A new insight into the potential drivers of antibiotic resistance gene enrichment in the collembolan gut association with antibiotic and non-antibiotic agents

Effects of non-antibiotic pharmaceuticals on antibiotic resistance genes (ARGs) in soil ecosystem are still unclear. In this study, we explored the microbial community and ARGs variations in the gut of the model soil collembolan Folsomia candida following soil antiepileptic drug carbamazepine (CBZ) contamination, while comparing with antibiotic erythromycin (ETM) exposure. Results showed that, CBZ and ETM all significantly influenced ARGs diversity and composition in the soil and collembolan gut, increasing the relative abundance of ARGs. However, unlike ETM, which influences ARGs via bacterial communities, exposure to CBZ may have primarily facilitated enrichment of ARGs in gut through mobile genetic elements (MGEs). Although soil CBZ contamination did not pose an effect on the gut fungal community of collembolans, it increased the relative abundance of animal fungal pathogens contained therein. Soil ETM and CBZ exposure both significantly increased the relative abundance of Gammaproteobacteria in the collembolan gut, which may be used to indicate soil contamination. Together, our results provide a fresh perspective for the potential drivers of non-antibiotic drugs on ARG changes based on the actual soil environment, revealing the potential ecological risk of CBZ on soil ecosystems involving ARGs dissemination and pathogens enrichment.

Geographical distribution of Ixodes persulcatus and associated pathogens: Analysis of integrated data from a China field survey and global published data

The increasing incidence and range expansion of tick-borne diseases have caused global threats to human and animal health under the background of climate and socioeconomic changes. As an efficient vector in transmission of tick-borne diseases, a growing burden caused by Ixodes persulcatus and associated pathogens could not be underestimated. This study summarized the distribution, hosts, and pathogens of I. persulcatus, and predicted the suitable habitats of this tick species worldwide. An integrated database involving a field survey, reference book, literature review, and related website was constructed. Location records of I. persulcatus and associated pathogens were incorporated into distribution maps using ArcGIS software. Positive rates for I. persulcatus-associated agents were estimated by meta-analysis. The global distribution of the tick species was predicted using Maxent model. I. persulcatus was distributed in 14 countries across the Eurasian continent, involving Russia, China, Japan, and several Baltic Sea states, which ranged between 21°N to 66°N. The tick species fed on 46 species of hosts, and 51 tick-borne agents could be harbored by I. persulcatus. The predictive model showed that I. persulcatus could be predominantly distributed in northern Europe, western Russia, and northern China. Our study fully clarified the potential public health risks posed by I. persulcatus and I. persulcatus-borne pathogens. Surveillance and control measures of tick-borne diseases should be enhanced to promote the health of humans, animals, and ecosystems.

Nucleoredoxin gene SINRX1 negatively regulates tomato immunity by activating SA signaling pathway

The tomato (Solanum lycopersicum) is widely consumed globally and renowned for its health benefits, including the reduction of cardiovascular disease and prostate cancer risk. However, tomato production faces significant challenges, particularly due to various biotic stresses such as fungi, bacteria, and viruses. To address this challenges, we employed the CRISPR/Cas9 system to modify the tomato NUCLEOREDOXIN (SlNRX) genes (SlNRX1 and SlNRX2) belonging to the nucleocytoplasmic THIOREDOXIN subfamily. CRISPR/Cas9-mediated mutations in SlNRX1 (slnrx1) plants exhibited resistance against bacterial leaf pathogen Pseudomonas syringae pv. maculicola (Psm) ES4326, as well as the fungal pathogen Alternaria brassicicola. However, the slnrx2 plants did not display resistance. Notably, the slnrx1 demonstrated elevated levels of endogenous salicylic acid (SA) and reduced levels of jasmonic acid after Psm infection, in comparison to both wild-type (WT) and slnrx2 plants. Furthermore, transcriptional analysis revealed that genes involved in SA biosynthesis, such as ISOCHORISMATE SYNTHASE 1 (SlICS1) and ENHANCED DISEASE SUSCEPTIBILITY 5 (SlEDS5), were upregulated in slnrx1 compared to WT plants. In addition, a key regulator of systemic acquired resistance, PATHOGENESIS-RELATED 1 (PR1), exhibited increased expression in slnrx1 compared to WT. These findings suggest that SlNRX1 acts as a negative regulator of plant immunity, facilitating infection by the Psm pathogen through interference with the phytohormone SA signaling pathway. Thus, targeted mutagenesis of SlNRX1 is a promising genetic means to enhance biotic stress resistance in crop breeding.

Characterization of multidrug and heavy metal resistance of carbapenemases producing Klebsiella pneumoniae from poultry samples in Bangladesh

BACKGROUND

Resistance to multiple drugs in Klebsiella pneumoniae (KPN) is an important issue in human and animal medicine. KPN phenotypic and genotypic aspects in poultry samples have not been comprehensively explored in Bangladesh.

METHODS

This research focused on the prevalence of antibiotic resistance and the characterization of KPN in Bangladeshi poultry isolates using both phenotypic and genotypic approaches.

RESULTS

A total of 32 poultry samples were randomly obtained from a commercial poultry farm in Narsingdi, Bangladesh, and 43.90% (18/41) of the isolates were confirmed to be KPN, whereas all isolates were biofilm producers. The antibiotic sensitivity test revealed the most remarkable (100%) antibiotic resistance level against Ampicillin, Doxycycline and Tetracycline while remaining susceptible to Doripenem, Meropenem, Cefoxitin and Polymyxin B. Resistance to Nalidixic acid, Nitrofurantoin, Trimethoprim, Levofloxacin, Ciprofloxacin, Cefuroxime and Chloramphenicol ranges from 18% to 70%. Minimum inhibitory concentrations for carbapenem-resistant KPN ranged from 128 to 512 g/mL for Meropenem, Imipenem, Gentamycin and Ciprofloxacin, respectively. Carbapenemase-producing KPN isolates harboured a single or multiple β-lactamase genes, bla_SIM-1 , bla_IMP-4 and bla_OXA-48 as well as one ESBL gene (bla_TEM ) and plasmid-mediated quinolone resistance gene (qnrB). Furthermore, Cr and Co outperformed Cu and Zn in antibacterial effectiveness.

CONCLUSIONS

The results of this investigation showed that the high prevalence of multidrug-resistant pathogenic KPN in our chosen geographic location had displayed sensitivity to FOX/PB/Cr/Co, which might be regarded as an alternate treatment to reduce pressure of use on carbapenems.

Levels and distribution of Salmonella in naturally contaminated cashews

Raw materials associated with foodborne illness outbreaks are rarely available for evaluation. The levels and distribution of Salmonella were determined in naturally contaminated raw cashews linked to a salmonellosis outbreak associated with a fermented cashew cheese analog. Two unopened 22.7-kg boxes from a single lot of cashew kernel pieces were each divided into seven approximately equal units, 14 in total. Three 10-g subsamples per unit (n = 21) were evaluated for aerobic plate count (APC), coliform counts, and Escherichia coli counts, and 10 50-g subsamples per unit (n = 70) were enriched for the presence of Salmonella. Presumptive Salmonella-positive colonies were confirmed using CHROMagar Salmonella and real-time PCR (InvA) and then serotyped using antigenic methods and genome sequencing prediction tools. APC and coliform counts ranged from 1.81-5.47 (mean 2.44 ± 0.63) log CFU/g and 0.60-5.20 (mean 1.74 ± 0.80) log CFU/g, respectively. Salmonella was recovered from four units in Box 1 and all seven units in Box 2. One of 10 subsamples was positive in all but four of the positive units; one (Box 1) and three (Box 2) units had two positive subsamples. The level of Salmonella in the two boxes combined was 0.0023 most probable number/g (95% confidence interval [0.0014, 0.0038]). Salmonella Urbana was isolated from three of five positive subsamples in Box 1 and eight of 10 positive subsamples in Box 2. Salmonella Fresno and Vinohrady were unique to single subsamples from Box 1, and Salmonella Nima was isolated from two subsamples from Box 2. Of the four serovars recovered, Salmonella Urbana and Salmonella Vinohrady were in common with outbreak-associated clinical or product isolates. Understanding the distribution and concentration of Salmonella in naturally contaminated cashews provides important information for hazard analysis and risk assessments for soaked and fermented cashew products.

The tracheal immune system of insects - A blueprint for understanding epithelial immunity

The unique design of respiratory organs in multicellular organisms makes them prone to infection by pathogens. To cope with this vulnerability, highly effective local immune systems evolved that are also operative in the tracheal system of insects. Many pathogens and parasites (including viruses, bacteria, fungi, and metazoan parasites) colonize the trachea or invade the host via this route. Currently, only two modules of the tracheal immune system have been characterized in depth: 1) Immune deficiency pathway-mediated activation of antimicrobial peptide gene expression and 2) local melanization processes that protect the structure from wounding. There is an urgent need to increase our understanding of the architecture of tracheal immune systems, especially regarding those mechanisms that enable the maintenance of immune homeostasis. This need for new studies is particularly exigent for species other than Drosophila.

Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers

BACKGROUND

The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs.

RESULTS

Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains.

CONCLUSIONS

This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.

A new workflow for assigning removal credits to assess overall performance of managed aquifer recharge (MAR)

Pathogen removal in managed aquifer recharge (MAR) systems is dependent upon numerous operational, physicochemical water quality, and biological parameters. Due to the site-specific conditions affecting these parameters, guidelines for specifying pathogen removal have historically taken rather precautionary and conservative approaches in order to protect groundwater quality and public health. A literature review of regulated pathogens in MAR applications was conducted and compared to up-and-coming indicators and surrogates for pathogen assessment, all of which can be gathered into a toolbox from which regulators and operators alike can select appropriate pathogens for monitoring and optimization of MAR practices. Combined with improved knowledge of pathogen fate and transport obtained through lab- and pilot-scale studies and supported by modeling, this foundation can be used to select appropriate, site-specific pathogens for regarding a more efficient pathogen retention, ultimately protecting public health and reducing costs. This paper outlines a new 10 step-wise workflow for moving towards determining robust removal credits for pathogens based on risk management principles. This approach is tailored to local conditions while reducing overly conservative regulatory restrictions or insufficient safety contingencies. The workflow is intended to help enable the full potential of MAR as more planned water reuse systems are implemented in the coming years.

Anthropogenic and natural disturbances along a river and its estuary alter the diversity of pathogens and antibiotic resistance mechanisms

Antibiotic resistance (AMR) in pathogens threatens human health worldwide, and antibiotic-resistant bacteria (ARB) are widespread in the environment. In particular, anthropogenically-disturbed rivers became reservoirs of ARBs and hotspots of antibiotic resistance gene (ARG) transmission. However, the diversity and sources of ARB, and the mechanisms of ARG transmission are not fully known. Here, we used deep metagenomic sequencing to study the dynamics of pathogens and their antibiotic resistance mechanisms along the Alexander River (Israel), affected by sewage and animal farm runoffs. Putative pathogens such as Aeromicrobium marinum and Mycobacterium massilipolynesiensis were enriched in western stations, following the inputs of polluted Nablus River. Aeromonas veronii was dominant in eastern stations in Spring. Several AMR mechanisms showed distinct patterns in Summer-Spring (dry season) and Winter (rainy season). We found low abundance beta-lactamases conferring carbapenem resistance: e.g., OXA-912 was linked to A. veronii in Spring; OXA-119 and OXA-205 to Xanthomonadaceae in Winter. We classified 33 % of ARG-containing contigs as putative plasmid sequences, indicating the high potential for resistome transmission. A limited number of ARGs were linked to putative phages. Our results suggest that this model river is a hotspot for AMR activity and transmission, and highlight the merit of deep sequencing for AMR discovery.

Exposure to cypermethrin pesticide disturbs the microbiome and disseminates antibiotic resistance genes in soil and the gut of Enchytraeus crypticus

Worldwide, pyrethroids, such as cypermethrin, are the second most applied group of insecticides, however, their effects on the soil microbiome and non-target soil fauna remain largely unknown. Herein, we assessed the change of bacterial communities and antibiotic resistance genes (ARGs) of soil and in the gut of the model soil species Enchytraeus crypticus using a combination of 16S rRNA gene amplicon sequencing, and high-throughput qPCR of ARGs. Results indicate that cypermethrin exposure enriches potential pathogens (e.g. Bacillus anthracis) in the soil and gut microbiome of E. crypticus, heavily disrupting the latter's microbiome structure, and even disrupts activities of the E. crypticus immune system. The co-occurrence of potential pathogens (e.g. Acinetobacter baumannii), ARGs, and mobile genetic elements (MGEs) revealed the increased risk of pathogenicity as well as antibiotic resistance in potential pathogens. Moreover, structural equation modeling demonstrated that the dissemination of ARGs was not only promoted by MGEs, but also by the ratio of the core to non-core bacterial abundance. Collectively, these results provide an in-depth view of the previously unappreciated environmental risk of cypermethrin on the dissemination of ARGs in the soil and non-target soil fauna.

Food safety incidents in the red meat industry: A review of foodborne disease outbreaks linked to the consumption of red meat and its products, 1991 to 2021

Red meat is a significant source of human nutrition, and the red meat industry contributes to the economy of nations. Nonetheless, there is a widespread global concern about public health issues posed by severe food safety incidents within the red meat industry. Most of these incidents are associated with foodborne disease outbreaks that impact individual consumers, food businesses and society. This study adopts a systematic search and review approach to identify three decades of published investigation reports of global foodborne disease outbreaks linked with the consumption of red meat and products made from them. The review aims to evaluate the critical features of these outbreak incidents to get insight into their contributing factors and root causes. In particular, this review discusses the transmission setting (origin of pathogenic agents), the food vehicles mostly incriminated, the causative pathogens (bacteria, viruses, and parasites) causing the most illnesses, and the most commonly reported contributing factors to the outbreaks. This information can help researchers and food business operators (FBOs) inform future risk assessment studies and support risk management activities in developing risk-mitigating strategies for the industry. Findings from this study suggest that implementing food safety management strategies which include adequate control measures at all stages of the food chain, from farm to fork, is imperative in preventing outbreak incidents. Of equal importance is the need for enhanced and sustained public education about the risk of foodborne illnesses associated with meat and its products whilst discouraging the consumption of raw meat products, especially by high-risk groups.

Reshaping surveillance for infectious diseases: less chasing of pathogens and more monitoring of drivers

Animal health surveillance, despite its name, tends to focus on looking for disease. Often this involves searching for cases of infection with known pathogens (‘pathogen chasing'). Such an approach is both resource intensive and limited by the requirement for prior knowledge of disease likelihood. In this paper, the authors propose the gradual reshaping of surveillance towards the systems level, focusing on the processes (‘drivers') that promote disease or health, rather than on the presence or absence of specific pathogens. Examples of relevant drivers include land-use change, increasing global interconnectedness, and finance and capital flows. Importantly, the authors suggest that surveillance should focus on detecting changes in patterns or quantities associated with such drivers. This would generate systems-level, risk-based surveillance information to identify areas where additional attention may be needed, and, over time, inform the implementation of prevention efforts. The collection, integration and analysis of data on drivers is likely to require investment in improving data infrastructures. A period of overlap would allow the two systems (traditional surveillance and driver monitoring) to be compared and calibrated. This would also lead to a better understanding of the drivers and their linkages, and thereby generate new knowledge that can improve surveillance and inform mitigation efforts. Since surveillance of drivers may give signals when changes are occurring, which could act as alerts and enable targeted mitigation, this might even enable disease to be prevented before it happens by directly intervening in the drivers themselves. Such surveillance focused on the drivers could be expected to bring additional benefits, since the same drivers promote multiple diseases. Further, focusing on drivers rather than pathogens should enable control of currently unknown diseases, making this approach particularly timely, given the increasing risk of emergence of new diseases.

An achromatic colorimetric nanosensor for sensitive multiple pathogen detection by coupling plasmonic nanoparticles with magnetic separation

Rapid screening of multiple pathogens will greatly improve the efficiency of pandemic prevention and control. Colorimetric methods exhibit the advantages of convenience, portability, low cost, time efficiency, and free of sophisticated instruments, yet usually have difficulties in simultaneous detection and suffer from monotonous color changes with low visual resolution and sensitivity. Hence, coupled three kinds of plasmonic nanoparticles (NPs) with magnetic separation, we developed an achromatic colorimetric nanosensor with highly enhanced visual resolution for simultaneous detection of SARS-CoV-2, Staphylococcus aureus, and Salmonella typhimurium. The achromatic nanosensor was composed of SARS-CoV-2-targeting red gold NPs, S. aureus-targeting yellow silver NPs and S. typhimurium-targeting blue silver triangle NPs mixed as black color. In the detection, three corresponding magnetic probes were added into the above mixture. In the presence of a target pathogen, it would be recognized and combined with corresponding colored reporters and magnetic probes to form sandwich complexes, which were removed by magnetic separation, and the sensor changed from black to a chromatic color (the color of the reporters remained in supernatant). Consequently, different target pathogen induced different color. For example, SARS-CoV-2, S. aureus, and S. typhimurium respectively produced green, purple, and orange. While coexistence of S. aureus and S. typhimurium produced red, and coexistence of S. aureus and SARS-CoV-2 produced blue, etc. Therefore, by observing the color change or measuring the absorption spectra, multiple pathogen detection was achieved conveniently. Compared with most colorimetric sensors, this achromatic nanosensor involved rich color change, thus significantly enhancing visual resolution and inspection sensitivity. Therefore, this sensor opened a promising avenue for efficient monitoring and early warning of food safety and quality.

