Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates.

BACKGROUND: Oxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However, even small levels of error can obscure the phylogenetic relationships between closely related isolates. Polishing tools have been developed to correct these errors, but it is uncertain if they obtain the accuracy needed for the high-resolution source tracking of foodborne illness outbreaks. RESULTS: We tested 132 combinations of assembly and short- and long-read polishing tools to assess their accuracy for reconstructing the genome sequences of 15 highly similar Salmonella enterica serovar Newport isolates from a 2020 onion outbreak. While long-read polishing alone improved accuracy, near perfect accuracy (99.9999% accuracy or ~ 5 nucleotide errors across the 4.8 Mbp genome, excluding low confidence regions) was only obtained by pipelines that combined both long- and short-read polishing tools. Notably, medaka was a more accurate and efficient long-read polisher than Racon. Among short-read polishers, NextPolish showed the highest accuracy, but Pilon, Polypolish, and POLCA performed similarly. Among the 5 best performing pipelines, polishing with medaka followed by NextPolish was the most common combination. Importantly, the order of polishing tools mattered i.e., using less accurate tools after more accurate ones introduced errors. Indels in homopolymers and repetitive regions, where the short reads could not be uniquely mapped, remained the most challenging errors to correct. CONCLUSIONS: Short reads are still needed to correct errors in nanopore sequenced assemblies to obtain the accuracy required for source tracking investigations. Our granular assessment of the performance of the polishing pipelines allowed us to suggest best practices for tool users and areas for improvement for tool developers.

Clinical and Laboratory Effects of Foodborne Illness in Children.

The World Health Organization estimates that 31 foodborne pathogen account for 600 million cases of illness annually. This study, conducted in a pediatric emergency department in Turkey, addresses the limited research on pediatric foodborne diseases (FD) in the country, exposing a significant knowledge gap. Analyzing 17,091 pediatric cases, 106 FD cases were identified, predominantly affecting boys (94.3%) with an average age of 7.65 ± 6.51 years. Remarkably, no patients required pediatric intensive care admission, and no mortalities were recorded. Hyponatremia emerged as a prevalent electrolyte disorder in pediatric FD, while hyperkalemia was notably observed in children under 5. The study emphasizes the severity of FD in children under 5, reflected in longer hospital stays, underscoring the urgent need for targeted interventions and improved detection methods in pediatric FD.

Foodborne Outbreak by Salmonella enterica Serovar Weltevreden in West Bengal, India.

Foodborne gastroenteritis outbreaks owing to Salmonella enterica serovar Weltevreden (Salmonella Weltevreden) represent a significant global public health problem. In the past two decades, Salmonella Weltevreden has emerged as a dominant foodborne pathogen, especially in South-East Asian countries. This report describes a community foodborne outbreak of gastroenteritis caused by Salmonella Weltevreden in August 2022 following consumption of panipuri from a street vendor in the Polba block in Hooghly district, West Bengal, India. This food item was consumed by 185 people, of whom 129 had acute watery diarrhea with other clinical symptoms and 65 of them were admitted to different District hospitals for treatment. Stool specimens collected from hospitalized cases were positive for S. enterica, and further serotyped as Salmonella Weltevreden. All the Salmonella Weltevreden strains possessed the Salmonella pathogenicity islands associated genes (invA/E, orgA, ttrc, ssaQ, mgtC, misL, spi4D), the enterotoxin (stn), and hyperinvasive locus gene (hilA). Except erythromycin, all the strains were susceptible for commonly used antimicrobials in the treatment of diarrhea. The XbaI-based pulsed-field gel electrophoresis analysis indicated that all the isolates responsible for the recent outbreak were similar, but diverged from other Salmonella Weltevreden that were previously reported in West Bengal. This report indicates that foodborne infection is a major public health concern in India and demands to strengthen capacity-building measures at the local health care levels for linking causative agents of outbreaks.

Experimental Evidence of the Diarrheal Activity of Sarcocystis sp. in Sika Deer (Cervus nippon).

