Multigene phylogeny, morphology, and pathogenicity trials reveal novel Cytospora species involved in perennial canker disease of apple trees in Iran

In recent years, canker and die-back diseases have become a growing threat for the productivity and longevity of apple orchards in Iran. In this study, 131 Cytospora isolates were recovered from symptomatic tissues of apple trees in apple orchards of Iran. Multigene phylogenetic inference based on combined sequence data of ITS, act, rpb2, and tef1-α loci, supplemented with morphological characteristics and pathogenicity assay revealed four novel Cytospora species which were described as C. avicennae, C. azerbaijanica, C. ershadii, and C. iranica, and four known species, namely C. chrysosperma, C. parasitica, C. paratranslucens, and C. sorbicola. Also, C. sorbicola is newly reported on apple trees worldwide. Koch's postulates were fulfilled to confirm that all eight species in this study were pathogenic on apple trees in Iran, among which C. sorbicola was the most intensive species. The results of this study further highlight rich diversity among Cytospora species occurring on apple trees, revealing several novel Cytospora species on this host. The host range, geographical distribution, and economic significance of novel species on apple industry remains to be studied.

Increased occurrence of Treponema spp. and double-species infections in patients with Alzheimer's disease

Although the link between microbial infections and Alzheimer's disease (AD) has been demonstrated in multiple studies, the involvement of pathogens in the development of AD remains unclear. Here, we investigated the frequency of the 10 most commonly cited viral (HSV-1, EBV, HHV-6, HHV-7, and CMV) and bacterial (Chlamydia pneumoniae, Helicobacter pylori, Borrelia burgdorferi, Porphyromonas gingivalis, and Treponema spp.) pathogens in serum, cerebrospinal fluid (CSF) and brain tissues of AD patients. We have used an in-house multiplex PCR kit for simultaneous detection of five bacterial and five viral pathogens in serum and CSF samples from 50 AD patients and 53 healthy controls (CTRL). We observed a significantly higher frequency rate of AD patients who tested positive for Treponema spp. compared to controls (AD: 62.2 %; CTRL: 30.3 %; p-value = 0.007). Furthermore, we confirmed a significantly higher occurrence of cases with two or more simultaneous infections in AD patients compared to controls (AD: 24 %; CTRL 7.5 %; p-value = 0.029). The studied pathogens were detected with comparable frequency in serum and CSF. In contrast, Borrelia burgdorferi, human herpesvirus 7, and human cytomegalovirus were not detected in any of the studied samples. This study provides further evidence of the association between microbial infections and AD and shows that paralleled analysis of multiple sample specimens provides complementary information and is advisable for future studies.

[A 10-year retrospective study of pathogens and antimicrobial resistance in neonatal sepsis]

OBJECTIVES

To investigate the changes in the pathogen spectrum and antimicrobial resistance over time in neonatal sepsis.

METHODS

The medical data were collected from the neonates who were diagnosed with sepsis in the Second Xiangya Hospital of Central South University from January 2010 to December 2019. The incidence rate of sepsis, the pathogen spectrum, and the characteristics of antimicrobial resistance were analyzed.

RESULTS

The incidence rate of neonatal sepsis was 4.02% (447/11 111). The top four pathogens detected were coagulase-negative staphylococci (CoNS), Klebsiella pneumoniae, Escherichia coli, and Candida. The incidence rate of sepsis and the pathogen spectrum showed no significant changes over time. Klebsiella pneumoniae was the most frequent pathogen in preterm infants, very low birth weight infants, and small-for-gestational-age infants, accounting for 33.9%, 29.5%, and 42.5%, respectively. CoNS, Klebsiella pneumoniae, and Escherichia coli had a high resistance rate to penicillins and third-generation cephalosporins.

CONCLUSIONS

The incidence of neonatal sepsis is high, and the main pathogen is CoNS. The pathogens of neonatal sepsis have a high resistance rate to penicillins and third-generation cephalosporins. It is recommended to enhance the prevention and control of neonatal infection, strengthen the surveillance of pathogens, and further standardize the rational use of antibiotics.

S-33 identifies proteins related to pathogenicity

Enterobacter species are responsible for causing infections of the lower respiratory tract, urinary tract, meninges, etc. Proteins secreted by these species may act as determinants of host-pathogen interaction and play a role in virulence. Among the secreted proteins, the Type VI secretion system (T6SS) acts as a molecular nanomachine to deliver many effector proteins directly into prey cells in a contact-dependent manner. The secreted proteins may provide an idea for the interaction of bacteria to their environment and an understanding of the role of these proteins for their role in bacterial physiology and behaviour. Therefore, aim of this study was to characterize the secreted proteins in the culture supernatant by a T6SS bacterium Enterobacter sp. S-33 using nano-LC-MS/MS tool. Using a combined mass spectrometry and bioinformatics approach, we identified a total of 736 proteins in the secretome. Bioinformatics analysis predicting subcellular localization identified 110 of the secreted proteins possessed signal sequences. By gene ontology analysis, more than 80 proteins of the secretome were classified into biological or molecular functions. More than 20 percent of secretome proteins were virulence proteins including T6SS proteins, proteins involved in adherence and fimbriae formation, molecular chaperones, outer membrane proteins, serine proteases, antimicrobial, biofilm, exotoxins, etc. In summary, the results of the present study of the S-33 secretome provide a basis for understanding the possible pathogenic mechanisms and future investigation by detailed experimental approach will provide a confirmation of secreted virulence proteins in the exact role of virulence using the in vivo model.

Skin microbiota interact with microbes on office surfaces

The indoor environment is recognized as a potential contributor to human health impacts through resident microbiomes. Indoor surface microbial communities are formed from several sources, environmental and anthropogenic. In this study, we characterized the bacterial and fungal communities from various sources typical of a working office environment including dust, fingers, and computer keyboards and mice. The composition of the dust bacterial community was significantly different from the other tested surfaces (P < 0.05), whereas the dust fungal community was only significantly different from fingers (P < 0.05). Bacterial and fungal communities were both shaped by deterministic processes, and bacterial communities had a higher migration rate. Results of a network analysis showed that the microbial community interactions of keyboards and mice were mainly competitive. Fast expectation-maximization microbial source tracking (FEAST) identified the sources of > 70 % of the keyboard and mouse microbial communities. Biomarkers for each sample types were identified by LDA Effect Size (LEfSE) analysis, some of which were soil-derived and potential anthropogenic pathogens, indicating the potential for exchange of microbes among outdoor, human and indoor surfaces. The current study shows that the source of microorganisms at the office interface is highly traceable and that their migration is linked to human activity. The migration of potentially pathogenic microbes were identified, emphasising the importance of personal hygiene.

pathogens in the ticks Dermacentor reticulatus and Ixodes ricinus in the UK

The emergence of Babesia pathogens novel to the UK is of growing concern; these include Babesia canis and Babesia caballi. However, a better understanding of changes in the prevalence of endemic Babesia species such as Babesia venatorum and Babesia divergens is also of importance. Here, the prevalence of Babesia pathogens in both Dermacentor reticulatus and Ixodes ricinus ticks was assessed. Dermacentor reticulatus were collected from six sites known to harbour populations of this species in west Wales and southern England. DNA was extracted from 879 individual ticks and subjected to PCR and sequence analysis. Seven Babesia species were detected in 7.5% of the ticks, including B. caballi (0.68%), B. bovis (1.7%), B. microti (1.02%), B. bigemina (0.34%), B. capreoli (0.34%), and one isolate of B. canis (0.34%). Two of the field sites with grazing equines present had ticks that were positive for B. caballi. For I. ricinus, up to 200 nymphs were collected from each of 24 cattle farms in south-west England. Nymphs were divided into 6 pools of 30 from each farm for DNA extraction, PCR, and sequencing. Samples from seven out of the 24 farms tested positive for Babesia, and most were positive for more than one species. Babesia divergens was identified from five farms, and three of these farms had two pooled samples positive for B. divergens, which given the low overall prevalence rate suggests that B. divergens may be highly clustered within the tick population. Most of the remaining positive samples were Babesia venatorum, demonstrating that this zoonotic pathogen is widespread in livestock habitats. The data suggest that B. canis is not yet widely prevalent in established D. reticulatus populations in the UK, but that there is a need to raise awareness of the risk of equine piroplasmosis in areas with endemic D. reticulatus foci, since B. caballi appears more widely established.