Application of essential oils as sanitizer alternatives on the postharvest washing of fresh produce

Growers commonly wash fresh produce with chemical sanitizers during postharvest handling. However, these sanitizers can be harsh to washing systems and pose a health risk to workers. Essential oils (EOs) can be used as alternatives to chemical sanitizers in produce washing. Previous studies reveal that the EOs from thyme, oregano, cinnamon, and clove are the main EOs evaluated in the studies as potential sanitizers for the washing of produce. The use of EOs and surfactants, such as tween80 and cetylpyridinium chloride, might be used to improve the antimicrobial activity of emulsions. However, studies are still required to evaluate the potential effect of different chemical components of EOs and preparations. Also, it is recommended that researchers focus on overcoming obstacles regarding EOs application in washing systems, including the high levels of EO required to reduce bacterial growth, undesired organoleptic impact on produce, and the poor solubility of EOs in aqueous solution.

The hidden diversity of microbes in ballast water and sediments revealed by metagenomic sequencing

With the rapid globalization of trade, the worldwide spread of pathogens through ballast water is becoming a major concern. Although the international maritime organization (IMO) convention has been adopted to prevent the spread of harmful pathogens, the limited species resolution of the current microbe-monitoring methods challenged the ballast water and sediments management (BWSM). In this study, we explored metagenomic sequencing to investigate the species composition of microbial communities in four international vessels for BWSM. Our results showed the largest species diversity (14,403) in ballast water and sediments, including bacteria (11,710), eukaryotes (1007), archaea (829), and viruses (790). A total of 129 phyla were detected, among which the Proteobacteria, followed by Bacteroidetes, and Actinobacteria were the most abundant. Notably, 422 pathogens that are potentially harmful to marine environments and aquaculture were identified. The co-occurrence network analysis showed that most of these pathogens were positively correlated with the commonly used indicator bacteria Vibrio cholerae, Escherichia coli, and intestinal Enterococci species, validating the D-2 standard in BWSM. The functional profile showed prominent pathways of methane and sulfur metabolism, indicating that the microbial community in the severe tank environment still utilizes the energy to sustain such a high level of microbe diversity. In conclusion, metagenomic sequencing provides novel information for BWSM.

Shrimp MultiPath™ multiplexed PCR white spot syndrome virus detection in penaeid shrimp

White spot syndrome virus (WSSV), which causes white spot disease, is one of the notoriously feared infectious agents in the shrimp industry, inflicting estimated production losses world-wide of up to US$1 billion annually. Cost-effective accessible surveillance testing and targeted diagnosis are key to alerting shrimp industries and authorities worldwide early about WSSV carrier status in targeted shrimp populations. Here we present key validation pathway metrics for the Shrimp MultiPathTM (SMP) WSSV assay as part of the multi-pathogen detection platform. With superior throughput, fast turn-around time, and extremely low cost per test, the SMP WSSV assay achieves a high level of analytical sensitivity (~2.9 copies), perfect analytical specificity (~100%), and good intra- and inter-run repeatability (coefficient of variation <5%). The diagnostic metrics were estimated using Bayesian latent class analysis on data from 3 experimental shrimp populations from Latin America with distinct WSSV prevalence and yielded a diagnostic sensitivity of 95% and diagnostic specificity of 99% for SMP WSSV, which was higher than these parameters for the TaqMan quantitative PCR (qPCR) assays currently recommended by the World Organisation for Animal Health and the Commonwealth Scientific and Industrial Research Organisation. This paper additionally presents compelling data for the use of synthetic double-stranded DNA analyte spiked into pathogen-naïve shrimp tissue homogenate as a means to substitute clinical samples for assay validation pathways targeting rare pathogens. SMP WSSV shows analytical and diagnostic metrics comparable to qPCR-based assays and demonstrates fit-for-purpose performance for detection of WSSV in clinically diseased and apparently healthy animals.

Rab GTPase-regulated phagosome-lysosome fusion is bypassed by micromolar calcium

Several ATP- and cytosol-dependent fusion processes between membranes of the endocytic and exocytic pathways have been biochemically reconstituted. We here present a phagosome-lysosome-fusion reaction driven by micromolar Ca2+ in the absence of ATP and cytosol. Investigating classical and Ca2+-driven fusion (CaFu) side-by-side in vitro, using the same membrane preparations, we show that CaFu is faster than standard fusion (StaFu), leads to larger fusion products, and is not blocked by established inhibitors of StaFu. Approximately 120 µM Ca2+ supports maximal membrane attachment and 15 µM Ca2+ maximal membrane fusion, assigning Ca2+ both a membrane binding and a fusion-promoting activity. StaFu and CaFu are inhibited by a mutant form α-SNAP that does not support SNARE (SNAP receptor) activation, and both are inhibited by a mixture of the cytosolic domains of three cognate Q-SNARE proteins, demonstrating a role of SNAREs in Ca2+-driven membrane merger. CaFu is independent of the calcium-regulated proteins synaptotagmin-7, calmodulin, and annexins A2 and A7. We propose that CaFu corresponds to the last step of phagosome-lysosome fusion, when a raised Ca2+ concentration from the compartment lumen activates SNAREs for fusion.

Migration risk of Escherichia coli O157:H7 in unsaturated porous media in response to different colloid types and compositions

The vadose zone is a critical zone for microbial entry into the subsurface environment, and various types of inorganic and organic colloids can affect the migration of pathogenic bacteria. In the study, we explored the migration behavior of Escherichia coli O157:H7 with humic acids (HA), iron oxides (Fe₂O₃) or their mixture, uncovering their migration mechanisms in the vadose zone. The effect of complex colloids on the physiological properties of E. coli O157:H7 was analyzed based on the measured particle size, zeta potential and contact angle. HA colloids significantly promoted the migration of E. coli O157:H7, where Fe₂O₃ was opposite. The migration mechanism of E. coli O157:H7 with HA and Fe₂O₃ is obviously different. Multiple colloids dominated by organic colloid will further highlight its promoting effect on E. coli O157:H7 under the guidance of electrostatic repulsion due to the influence of colloidal stability. Multiple colloids dominated by metallic colloid will inhibit the migration of E. coli O157:H7 under the control of capillary force due to the restriction of contact angle. The risk of secondary release of E. coli O157:H7 can be effectively reduced when the ratio of HA/Fe₂O₃ is ≥ 1. Combining this conclusion with the distribution characteristics of soil in China, an attempt was made to analyse the migration risk of E. coli O157:H7 on a national scale. In China, from north to south, the migration capacity of E. coli O157:H7 gradually decreased, and the risk of secondary release gradually increased. These results provide ideas for the subsequent study of the effect of other factors on the migration of pathogenic bacteria on a national scale and provide risk information about soil colloids for the construction of pathogen risk assessment model under comprehensive conditions in the future.

The Evolution of the Age of Onset of Resistance to Infectious Disease

Many organisms experience an increase in disease resistance as they age, but the time of life at which this change occurs varies. Increases in resistance are partially due to prior exposure and physiological constraints, but these cannot fully explain the observed patterns of age-related resistance. An alternative explanation is that developing resistance at an earlier age incurs costs to other life-history traits. Here, we explore how trade-offs with host reproduction or mortality affect the evolution of the onset of resistance, depending on when during the host's life cycle the costs are paid (only when resistance is developing, only when resistant or throughout the lifetime). We find that the timing of the costs is crucial to determining evolutionary outcomes, often making the difference between resistance developing at an early or late age. Accurate modelling of biological systems therefore relies on knowing not only the shape of trade-offs but also when they take effect. We also find that the evolution of the rate of onset of resistance can result in evolutionary branching. This provides an alternative, possible evolutionary history of populations which are dimorphic in disease resistance, where the rate of onset of resistance has diversified rather than the level of resistance.

Transport of microplastics in the body and interaction with biological barriers, and controlling of microplastics pollution

Microplastics (MPs) are one novel environmental pollutant sized < 5 mm that is ubiquitously present in numerous environmental media and particularly susceptible to interact with various toxic chemicals. Importantly, MPs can enter the food chain, and are bio-enriched and bio-accumulated with trophic levels, eventually endangering ecosystems and human health. However, there need to be more understanding regarding the bio-interaction of MPs with the host, particularly for biological barriers. This review aimed to summarize the latest findings regarding the main exposure routes of MPs that generated health burdens on humans. Furthermore, their interactions with biological barriers that generate adverse health effects and the underlying mechanisms were also reviewed. Additionally, we provided a comprehensive overview of recent advances regarding the removing and controlling of MPs. Finally, we discussed the future directions for MPs hazard prevention to provide helpful information for regulating decision-making and guiding safer plastics applications.

Prevalence of Anaplasma phagocytophilum, Borrelia burgdorferi sensu lato, Rickettsia spp. and Babesia spp. in cattle serum and questing ticks from Belgium

BACKGROUND

Anaplasmosis, borreliosis, rickettsiosis and babesiosis are tick-borne diseases of medical, veterinary and economic importance. In Belgium, little is known on the prevalence of these diseases in animals and previous screenings relate only to targeted geographic regions, clinical cases or a limited number of tested samples. We therefore performed the first nationwide seroprevalence study of Anaplasma spp., A. phagocytophilum, Borrelia spp., Rickettsia spp. and Babesia spp. in Belgian cattle. We also screened questing ticks for the aforementioned pathogens.

