Disentangling survival of Escherichia coli O157:H7 in soils: From a subpopulation perspective

Dairy effluent management systems as a potential persistence source of Shiga toxin-producing Escherichia coli (STEC) strains

Shiga toxin-producing Escherichia coli (STEC) is a group of pathogenic enterobacteria of significant public health importance due to their association with highly prevalent human diseases. STEC is ubiquitous in livestock environments, and its presence in the environment emphasizes the importance of properly managing agricultural effluents to reduce health risks from contamination. In order to detect STEC in the effluent treatment systems of two dairy farms ("A" and "B") in the southwest of Buenos Aires province, samples ("A", n=88; "B", n=72) were taken at two different times of the year (winter and spring) and at various points in the treatment systems. Analysis markers for virulence genes (stx, eae, saa, and ehxA) revealed the presence of STEC in 13.1% of the samples, showing an increase in spring and differences between dairy farms possibly related to their maintenance conditions. After manure, sediments showed the highest proportion of STEC-positive samples, which is relevant due to the ability of these strains to survive in the environment through biofilm formation. Eight genetic profiles were identified among all STEC-positive samples, which are associated with STEC strains that can cause hemolytic uremic syndrome (HUS) and other gastrointestinal diseases. This demonstrates the role of dairy farm environments in the region as reservoirs of pathogenic STEC strains and their impact on public health.

Carbon dots and covalent organic frameworks based FRET immunosensor for sensitive detection of Escherichia coli O157:H7

The combination of carbon dots (CDs) with covalent organic frameworks (COFs) was used to design an innovative sensor based on fluorescence resonance energy transfer (FRET) for the detection of Escherichia coli O157:H7 (E. coli O157:H7) in food samples. Carbon dots were used as fluorescence donors, covalent organic frameworks as fluorescence acceptors. The antibody (Ab) specific to E. coli O157:H7 was used to form a CD-Ab-COF immunosensor by linking CDs and COFs. The antibody was specifically bound with E. coli O157:H7, which caused the connection between CDs and COFs to be interrupted, and the carbon dots exhibited fluorescence restoration. The sensor exhibited a linear detection range spanning from 0 to 106 CFU/mL, with the limit of detection (LOD) of 7 CFU/mL. The analytical performance of the developed immunosensor was evaluated using spiked food samples with different concentrations of E. coli O157:H7, validating the capability of assessing risks in food testing.

An integrated magnetic separation enzyme-linked colorimetric sensing platform for field detection of Escherichia coli O157: H7 in food

An intelligent colorimetric sensing platform integrated with in situ immunomagnetic separation function was developed for ultrasensitive detection of Escherichia coli O157: H7 (E. coli O157: H7) in food. Captured antibody modified magnetic nanoparticles (cMNPs) and detection antibody/horseradish peroxidase (HRP) co-functionalized AuNPs (dHAuNPs) were firstly synthesized for targeted enrichment and colorimetric assay of E. coli O157: H7, in which remarkable signal amplification was realized by loading large amounts of HRP on the surface of AuNPs. Coupling with the optical collimation attachments and embedded magnetic separation module, a highly integrated optical device was constructed, by which in situ magnetic separation and high-quality imaging of 96-well microplates containing E. coli O157: H7 was achieved with a smartphone. The concentration of E. coli O157: H7 could be achieved in one-step by performing digital image colorimetric analysis of the obtained image with a custom-designed app. This biosensor possesses high sensitivity (1.63 CFU/mL), short detecting time (3 h), and good anti-interference performance even in real-sample testing. Overall, the developed method is expected to be a novel field detection platform for foodborne pathogens in water and food as well as for the diagnosis of infections due to its portability, ease of operation, and high feasibility.

Drivers and consequences of microbial community coalescence

Microbial communities are undergoing unprecedented dispersion and amalgamation across diverse ecosystems, thereby exerting profound and pervasive influences on microbial assemblages and ecosystem dynamics. This review delves into the phenomenon of community coalescence, offering an ecological overview that outlines its four-step process and elucidates the intrinsic interconnections in the context of community assembly. We examine pivotal mechanisms driving community coalescence, with a particular emphasis on elucidating the fates of both source and resident microbial communities and the consequential impacts on the ecosystem. Finally, we proffer recommendations to guide researchers in this rapidly evolving domain, facilitating deeper insights into the ecological ramifications of microbial community coalescence.

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.