Predicting the current and future risk of ticks on livestock farms in Britain using random forest models

The most abundant tick species in northern Europe, Ixodes ricinus, transmits a range of pathogens that cause disease in livestock. As I. ricinus distribution is influenced by climate, tick-borne disease risk is expected to change in the future. The aims of this work were to build a spatial model to predict current and future risk of ticks on livestock farms across Britain. Variables relating both to tick hazard and livestock exposure were included, to capture a niche which may be missed by broader scale models. A random forest machine learning model was used due to its ability to cope with correlated variables and interactions. Data on tick presence and absence on sheep and cattle farms was obtained from a retrospective questionnaire survey of 926 farmers. The ROC of the final model was 0.80. The model outputs matched observed patterns of tick distribution, with areas of highest tick risk in southwest and northwest England, Wales, and west Scotland. Overall, the probability of tick presence on livestock farms was predicted to increase by 5-7 % across Britain under future climate scenarios. The predicted increase is greater at higher altitudes and latitudes, further increasing the risk of tick-borne disease on farms in these areas.

Isolation and characterization of Vibrio owensii from Palk Bay and its infection study against post larvae of Litopenaeus vannamei

Vibrio is heterotrophic ubiquitous marine bacteria that plays dual role as putative halobiont and potential pathogen. Environment and diseases are inextricable hence the role of vibrio as a potential pathogen in the natural environment must be comprehended. Hence the present study aims at investigating the pathogenicity of Vibrio owensii on the post larvae of Litopenaeus vannamei. V. owensii isolated from the marine natural habitat of the Palk Bay province in India was highly resistant to ampicillin, methicillin, tetracycline and vancomycin. The strain also lacked pathogenicity against the post larvae of L. vannamei due to the absence of major virulence factors viz. Chitinase, phospholipase and hemolytic activity. Presumably this is the first report on the occurrence of V. owensii in the Indian waters therefore there arises a need to carry out more serious research on the pathogenicity of this species on other commercial crustaceans reared in the Indian aquaculture settings in order to apprehend its role as potential pathogen or the contrary.

An ultrasensitive fluorescence detection template of pathogenic bacteria based on dual catalytic hairpin DNA Walker@Gold nanoparticles enzyme-free amplification

Integrating the advantages of catalytic hairpin components and multi-foot DNA walker, we designed a 16S rRNA detection probe template for pathogen bacteria, which utilizes DNA ligation quencher and dual catalytic hairpin@DNA walker to induce signal recovery. The dual catalytic hairpin@DNA walker uses the walking position of the target on the AuNP as a foothold to promote the reaction, so that the biosensing of the low-abundance target sequence can induce signal recovery. During the entire experiment, no enzyme is required, which can avoid the limitation of enzyme degradation under unfavorable conditions and the inability to detect the target. Most importantly, the detection template has the advantages of high sensitivity, and its detection limit is significantly better than that of single hairpin DNA walker probe. As the detection system can sensitively and rapidly detect its targeted bacteria and not rely on any enzyme and sophisticated instrumentation, it has great potential for sensitive and specific pathogenic bacteria detection.

Glucosinolates and Biotic Stress Tolerance in Brassicaceae with Emphasis on Cabbage: A Review

Glucosinolates (GSLs) and GSL-associated genes are receiving increasing attention from molecular biologists due to their multifunctional properties. GSLs are secondary metabolites considered to be highly active in most Brassica species. Their importance has motivated the discovery and functional analysis of the GSLs and GSL hydrolysis products involved in disease development in brassicas and other plants. Comprehensive knowledge of the GSL content of Brassica species and the molecular details of GSL-related genes will help elucidate the molecular control of this plant defense system. This report provides an overview of the current status of knowledge on GSLs, GSL biosynthesis, as well as hydrolysis related genes, and GSL hydrolysis products that regulate fungal, bacterial, and insect resistance in cabbage and other brassicas.

PATHOGENS IN QUAILS OF THE TRANS-PECOS ECOREGION OF TEXAS

Texas quail populations have declined over the past few decades. While habitat loss has been identified as the primary cause, it has been speculated that pathogens may also play a role in this decline. To help address this, we collected scaled quail, Callipepla squamata, Gambel's quail, Callipepla gambelii, and Montezuma quail, Cyrtonyx montezumae, from across the Trans-Pecos ecoregion of Texas via hunter-harvest. Quail samples were then necropsied to document pathogens not previously recorded in the host species. Pathogens were submitted to the Texas A&M University Veterinary Medicine Diagnostic Lab (TVMDL), where parasite identification and histopathological analyses were conducted. From this, we identified several parasites that had never been documented in the quails of the Trans-Pecos ecoregion of Texas. This study was the first to document Mycobacterium sp. and Sarcocystis sp. in scaled quail, Subulura sp. and Physaloptera sp. in Montezuma quail, and Oxyspirura petrowi and Aulonocephalus pennula in a Texas Gambel's quail.

Antifungal activity of lactic acid bacteria and their application in food biopreservation

Lactic acid bacteria (LAB) are ubiquitous bacteria associated with spontaneous lactic fermentation of vegetables, dairy and meat products. They are generally recognized as safe (GRAS), and they are involved in transformation of probiotic lacto-fermented foods, highly desired for their nutraceutical properties. The antifungal activity is one of the exciting properties of LAB, because of its possible application in food bio-preservation, as alternative to chemical preservatives. Many recent research works have been developed on antifungal activity of LAB, and they demonstrate their capacity to produce various antifungal compounds, (i.e. organic acids, PLA, proteinaceous compounds, peptides, cyclic dipeptides, fatty acids, and other compounds), of different properties (hydrophilic, hydrophobic and amphiphilic). The effectiveness of LAB in controlling spoilage and pathogenic fungi, demonstrated in different agricultural and food products, can be due to the synergistic effect between their antifungal compounds of different properties; where the amphiphilic-compounds allow the contact between the target microbial cell (hydrophilic compartment) and antifungal hydrophobic-compounds. Further studies on the interaction between compounds of these three properties are to de be developed, in order to highlight more their mechanism of action, and make LAB more profitable in improving shelf life and nutraceutical properties of foods.

Pathogen Distribution and Antimicrobial Resistance of Early Onset Sepsis in Very Premature Infants: A Real-World Study

INTRODUCTION

Early onset sepsis (EOS) remains a potentially fatal newborn condition, especially in very preterm infants. Data on the pathogen distribution and antibiotic susceptibility patterns of EOS among very preterm infants are scarce but essential for the choice of empirical antibiotic administration. We sought to assess the epidemiologic characteristics and antibiotic susceptibility patterns of pathogens causing EOS among a cohort of very preterm infants in China.

METHODS

This prospective, observational study included a cohort of infants born at a gestational age (GA) less than 32 weeks of 32 newborn intensive care units (NICUs) in China between January 1, 2018 and December 31, 2020. EOS was defined by isolation of pathogenic species from blood culture within 72 h of birth.

RESULTS

A total of 108 EOS cases (18.4 per 1000 admissions) were identified among 5865 very preterm infants. Incidence of EOS increased with the decrease of GA and birthweight. Escherichia coli (n = 44, 40.7%) was the most common pathogen, followed by Klebsiella spp. (n = 10, 9.3%). The distribution and proportion of pathogenic bacteria varied significantly by GA. E. coli and Klebsiella spp. showed high resistance to ampicillin and third-generation cephalosporins, while they showed good susceptibility to carbapenem antibiotics and piperacillin-tazobactam.

CONCLUSION

Our data demonstrated that pathogens causing neonatal EOS showed high rates of resistance to ampicillin and third-generation cephalosporins. This raised questions about the best empirical antibiotic choice for preterm infants suspected of having EOS in low- and middle-income countries (LMICs).

Origin, fluxes, and reservoirs of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa in aquatic ecosystems of a French floodplain

The release and spread of opportunistic pathogens - some of which are resistant to antibiotics - in the environment is a major public health challenge worldwide. In this study, we found evidence of the origin of such microorganisms and characterized their dispersal and survival in floodplain ecosystems to understand their fate in the environment. We determined the concentrations of Escherichia coli, extended-spectrum β-lactamases (ESBL)-producing E. coli, Klebsiella pneumoniae, ESBL-producing K. pneumoniae, and Pseudomonas aeruginosa in a floodplain of Eastern France using a culture-based method. Furthermore, we assessed the population structure of E. coli isolates by quadruplex PCR, their plasmid replicon content by PCR-based replicon typing, and the nature of their bla_ESBL genes by PCR and sequencing. The main aquatic ecosystems of the floodplain (river, tributaries, riverine wetlands, and groundwater) were sampled monthly over a one-year cycle. The majority of E. coli isolates retrieved in the studied floodplain were likely of human origin. Moreover, contamination of floodplain aquatic ecosystems by opportunistic pathogens mainly resulted from hydrological fluxes during high-flow periods, suggesting that dispersal and dilution predominated. During low-flow periods, E. coli may be able to survive for several months in isolated ecosystems in which it may find favourable conditions to thrive. The most nutrient-rich and isolated wetlands are consequently potential pathogen reservoirs. The production of ESBL was not a disadvantage for E. coli in low-anthropized floodplain ecosystems.

