of the biological function of chicken lincRNA-73240 and provide a theoretical basis for further research on the molecular mechanisms of the chicken immune response. Full article

In this study, we reported the complete genome sequence of Shewanella oncorhynchi for the first time. S. oncorhynchi Z-P2 is a bacterium that produces the siderophore putrebactin. Its genome consists of a circular chromosome of 5,034,612 bp with a G + C content of 45.4%. A total of 4544 protein-coding genes, 109 tRNAs and 31 rRNAs were annotated by the RAST. Five non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene clusters were identified by the antiSMASH analysis. The pan-genome analysis of Z-P2 and 10 Shewanella putrefaciens revealed 9228 pan-gene clusters and 2681 core gene clusters, with Z-P2 having 618 unique gene clusters. Additionally, the gene cluster involved in putrebactin biosynthesis in Z-P2 was annotated, and the mechanism of putrebactin biosynthesis was analyzed. The putrebactin produced by Z-P2 was detected using UPLC-MS analysis, with an [M + H]⁺ molecular ion at m/z 373.21. These findings provide valuable support for further research on the genetic engineering of putrebactin biosynthetic genes of Z-P2 and their potential applications. Full article

Poultry rendering is the process of upcycling inedible poultry carcass materials into useful animal food/feed components as well as other valuable commercial products. Microbiological safety validation is nonetheless critical to ensuring the prevention of food safety hazard(s) transmission. This study determined the death kinetics of the thermotolerant Salmonella enterica serovar Senftenberg isolate 775W in chicken feathers and blood in low-temperature dry rendering (i.e., no direct contact with heating medium) to validate pathogen inactivation in commercial processing. Chicken feathers and blood were inoculated with Salmonella Senftenberg 775W and heated to 60, 70, or 80 °C for up to 60, 20, and 5 min, respectively. Three identically completed replicates (N = 3) for each product were conducted. Pathogen inactivation data were fitted to a non-linear model, providing for the detection and characterization of shoulder, log-linear death, and tailing components in death curves. The analysis showed a >7-log₁₀ reduction in Salmonella was achieved across all processing temperatures, with t_7D values (time for 7.0 log-cycle lethality) ranging from 21.68, 7.30, and 4.26 min for feathers and 18.38, 5.03, and 2.79 min in blood at 60, 70, and 80 °C, respectively. Study findings validate that low-temperature processing conditions can inactivate Salmonella in poultry-rendered offal. Full article

Food is often contaminated with Escherichia coli (E. coli) bacteria strains, which have been associated with different diseases, including urinary tract infections. The consumption of meat by humans is a potential route of transmission of antimicrobial resistance, and food-producing animals have been associated as a major reservoir of resistant bacterial strains. The aim of this study was to determine the presence of the E. coli strains producing the CNF-1 toxin in pig kidneys. Pig kidneys were collected from a Mexican slaughterhouse and classified according to their coloration into reddish kidneys (RK) and yellowish kidneys (YK). A tissue sample from each kidney was processed for histological analysis, the presence of E. coli was determined by conventional PCR assay, and the CNF-1 toxin was detected by both conventional PCR and Western blotting. Herein, an inflammatory cell infiltrate was found in all collected kidneys, regardless of macroscopic differences. Surprisingly, E. coli and the CNF-1 toxin were detected in all kidney samples. We clearly demonstrate contamination by CNF-1 toxin-producing E. coli in pork kidneys from a slaughterhouse, even in those without apparent damage. This suggests that pork may serve as a reservoir for pathogens, representing an important risk to human health. Full article

In contrast to “frank” pathogens, like Salmonella entrocolitica, Shigella dysenteriae, and Vibrio cholerae, that always have a probability of disease, “opportunistic” pathogens are organisms that cause an infectious disease in a host with a weakened immune system and rarely in a healthy host. Historically, drinking water treatment has focused on control of frank pathogens, particularly those from human or animal sources (like Giardia lamblia, Cryptosporidium parvum, or Hepatitis A virus), but in recent years outbreaks from drinking water have increasingly been due to opportunistic pathogens. Characteristics of opportunistic pathogens that make them problematic for water treatment include: (1) they are normally present in aquatic environments, (2) they grow in biofilms that protect the bacteria from disinfectants, and (3) under appropriate conditions in drinking water systems (e.g., warm water, stagnation, low disinfectant levels, etc.), these bacteria can amplify to levels that can pose a public health risk. The three most common opportunistic pathogens in drinking water systems are Legionella pneumophila, Mycobacterium avium, and Pseudomonas aeruginosa. This report focuses on these organisms to provide information on their public health risk, occurrence in drinking water systems, susceptibility to various disinfectants, and other operational practices (like flushing and cleaning of pipes and storage tanks). In addition, information is provided on a group of nine other opportunistic pathogens that are less commonly found in drinking water systems, including Aeromonas hydrophila, Klebsiella pneumoniae, Serratia marcescens, Burkholderia pseudomallei, Acinetobacter baumannii, Stenotrophomonas maltophilia, Arcobacter butzleri, and several free-living amoebae including Naegleria fowleri and species of Acanthamoeba. The public health risk for these microbes in drinking water is still unclear, but in most cases, efforts to manage Legionella, mycobacteria, and Pseudomonas risks will also be effective for these other opportunistic pathogens. The approach to managing opportunistic pathogens in drinking water supplies focuses on controlling the growth of these organisms. Many of these microbes are normal inhabitants in biofilms in water, so the attention is less on eliminating these organisms from entering the system and more on managing their occurrence and concentrations in the pipe network. With anticipated warming trends associated with climate change, the factors that drive the growth of opportunistic pathogens in drinking water systems will likely increase. It is important, therefore, to evaluate treatment barriers and management activities for control of opportunistic pathogen risks. Controls for primary treatment, particularly for turbidity management and disinfection, should be reviewed to ensure adequacy for opportunistic pathogen control. However, the major focus for the utility’s opportunistic pathogen risk reduction plan is the management of biological activity and biofilms in the distribution system. Factors that influence the growth of microbes (primarily in biofilms) in the distribution system include, temperature, disinfectant type and concentration, nutrient levels (measured as AOC or BDOC), stagnation, flushing of pipes and cleaning of storage tank sediments, and corrosion control. Pressure management and distribution system integrity are also important to the microbial quality of water but are related more to the intrusion of contaminants into the distribution system rather than directly related to microbial growth. Summarizing the identified risk from drinking water, the availability and quality of disinfection data for treatment, and guidelines or standards for control showed that adequate information is best available for management of L. pneumophila. For L. pneumophila, the risk for this organism has been clearly established from drinking water, cases have increased worldwide, and it is one of the most identified causes of drinking water outbreaks. Water management best practices (e.g., maintenance of a disinfectant residual throughout the distribution system, flushing and cleaning of sediments in pipelines and storage tanks, among others) have been shown to be effective for control of L. pneumophila in water supplies. In addition, there are well documented management guidelines available for the control of the organism in drinking water distribution systems. By comparison, management of risks for Mycobacteria from water are less clear than for L. pneumophila. Treatment of M. avium is difficult due to its resistance to disinfection, the tendency to form clumps, and attachment to surfaces in biofilms. Additionally, there are no guidelines for management of M. avium in drinking water, and one risk assessment study suggested a low risk of infection. The role of tap water in the transmission of the other opportunistic pathogens is less clear and, in many cases, actions to manage L. pneumophila (e.g., maintenance of a disinfectant residual, flushing, cleaning of storage tanks, etc.) will also be beneficial in helping to manage these organisms as well. Full article