METHODS

ELISAs and IFATs were performed on a representative sample set of cattle sera stratified proportionally to the number of cattle herds per province. Questing ticks were collected in areas where the highest prevalence for the forenamed pathogens in cattle serum were observed. Ticks were analyzed by quantitative PCR for A. phagocytophilum (n = 783), B. burgdorferi sensu lato (n = 783) and Rickettsia spp. (n = 715) and by PCR for Babesia spp. (n = 358).

RESULTS

The ELISA screening for antibodies to Anaplasma spp. and Borrelia spp. in cattle sera showed an overall seroprevalence of 15.6% (53/339) and 12.9% (52/402), respectively. The IFAT screening for antibodies against A. phagocytophilum, Rickettsia spp. and Babesia spp. resulted in an overall seroprevalence of 34.2% (116/339), 31.2% (99/317) and 3.4% (14/412), respectively. At the provincial level, the provinces of Liege and Walloon Brabant harboured the highest seroprevalence of Anaplasma spp. (44.4% and 42.7% respectively) and A. phagocytophilum (55.6% and 71.4%). East Flanders and Luxembourg exhibited the highest seroprevalence of Borrelia spp. (32.4%) and Rickettsia spp. (54.8%) respectively. The province of Antwerp showed the highest seroprevalence of Babesia spp. (11%). The screening of field-collected ticks resulted in a prevalence of 13.8% for B. burgdorferi s.l., with B. afzelii and B. garinii being the most common genospecies (65.7% and 17.1%, respectively). Rickettsia spp. was detected in 7.1% of the tested ticks and the only identified species was R. helvetica. A low prevalence was found for A. phagocytophilum (0.5%) and no Babesia positive tick was detected.

CONCLUSIONS

The seroprevalence data in cattle indicate hot spots for tick-borne pathogens in specific provinces and highlights the importance of veterinary surveillance in anticipating the emergence of diseases among humans. The detection of all pathogens, with the exception of Babesia spp. in questing ticks, underlines the need of raising awareness among public and professionals on other tick-borne diseases along with lyme borreliosis.

Fast and easy bioassay for the necrotizing fungus Botrytis cinerea on poplar leaves

BACKGROUND

Necrotizing pathogens pose an immense economic and ecological threat to trees and forests, but the molecular analysis of these pathogens is still in its infancy because of lacking model systems. To close this gap, we developed a reliable bioassay for the widespread necrotic pathogen Botrytis cinerea on poplars (Populus sp.), which are established model organisms to study tree molecular biology.

RESULTS

Botrytis cinerea was isolated from Populus x canescens leaves. We developed an infection system using fungal agar plugs, which are easy to handle. The method does not require costly machinery and results in very high infection success and significant fungal proliferation within four days. We successfully tested the fungal plug infection on 18 poplar species from five different sections. Emerging necroses were phenotypically and anatomically examined in Populus x canescens leaves. We adapted methods for image analyses of necrotic areas. We calibrated B. cinerea DNA against Ct-values obtained by quantitative real-time polymerase chain reaction and measured the amounts of fungal DNA in infected leaves. Increases in necrotic area and fungal DNA were strictly correlated within the first four days after inoculation. Methyl jasmonate pretreatment of poplar leaves decreased the spreading of the infection.

CONCLUSIONS

We provide a simple and rapid protocol to study the effects of a necrotizing pathogen on poplar leaves. The bioassay and fungal DNA quantification for Botrytis cinerea set the stage for in-depth molecular studies of immunity and resistance to a generalist necrotic pathogen in trees.

Multi-drug resistant ESKAPE pathogens and the uses of plants as their antimicrobial agents

Infections by ESKAPE (Enterococcus sp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens cause major concern due to their multi-drug resistance (MDR). The ESKAPE pathogens are frequently linked to greater mortality, diseases, and economic burden in healthcare worldwide. Therefore, the use of plants as a natural source of antimicrobial agents provide a solution as they are easily available and safe to use. These natural drugs can also be enhanced by incorporating silver nanoparticles and combining them with existing antibiotics. By focussing the attention on the ESKAPE organisms, the MDR issue can be addressed much better.

In vitro application of proline in potato tubers under newly emerging bacteria Lelliottia amnigena infection

Biotic stress deleteriously affects growth, development, and productivity in plants. Proline (Pro) plays a significant role in enhancing plant resistance to pathogen infection. However, its effects on reducing Lelliottia amnigena-induced oxidative stress in potato tubers remain unknown. The present study aims to evaluate the in vitro Pro treatment in potato tubers exposed to a newly emerging bacterium, L. amnigena. Sterilized healthy potato tubers were inoculated with 0.3 mL of L. amnigena suspension (3.69 × 10⁷ CFU mL^-1) 24 h before Pro (5.0 mM) application. The L. amnigena treatment significantly increased the contents of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) in the potato tubers by 80.6 and 85.6%, respectively, compared to the control. Application of proline (Pro) decreased MDA and H₂O₂ contents by 53.6 and 55.9%, respectively, compared to the control. Application of Pro to L. amnigena-stressed potato tubers increased the activities of NADPH oxidase (NOX), superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), polyphenol oxidase (PPO), phenylalanine ammonia-lyase (PAL), cinnamyl alcohol dehydrogenase (CAD), 4-coumaryl-CoA ligase (4CL) and cinnamate-4-hydroxylase (C4H) C4H by 94.2, 96.3, 97.3, 97.1, 96.6, 79.3, 96.4, 93.6, and 96.2%, respectively, compared to the control. In comparison to the control, the genes PAL, SOD, CAT, POD, and NOX were significantly increased in the Pro-treated tubers at 5.0 mM concentration. Tubers treated with Pro + L. amnigena increased the transcript levels of PAL, SOD, CAT, POD, and NOX by 2.3, 2.2, 2.3, 2.5, and 2.8-fold respectively, compared to the control. Our findings suggested that pretreatment of tubers with Pro might reduce lipid peroxidation and oxidative stress by enhancing enzymatic antioxidant activity and gene expression.

WildHealthNet: Supporting the development of sustainable wildlife health surveillance networks in Southeast Asia

Wildlife and wildlife interfaces with people and livestock are essential surveillance targets to monitor emergent or endemic pathogens or new threats affecting wildlife, livestock, and human health. However, limitations of previous investments in scope and duration have resulted in a neglect of wildlife health surveillance (WHS) systems at national and global scales, particularly in lower and middle income countries (LMICs). Building on decades of wildlife health activities in LMICs, we demonstrate the implementation of a locally-driven multi-pronged One Health approach to establishing WHS in Cambodia, Lao PDR and Viet Nam under the WildHealthNet initiative. WildHealthNet utilizes existing local capacity in the animal, public health, and environmental sectors for event based or targeted surveillance and disease detection. To scale up surveillance systems to the national level, WildHealthNet relies on iterative field implementation and policy development, capacity bridging, improving data collection and management systems, and implementing context specific responses to wildlife health intelligence. National WHS systems piloted in Cambodia, Lao PDR, and Viet Nam engaged protected area rangers, wildlife rescue centers, community members, and livestock and human health sector staff and laboratories. Surveillance activities detected outbreaks of H5N1 highly pathogenic avian influenza in wild birds, African swine fever in wild boar (Sus scrofa), Lumpy skin disease in banteng (Bos javanicus), and other endemic zoonotic pathogens identified as surveillance priorities by local stakeholders. In Cambodia and Lao PDR, national plans for wildlife disease surveillance are being signed into legislation. Cross-sectoral and trans-disciplinary approaches are needed to implement effective WHS systems. Long-term commitment, and paralleled implementation and policy development are key to sustainable WHS networks. WildHealthNet offers a roadmap to aid in the development of locally-relevant and locally-led WHS systems that support the global objectives of the World Organization for Animal Health's Wildlife Health Framework and other international agendas.

Rodent-targeted approaches to reduce acarological risk of human exposure to pathogen-infected Ixodes ticks

In the United States, rodents serve as important hosts of medically important Ixodes ticks, including Ixodes scapularis and Ixodes pacificus, as well as reservoirs for human pathogens, including Anaplasma phagocytophilum, Borrelia burgdorferi sensu stricto (s.s.), and Babesia microti. Over the last four decades, different methods to disrupt enzootic transmission of these pathogens between tick vectors and rodent reservoirs have been developed and evaluated. Early work focused on self-application of topical acaricide by rodents to kill infesting ticks; this resulted in two different types of commercial products based on (i) delivery of permethrin to rodents via impregnated cotton offered as nesting material or (ii) application of fipronil to rodents via an impregnated wick as they navigate through a bait box to reach a food source. More recent work has focused on approaches where acaricides, antibiotics, or a vaccine against Bo. burgdorferi s.s. are delivered orally via rodent food baits. Of these, the oral vaccine and oral acaricide are nearest to commercialization. Other approaches in early stages of development include anti-tick vaccines for rodents and use of heritable genome editing to engineer white-footed mice (Peromyscus leucopus) that are refractory to Bo. burgdorferi s.s. In this review, I first outline general benefits and drawbacks of rodent-targeted tick and pathogen control methods, and then describe the empirical evidence for different approaches to impact enzootic pathogen transmission and acarological risk of human exposure to pathogen-infected Ixodes ticks. Rodent-targeted methods remain promising components of integrated tick management approaches but there are concerns about the robustness of the impact of existing rodent-targeted products across habitats and variable tick host communities, and in some cases also for the implementation cost in relation to what homeowners in Lyme disease endemic areas say they are willing to pay for tick control.