Recently, the wild deer population has been increasing in Japan, causing serious feeding-related damage to the agricultural and forestry industries. In conjunction with the government's promotion of hunting for population control, the effective utilization of resources and promotion of the game meat industry as a sixth sector of industrialization are desired by local governments. However, several cases in which patients showed intestinal symptoms such as diarrhea due to the consumption of sika deer meat infected with protozoan Sarcocystis spp. have been reported, and the pathogenic microorganisms found in wild deer should be investigated. In this study, Sarcocystis sp. parasitized Kyushu sika deer (Cervus nippon nippon) in Nagasaki Prefecture, Japan, was examined for its enterotoxicity. A phylogenetic analysis based on the sequence of the 18S rRNA gene and cox1 showed that the species was highly homologous to Sarcocystis japonica and/or Sarcocystis sp. HM050622. We attempted to confirm the diarrhea-evoking toxicity of Sarcocystis sp. in sika deer meat, which has been previously reported in human case reports. A mouse ileal loop assay showed that Sarcocystis sp. in sika deer meat induced significant fluid accumulation in the loop at doses of ∼5 × 106 bradyzoites. Western blotting showed that these Sarcocystis parasites possess actin-depolymerizing factor, a diarrhea-evoking factor, similar to Sarcocystis fayeri, which exists in horsemeat. However, the pathogenic conditions of the ileal loop were different from those of similar experiments with S. fayeri. This study suggests that S. japonica parasitizing C. n. nippon may cause diarrhea via a different mechanism from that of S. fayeri.

Molecular Characteristics of Staphylococcus aureus Isolates form Food-Poisoning Outbreaks (2011-2022) in Sichuan, China.

Staphylococcal food poisoning (SFP) is one of the most common foodborne diseases in the world. This study aimed to investigate the molecular epidemiological characteristics of Staphylococcus aureus isolated from SFP. A total of 103 S. aureus isolates were obtained during 2011-2022 in Sichuan, southwest China. All isolates were tested for the genomic characteristics and phylogenetic analysis by performing whole-genome sequencing. Multilocus sequence typing analysis showed 17 multilocus sequence types (STs), ST7 (23.30%), ST5 (22.33%), and ST6 (16.50%) being the most common. A total of 45 virulence genes were detected, 22 of which were staphylococcal enterotoxin (SE) genes. Among the identified SE genes, selX exhibited the highest prevalence (86.4%). All isolates carried at least one SE gene. The results of the antimicrobial resistance (AMR) gene detection revealed 41 AMR genes of 12 classes. ß-lactam resistance genes (blal, blaR1, blaZ) and tetracycline resistance gene (tet(38)) exhibited a higher prevalence rate. Core genome single nucleotide polymorphism showed phylogenetic clustering of the isolates with the same region, year, and ST. The results indicated that the SFP isolates in southwest of China harbored multiple toxin and resistance genes, with a high prevalence of new SEs. Therefore, it is important to monitor the antimicrobial susceptibility and SE of S. aureus to reduce the potential risks to public health.

Usefulness and Limitations of PFGE Diagnosis and Nucleotide Sequencing Method in the Analysis of Food Poisoning Pathogens Found in Cooking Employees.

In the case of a food poisoning outbreak, it is essential to understand the relationship between cooking workers and food poisoning. Many biological diagnostic methods have recently been developed to detect food poisoning pathogens. Among these diagnostic tools, this study presents PCR-based pulsed-field gel electrophoresis and nucleotide sequencing diagnostic analysis results for diagnosing food poisoning outbreaks associated with cooking employees in Chungcheongnam-do, Republic of Korea. Pulsed-field gel electrophoresis was useful in identifying the food poisoning outbreaks caused by Staphylococcus aureus and Enteropathogenic Escherichia coli. In the case of Norovirus, nucleotide sequencing was used to identify the relationship between cooking workers and the food poisoning outbreak. However, it is difficult to determine whether cooking employees directly caused the food poisoning outbreaks based on these molecular biological diagnostic results alone. A system is needed to integrate epidemiological and diagnostic information to identify a direct correlation between the food poisoning outbreak and cooking employees.

[Establishment of Rapid Simultaneous Analysis Method for Plant Toxins by LC-TOF-MS].