Optimized mechanism for fast removal of infectious pathogen-laden aerosols in the negative-pressure unit

It has been frequently emphasized that highly contagious respiratory disease pathogens (such as SARS-CoV-2) are transmitted to the other hosts in the form of micro-sized aerosols (< 5 μm) in the air without physical contacts. Hospital environments such as negative-pressure unit are considered being consistently exposed to pathogens, so it is essential to quickly discharge them through the effective ventilation system. To achieve that, in the present study, we propose the optimized ventilation mechanism and design for the fastest removal of pathogen-laden aerosol using numerical simulations. We quantitatively evaluated the aerosol removal performance of various ventilation configurations (combinations of air exhaust and supply ducts), and found that the key mechanism is to form the coherent (preferentially upward) airflow structure to surround the respiratory flow containing the aerosol cluster. We believe that the present findings will play a critical role in developing the high-efficiency negative-pressure facility irrespective of its size and environments.

The difference in pathogenic bacteria between chronic rhinosinusitis in patients with and without Sjogren's syndrome: a retrospective case-control study

Background

Chronic rhinosinusitis (CRS) affects the quality of life of many people worldwide and can cause comorbidities. Our previous research proved that Sjogren’s syndrome (SS) is a predisposing factor for CRS, with a 2.5-fold associated risk. Antibiotics are important in CRS treatment; however, there is a paucity of research on the pathogenic bacteria of SS-CRS in the past. We conducted this study to investigate the pathogenic difference of SS-CRS and non-SS-CRS and aimed to give clinicians references when selecting antibiotics to treat SS-CRS.

Materials and methods

A total of 14,678 patients hospitalized for CRS operation from 2004 to 2018 were identified from the Chang Gung Research Database. These CRS cases were classified as either SS-CRS or non-SS-CRS. We analyzed their bacterial distribution by studying the results of the pus cultures performed alongside surgery.

Results

The top three facultative anaerobic or aerobic isolated bacteria in the SS-CRS group were coagulase-negative Staphylococcus (CoNS: 34.3%), Pseudomonas aeruginosa (28.6%), methicillin-sensitive Staphylococcus aureus (MSSA: 20%), and Staphylococcus epidermidis (20%). In the non-SS-CRS group, S. epidermidis (29.3%), CoNS (25.7%), and MSSA (14.2%) were identified. The top three anaerobic bacterial genera were Cutibacterium (54.3%), Peptostreptococcus (11.4%), and Fusobacterium (11.4%) in the SS-CRS group and Cutibacterium (53.8%), Peptostreptococcus (25%), and Prevotella (12.9%) in the non-SS-CRS group.

Conclusions

P.aeruginosa is a major pathogen in SS-CRS patients. In addition, physicians should be aware of potential Fusobacterium and antibiotic-resistant bacterial infection in patients with SS-CRS.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07652-4.

Microplastics act as a carrier for wastewater-borne pathogenic bacteria in sewage

Microplastic pollution, a pressing global environmental problem, has a severe impact on both aquatic ecosystems and public health worldwide. Due to the small size of microplastics, they are able to pass through the filtration systems of municipal wastewater treatment works (WWTWs). In recent years, studies have focused on the environmental abundance and ecotoxicological effects of microplastics, but there are limited studies investigating the colonization of microplastics by bacteria, especially those pathogenic ones. In this study, we examined the colonization and composition of the bacterial communities on polyethylene microbeads after incubation in raw sewage collected from three municipal WWTWs in Hong Kong (Sha Tin Sewage Treatment Works, Stonecutters Island Sewage Treatment Works, and Shek Wu Hui Sewage Treatment Works). Scanning electron microscopy (SEM) results indicate that bacterial cells were colonized on the surfaces of the microbeads and formed biofilms after sewage incubation. Metagenomic sequencing data demonstrated an increase in bacterial diversity after 21 days of sewage incubation when compared to shorter incubation periods of 6, 11 and 16 days. Importantly, human and fish pathogens such as Arcobacter cryaerophilus, Aeromonas salmonicida, Vibrio areninigrae and Vibrio navarrensis were found in the resident bacterial communities. Taken together, our results demonstrate that microplastics could act as a carrier for wastewater-borne pathogenic bacteria in municipal sewage.

Differential responses of leaf photosynthesis to insect and pathogen outbreaks: A global synthesis

Outbreak of insects or pathogens (referred to as biotic disturbance), which is projected to continually increase in a warmer climate, may profoundly affect plant photosynthesis and production. However, the response of plant photosynthesis to biotic disturbance remains unclear, especially differences in response between insects and pathogens, which hinders the prediction of plant productivity in future climate. In this study, a meta-analysis approach was used to examine effects of insects and pathogens on photosynthetic rate per unit leaf area (Pn) and the associated characteristics from 115 studies. Our results showed that biotic disturbance significantly decreased Pn by 34.8% but increased Rd by 26.2%. Most of parameters associated with Pn were significantly reduced by biotic disturbance, including g_s, T_r, photosynthetic pigments (e.g., a+b, a, and b), and chlorophyll fluorescence properties (Fv/Fm, q_p). The disturbance type (insects vs pathogens) was the most important factor affecting the response of Pn, with a greater decrease in Pn by pathogens (-37.5%) than insects (-28.0%). The response ratio of Pn was positively correlated with that of g_s and Tr for both insects and pathogens, while negatively with C_i and positively with Chl a+b, Φ_PSII, and q_p for only pathogens. In addition, the higher sensitivity of Pn to biotic disturbance in crop than non-crop plants poses a great challenge to agricultural system in the future. The weighted response ratio of Pn and relationships of Pn with other associated paramerters under insect and pathogen disturbance will facilitate vegetation models to integrate the effects of biotic disturbance on primary production, improving predicition of the ecosystem carbon cyling in combining with leaf area measurement.

Ecofriendly phytofabrication of silver nanoparticles using aqueous extract of Cuphea carthagenensis and their antioxidant potential and antibacterial activity against clinically important human pathogens

The green synthesis of nanoparticles (NPs) is the safest, ecofriendly, cost-effective, and non-hazardous approach of nanotechnology. In the current study, we described the green synthesis of silver nanoparticles (AgNPs) using Cuphea carthagenensis aqueous leaf extract as a reducing, capping, and stabilizing agent. The study aims at the synthesis, characterization, optimization, and determination of the antibacterial activity of Cc-AgNPs against clinically important human pathogens. Coating of cotton fabrics with Cc-AgNPs and their efficacy against skin infection causing organisms was also evaluated. Furthermore, antioxidant activity, growth assay and time kill assay of Cc-AgNPs were also performed in the study. The biosynthesized Cc-AgNPs were characterized by UV-visible spectrometry, energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FTIR). The spectroscopic and microscopic analysis demonstrated biosynthesis of face-centered cubic (fcc) crystalline spherical Cc-AgNPs with an average particle size of 10.65 ± 0.1 nm. Optimized peak synthesis of Cc-AgNPs was reported at pH7, 55 °C, 4 mM silver nitrate, and 5:45 (plant extract: silver nitrate). Cc-AgNPs exhibited potent antioxidant effect and antibacterial activity against both Gram-positive and Gram-negative bacteria. The lowest MIC (15 μg/ml) and MBC (25 μg/ml) values were reported against S. typhimurium. The Cc-AgNPs coated fabrics demonstrated potent antibacterial activity against tested strains. This application could be helpful in wound healing management. Furthermore, the hemolytic analysis demonstrated that Cc-AgNPs exhibit non-toxic nature against Red Blood Cells (RBCs) at the tested concentrations. In conclusion, the investigation demonstrated a fast, stable, and eco-friendly approach to the biosynthesis of Cc-AgNPs along with their antibacterial and antioxidant properties.