The Tick-Borne Pathogens: An Overview of China's Situation

BACKGROUND

Ticks are important medical arthropods that can transmit hundreds of pathogens, such as parasites, bacteria, and viruses, leading to serious public health burdens worldwide. Unexplained fever is the most common clinical manifestation of tick-borne diseases. Since the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the surge of coronavirus disease 2019 (COVID-19) cases led to the hospital overload and fewer laboratory tests for tick-borne diseases. Therefore, it is essential to review the tick-borne pathogens and further understand tick-borne diseases.

PURPOSE

The geographic distribution and population of ticks in the Northern hemisphere have expanded while emerging tick-borne pathogens have been introduced to China continuously. This paper focused on the tick-borne pathogens that are threatening public health in the world. Their medical significant tick vectors, as well as the epidemiology, clinical manifestations, diagnosis, treatment, prevention, and control measures, are emphasized in this document.

METHODS

In this study, all required data were collected from articles indexed in English databases, including Scopus, PubMed, Web of Science, Science Direct, and Google Scholar.

RESULTS

Ticks presented a great threat to the economy and public health. Although both infections by tick-borne pathogens and SARS-CoV-2 have fever symptoms, the history of tick bite and its associated symptoms such as encephalitis or eschar could be helpful for the differential diagnosis. Additionally, as a carrier of vector ticks, migratory birds may play a potential role in the geographical expansion of ticks and tick-borne pathogens during seasonal migration.

CONCLUSION

China should assess the risk score of vector ticks and clarify the potential role of migratory birds in transmitting ticks. Additionally, the individual and collective protection, vector control, comprehensive surveillance, accurate diagnosis, and symptomatic treatment should be carried out, to meet the challenge.

Prevalence of Anaplasma phagocytophilum, Borrelia burgdorferi sensu lato, Rickettsia spp. and Babesia spp. in cattle serum and questing ticks from Belgium

BACKGROUND

Anaplasmosis, borreliosis, rickettsiosis and babesiosis are tick-borne diseases of medical, veterinary and economic importance. In Belgium, little is known on the prevalence of these diseases in animals and previous screenings relate only to targeted geographic regions, clinical cases or a limited number of tested samples. We therefore performed the first nationwide seroprevalence study of Anaplasma spp., A. phagocytophilum, Borrelia spp., Rickettsia spp. and Babesia spp. in Belgian cattle. We also screened questing ticks for the aforementioned pathogens.

METHODS

ELISAs and IFATs were performed on a representative sample set of cattle sera stratified proportionally to the number of cattle herds per province. Questing ticks were collected in areas where the highest prevalence for the forenamed pathogens in cattle serum were observed. Ticks were analyzed by quantitative PCR for A. phagocytophilum (n = 783), B. burgdorferi sensu lato (n = 783) and Rickettsia spp. (n = 715) and by PCR for Babesia spp. (n =358).

RESULTS

The ELISA screening for antibodies to Anaplasma spp. and Borrelia spp. in cattle sera showed an overall seroprevalence of 15.6% (53/339) and 12.9% (52/402), respectively. The IFAT screening for antibodies against A. phagocytophilum, Rickettsia spp. and Babesia spp. resulted in an overall seroprevalence of 34.2% (116/339), 31.2% (99/317) and 3.4% (14/412), respectively. At the provincial level, the provinces of Liege and Walloon Brabant harboured the highest seroprevalence of Anaplasma spp. (44.4% and 42.7% respectively) and A. phagocytophilum (55.6% and 71.4%). East Flanders and Luxembourg exhibited the highest seroprevalence of Borrelia spp. (32.4%) and Rickettsia spp. (54.8%) respectively. The province of Antwerp showed the highest seroprevalence of Babesia spp. (11%). The screening of field-collected ticks resulted in a prevalence of 13.8% for B. burgdorferi s.l., with B. afzelii and B. garinii being the most common genospecies (65.7% and 17.1%, respectively). Rickettsia spp. was detected in 7.1% of the tested ticks and the only identified species was R. helvetica. A low prevalence was found for A. phagocytophilum (0.5%) and no Babesia positive tick was detected.

CONCLUSIONS

The seroprevalence data in cattle indicate hot spots for tick-borne pathogens in specific provinces and highlights the importance of veterinary surveillance in anticipating the emergence of diseases among humans. The detection of all pathogens, with the exception of Babesia spp. in questing ticks, underlines the need of raising awareness among public and professionals on other tick-borne diseases along with lyme borreliosis.

Manure and biochar have limited effect on lettuce leaf endophyte resistome

Soil amendment with manure compost and biochar is widely adopted to improve soil fertility and promote plant growth, and their effects on soil microbial communities and resistome have been well documented. However, there is sparse information regarding their effects on vegetable endophytes, which represent a major source of human exposure to pathogens and antibiotic resistance genes (ARGs) when eaten raw. Here, we investigated the impacts of manure compost or biochar addition on the bacterial community compositions and ARGs in the soil-lettuce continuum including soil, seed, leaf, and root samples. A total of 137 ARGs and 31 mobile genetic elements (MGEs) were detected in all the samples after 60 days of cultivation. The relative abundance of ARGs and the diversity of bacteria communities presented a consistent decreasing trend from soil to root endophytes, then leaf endophytes. Manure compost addition increased the diversity and abundance of ARGs in soil, while significant changes in the ARG profiles and bacterial communities were not observed in leaf endophytes after manure compost or biochar addition, or both. Bipartite networks analysis suggested that seed microbiome was one of the major sources of plant endophytes and ARGs. Twenty potential human pathogens were isolated from lettuce, indicating potential exposure risk to pathogens via the consumption of raw lettuce. These results suggest limited impacts of manure compost and biochar addition on lettuce endophytes and highlight the contribution of seed microbiome to endophyte ARG profiles.

Clinical Evaluation of Metagenomic Next-Generation Sequencing for the detection of pathogens in BALF in severe community acquired pneumonia

BACKGROUND

Rapid and accurate identification of pathogens is very important for the treatment of Severe community-acquired pneumonia (SCAP) in children. Metagenomic Next-generation sequencing (mNGS) has been applied in the detection of pathogenic bacteria in recent years, while the overall evaluation the application of SCAP in children is lacking.

METHODS

In our study, 84 cases of SCAP were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using mNGS; and sputum, blood, and BALF samples were analysed using conventional technology (CT).

RESULTS

Among the 84 children, 41 were boys, and 43 were girls, with an average age ranging from 2 months to 14 years. The pathogen detection rate of mNGS was higher than that of CT (83.3% [70/84] vs. 63.1% [53/84], P = 0.003). The mNGS was much greater than that of the CT in detecting Streptococcus pneumoniae (89.2% [25/29] vs. 44.8% [13/29], P = 0.001) and Haemophilus influenzae (91.7% [11/12] vs. 33.3% [4/12], P < 0.005). The mNGS also showed superior fungal detection performance compared with that of the CT (81.8% [9/11] vs. 18.2% [2/11], P = 0.004). The mNGS test can detect viruses, such as bocavirus, rhinovirus, and human metapneumovirus, which are not frequently recognised using CT. However, the mNGS detection rate was lower than that of the CT (52.4% [11/21] vs. 95.2% [20/21], P = 0.004) for Mycoplasma pneumoniae (MP). The detection rate of mNGS for mixed infection was greater than that of the CT, although statistical significance was not observed (26.3% [20/39] vs. 21.1% [16/39], P > 0.005). Treatment for 26 (31.0%) children was changed based on mNGS results, and their symptoms were reduced; nine patients had their antibiotic modified, five had antibiotics added, nine had their antifungal medication, and seven had their antiviral medication.

CONCLUSION

mNGS has unique advantages in the detection of SCAP pathogens in children, especially S. pneumoniae, H. influenzae, and fungi. However, the detection rate of MP using mNGS was lower than that of the CT. Additionally, mNGS can detect pathogens that are not generally covered by CT, which is extremely important for the modification of the treatment strategy.