Assuming food poisoning caused by toxic plants, an LC-TOF-MS-based method for the rapid and simultaneous analysis of 16 plant toxins was established. After adding water-methanol (1 : 9) and n-hexane, the samples were homogenized and extracted, and then subjected to centrifugal separation. Without any purification procedures, LC-TOF-MS measurements were performed, and qualitative and quantitative analyses using monoisotopic ion [M+H]+ (m/z) were conducted. The addition-recovery test using curry showed that qualitative analysis was possible under a setting with a retention time of ±0.2 minutes or less and mass accuracy of 5 ppm or lower and that quantitative analysis was possible with a recovery rate of 68-142% and a repeatability of 1.4-10.1%. Furthermore, measurements of the amount of plant toxins in the boiled plants and broths of cooked toxic plants demonstrated the transfer of plant toxins to broths. These suggest that in the event of food poisoning, broths may be used as an analysis sample, even when plants are not available.

[Determination of tetrodotoxin in urine by liquid chromatography-tandem mass spectrometry with internal standard calibration].

OBJECTIVE: An analytical method was developed for tetrodotoxin(TTX) in urine by liquid chromatography-tandem mass spectrometry(LC-MS/MS) with internal standard calibration. METHODS: TTX in the sample was extracted with the mixture of acetic acid/methanol/acetonitrile(0.005 mL/0.8 mL/1.8 mL), cleaned by solid phase extraction(SPE) with cation exchange cartridge, eluted with 50% acetonitrile/water containing 0.3% hydrochloric acid, and neutralized with ammonia. The extract was separated by a Waters XBridge~(TM) BEH Amide column(150 mm×3.0mm, 1.7 µm) and measured by MS/MS. By optimizing sample extraction and SPE cleanup conditions, the problems of low recovery and strong suppression effects of MS signal for TTX in urine were resolved when cleaned with cation exchange cartridge. RESULTS: Quantitatively calibrated by the internal standard of Kasugamycin, good linear relationship was found for TTX in urine at the range of 0.2-200 µg/L with the correlation coefficient(r~2) of 0.997. The limits of detection and quantitation for TTX in sample matrix were 0.1 and 0.2µg/L, respectively. The average recoveries at three spiking levels(0.2, 10.0 and 200 µg/L) were 89.3%-95.3% with relative standard deviation(n=6) less than 5.1%. The concentrations of TTX in urine from 11 poisoning patients were 0.4-138 µg/L. The detection rate was 100% in urine collected within 3 days after poisoning. CONCLUSION: The established method was simple, accurate and sensitive. It can provide reliable technical support for the rapid treatment of TTX poisoning events and the study of toxin metabolism in vivo.

Emergence of Novel Type C Botulism Strain in Household Outbreak, Japan.

In 2021, an outbreak of food poisoning caused by Clostridium botulinum type C occurred in Kumamoto, Japan. Analysis of the isolated strain revealed that it possessed the bont/C gene and was slightly different from the reference bont/C gene. The risk for human infection with this new toxin type may be low.

Types A and F Clostridium perfringens in healthcare wastewater from Ghana.

IMPORTANCE: Clostridium perfringens causes gas gangrene and food poisoning in humans, and monitoring this bacterium is important for public health. Although whole-genome sequencing is useful to comprehensively understand the virulence, resistome, and global genetic relatedness of bacteria, limited genomic data from environmental sources and developing countries hamper our understanding of the richness of the intrinsic genomic diversity of this pathogen. Here, we successfully accumulated the genetic data on C. perfringens strains isolated from hospital effluent and provided the first evidence that predicted pathogenic C. perfringens may be disseminated in the clinical environment in Ghana. Our findings suggest the importance of risk assessment in the environment as well as the clinical setting to mitigate the potential outbreak of C. perfringens food poisoning in Ghana.

Atypical diarrhoeagenic Escherichia coli in milk related to a large foodborne outbreak.

A foodborne outbreak related to milk cartons served in school lunches occurred in June 2021, which involved more than 1,800 cases from 25 schools. The major symptoms were abdominal pain, diarrhoea, vomiting, and fever. Although major foodborne toxins and pathogens were not detected, a specific Escherichia coli strain, serotype OUT (OgGp9):H18, was predominantly isolated from milk samples related to the outbreak and most patients tested. The strains from milk and patient stool samples were identified as the same clone by core genome multilocus sequence typing and single-nucleotide polymorphism analysis. The strain was detected in milk samples served for two days related to the foodborne outbreak at a rate of 69.6% and levels of less than ten most probable number/100 mL but not on days unrelated to the outbreak. The acid tolerance of the strain for survival in the stomach was similar to that of enterohaemorrhagic E. coli O157:H7, and the same inserts in the chu gene cluster in the acid fitness island were genetically revealed. The pathogenicity of the strain was not clear; however, it was indicated that the causative pathogen was atypical diarrhoeagenic E. coli OUT (OgGp9):H18.