Indigenous microbial community governs the survival of Escherichia coli O157:H7 in constructed wetlands

The survival pattern of Escherichia coli O157:H7 (E. coli O157:H7) and its regulatory factors in natural environments have been widely studied. However, there is little information about the survival of E. coli O157:H7 in artificial environments, especially in wastewater treatment facilities. In this study, a contamination experiment was performed to explore the survival pattern of E. coli O157:H7 and its central control factors in two constructed wetlands (CWs) under different hydraulic loading rates (HLRs). The results showed that the survival time of E. coli O157:H7 was longer in the CW under the higher HLR. Substrate ammonium nitrogen and available phosphorus were the main factors that influenced the survival of E. coli O157:H7 in CWs. Despite the minimal effect of microbial α-diversity, some keystone taxa, such as Aeromonas, Selenomonas, and Paramecium, governed the survival of E. coli O157:H7. In addition, the prokaryotic community had a more significant impact on the survival of E. coli O157:H7 than the eukaryotic community. The biotic properties had a more substantial direct power on the survival of E. coli O157:H7 than the abiotic factors in CWs. Collectively, this study comprehensively disclosed the survival pattern of E. coli O157:H7 in CWs, which is an essential addition to the environmental behavior of E. coli O157:H7, providing a theoretical basis for the prevention and control of biological contamination in wastewater treatment processes.

Identification of Malassezia globosa as a Gastric Fungus Associated with PD-L1 Expression and Overall Survival of Patients with Gastric Cancer

BACKGROUND

Microbiotas affected the prognosis of cancer patients by regulating programmed death ligand-1 (PD-L1) expression. However, the relationship between gastric fungi and PD-L1 expression is still unclear in gastric cancer (GC). We aimed at exploring the association of gastric fungi with PD-L1 expression and overall survival in GC.

METHODS

A total of 61 GC patients were divided into the two groups based on the PD-L1 combined positive scores (CPS). Fungal profiling was performed by internal transcribed spacer rDNA sequencing, and the survival analyses were performed by Kaplan-Meier curves.

RESULTS

We observed a taxonomic difference of fungi between the PD-L1-High (CPS ≥ 10) and PD-L1-Low group (CPS < 10) by principal coordinates analysis (PCoA) (P = 0.014 for Bray-Curtis and P = 0.042 for Jaccard). Malassezia had a higher abundance in the PD-L1-High group compared to the PD-L1-Low group (P = 0.045). Malassezia globosa elevated significantly in the PD-L1-High group. GC patients with PD-L1 low expression and low abundance of Malassezia globosa had a longer overall survival (OS) than others (P = 0.047). Malassezia globosa was associated with PD-L1 expression (Odds Ratio = 3.509, 95% Confidence Interval: 1.056-11.656, P = 0.040). Malassezia globosa was associated with the tumor size (P = 0.031) and PD-L1 status (P = 0.024). GC patients with a high abundance of Malassezia globosa had shorter OS than others (P = 0.028). Malassezia globosa was an independent factor (Hazard Ratio = 3.080, 95% Confidence Interval: 1.140-8.323, P = 0.027) for OS after adjusting for tumor stage. Malassezia globosa was figured out to be associated with- fatty acid and lipid biosynthesis and degradation via LIPASYN pathway. Conclusions. Malassezia globosa was identified as a PD-L1 expression-associated gastric fungus and associated with OS of GC patients, which calls for more studies to further explore its potential in PD-L1/PD-1 targeted immunotherapy.

Impact of temperature, soil type and compost amendment on the survival, growth and persistence of Listeria monocytogenes of non-environmental (food-source associated) origin in soil

Listeria monocytogenes of varied sources including food-related sources may reach the soil. Associated food safety and environmental health risks of such contamination depend significantly on the capacity of L. monocytogenes to survive in the soil. This study assessed the survival of 13 L. monocytogenes strains isolated from food and food processing environments and a cocktail of three of the strains in two types of soils (loam and sandy) under controlled temperature conditions: 5, 10, 20, 25, 30℃ and 'uncontrolled' ambient temperature conditions in a tropical region. The impact of compost amendment on the survival of L. monocytogenes in the two different types of soils was also assessed. Soil type, temperature and compost amendment significantly (P <0.001) impacted the survival of L. monocytogenes in soil. Temperature variations affected the survival of L. monocytogenes in soil, where some strains such as strain 732, a L. monocytogenes 1/2a strain survived better at lower temperature (5°C), for which counts of up to 10.47 ± 0.005 log CFU/g were recovered in compost-amended sandy soil, 60 days post-inoculation. Some other strains such as strain 441, a L. monocytogenes 1/2a survived best at intermediate temperature (25 and 30 °C), while others such as 2739 (L. monocytogenes 1/2b) thrived at higher temperature (between 30 °C - 37 °C). There were significant correlations between the influence of temperature and soil type, where lower temperature conditions (5°C - 20°C) were generally more suitable for survival in sandy soil compared to higher temperature conditions. For some of the strains that thrived better in sandy soil at lower temperature, Pearson correlation analysis found significant correlations between temperature and soil type. Steady, controlled temperature generally favored the survival of the strains compared to uncontrolled ambient temperature conditions, except for the cocktail. The cocktail persisted until the last day of post-inoculation storage (60th day) in all test soils and under all incubation temperature conditions. Loam soil was more favorable for the survival of L. monocytogenes and compost amendment improved the survival of the strains, especially in compost-amended sandy soil. Listeria monocytogenes may exhibit variable survival capacity in soil, depending on conditions such as soil type, compost amendment and temperature.