Aptamer-based CRISPR-Cas powered diagnostics of diverse biomarkers and small molecule targets

CRISPR-Cas systems have been widely used in genome editing and transcriptional regulation. Recently, CRISPR-Cas effectors are adopted for biosensor construction due to its adjustable properties, such as simplicity of design, easy operation, collateral cleavage activity, and high biocompatibility. Aptamers' excellent sensitivity, specificity, in vitro synthesis, base-pairing, labeling, modification, and programmability has made them an attractive molecular recognition element for inclusion in CRISPR-Cas systems. Here, we review current advances in aptamer-based CRISPR-Cas sensors. We briefly discuss aptamers and the knowledge of Cas effector proteins, crRNA, reporter probes, analytes, and applications of target-specific aptamers. Next, we provide fabrication strategies, molecular binding, and detection using fluorescence, electrochemical, colorimetric, nanomaterials, Rayleigh, and Raman scattering. The application of CRISPR-Cas systems in aptamer-based sensing of a wide range of biomarkers (disease and pathogens) and toxic contaminants is growing. This review provides an update and offers novel insights into developing CRISPR-Cas-based sensors using ssDNA aptamers with high efficiency and specificity for point-of-care setting diagnostics.

Membrane Proteins as a Regulator for Antibiotic Persistence in Gram-Negative Bacteria

Antibiotic treatment failure threatens our ability to control bacterial infections that can cause chronic diseases. Persister bacteria are a subpopulation of physiological variants that becomes highly tolerant to antibiotics. Membrane proteins play crucial roles in all living organisms to regulate cellular physiology. Although a diverse membrane component involved in persistence can result in antibiotic treatment failure, the regulations of antibiotic persistence by membrane proteins has not been fully understood. In this review, we summarize the recent advances in our understanding with regards to membrane proteins in Gram-negative bacteria as a regulator for antibiotic persistence, highlighting various physiological mechanisms in bacteria.

First draft genome of Thecaphora frezii, causal agent of peanut smut disease

OBJECTIVES

The fungal pathogen Thecaphora frezii Carranza & Lindquist causes peanut smut, a severe disease currently endemic in Argentina. To study the ecology of T. frezii and to understand the mechanisms of smut resistance in peanut plants, it is crucial to know the genetics of this pathogen. The objective of this work was to isolate the pathogen and generate the first draft genome of T. frezii that will be the basis for analyzing its potential genetic diversity and its interaction with peanut cultivars. Our research group is working to identify peanut germplasm with smut resistance and to understand the genetics of the pathogen. Knowing the genome of T. frezii will help analyze potential variants of this pathogen and contribute to develop enhanced peanut germplasm with broader and long-lasting resistance.

DATA DESCRIPTION

Thecaphora frezii isolate IPAVE 0401 (here referred as T.f.B7) was obtained from a single hyphal-tip culture, its DNA was sequenced using Pacific Biosciences Sequel II (PacBio) and Illumina NovaSeq6000 (Nova). Data from both sequencing platforms were combined and the de novo assembling estimated a 29.3 Mb genome size. Completeness of the genome examined using Benchmarking Universal Single-Copy Orthologs (BUSCO) showed the assembly had 84.6% of the 758 genes in fungi_odb10.

First evidence of ranavirus in native and invasive amphibians in Colombia

Ranaviruses can cause mass mortality events in amphibians, thereby becoming a threat to populations that are already facing dramatic declines. Ranaviruses affect all life stages and persist in multiple amphibian hosts. The detrimental effects of ranavirus infections to amphibian populations have already been observed in the UK and in North America. In Central and South America, the virus has been reported in several countries, but the presence of the genus Ranavirus (Rv) in Colombia is unknown. To help fill this knowledge gap, we surveyed for Rv in 60 species of frogs (including one invasive species) in Colombia. We also tested for co-infection with Batrachochytrium dendrobatidis (Bd) in a subset of individuals. For Rv, we sampled 274 vouchered liver tissue samples collected between 2014 and 2019 from 41 localities covering lowlands to mountaintop páramo habitat across the country. Using quantitative polymerase chain reaction (qPCR) and end-point PCR, we detected Rv in 14 individuals from 8 localities, representing 6 species, including 5 native frogs of the genera Osornophryne, Pristimantis and Leptodactylus, and the invasive American bullfrog Rana catesbeiana. Bd was detected in 7 of 140 individuals, with 1 co-infection of Rv and Bd in an R. catesbeiana specimen collected in 2018. This constitutes the first report of ranavirus in Colombia and should set off alarms about this new emerging threat to amphibian populations in the country. Our findings provide some preliminary clues about how and when Rv may have spread and contribute to understanding how the pathogen is distributed globally.

Detection of potential pathogen in pancreatic fluid aspiration with metagenomic next-generation sequencing in patients with suspected infected pancreatic necrosis

BACKGROUND

Timely and accurate microbial diagnosis is important in managing patients with infected pancreatic necrosis (IPN).

AIMS

To evaluate the diagnostic performance of Metagenomic next-generation sequencing (mNGS) in patients with suspected IPN.

METHODS

The clinical data of 40 patients with suspected IPN who underwent CT-guided pancreatic fluid aspiration were retrospectively analyzed. Microbial culture and mNGS were simultaneously applied to identify the potential pathogens. The diagnostic performance of the mNGS was assessed by sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV).

RESULTS

The mNGS report can be obtained significantly earlier than culture methods (42 (36-62 h) vs. 60 (42-124 h), P = 0.032). Across all the study samples, seven species of bacteria and two species of fungi were reported accordingly to the culture results, while 22 species of bacteria and two species of fungi were detected by mNGS. The sensitivity, specificity, NPV, and PPV of mNGS were 88.0%, 100%, 83.33%, and 100%, respectively.

CONCLUSIONS

The diagnostic accuracy of mNGS in patients with suspected IPN is satisfactory. Moreover, mNGS may broaden the range of identifiable infectious pathogens and provide a more timely diagnosis.

Fungal Communities of Spring Barley from Seedling Emergence to Harvest During a Severe Puccinia hordei Epidemic

All plant tissues from leaves, stems, and roots are hosting a wide diversity of fungal species. Our understanding of the assembly of this diversity of fungi during the plant growth cycle is limited. Here, we characterized the mycobiome of three spring barley cultivars grown in Zealand, Denmark, at weekly intervals during a growth season from seedling emergence to senescence and seed maturity. A notable proportion of members of the fungal communities were shared among different plant organs, but community dynamics were tissue-specific. A severe attack of Puccinia hordei occurring during the vegetative stage had profound effects on the mycobiome, and P. hordei biomass displaced that of other taxa. Plant tissue type was the most important factor determining the mycobiome, but also plant age was contributing significantly. Using a random forest model, we found that specific members of the mycobiome were responding differently to plant age, for instance, Olpidium and Articulospora in roots, Dioszegia and Sporobolomyces in leaves, Pyrenophora in stems, and Epicoccum in heads. A co-occurrence network analysis revealed complex interactions among fungal OTUs, and network connectivity was changing as per plant growth stage and plant tissue type. This study contributes to the understanding of assembly of fungal communities in cereals by providing a detailed description of fungal communities associated with barley. This knowledge will be vital for microbiome assisted plant health management and our study will serve as an important baseline for future efforts to harness microbiota in cereal health.

Determination of Verification Parameters for Using the Manual Sampling Device for Fresh Raw Beef Trim

Multifaceted food safety systems are used by the beef processing industry to minimize risk of bacterial contamination of the finished product. These systems are comprised of several parts including the conditional release of product requiring a sample to produce a negative result on a pathogen test prior to sending the product into the food supply. The methods of sample collection require verification activities that ensure the sampling protocols are performed adequately. The research described herein was done to determine the parameters for use in verifying adequate beef trim sampling for the Manual Sampling Device (MSD) method. In addition, the efficacy of repeated sampling via multiple applications of the MSD procedure on a fresh raw beef trim combo was investigated. The results show that MSD sample collection thatcoversless than the entire combo surface, but at least one-halfof the combo surface and is collected for a minimum of 90 s, is adequate for the recovery of organisms and prevalence targets from fresh raw beef trim. In addition, the evidence that MSD sample collection thatoccurs forless than the recommended time, butnot less than 30 s per side of the swab, is adequate for the recovery of organisms and prevalence targets from raw beef trim. Finally, results show that in a scenario where an in-plant MSD sample and a regulatory MSD sample are required from the same combo, two MSD samples can be collected from the same combo bin with similar test results for both samples. While the recommended MSD protocol specifications will not be changed, the data presented herein provide support for some flexibility in accepting test results when verification activities indicate that sampling did not occur as specified in the recommended procedure.

Genomic insight into the environmental adaptations and toxigenic features of endophytic Bacillus cereus CaB1 isolated from Capsicum annuum L

In the study, a previously isolated plant beneficial endophytic B. cereus CaB1 was selected for the detailed analysis by whole-genome sequencing. The WGS has generated a total of 1.9 GB high-quality data which was assembled into a 5,257,162 bp genome with G + C content of 35.2%. Interestingly, CaB1 genome was identified to have 40 genes with plant beneficial functions by bioinformatic analysis. At the same time, it also showed the presence of various virulence factors except the diarrhoeal toxin, cereulide. Upon comparative analysis of CaB1 with other B. cereus strains, it was found to have random distributions of virulence and plant growth promoting traits. The core genome phylogenetic analysis of the Bacillus cereus strains further showed the close relation of plant associated strains with isolates from spoiled food products. The observed genome flexibility of B. cereus thus indicates its ability to make use of diverse hosts, which can result either in beneficial or harmful effects.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03463-9.