Genomic analysis and biological characterization of a novel Schitoviridae phage infecting Vibrio alginolyticus.

Vibrio alginolyticus is a Gram-negative bacterium commonly associated with mackerel poisoning. A bacteriophage that specifically targets and lyses this bacterium could be employed as a biocontrol agent for treating the bacterial infection or improving the shelf-life of mackerel products. However, only a few well-characterized V. alginolyticus phages have been reported in the literature. In this study, a novel lytic phage, named ΦImVa-1, specifically infecting V. alginolyticus strain ATCC 17749, was isolated from Indian mackerel. The phage has a short latent period of 15 min and a burst size of approximately 66 particles per infected bacterium. ΦImVa-1 remained stable for 2 h at a wide temperature (27-75 °C) and within a pH range of 5 to 10. Transmission electron microscopy revealed that ΦImVa-1 has an icosahedral head of approximately 60 nm in diameter with a short tail, resembling those in the Schitoviridae family. High throughput sequencing and bioinformatics analysis elucidated that ΦImVa-1 has a linear dsDNA genome of 77,479 base pairs (bp), with a G + C content of ~ 38.72% and 110 predicted gene coding regions (106 open reading frames and four tRNAs). The genome contains an extremely large virion-associated RNA polymerase gene and two smaller non-virion-associated RNA polymerase genes, which are hallmarks of schitoviruses. No antibiotic genes were found in the ΦImVa-1 genome. This is the first paper describing the biological properties, morphology, and the complete genome of a V. alginolyticus-infecting schitovirus. When raw mackerel fish flesh slices were treated with ΦImVa-1, the pathogen loads reduced significantly, demonstrating the potential of the phage as a biocontrol agent for V. alginolyticus strain ATCC 17749 in the food. KEY POINTS: • A novel schitovirus infecting Vibrio alginolyticus ATCC 17749 was isolated from Indian mackerel. • The complete genome of the phage was determined, analyzed, and compared with other phages. • The phage is heat stable making it a potential biocontrol agent in extreme environments.

The affinity of histamine to serum albumin: Capillary electrophoresis-frontal analysis and in-silico molecular docking approaches.

Histamine is a biogenic amine found in various body tissues and responsible for many critical vital activities. It is also responsible for allergic reactions in the body. Ingestion of foods containing high amounts of histamine can cause fatal allergic reactions. Albumin in plasma controls drugs and free concentrations of bioactive constituents taken to the body with food. Hence, this study aimed to characterise the interactions of histamine with bovine serum albumin. Capillary electrophoresis in the frontal analysis mode was employed in this study as a practical approach for assessing histamine-bovine serum albumin affinity. The plateau-shaped free histamine peak was well separated from the bovine serum albumin (BSA)-histamine complex peak. The free histamine concentration was obtained by following the height of the free histamine peak. Whereas the bound histamine concentrations were obtained by calculating the difference between the height of total and free histamine peaks. Histamine bound to BSA at one independent site with a Kb value of 2.50 × 103 L/mol. Moreover, an in-silico molecular docking method was performed, and it was revealed that the binding site of histamine was located closer to Lysine-131 in subdomain IIA of bovine serum albumin.

The Epidemiological and Clinical Characteristics of the Largest Outbreak of Enterohemorrhagic Escherichia coli in Korea.