Plant community-mediated effects of grazing on plant diseases

Grazing is one of the most important management practices for grasslands. To date, most studies on how grazing affects plant diseases have focused on a single plant species, ignoring plant community characteristics and phylogeny. We used data from a 6-year yak grazing experiment (0, 1, 2, and 3 yak(s) ha^- 1 treatment) in an alpine meadow ecosystem of Qinghai-Tibetan Plateau, from which we tested grazing effects on foliar fungal diseases at both population and community levels. By measuring plant community variables (including richness, evenness, phylogenetic diversity, and composition) and disease severity, we evaluated the relative importance of plant community-mediated effects of yak grazing on community pathogen load with a multi-model inference approach. We found significant differences in pathogen load among different grazing treatments; we recorded the highest and lowest pathogen loads in the 1 yak ha^- 1 treatment and in the 3 yaks ha^- 1 treatment, respectively. Pielou's evenness index and community proneness (i.e., an estimate of the capacity of plant communities to support diseases) best explained variation in pathogen load, indicating that plant community-mediated effects (through evenness and proneness) of yak grazing determined pathogen load. Our study provides empirical evidence that grazing influences foliar fungal disease prevalence through plant community evenness and composition, which demonstrates the necessity of incorporating host plant community characteristics into disease load prediction frameworks.

Bacterial AB toxins and host-microbe interactions

AB toxins are protein virulence factors secreted by many bacterial pathogens, contributing to the pathogenicity of the cognate bacteria. AB toxins consist of two functionally distinct components: the enzymatic "A" component for pathogenicity and the receptor-binding "B" component for toxin delivery. Consistently, unlike other virulence factors such as effectors, AB toxins do not require additional systems to deliver them to the target host cells. Target host cells are located in the infection site and/or located distantly from infected host cells. The first part of this review discusses the structural and functional features of single-peptide and multiprotein AB toxins in the context of host-microbe interactions, using several well-characterized examples. The second part of this review discusses toxin neutralization strategies, as well as applications of AB toxins relevant to developing intervention strategies against diseases.

Epidemics and policy: the dismal trade-offs

I propose a stochastic SIR-Macro model to study the effects of alternative mitigation policies to cope with an epidemic. Lockdowns that force firms to close and that discontinue social activities slow down the progression of the epidemic at the cost of reducing GDP and increasing debt and, on average, decrease mortality. Testing-Tracing-Quarantine policies decrease mortality at a lower cost, but they are effective only if thorough. I find that lockdowns work best in case of a bigger average family size, of a diffused labor market participation and of a bigger average firm size.

Refining real-time predictions of Vibrio vulnificus concentrations in a tropical urban estuary by incorporating dissolved organic matter dynamics

The south shore of O'ahu, Hawai'i is one of the most visited coastal tourism areas in the United States with some of the highest instances of recreational waterborne disease. A population of the pathogenic bacterium Vibrio vulnificus lives in the estuarine Ala Wai Canal in Honolulu which surrounds the heavily populated tourism center of Waikīkī. We developed a statistical model to predict V. vulnificus dynamics in this system using environmental measurements from moored oceanographic and atmospheric sensors in real time. During a year-long investigation, we analyzed water from 9 sampling events at 3 depths and 8 sites along the canal (n = 213) for 36 biogeochemical variables and V. vulnificus concentration using quantitative polymerase chain reaction (qPCR) of the hemolysin A gene (vvhA). The best multiple linear regression model of V. vulnificus concentration, explaining 80% of variation, included only six predictors: 5-day average rainfall preceding water sampling, daily maximum air temperature, water temperature, nitrate plus nitrite, and two metrics of humic dissolved organic matter (DOM). We show how real-time predictions of V. vulnificus concentration can be made using these models applied to the time series of water quality measurements from the Pacific Islands Ocean Observing System (PacIOOS) as well as the PacIOOS plume model based on the Waikīkī Regional Ocean Modeling System (ROMS) products. These applications highlight the importance of including DOM variables in predictive modeling of V. vulnificus and the influence of rain events in elevating nearshore concentrations of V. vulnificus. Long-term climate model projections of locally downscaled monthly rainfall and air temperature were used to predict an overall increase in V. vulnificus concentration of approximately 2- to 3-fold by 2100. Improving these predictive models of microbial populations is critical for management of waterborne pathogen risk exposure, particularly in the wake of a changing global climate.

Insight into melatonin-mediated response and signaling in the regulation of plant defense under biotic stress

Melatonin plays a crucial role in the mitigation of plant biotic stress through induced defense responses and pathogen attenuation. Utilizing the current knowledge of signaling and associated mechanism of this phytoprotectant will be invaluable in sustainable plant disease management. Biotic stress in plants involves complex regulatory networks of various sensory and signaling molecules. In this context, the polyfunctional, ubiquitous-signaling molecule melatonin has shown a regulatory role in biotic stress mitigation in plants. The present review conceptualized the current knowledge concerning the melatonin-mediated activation of the defense signaling network that leads to the resistant or tolerant phenotype of the infected plants. Fundamentals of signaling networks involved in melatonin-induced reactive oxygen species (ROS) or reactive nitrogen species (RNS) scavenging through enzymatic and non-enzymatic antioxidants have also been discussed. Increasing evidence has suggested that melatonin acts upstream of mitogen-activated proteinase kinases in activation of defense-related genes and heat shock proteins that provide immunity against pathogen attack. Besides, the direct application of melatonin on virulent fungi and bacteria showed disrupted spore morphology, destabilization of cell ultrastructure, reduced biofilm formation, and enhanced mortality that led to attenuate disease symptoms on melatonin-treated plants. The transcriptome analysis has revealed the down-regulation of pathogenicity genes, metabolism-related genes, and up-regulation of fungicide susceptibility genes in melatonin-treated pathogens. The activation of melatonin-mediated systemic acquired resistance (SAR) through cross-talk with salicylic acid (SA), jasmonic acid (JA) has been essential for viral disease management. The high endogenous melatonin concentration has also been correlated with the up-regulation of genes involved in pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). The present review highlights the versatile functions of melatonin towards direct inhibition of pathogen propagule along with active participation in mediating oxidative burst and simulating PTI, ETI and SAR responses. The hormonal cross-talk involving melatonin mediated biotic stress tolerance through defense signaling network suggests its suitability in a sustainable plant protection system.

New insights into the inhibitory roles and mechanisms of D-amino acids in bacterial biofilms in medicine, industry, and agriculture

Biofilms are complex aggregates of microbes that are tightly protected by an extracellular matrix (ECM) and may attach to a surface or adhere together. A higher persistence of bacteria on biofilms makes them resistant not only to harsh conditions but also to various antibiotics which led to the emergence of problems in different applications. Recently, it has been discovered that many bacteria produce and release various D-amino acids (D-AAs) to inhibit biofilm formation, which made a great deal of interest in research into the control of bacterial biofilms in diverse fields, such as human health, industrial settings, and medical devices. D-AAs have various mechanisms to inhibit bacterial biofilms such as: (i) interfering with protein synthesis (ii) Inhibition of extracellular polymeric materials (EPS) productions (protein, eDNA, and polysaccharide) (iii) Inhibition of quorum sensing (autoinducers), and (iv) interfere with peptidoglycan synthesis, these various modes of action, enables these small molecules to inhibit both Gram-negative and Gram-positive bacterial biofilms. Since most biofilms are multi-species, D-AAs in combination with other antimicrobial agents are good choices to combat a variety of bacterial biofilms without displaying toxicity on human cells. This review article addressed the role of D-AAs in controlling several bacterial biofilms and described the possible or definite mechanisms involved in this process.

Robust network stability of mosquitoes and human pathogens of medical importance

Background

The exact number of mosquito species relevant to human health is unknown, posing challenges in understanding the scope and breadth of vector–pathogen relationships, and how resilient mosquito vector–pathogen networks are to targeted eradication of vectors.

Methods

We performed an extensive literature survey to determine the associations between mosquito species and their associated pathogens of human medical importance. For each vector–pathogen association, we then determined the strength of the associations (i.e., natural infection, lab infection, lab dissemination, lab transmission, known vector). A network analysis was used to identify relationships among all pathogens and vectors. Finally, we examined how elimination of either random or targeted species affected the extinction of pathogens.

Results

We found that 88 of 3578 mosquito species (2.5%) are known vectors for 78 human disease-causing pathogens; however, an additional 243 species (6.8%) were identified as potential or likely vectors, bringing the total of all mosquitos implicated in human disease to 331 (9.3%). Network analysis revealed that known vectors and pathogens were compartmentalized, with the removal of six vectors being enough to break the network (i.e., cause a pathogen to have no vector). However, the presence of potential or likely vectors greatly increased redundancies in the network, requiring more than 41 vectors to be eliminated before breaking the network.