Dysbiosis of Gastric Mucosal Fungal Microbiota in the Gastric Cancer Microenvironment

Background

Microbes have been shown to contribute to gastric cancer (GC), gastric bacteria and viruses are associated with gastric carcinogenesis. However, the relationship between gastric fungi and GC is still unclear. Our aim was to evaluate the gastric fungal microbiota in the GC microenvironment.

Methods

Gastric fungal microbiome profiling was performed with internal transcribed spacer (ITS) rDNA sequencing in primary tumor and corresponding paired normal mucosal tissues from 61 GC patients. Differences in microbial composition, taxa diversity, and predicted function were further analyzed.

Results

Dysbiosis of gastric mucosal fungal microbiome was observed between the tumor and normal groups in GC. The tumor group had a higher abundance of certain taxa than the normal group. In the taxa classification, the abundances of Pezizomycetes, Sordariales, Chaetomiaceae, and Rozellomycota were lower in the tumor group than in the normal group. At the genus level, Solicoccozyma (P = 0.033) was found in higher abundance and was differentially enriched in the tumor group with Lefse analysis. Additionally, Solicoccozyma accounted for 0.3% of gastric fungi in the GC microenvironment. Twenty-seven of the 61 GC patients showed positive Solicoccozyma expression in tumors. Solicoccozyma-positive expression in tumors was associated with the Bormann classification and nerve invasion. Solicoccozyma was considered a gastric fungal marker to classify stage I and stage II-IV GC patients with an area under the receiver-operating curve (AUC) of 0.7061, as well as to classify the nerve invasive and nonnerve invasive tumors from GC patients with an AUC of 0.6978. Functional prediction indicated that the positive expression of Solicoccozyma in tumors was associated with the amino acid- and carbohydrate-related metabolic pathways in GC.

Conclusions

This study revealed a novel perspective on the role of Solicoccozyma in tumors and a theoretical basis for therapeutic targets against GC.

The detection and stability of the SARS-CoV-2 RNA biomarkers in wastewater influent in Helsinki, Finland

Wastewater-based surveillance of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is used to monitor the population-level prevalence of the COVID-19 disease. In many cases, due to lockdowns or analytical delays, the analysis of wastewater samples might only be possible after prolonged storage. In this study, the effect of storage conditions on the RNA copy numbers of the SARS-CoV-2 virus in wastewater influent was studied and compared to the persistence of norovirus over time at 4 °C, -20 °C, and -75 °C using the reverse-transcription quantitative PCR (RT-qPCR) assays E-Sarbeco, N2, and norovirus GII. For the first time in Finland, the presence of SARS-CoV-2 RNA was tested in 24 h composite influent wastewater samples collected from Viikinmäki wastewater treatment plant, Helsinki, Finland. The detected and quantified SARS-CoV-2 RNA copy numbers of the wastewater sample aliquots taken during 19-20 April 2020 and stored for 29, 64, and 84 days remained surprisingly stable. In the stored samples, the SARS betacoronavirus and SARS-CoV-2 copy numbers, but not the norovirus GII copy numbers, seemed slightly higher when analyzed from the pre-centrifuged pellet-that is, the particulate matter of the influent-as compared with the supernatant (i.e., water fraction) used for ultrafiltration, although the difference was not statistically significant. Furthermore, when wastewater was spiked with SARS-CoV-2, linear decay at 4 °C was observed on the first 28 days, while no decay was visible within 58 days at -20 °C or -75 °C. In conclusion, freezing temperatures should be used for storage when immediate SARS-CoV-2 RNA analysis from the wastewater influent is not possible. Analysis of the particulate matter of the sample, in addition to the water fraction, can improve the detection frequency.