BACKGROUND: The largest outbreak of enterohemorrhagic Escherichia coli (EHEC) O157:H7 occurred at a preschool in South Korea from June 12 to 29, 2020. This study aimed to analyze the epidemiological and clinical characteristics of EHEC infection in this outbreak. METHODS: Epidemiological investigation was performed on all 184 children and 19 workers at the preschool using a standard questionnaire to assess symptoms, food intake, attendance, and special activity history. Pulsed-field gel electrophoresis analysis of confirmed cases was performed to determine genetic relevance. RESULTS: During this outbreak, 103 children were affected, whereas only one infection was identified in adults. Of the 103 pediatric patients, 85 had symptoms (82.5%), including diarrhea, abdominal pain, bloody stool, fever, and vomiting. Thirty-two patients (31.1%) were hospitalized, 15 (14.6%) were diagnosed with hemolytic uremic syndrome, and 4 (3.9%) received dialysis treatment. Pulsed-field gel electrophoresis analysis identified 4 genotypes with high genetic relevance (92.3%). Epidemiological investigation revealed that this outbreak might have occurred from ingesting foods stored in a refrigerator with a constant temperature above 10°C, which was conducive to bacterial growth. Despite several measures after outbreak recognition, new infections continued to appear. Therefore, the preschool was forced to close on June 19 to prevent further person-to-person transmission. CONCLUSION: Our findings from the response to the largest outbreak will help prepare countermeasures against future EHEC outbreak.

Molecular Mechanisms of Scombroid Food Poisoning.

Scombroid food poisoning (SFP) is a foodborne disease that develops after consumption of fresh fish and, rarely, seafood that has fine organoleptic characteristics but contains a large amount of exogenous histamine. SFP, like other food pseudo-allergic reactions (FPA), is a disorder that is clinically identical to allergic reactions type I, but there are many differences in their pathogenesis. To date, SFP has been widespread throughout the world and is an urgent problem, although exact epidemiological data on incidence varies greatly. The need to distinguish SFP from true IgE-associated allergy to fish and seafood is one of the most difficult examples of the differential diagnosis of allergic conditions. The most important difference is the absence of an IgE response in SFP. The pathogenesis of SFP includes a complex system of interactions between the body and chemical triggers such as exogenous histamine, other biogenic amines, cis-urocanic acid, salicylates, and other histamine liberators. Because of the wide range of molecular pathways involved in this process, it is critical to understand their differences. This may help predict and prevent poor outcomes in patients and contribute to the development of adequate hygienic rules and regulations for seafood product safety. Despite the vast and lengthy history of research on SFP mechanisms, there are still many blank spots in our understanding of this condition. The goals of this review are to differentiate various molecular mechanisms of SFP and describe methods of hygienic regulation of some biogenic amines that influence the concentration of histamine in the human body and play an important role in the mechanism of SFP.

[Development of a Simple Identification Method for Omphalotus guepiniformis by Color Reaction].

A simple method of identification using a color reaction was developed for Omphalotus guepiniformis. Only Omphalotus guepiniformis turned turquoise green. Other edible mushrooms resembling the mushroom did not change color when the beam reagent (5 w/v% potassium hydroxide ethanolic solution) was dripped onto the mushroom pileus. Furthermore, ethanol extract and mock cooking products of this mushroom exhibited the same color reaction. These results demonstrate this method as useful for identifying Omphalotus guepiniformis during mushroom hunting or during investigations of food poisoning.

[Color Reaction Identification of Omphalotus guepiniformis Causing Food Poisoning].

Simple identification using a color reaction was applied to investigate poisoning, putatively caused by Omphalotus guepiniformis. Some leftover uncooked mushrooms had turned turquoise green when a beam reagent (5 w/v% potassium hydroxide ethanolic solution) was dripped onto the mushroom pileus. Furthermore, ethanol extract of the mushrooms exhibited the same color reaction. Then, illudin S, a toxic compound contained in O. guepiniformis, was detected in uncooked leftover mushrooms using LC-MS/MS analysis. Therefore, this case was inferred as caused by O. guepiniformis. These results indicate the identification method described above as useful for screening tests for investigating food poisoning caused by O. guepiniformis.

[Rapid confirmation method of food poisoning caused by Bacillus cereus cereulide in rice and flour products].