Conclusion

Although < 10% of mosquitoes are involved in transmitting pathogens that cause human disease, our findings point to inherent robustness in global mosquito vector–pathogen networks.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05333-4.

Spatial dynamics of inflammation-causing and commensal bacteria in the gastrointestinal tract

In recent years, new research programmes have been initiated to understand the role of gut bacteria in health and disease, enabled in large part by the emergence of high-throughput sequencing. As new genomic and other data emerge it will become important to explain observations in terms of underlying population mechanisms; for instance, it is of interest to understand how resident bacteria interact with their hosts and pathogens, and how they play a protective role. Connecting underlying processes with observed patterns is aided by the development of mathematical models. Here, we develop a spatial model of microbial populations in the gastrointestinal tract to explore conditions under which inflammation-causing bacteria can invade the gut and under which such pathogens become persistent. We find that pathogens invade both small and large intestine from even a relatively small inoculum size but are usually eliminated by the host response. When the immune response is weak, the pathogen is able to persist for a long period. Spatial structure affects these dynamics by creating moving refugia which facilitate bouts of pathogen resurgence and inflammation in persistent infections. Space also plays a role in repopulation by commensals after infection. We further find that the rate of decay of inflammation has a stronger effect on outcomes than the initiation of inflammation or other parameters. Finally, we explore the impact of partially inflammation-resistant commensals on these dynamics.

Integrins are double-edged swords in pulmonary infectious diseases

Integrins are an important family of adhesion molecules that are widely distributed on immune cells in the lungs. Of note, accumulating evidences have shown that integrins are double-edged swords in pulmonary infectious diseases. On one hand, integrins promote the migration of immune cells to remove the invaded pathogens in the infected lungs. However, on the other hand, integrins also act as the targets for pathogens to escape from host immune system, which is a potential factor leading to further tissue damage. Thus, the innovative therapeutic strategies based on integrins has inspired well-founded hopes to treat pulmonary infectious diseases. In this review, we illustrate the involvement of integrins in pulmonary infectious diseases, and further discuss the innovative therapeutic targets based on integrins.

A health survey of the reef forming scleractinian cold-water corals Lophelia pertusa and Madrepora oculata in a remote submarine canyon on the European continental margin, NE Atlantic

Monitoring of cold-water corals (CWCs) for pathogens and diseases is limited due to the environment, protected nature of the corals and their habitat and as well as the challenging and sampling effort required. It is recognised that environmental factors such as temperature and pH can expedite the ability of pathogens to cause diseases in cold-water corals therefore the characterisation of pathogen diversity, prevalence and associated pathologies is essential. The present study combined histology and polymerase chain reaction (PCR) diagnostic techniques to screen for two significant pathogen groups (bacteria of the genus Vibrio and the protozoan Haplosporidia) in the dominant NE Atlantic deep-water framework corals Lophelia pertusa (13 colonies) and Madrepora oculata (2 colonies) at three sampling locations (canyon head, south branch and the flank) in the Porcupine Bank Canyon (PBC), NE Atlantic. One M. oculata colony and four L. pertusa colonies were collected from both the canyon flank and the south branch whilst five L. pertusa colonies were collected from the canyon head. No pathogens were detected in the M. oculata samples. Neither histology nor PCR detected Vibrio spp. in L. pertusa, although Illumina technology used in this study to profile the CWCs microbiome, detected V. shilonii (0.03%) in a single L. pertusa individual, from the canyon head, that had also been screened in this study. A macroborer was observed at a prevalence of 0.07% at the canyon head only. Rickettsiales-like organisms (RLOs) were visualised with an overall prevalence of 40% and with a low intensity of 1 to 4 (RLO) colonies per individual polyp by histology. L. pertusa from the PBC canyon head had an RLO prevalence of 13.3% with the highest detection of 26.7% recorded in the south branch corals. Similarly, unidentified cells observed in L. pertusa from the south branch (20%) were more common than those observed in L. pertusa from the canyon head (6.7%). No RLOs or unidentified cells were observed in corals from the flank. Mean particulate organic matter concentration is highest in the south branch (2,612 μg l^-1) followed by the canyon head (1,065 μg l^-1) and lowest at the canyon flank (494 μg l^-1). Although the route of pathogen entry and the impact of RLO infection on L. pertusa is unclear, particulate availability and the feeding strategies employed by the scleractinian corals may be influencing their exposure to pathogens. The absence of a pathogen in M. oculata may be attributed to the smaller number of colonies screened or the narrower diet in M. oculata compared to the unrestricted diet exhibited in L. pertusa, if ingestion is a route of entry for pathogen groups. The findings of this study also shed some light on how environmental conditions experienced by deep sea organisms and their life strategies may be limiting pathogen diversity and prevalence.

Pathogen infection routes and host innate immunity: Lessons from insects

Recent advances in insect-pathogen interactions have started to reveal the role of insect tissues and organs as natural infection routes for parasites and microbial pathogens. Here we summarize this information highlighting the micro- and macro-parasites that enter insects through distinct infection routes and link them to innate immune activity. We also examine whether the infection route determines the insect immune response and if the resulting immunological and physiological processes underpinning these different routes of infection are clearly distinct. Understanding how the infection route is associated with the robustness in insect host defense will help us identify conserved evolutionary and ecological patterns in order to design novel strategies for the management of destructive agricultural pests and disease vectors.

Technical suitability and reliability of an in vivo and non-invasive biosensor-type glucose assessment as a potential biomarker for multiple stressors in fishes: an evaluation on Salmonids

Regardless of the wide use of glucose measurements in stress evaluation, there are some inconsistencies in its acceptance as a stress marker. To meet the challenge and test the reliability/suitability of glucose measurement in practice, we simulated different environmental/anthropogenic exposure scenarios in this study. We aimed to provoke stress in fish followed by a 2-week stress recovery period and under the cumulative effect of leachate fish exposed to pathogenic oomycetes (Saprolegnia parasitica) to represent a possible infection in fish. We selected stream-resident and anadromous brown trout ecotypes (Salmo trutta) representing salmonids with different migratory behaviour strategies. Here, we analysed glucose content in fish-holding water, blood and gills to determine glucose suitability as a potential biomarker of fish response to environmental challenges. Additionally, swimming behavioural parameters and haematocrit were measured. The results indicated that the quantity of glucose released in the holding water of stressed fish increased considerably and remained substantially higher throughout the stress recovery period than the control level. Correspondingly, the circulating levels of glucose in blood and gills decreased over time in fish exposed to different stressors. A significant decrease in swimming activity of fish was observed during the first hours of leachate exposure and increased in fish exposed to S. parasitica compared to control. Our study is the first to ensure the validity and reliability of glucose response in evaluating physiological stress in fish under chemical and biological stimuli, indicating its sensitivity and response range of glucose measurement in fish-holding water.

Determinants of endophytic and pathogenic lifestyle in root colonizing fungi

Plant-fungal interactions in the soil crucially impact crop productivity and can range from highly beneficial to detrimental. Accumulating evidence suggests that some root-colonizing fungi shift between endophytic and pathogenic behaviour depending on the host species and that combinations of effector proteins collectively shape the fungal lifestyle on a given plant. In this review we discuss recent advances in our understanding of how fungal infection strategies on roots can lead to contrasting outcomes for the host. We highlight functional similarities and differences in compatibility determinants that control the colonization of specific-cell layers within plant roots, ultimately shaping the continuum between endophytic and pathogenic lifestyle.

Application of Nanopore Sequencing Technology in the Clinical Diagnosis of Infectious Diseases

Infectious diseases are an enormous public health burden and a growing threat to human health worldwide. Emerging or classic recurrent pathogens, or pathogens with resistant traits, challenge our ability to diagnose and control infectious diseases. Nanopore sequencing technology has the potential to enhance our ability to diagnose, interrogate, and track infectious diseases due to the unrestricted read length and system portability. This review focuses on the application of nanopore sequencing technology in the clinical diagnosis of infectious diseases and includes the following: (i) a brief introduction to nanopore sequencing technology and Oxford Nanopore Technologies (ONT) sequencing platforms; (ii) strategies for nanopore-based sequencing technologies; and (iii) applications of nanopore sequencing technology in monitoring emerging pathogenic microorganisms, molecular detection of clinically relevant drug-resistance genes, and characterization of disease-related microbial communities. Finally, we discuss the current challenges, potential opportunities, and future outlook for applying nanopore sequencing technology in the diagnosis of infectious diseases.