Using machine learning models to predict the effects of seasonal fluxes on Plesiomonas shigelloides population density

Seasonal variations (SVs) affect the population density (PD), fate, and fitness of pathogens in environmental water resources and the public health impacts. Therefore, this study is aimed at applying machine learning intelligence (MLI) to predict the impacts of SVs on P. shigelloides population density (PDP) in the aquatic milieu. Physicochemical events (PEs) and PDP from three rivers acquired via standard microbiological and instrumental techniques across seasons were fitted to MLI algorithms (linear regression (LR), multiple linear regression (MR), random forest (RF), gradient boosted machine (GBM), neural network (NN), K-nearest neighbour (KNN), boosted regression tree (BRT), extreme gradient boosting (XGB) regression, support vector regression (SVR), decision tree regression (DTR), M5 pruned regression (M5P), artificial neural network (ANN) regression (with one 10-node hidden layer (ANN10), two 6- and 4-node hidden layers (ANN64), and two 5- and 5-node hidden layers (ANN55)), and elastic net regression (ENR)) to assess the implications of the SVs of PEs on aquatic PDP. The results showed that SVs significantly influenced PDP and PEs in the water (p < 0.0001), exhibiting a site-specific pattern. While MLI algorithms predicted PDP with differing absolute flux magnitudes for the contributing variables, DTR predicted the highest PDP value of 1.707 log unit, followed by XGB (1.637 log unit), but XGB (mean-squared-error (MSE) = 0.0025; root-mean-squared-error (RMSE) = 0.0501; R² =0.998; medium absolute deviation (MAD) = 0.0275) outperformed other models in terms of regression metrics. Temperature and total suspended solids (TSS) ranked first and second as significant factors in predicting PDP in 53.3% (8/15) and 40% (6/15), respectively, of the models, based on the RMSE loss after permutations. Additionally, season ranked third among the 7 models, and turbidity (TBS) ranked fourth at 26.7% (4/15), as the primary significant factor for predicting PDP in the aquatic milieu. The results of this investigation demonstrated that MLI predictive modelling techniques can promisingly be exploited to complement the repetitive laboratory-based monitoring of PDP and other pathogens, especially in low-resource settings, in response to seasonal fluxes and can provide insights into the potential public health risks of emerging pathogens and TSS pollution (e.g., nanoparticles and micro- and nanoplastics) in the aquatic milieu. The model outputs provide low-cost and effective early warning information to assist watershed managers and fish farmers in making appropriate decisions about water resource protection, aquaculture management, and sustainable public health protection.

Wild oyster population resistance to ocean acidification adversely affected by bacterial infection

The carbon dioxide induced ocean acidification (OA) process is well known to have profound effects on physiology, survival and immune responses in marine organisms, and particularly calcifiers including edible oysters. At the same time, some wild populations could develop a complex and sophisticated immune system to cope with multiple biotic and abiotic stresses, such as bacterial infections and OA, over the long period of coevolution with the environment. However, it is unclear how immunological responses and the underlying mechanisms are altered under the combined effect of OA and bacterial infection, especially in the ecologically and economically important edible oysters. Here, we collected the wild population of oyster species Crassostrea hongkongensis (the Hong Kong oyster) from their native estuarine area and carried out a bacterial challenge with the worldwide pervasive pathogen of human foodborne disease, Vibrio parahaemolyticus, to investigate the host immune responses and molecular mechanisms under the high-CO₂ and low pH-driven OA conditions. The wild population had a high immune resistance to OA, but the resistance is compromised under the combined effect of OA and bacterial infection both in vivo or in vitro. We classified all transcriptomic genes based on expression profiles and functional pathways and identified the specifically switched on and off genes and pathways under combined effect. These genes and pathways were mainly involved in multiple immunological processes including pathogen recognition, immune signal transduction and effectors. This work would help understand how the immunological function and mechanism response to bacterial infection in wild populations and predict the dynamic distribution of human health-related pathogens to reduce the risk of foodborne disease under the future climate change scenario.

Microfiber-loaded bacterial community in indoor fallout and air-conditioner filter dust

Microfibers (MFs) are widely existed in indoor air; however, characteristic of microbiota on MFs is largely unknown. In this study, air-borne MFs were collected from fallout or air-conditioner (AC) filter dust in three types of indoor space including living room, dormitory and office. Both plastic and natural MFs were identified by Fourier transform infrared spectroscopy. Ultramicroscopic observation showed dense biofilms adhering on surfaces of MFs. Fallout MFs contained more bacteria but fewer fungi than MFs from AC filter dust. MFs-loaded bacteria were of highest abundance in living rooms, following dormitories and offices. Bacterial community and its diversity were further analyzed by 16S rRNA High-throughput sequencing. Up to 4540 of bacterium OTUs were shared in these MFs samples, unique OTUs in fallout and AC filter samples accounting for 26.3 % and 25.7 % of the total. Compared to MFs fallout, AC filter MFs contained more species of pathogenic bacteria, such as Betaproteobacteriales and Ralstonia, with obviously different β-diversity between two groups. Phenotypic analysis showed that fallout and AC filter MFs bacteria presented high index values of film formation, oxidative stress tolerance and potential pathogenicity. Overall, these results suggest that abundant bacteria including pathogen can be loaded on MFs, and would pose health risks through delivery of indoor MFs.

Research progress on Mincle as a multifunctional receptor

Macrophage-induced C-type lectin (Mincle), a lipopolysaccharide-induced protein, is widely expressed on antigen-presenting cells. Mincle acts as a pattern recognition receptor that recognizes pathogen-associated molecular patterns of pathogens such as bacteria and fungi, mainly glycolipids, which induces an acquired immune response against microbial infection. Interestingly, Mincle can also identify patterns of lipid damage-associated molecule patterns released by injured cells, such as Sin3-associated protein 130 and β-glucosylceramides, which induces sterile inflammation and ultimately accelerates the progression of stroke, obesity, hepatitis, kidney injury, autoimmune diseases and tumors by promoting tissue inflammation. This article will review the various functions of Mincle, such as mediating sterile inflammation of tissues to accelerate disease progression, initiating immune responses to fight infection and promoting tumor progression.

Health Monitoring for Laboratory Salamanders

Laboratory animal health monitoring programs are necessary to protect animal health and welfare, the validity of experimental data, and human health against zoonotic infections. Health monitoring programs should be designed based on a risk assessment and knowledge about the biology and transmission of salamander pathogens. Both traditional and molecular diagnostic platforms are available for salamanders, and they provide complementary information. A comprehensive approach to health monitoring leverages the advantages of multiple platforms to provide a more complete picture of colony health and pathogen status. This chapter presents key considerations in the design and implementation of a colony health monitoring program for laboratory salamanders, including protocols for necropsy and sample collection.

Analysis of Corynebacterium silvaticum genomes from Portugal reveals a single cluster and a clade suggested to produce diphtheria toxin

Background

Corynebacterium silvaticum is a pathogenic, gram-positive bacterial species that causes caseous lymphadenitis in wild boars, domestic pigs and roe deer in Western Europe. It can affect animal production and cause zoonosis. Genome analysis has suggested that one strain from Portugal and one from Austria could probably produce the diphtheria toxin (DT), which inhibits protein synthesis and can cause death.

Methods

To further investigate the species genetic diversity and probable production of DT by Portuguese strains, eight isolates from this country were sequenced and compared to 38 public ones.

Results

Strains from Portugal are monophyletic, nearly identical, form a unique cluster and have 27 out of 36 known Corynebacterium virulence or niche factors. All of them lack a frameshift in the tox gene and were suggested to produce DT. A phylogenetic analysis shows that the species has diverged into two clades. Clade 1 is composed of strains that were suggested to have the ability to produce DT, represented by the monophyletic strains from Portugal and strain 05-13 from Austria. Clade 2 is composed of strains unable to produce DT due to a frameshifted tox gene. The second clade is represented by strains from Austria, Germany and Switzerland. Ten genome clusters were detected, in which strains from Germany are the most diverse. Strains from Portugal belong to an exclusive cluster. The pangenome has 2,961 proteins and is nearly closed (α = 0.968). Exclusive genes shared by clusters 1 and 2, and Portuguese strains are probably not related to disease manifestation as they share the same host but could play a role in their extra-host environmental adaptation. These results show the potential of the species to cause zoonosis, possibly diphtheria. The identified clusters, exclusively shaded genes, and exclusive STs identified in Portugal could be applied in the identification and epidemiology of the species.