OBJECTIVE: To develop a method for rapid determination of Bacillus cereus cereulide in rice and flour products by ultra-performance liquid chromatography-tandem mass spectrometry, providing emergency measures for food poisoning caused by cereulide. METHODS: Single rice and flour samples were extracted with acetonitrile aqueous solution, salting out, after centrifuged and filmed, the organic phase was directly determined. The complex matrix samples fried rice and noodles were extracted with acetonitrile aqueous solution, cleaned up with HLB column, a ACQUITY UPLC Peptide BEH C_(18) 300Å column(2.1 mm×100 mm, 1.7 µm)was used for liquid chromatography separation, multiple reaction monitoring(MRM) mode was used for detection in electrospray ionization with positive ion mode, and quantified by the solvent standard curve method. RESULTS: At the spiked level of 0.5, 1.0 and 5.0 µg/kg, the recoveries of cereulide in negative steamed rice, steamed bread and noodles samples were 87.4%-98.3%, and the relative standard deviations were 1.4%-4.2%. At the spiking levels of 1.0, 2.0 and 5.0 µg/kg, the recoveries of cereulide in the negative samples such as fried steamed rice and fried noodles were 89.5%-99.3% with the relative standard deviations of 1.1%-7.5%(n=6). The detection limit of cereulide was 0.2-0.3 µg/kg, and the quantification limit was 0.5-1.0 µg/kg. The established method was applied to the detection of the actual samples causing food poisoning in a certain place in Beijing. The content of cereulide in poisoned food samples was 1287-7398 µg/kg, the content of cereulide in two raw materials cold noodles was 0.4 and 9.4 µg/kg. CONCLUSION: The method is simple, rapid, high sensitivity and accurate, and can realize the rapid treatment of food poisoning caused by cereulide.

Foodborne botulism in Poland in 2018-2021.

Objectives: The aim of this study is to assess the epidemiological situation of foodborne botulism in Poland in 2018-2021, compared to previous years. Materials and methods: The assessment is based on an analysis of aggregated surveillance data from the annual bulletin "Infectious Diseases and Poisons in Poland" from 2013-2021, as well as botulism case reports collected by sanitary-epidemiological stations and sent to the Department of Epidemiology of Infectious Diseases and Surveillance of the NIPH NIH - NRI or provided by EpiBase. Results: A total of 54 foodborne botulism cases were registered between 2018 and 2021, including 31 (57.4%) cases of laboratory-confirmed botulism intoxication. Most cases (46 cases, 85.2%) were sporadic. The declining trend in the number of notifications continued throughout the time period, and the incidence recorded in 2021 (0.02 per 100,000 population) was the lowest since the introduction of mandatory reporting and registration of botulism in Poland. The highest median annual incidence was recorded in the Warmisko-Mazurskie (0.18), but many voivodeships reported only single notifications or none. The decreasing trend in rural areas relative to the level of incidence in urban areas continued. Men (incidence in men more than twice that of women) and people aged 50-59 predominated. All patients were hospitalized. According to the State Sanitary Inspection, there were 3 deaths (mortality of 5.6%). Conclusions: In 2018-2021, the downward trend in the number of foodborne botulism notifications in Poland continued. At the same time, the considerable proportion of cases reported by physicians without laboratory confirmation and not meeting the definition of botulism adopted in other EU countries is noteworthy. The incidence in rural areas decreases to the level of incidence in urban areas, and the previously observed geographical distribution of cases diminishes.

Bacterial Foodborne Illness in Malaysia: Terminalia spp. as a Potential Resource for Treating Infections and Countering Antibiotic Resistance.

Acute diarrhoea is becoming a major public health problem in Malaysia, with more than 13.5 million cases reported annually. Foodborne bacterial pathogens are a predominant cause of diarrhoea, with infections causing prolonged illness durations and higher patient mortality rates, placing a tremendous burden on the Malaysian economy. Due to increasing incidences of diarrhoea in Malaysia caused by foodborne pathogens and the increasing levels of resistance towards antibiotics from many different classes, new drugs and/or therapies are urgently required. The evidence for plants as new sources of antibiotics has increased dramatically in recent years and there has been a substantial increase in interest in traditional and herbal medicines. Several Terminalia spp. are native to Malaysia, with previous research demonstrating that Terminalia spp. are rich in therapeutic phytochemicals and possess antibacterial properties. However, limited research has been conducted on the native Malaysian Terminalia spp. for their potential as new antibacterial therapies. The current review discusses the types of bacteria, including antibiotic-resistant strains, that cause food poisoning in Malaysia, and reports the phytochemical content and antibacterial properties of eight of these useful plant species. Future directions pertaining to drug discovery pathways are also suggested.