Antimicrobial activity of supernatants produced by bacteria isolated from Brazilian stingless bee's larval food

Background

The discovery of new molecules with antimicrobial properties has been a promising approach, mainly when related to substances produced by bacteria. The use of substances produced by bees has evidenced the antimicrobial action in different types of organisms. Thus, the use of bacteria isolated from larval food of stingless bees opens the way for the identification of the new molecules. The effect of supernatants produced by these bacteria was evaluated for their ability to inhibit the growth of bacteria of clinical interest. Furthermore, their effects were evaluated when used in synergy with antibiotics available in the pharmaceutical industry.

Results

A few supernatants showed an inhibitory effect against susceptible and multiresistant strains in the PIC assay and the modulation assay. Emphasizing the inhibitory effect on multidrug-resistant strains, 7 showed an effect on multidrug-resistant Escherichia coli (APEC), Klebsiella pneumoniae carbapenemase (KPC), multidrug-resistant Pseudomonas aeruginosa, and multidrug-resistant Staphylococcus aureus (MRSA) in the PIC assay. Of the supernatants analyzed, some presented synergism for more than one species of multidrug-resistant bacteria. Nine had a synergistic effect with ampicillin on E. coli (APEC) or S. aureus (MRSA), 5 with penicillin G on E. coli (APEC) or KPC, and 3 with vancomycin on KPC.

Conclusion

In summary, the results indicate that supernatants produced from microorganisms can synthesize different classes of molecules with potent antibiotic activity against multiresistant bacteria. Thus, suggesting the use of these microorganisms for use clinical tests to isolate the molecules produced and their potential for use.

Carbon Dots in the Detection of Pathogenic Bacteria and Viruses

Bacterial and viruses pathogens are a significant hazard to human safety and health. In the imaging and detection of pathogenic microorganisms, the application of fluorescent nanoparticles is very useful. Carbon dots and quantum dots are preferred in this regard as labels, amplifiers, and/or electrode modifiers because of their outstanding features. However, precise diagnostics to identify numerous harmful bacteria simultaneously still face considerable hurdles, yet it is an inevitable issue. With the growing development of biosensors, nanoproduct-based bio-sensing has recently become one of the most promising methods for accurately identifying and quantifying various pathogens at low cost, high sensitivity, and selectivity, with time savings. The most recent applications of carbon dots in optical and electrochemical-based sensors are discussed in this review, along with some examples of pathogen sensors.HighlightsSimultaneous and early detection of pathogens is a critical issue in the management of readily spread to prevent epidemics.Carbon dots-based biosensors are more preferred in detection of pathogens due to high selectivity and sensitivity, as well as quick and cheap point-of-care platform.Summary of recent advances in the design of optical and electrochemical biosensors for the detection of pathogens.

Ozone disinfection of waterborne pathogens and their surrogates: A critical review

Viruses, Giardia cysts, and Cryptosporidium parvum oocysts are all major causes of waterborne diseases that can be uniquely challenging in terms of inactivation/removal during water and wastewater treatment and water reuse. Ozone is a strong disinfectant that has been both studied and utilized in water treatment for more than a century. Despite the wealth of data examining ozone disinfection, direct comparison of results from different studies is challenging due to the complexity of aqueous ozone chemistry and the variety of the applied approaches. In this systematic review, an analysis of the available ozone disinfection data for viruses, Giardia cysts, and C. parvum oocysts, along with their corresponding surrogates, was performed. It was based on studies implementing procedures which produce reliable and comparable datasets. Datasets were compiled and compared with the current USEPA Ct models for ozone. Additionally, the use of non-pathogenic surrogate organisms for prediction of pathogen inactivation during ozone disinfection was evaluated. Based on second-order inactivation rate constants, it was determined that the inactivation efficiency of ozone decreases in the following order: Viruses >> Giardia cysts > C. parvum oocysts. The USEPA Ct models were found to be accurate to conservative in predicting inactivation of C. parvum oocysts and viruses, respectively, however they overestimate inactivation of Giardia cysts at ozone Ct values greater than ∼1 mg min L-1. Common surrogates of these pathogens, such as MS2 bacteriophage and Bacillus subtilis spores, were found to exhibit different inactivation kinetics to mammalian viruses and C. parvum oocysts, respectively. The compilation of data highlights the need for further studies on disinfection kinetics and inactivation mechanisms by ozone to better fit inactivation models as well as for proper selection of surrogate organisms.

Combined administration routes of marine yeasts enhanced immune-related genes and protection of white shrimp (Penaeus vannamei) against Vibrio parahaemolyticus

Antibiotic usage to control infectious diseases in shrimp aquaculture has led to serious problems on antimicrobial resistance. An alternative to mitigate this issue is the use of probiotics, which can be easily administered by feed and water. This study examines immunomodulatory and protective effects of the marine yeasts Debaryomyces hansenii CBS8339 (Dh) and Yarrowia lipolytica Yl-N6 (Yl) -alone and mixed-in white shrimp Penaeus vannamei post-larvae. Administration routes (fed and water alone or in combination), supplementation frequency and time elapsed after the last dietary supplement were tested on growth and gene expression of penaeidin, lectin, lysozyme, superoxide dismutase, catalase, and peroxidase, as well as survival upon Vibrio parahaemolyticus IPNGS16 challenge. Penaeidin and lectin genes were upregulated in post-larvae fed orally with Yl or combined Dh + Yl. Higher growth and survival for yeast supplementation treatments were observed compared to the control group, mainly when yeasts (Dh + Yl) and administration routes (feed and water) were combined. In conclusion, mixed yeast and combined administration routes improved growth and immunity against V. parahaemolyticus.

Infection cycle of Marteilia pararefringens in blue mussels Mytilus edulis in a heliothermic marine oyster lagoon in Norway

Agapollen is a traditional heliothermic marine oyster lagoon in western Norway, representing the northernmost site of any Marteilia sp. protists detected in Europe. The semi-closed lagoon is a unique site to study the life cycle and development of M. pararefringens in naïve mussels. Two baskets with uninfected mussels were deployed in the lagoon outlet in May and October 2018, respectively, and sampled every 6 wk. The parasite was first detected in the mussels by PCR in early July and by histology in late August. By then, M. pararefringens had developed into mature stages, indicating a rapid development during mid-summer. Sporulation occurred during autumn. Mussels deployed in October never became infected, indicating that transmission was restricted to the warmest period of the year. Pronounced pathology was observed in infected mussels, including degenerated digestive tubules and infiltration of haemocytes. Mussel mortality was observed in the baskets, but whether this was due to infections of M. pararefringens or other environmental factors could not be determined. Plankton samples from the lagoon were also collected for PCR analysis. These samples, dominated by copepods, were positive for M. pararefringens in summer. In sorted samples, M. pararefringens was detected in the Acartia spp. and Paracartia grani fractions between July and October. These plankton copepods are therefore potentially involved in the life cycle of M. pararefringens.

[Clinical and microbiological characteristics of children with drowning-associated aspiration pneumonia]

OBJECTIVES

To study the clinical and microbiological characteristics of children with drowning-associated aspiration pneumonia, so as to provide a reference for empirical selection of antibacterial agents.

METHODS

A retrospective analysis was performed on the medical data of 185 children with drowning-associated aspiration pneumonia who were admitted to Children's Hospital of Chongqing Medical University from January 2010 to October 2020. According to the drowning environment, these children were divided into four groups: fecal group (n=44), freshwater group (n=69), swimming pool group (n=41), and contaminant water group (n=31). The clinical characteristics and pathogen detection results were reviewed and compared among the four groups.

RESULTS

The 185 children had an age of 4 months to 17 years (median 34 months). Sputum cultures were performed on 157 children, and 103 were tested positive (65.6%), with 87 strains of Gram-negative bacteria (68.5%), 37 strains of Gram-positive bacteria (29.1%), and 3 strains of fungi (2.4%). Gram-negative bacteria were the main pathogen in the fecal group and the contaminant water group, accounting for 88.2% (30/34) and 78.3% (18/23), respectively. The freshwater group had a significantly higher detection rate of Gram-positive bacteria than the fecal group (P<0.008), and the swimming pool group had an equal detection rate of Gram-negative bacteria and Gram-positive bacteria.

CONCLUSIONS

For pulmonary bacterial infection in children with drowning in feces or contaminant water, antibiotics against Gram-negative bacteria may be applied empirically, while for children with drowning in a swimming pool or freshwater, broad-spectrum antibiotics may be used as initial treatment, and subsequently the application of antibiotics may be adjusted according to the results of the drug sensitivity test.