An overview of complement systems in teleosts

Complement plays an important role in the innate immune system, and it comprises about 35 individual proteins. In mammals, complement is activated via three different pathways, the classical pathway, the alternative pathway, and the lectin pathway. All three activation pathways produce C3-convertase in different forms. C3-convertase cleaves C3 to C3a and C3b and initiates a cascade of cleavage and activation, eventually resulting in the formation of the membrane attack complex. Complement activation results in the generation of activated fragments that are involved in microbial killing, phagocytosis, inflammatory reactions, immune complex clearance, and antibody production. Although the complement system has been studied extensively in mammals, complement is less well understood in teleosts. This review summarizes the current knowledge of the teleost complement components involved in phagocytosis, chemotaxis, and cell lysis. We report the characterized complement components in various teleost species. In addition, we provide a comprehensive compilation of complement regulators, and this information is used to analyze the role of complement regulators in pathogen infection. The influence of complement receptors on the immune responses of teleosts is reviewed. Finally, we propose directions for future study of the molecular evolution, structure, and function of complement components in teleosts. This review provides new insights into the complement system of recognition and defense, and such knowledge is essential for the development of new immune strategies in aquaculture.

Coronavirus disease 2019 (COVID-19) associated bacterial coinfection: Incidence, diagnosis and treatment

Coronavirus disease 2019 (COVID-19) emerged as a pandemic that spread rapidly around the world, causing nearly 500 billion infections and more than 6 million deaths to date. During the first wave of the pandemic, empirical antibiotics was prescribed in over 70% of hospitalized COVID-19 patients. However, research now shows a low incidence rate of bacterial coinfection in hospitalized COVID-19 patients, between 2.5% and 5.1%. The rate of secondary infections was 3.7% in overall, but can be as high as 41.9% in the intensive care units. Over-prescription of antibiotics to treat COVID-19 patients fueled the ongoing antimicrobial resistance globally. Diagnosis of bacterial coinfection is challenging due to indistinguishable clinical presentations with overlapping lower respiratory tract symptoms such as fever, cough and dyspnea. Other diagnostic methods include conventional culture, diagnostic syndromic testing, serology test and biomarkers. COVID-19 patients with bacterial coinfection or secondary infection have a higher in-hospital mortality and longer length of stay, timely and appropriate antibiotic use aided by accurate diagnosis is crucial to improve patient outcome and prevent antimicrobial resistance.

Trends of ocular fungal infections in North China (2001-2020)

OBJECTIVES

To analyze the epidemiologic features, culture positivity, the fungal spectrum of different sites of ocular infection in North China over 20 years from 2001 to 2020.

METHODS

11, 635 patients suspected of ocular fungal infection were reviewed. The demographic profile, fungal positive culture rate among different sites, the distribution, and trends of main pathogens among cornea and intraocular fluid were analyzed.

RESULTS

Among 11, 635 samples, the positive culture rate of ocular fungal infection was 23.6%. Most of samples (83.1%) were from cornea, and their culture positivity was 26.9%. Fungal keratitis occurred more often during the harvesting season (October to December; 34.0%) than in other seasons (average: 22.0%). Fusarium sp. (53.2%), Aspergillus sp. (15.9%) and Alternaria sp. (12.5%) were the most common fungal species of ocular mycotic infections in the past two decades in north China. 2562 organisms were identified from cornea, of which 1443 (56.3%) were Fusarium sp., 403 (15.7%) and 329 (12.8%) were Aspergillus sp., and Alternaria sp., respectively. Of the 120 fungi isolated from the intraocular fluid, the most common was Aspergillus sp. (33.3%), followed by Fusarium sp. (24.2%) and Candida sp. (15.0%).

CONCLUSIONS

Fusarium sp., Aspergillus sp. and Alternaria sp. were the most common organisms in cases of fungal keratitis, while Aspergillus sp., Fusarium sp. and Candida sp. were the most frequent isolates for fungal endophthalmitis.

SlS5H silencing reveals specific pathogen-triggered salicylic acid metabolism in tomato

BACKGROUND

Salicylic acid (SA) is a major plant hormone that mediates the defence pathway against pathogens. SA accumulates in highly variable amounts depending on the plant-pathogen system, and several enzyme activities participate in the restoration of its levels. Gentisic acid (GA) is the product of the 5-hydroxylation of SA, which is catalysed by S5H, an enzyme activity regarded as a major player in SA homeostasis. GA accumulates at high levels in tomato plants infected by Citrus Exocortis Viroid (CEVd), and to a lesser extend upon Pseudomonas syringae DC3000 pv. tomato (Pst) infection.

RESULTS

We have studied the induction of tomato SlS5H gene by different pathogens, and its expression correlates with the accumulation of GA. Transient over-expression of SlS5H in Nicotiana benthamiana confirmed that SA is processed by SlS5H in vivo. SlS5H-silenced tomato plants were generated, displaying a smaller size and early senescence, together with hypersusceptibility to the necrotrophic fungus Botrytis cinerea. In contrast, these transgenic lines exhibited an increased defence response and resistance to both CEVd and Pst infections. Alternative SA processing appears to occur for each specific pathogenic interaction to cope with SA levels. In SlS5H-silenced plants infected with CEVd, glycosylated SA was the most discriminant metabolite found. Instead, in Pst-infected transgenic plants, SA appeared to be rerouted to other phenolics such as feruloyldopamine, feruloylquinic acid, feruloylgalactarate and 2-hydroxyglutarate.

CONCLUSION

Using SlS5H-silenced plants as a tool to unbalance SA levels, we have studied the re-routing of SA upon CEVd and Pst infections and found that, despite the common origin and role for SA in plant pathogenesis, there appear to be different pathogen-specific, alternate homeostasis pathways.

Bees under interactive stressors: the novel insecticides flupyradifurone and sulfoxaflor along with the fungicide azoxystrobin disrupt the gut microbiota of honey bees and increase opportunistic bacterial pathogens

The gut microbiome plays an important role in bee health and disease. But it can be disrupted by pesticides and in-hive chemicals, putting honey bee health in danger. We used a controlled and fully crossed laboratory experimental design to test the effects of a 10-day period of chronic exposure to field-realistic sublethal concentrations of two nicotinic acetylcholine receptor agonist insecticides (nACHRs), namely flupyradifurone (FPF) and sulfoxaflor (Sulf), and a fungicide, azoxystrobin (Azoxy), individually and in combination, on the survival of individual honey bee workers and the composition of their gut microbiota (fungal and bacterial diversity). Metabarcoding was used to examine the gut microbiota on days 0, 5, and 10 of pesticide exposure to determine how the microbial response varies over time; to do so, the fungal ITS2 fragment and the V4 region of the bacterial 16S rRNA were targeted. We found that FPF has a negative impact on honey bee survival, but interactive (additive or synergistic) effects between either insecticide and the fungicide on honey bee survival were not statistically significant. Pesticide treatments significantly impacted the microbial community composition. The fungicide Azoxy substantially reduced the Shannon diversity of fungi after chronic exposure for 10 days. The relative abundance of the top 10 genera of the bee gut microbiota was also differentially affected by the fungicide, insecticides, and fungicide-insecticide combinations. Gut microbiota dysbiosis was associated with an increase in the relative abundance of opportunistic pathogens such as Serratia spp. (e.g. S. marcescens), which can have devastating consequences for host health such as increased susceptibility to infection and reduced lifespan. Our findings raise concerns about the long-term impact of novel nACHR insecticides, particularly FPF, on pollinator health and recommend a novel methodology for a refined risk assessment that includes the potential effects of agrochemicals on the gut microbiome of bees.

Respiratory infections in X-linked hyper-IgM syndrome with CD40LG mutation: a case series of seven children in China

BACKGROUND

X-linked hyper-immunoglobulin M (XHIGM), a primary immunodeficiency syndrome caused by mutations in the CD40 ligand gene(CD40LG), presents with recurrent respiratory infections in pediatric patients. We aimed to evaluate the spectrum of clinical features and respiratory pathogens in pediatric patients with XHIGM in China.

METHODS

We retrospectively reviewed seven pediatric patients who were diagnosed with XHIGM and received follow-up treatment at the Guangzhou Women and Children's Medical Center between January 2010 and January 2021. We determined their clinical characteristics, causative pathogens, and prognosis by performing peripheral immunological and genetic tests.

RESULTS

There were seven boys with age ranging from 4-20 months (median age, 13 months). Four of the seven respiratory infections were caused by Talaromyces marneffei(T. marneffei). Two patients had viral infections caused by cytomegalovirus (CMV) and human adenovirus respectively. One patient had a mixed infection caused by Pneumocystis carinii and CMV. Except for one child who died of respiratory failure, one patient received hematopoietic stem cell transplantation (HSCT) and recovered well, the other five patients survived with regular infusions of intravenous immunoglobulin (IVIg) during the follow-up period. Six patients had reduced antibody levels, especially IgG, IgA, and IgE levels. Increased serum IgM levels were detected in four cases, and three cases presented normal IgM levels at onset. All children were diagnosed with XHIGM with CD40LG variation. Three novel mutations were identified in the present study.

CONCLUSIONS

Our study suggests that respiratory infections usually begin within 2 years old, fungi and viruses are important pathogens causing respiratory infections in children with XHIGM. In endemic areas, T. marneffei is the common pathogen of respiratory tract infection in children with the disease.