Seasonal Variations in the Characteristics of Microbial Community Structure and Diversity in Atmospheric Particulate Matter from Clean Days and Smoggy Days in Beijing

Microorganisms are an important part of atmospheric particulate matter and are closely related to human health. In this paper, the variations in the characteristics of the chemical components and bacterial communities in PM₁₀ and PM_2.5 grouped according to season, pollution degree, particle size, and winter heating stage were studied. The influence of environmental factors on community structure was also analyzed. The results showed that seasonal variations were significant. NO₃^- contributed the most to the formation of particulate matter in spring and winter, while SO₄^2- contributed the most in summer and autumn. The community structures in summer and autumn were similar, while the community structure in spring was significantly different. The dominant phyla were similar among seasons, but their proportions were different. The dominant genera were no-rank_c_Cyanobacteria, Acidovorax, Escherichia-Shigella and Sphingomonas in spring; Massilia, Bacillus, Acinetobacter, Rhodococcus, and Brevibacillus in summer and autumn; and Rhodococcus in winter. The atmospheric microorganisms in Beijing mainly came from soil, water, and plants. The few pathogens detected were mainly affected by the microbial source on the sampling day, regardless of pollution level. RDA (redundancy analysis) showed that the bacterial community was positively correlated with the concentration of particulate matter and that the wind speed in spring was positively correlated with NO₃^- levels, NH₄⁺ levels, temperature, and relative humidity in summer and autumn, but there was no clear consistency among winter samples. This study comprehensively analyzed the variations in the characteristics of the airborne bacterial community in Beijing over one year and provided a reference for understanding the source, mechanism, and assessment of the health effects of different air qualities.

A review of the potential of conventional and advanced membrane technology in the removal of pathogens from wastewater

Consumption of pathogenic contaminated water has claimed the lives of many people. Hence, this scenario has emphasized the urgent need for research methods to avoid, treat and eliminate harmful pathogens in wastewater. Therefore, effective water treatment has become a matter of utmost importance. Membrane technology offers purer, cleaner, and pathogen-free water through the water separation method via a permeable membrane. Advanced membrane technology such as nanocomposite membrane, membrane distillation, membrane bioreactor, and photocatalytic membrane reactor can offer synergistic effects in removing pathogen through the integration of additional functionality and filtration in a single chamber. This paper also comprehensively discussed the application, challenges, and future perspective of the advanced membrane technology as a promising alternative in battling pathogenic microbial contaminants, which will also be beneficial and valuable in managing pandemics in the future as well as protecting human health and the environment. In addition, the potential of membrane technology in battling the ongoing global pandemic of coronavirus disease 2019 (COVID-19) was also discussed briefly.

Identification and characterisation of sPEPs in Cryptococcus neoformans

Short open reading frame (sORF)-encoded peptides (sPEPs) have been found across a wide range of genomic locations in a variety of species. To date, their identification, validation, and characterisation in the human fungal pathogen Cryptococcus neoformans has been limited due to a lack of standardised protocols. We have developed an enrichment process that enables sPEP detection within a protein sample from this polysaccharide-encapsulated yeast, and implemented proteogenomics to provide insights into the validity of predicted and hypothetical sORFs annotated in the C. neoformans genome. Novel sORFs were discovered within the 5' and 3' UTRs of known transcripts as well as in "non-coding" RNAs. One novel candidate, dubbed NPB1, that resided in an RNA annotated as "non-coding", was chosen for characterisation. Through the creation of both specific point mutations and a full deletion allele, the function of the new sPEP, Npb1, was shown to resemble that of the bacterial trans-translation protein SmpB.

Development of a proof-of-concept microfluidic portable pathogen analysis system for water quality monitoring

Waterborne diseases cause millions of deaths worldwide, especially in developing communities. The monitoring and rapid detection of microbial pathogens in water is critical for public health protection. This study reports the development of a proof-of-concept portable pathogen analysis system (PPAS) that can detect bacteria in water with the potential application in a point-of-sample collection setting. A centrifugal microfluidic platform is adopted to integrate bacterial cell lysis in water samples, nucleic acid extraction, and reagent mixing with a droplet digital loop mediated isothermal amplification assay for bacteria quantification onto a single centrifugal disc (CD). Coupled with a portable "CD Driver" capable of automating the assay steps, the CD functions as a single step bacterial detection "lab" without the need to transfer samples from vial-to-vial as in a traditional laboratory. The prototype system can detect Enterococcus faecalis, a common fecal indicator bacterium, in water samples with a single touch of a start button within 1 h and having total hands-on-time being less than 5 min. An add-on bacterial concentration cup prefilled with absorbent polymer beads was designed to integrate with the pathogen CD to improve the downstream quantification sensitivity. All reagents and amplified products are contained within the single-use disc, reducing the opportunity of cross contamination of other samples by the amplification products. This proof-of-concept PPAS lays the foundation for field testing devices in areas needing more accessible water quality monitoring tools and are at higher risk for being exposed to contaminated waters.

Enhanced decay of coronaviruses in sewers with domestic wastewater

Recent outbreaks caused by coronaviruses and their supposed potential fecal-oral transmission highlight the need for understanding the survival of infectious coronavirus in domestic sewers. To date, the survivability and decay of coronaviruses were predominately studied using small volumes of wastewater (normally 5-30 mL) in vials (in-vial tests). However, real sewers are more complicated than bulk wastewater (wastewater matrix only), in particular the presence of sewer biofilms and different operational conditions. This study investigated the decay of infectious human coronavirus 229E (HCoV-229E) and feline infectious peritonitis virus (FIPV), two typical surrogate coronaviruses, in laboratory-scale reactors mimicking the gravity (GS, gravity-driven sewers) and rising main sewers (RM, pressurized sewers) with and without sewer biofilms. The in-sewer decay of both coronaviruses was greatly enhanced in comparison to those reported in bulk wastewater through in-vial tests. 99% of HCoV-229E and FIPV decayed within 2 h under either GS or RM conditions with biofilms, in contrast to 6-10 h without biofilms. There is limited difference in the decay of HCoV and FIPV in reactors operated as RM or GS, with the T₉₀ and T₉₉ difference of 7-10 min and 14-20 min, respectively. The decay of both coronaviruses in sewer biofilm reactors can be simulated by biphasic first-order kinetic models, with the first-order rate constant 2-4 times higher during the first phase than the second phase. The decay of infectious HCoV and FIPV was significantly faster in the reactors with sewer biofilms than in the reactors without biofilms, suggesting an enhanced decay of these surrogate viruses due to the presence of biofilms and related processes. The mechanism of biofilms in virus adsorption and potential inactivation remains unclear and requires future investigations. The results indicate that the survivability of infectious coronaviruses detected using bulk wastewater overestimated the infectivity risk of coronavirus during wastewater transportations in sewers or the downstream treatment.

C-type lectin-(like) fold - Protein-protein interaction patterns and utilization

The C-type lectin-like fold (CTL fold) is a building block of many proteins, including saccharide-binding lectins, natural killer cell receptors, macrophage mannose receptor, selectins, collectins, snake venoms and others. Some are important players in innate immunity and are involved in the first-line response to virally infected cells or cancer cells, some play a role in antimicrobial defense, and some are potential targets for fight against problems connected with allergies, obesity, and autoimmunity. The structure of a CTL domain typically contains two α-helices, two small β-sheets and a long surface loop, with two or three disulfide bridges stabilizing the structure. This small domain is often involved in interactions with a target molecule, however, utilizing varied parts of the domain surface, with or without structural modifications. More than 500 three-dimensional structures of CTL fold-containing proteins are available in the Protein Data Bank, including a significant number of complexes with their key interacting partners (protein:protein complexes). The amount of available structural data enables a detailed analysis of the rules of interaction patterns utilized in activation, inhibition, attachment and other pathways or functionalities. Interpretation of known CTL receptor structures and all other CTL-containing proteins and complexes with described three-dimensional structures, complemented with sequence/structure/interaction correlation analysis offers a comprehensive view of the rules of interaction patterns of the CTL fold. The results are of value for prediction of interaction behavior of so far not understood CTL-containing proteins and development of new protein binders based on this fold, with applications in biomedicine or biotechnologies. It follows from the available structural data that almost the whole surface of the CTL fold is utilized in protein:protein interactions, with the heaviest frequency of utilization in the canonical interaction region. The individual categories of interactions differ in the interface buildup strategy. The strongest CTL binders rely on interfaces with large interaction area, presence of hydrophobic core, or high surface complementarity. The typical interaction surfaces of the fold are not conserved in amino acid sequence and can be utilized in design of new binders for biotechnological applications.

Size-dependent photothermal antibacterial activity of Ti3C2Tx MXene nanosheets against methicillin-resistant Staphylococcus aureus

Developing antibiotics-independent antibacterial materials is of great importance for combating drug-resistant bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA). MXene (transition metal carbides and nitrides), a class of novel 2D nanomaterials, has shown great potentials in biomedical areas. However, the effect of MXene size on its properties and bioactivity is still unknown. Herein, we report for the first time that the antibacterial photothermal therapy efficacy of Ti₃C₂T_x MXene nanosheets is size-dependent. Three MXene suspensions with small size of 196 nm (MX-s), medium size of 347 nm (MX-m) and large size of 497 nm (MX-l) were prepared via ultrasonication. Upon NIR irradiation for 5 min, the temperature of MXene suspensions (10 μg/mL) increased to 64, 60 and 56 °C for MX-s, MX-m and MX-l, respectively. Accordingly, the viability loss of MRSA induced by MX-s, MX-m and MX-l under NIR was 93%, 69% and 56%, respectively. The in vivo study in the MRSA-infected mouse model showed that the photothermal therapy efficacy of MX-s was comparable to that of the positive control vancomycin. This is the first report on the size-dependent photothermal effect and photothermal antibacterial activity of MXene, which may guide the development of MXene-based therapeutics in the future. In addition, the drug-free antibacterial therapy has great implications for the treatment of antibiotics-resistant bacteria infections.

(Alphaproteobacteria: Rickettsiales: Anaplasmataceae): an intracytoplasmic, hepatopancreatic, pathogen of the flatback mud crab, Eurypanopeus depressus

Bacterial pathogens are a long-standing threat to the longevity and survival of crustacean hosts. Their presence and continuing emergence require close monitoring to understand their impact on fished, cultured, and wild crustacean populations. We describe a new bacterial pathogen belonging to the Anaplasmataceae family (Alphaproteobacteria: Rickettsiales), providing pathological, ultrastructural, phylogenetic, and genomic evidence to determine a candidate genus and species ('Candidatus Mellornella promiscua'). This bacterium was found to infect the mud crab, Eurypanopeus depressus, on the North Carolina coastline (USA) at a prevalence of 10.8%. 'Candidatus Mellornella promiscua' was often observed in co-infection with the rhizocephalan barnacle, Loxothylacus panopaei. The bacterium was only found in the hepatopancreas of the mud crab host, causing cytoplasmic hypertrophy, tubule necrosis, large plaques within the cytoplasm of the host cell, and an abundance of sex-pili. The circular genome of the bacterium is 1,013,119bp and encodes 939 genes in total. Phylogenetically, the new bacterium branches within the Anaplasmataceae. The genome is dissimilar from other described bacteria, with 16S gene similarity observed at a maximum of 85.3% to a Wolbachia endosymbiont. We explore this novel bacterial pathogen using genomic, phylogenetic, ultrastructural, and pathological methods, discussing these results in light of current bacterial taxonomy, similarity to other bacterial pathogens, and the potential impact upon the surrounding disease ecology of the host and benthic ecosystem.

The circadian clock ticks in plant stress responses

The circadian clock, a time-keeping mechanism, drives nearly 24-h self-sustaining rhythms at the physiological, cellular, and molecular levels, keeping them synchronized with the cyclic changes of environmental signals. The plant clock is sensitive to external and internal stress signals that act as timing cues to influence the circadian rhythms through input pathways of the circadian clock system. In order to cope with environmental stresses, many core oscillators are involved in defense while maintaining daily growth in various ways. Recent studies have shown that a hierarchical multi-oscillator network orchestrates the defense through rhythmic accumulation of gene transcripts, alternative splicing of mRNA precursors, modification and turnover of proteins, subcellular localization, stimuli-induced phase separation, and long-distance transport of proteins. This review summarizes the essential role of circadian core oscillators in response to stresses in Arabidopsis thaliana and crops, including daily and seasonal abiotic stresses (low or high temperature, drought, high salinity, and nutrition deficiency) and biotic stresses (pathogens and herbivorous insects). By integrating time-keeping mechanisms, circadian rhythms and stress resistance, we provide a temporal perspective for scientists to better understand plant environmental adaptation and breed high-quality crop germplasm for agricultural production.

Inactivation of Salmonella enterica Serovar Typhimurium and Staphylococcus aureus in Rice by Radio Frequency Heating

ABSTRACT

The objectives of this study were to determine the effect of the milling degree (MD) of rice (Oryza sativa L.) on the heating rate, pathogen inactivation (Salmonella Typhimurium and Staphylococcus aureus), and color change resulting from radio frequency (RF) heating. Rice samples inoculated with pathogens were placed in a polypropylene jar and subjected to RF heating for 0 to 75 s. The heating rate of rice with a 2% MD was the highest during RF heating, followed by those with a 0, 8, and 10% MD; the reduction of pathogens showed the same trend. The reductions of pathogen levels in rice with MDs of 0 and 2% were significantly higher than those observed for rice with MDs of 8 and 10% under the same treatment conditions. For example, log reductions of Salmonella Typhimurium in rice by 55-s RF heating were 3.64, 5.19, 2.18, and 1.80 for MDs of 0, 2, 8, and 10%, respectively. At the same treatment conditions, log reductions of S. aureus were 2.77, 5.08, 1.15, and 0.90 for MDs of 0, 2, 8, and 10%, respectively. The color of rice measured according to L*, a*, and b* was not significantly altered after RF heating, regardless of the MD. Therefore, the MD of rice should be considered before RF heating is applied to inactivate foodborne pathogens.

HIGHLIGHTS

[Analysis of etiological characteristics and establishment of prediction model of postoperative infections in patients undergoing oral squamous cell carcinoma surgery with free flap reconstruction]

OBJECTIVE

To investigate the characteristics of pathogen infection and to establish a prediction model of infections in oral squamous cell carcinoma patients undergoing surgery with free flap reconstruction.

METHODS

The retrospective cohort study consisted of 1 596 patients undergoing tumor resection and free flap reconstruction for oral squamous cell carcinoma from January 2018 to December 2020. According to the postoperative infection, the patients were divided into the infected group (n=154) and non-infected group (n=1 442). The characteristics of pathogens were analyzed in the infected patients. The primary outcome variable was postoperative infection, and Logistic regression was used to determine risk factors of the infection. The prediction model was established and the discriminatory accuracy of the model was evaluated using receiver operating characteristic (ROC) curve.

RESULTS

Totally 154 cases were infected in the 1 596 cases undergoing surgery with free flap reconstruction, and the infection rate was 9.65%. The most frequent sites of infection were the surgical wound and respiratory tract. A total of 268 pathogens were isolated and cultured, including 240 strains of Gram-negative bacteria, accounting for 89.55%, mainly Pseudomonas aeruginosa and Klebsiella pneumoniae; 23 strains of Gram-positive bacteria, accounting for 8.58%, mainly Enterococcus faecalis and Staphylococcus aureus; and 5 strains of fungi, accounting for 1.87%. The isolated Pseudomonas aeruginosa had high resistant rate to imipenem and meropenem, and was sensitive to antibiotics, such as ciprofloxacin. The isolated Staphylococcus aureus had high resistant rate to erythromycin and clindamycin, and was sensitive to vancomycin. According to the multivariate Logistic analysis, four independent variables were significantly associated with an increased risk of postoperative infection (P < 0.05): clinical N category≥1, the American Society of Anesthesiologists (ASA) grade ≥2, tracheotomy and length of hospital stay >13 d. The prediction model was established based on these factors and the expression of the risk prediction model was as follows: predicted probability value P=1/(1+e^-a), a=-0.803+0.674×(clinical N category ≥1)+0.518×(the ASA grade ≥2)+0.918×(tracheotomy)+1.581×(length of hospital stay >13 d), Hosmer-Lemeshow χ²=10.647, P=0.223, the degree of fitting of the model was good. The area under the ROC curve was 0.818 and 95%CI of the model for predicting infection was 0.789-0.846.

CONCLUSION

Oral squamous cell carcinoma patients undergoing surgery with free flap reconstruction are prone to have a high incidence of postoperative infection and Gram-negative bacteria are the main pathogens causing an infection. The established prediction model is of good predictive effect. Rational antimicrobial use coupled with awareness of infection control measures is paramount to reduce the incidence of postoperative infection in the oral squamous cell carcinoma patients undergoing surgery with free flap reconstruction.