Occurrence Of Pathogens Research Articles

Inferring pathogen presence when sample misclassification and partial observation occur

Abstract Surveillance programmes are essential for detecting emerging pathogens and often rely on molecular methods to make inference about the presence of a target disease agent. However, molecular methods rarely detect target DNA perfectly. For example, molecular pathogen detection methods can result in misclassification (i.e. false positives and false negatives) or partial detection errors (i.e. detections with ‘ambiguous’, ‘uncertain’ or ‘equivocal’ results). Then, when data are to be analysed, these partial observations are either discarded or censored; this, however, disregards information that could be used to make inference about the true state of the system. There is a critical need for more direction and guidance related to how many samples are enough to declare a unit of interest ‘pathogen free’. Here, we develop a Bayesian hierarchal framework that accommodates false negative, false positive and uncertain detections to improve inference related to the occupancy of a pathogen. We apply our modelling framework to a case study of the fungal pathogen Pseudogymnoascus destructans (Pd) identified in Texas bats at the invasion front of white‐nose syndrome. To improve future surveillance programmes, we provide guidance on sample sizes required to be 95% certain a target organism is absent from a site. We found that the presence of uncertain detections increased the variability of resulting posterior probability distributions of pathogen occurrence, and that our estimates of required sample size were very sensitive to prior information about pathogen occupancy, pathogen prevalence and diagnostic test specificity. In the Pd case study, we found that the posterior probability of occupancy was very low in 2018, but occupancy probability approached 1 in 2020, reflecting increasing prior probabilities of occupancy and prevalence elicited from the site manager. Our modelling framework provides the user a posterior probability distribution of pathogen occurrence, which allows for subjective interpretation by the decision‐maker. To help readers apply and use the methods we developed, we provide an interactive RShiny app that generates target species occupancy estimation and sample size estimates to make these methods more accessible to the scientific community (https://rmummah.shinyapps.io/ambigDetect_sampleSize). This modelling framework and sample size guide may be useful for improving inferences from molecular surveillance data about emerging pathogens, non‐native invasive species and endangered species where misclassifications and ambiguous detections occur.

Occurrence and prevalence of antibiotic resistance genes and pathogens in an industrial park wastewater treatment plant

Antibiotic resistance genes (ARGs) and pathogens are emerging environmental pollutants that pose a threat to human health and ecosystem. Industrial park wastewater treatment plants (WWTPs) treat large amounts of comprehensive wastewater derived from industrial production and park human activity, which is possible a source of ARGs and pathogens. Therefore, this study investigated the occurrence and prevalence of ARGs, ARGs hosts and pathogens and assesses the ARGs health risk in the biological treatment process in a large-sale industrial park WWTP using metagenomic analysis and omics-based framework, respectively. Results show that the major ARG subtypes are multidrug resistance genes (MDRGs), macB, tetA(58), evgS, novA, msbA and bcrA and the ARGs main hosts were genus Acidovorax, Pseudomonas, Mesorhizobium. In particular, all determined ARGs genus level hosts are pathogens. The total removal percentage of ARGs, MDRGs and pathogens were 12.77 %, 12.96 % and 25.71 % respectively, suggesting that the present treatment could not efficiently remove these pollutants. The relative abundance of ARGs, MDRGs and pathogens varied along biological treatment process that ARGs and MDRGs were enriched in activated sludge and pathogens were enriched in both secondary sedimentation tank and activated sludge. Among 980 known ARGs, 23 ARGs (e.g., ermB, gadX and tetM) were assigned into risk Rank I with characters of enrichment in the human-associated environment, gene mobility and pathogenicity. The results indicate that industrial park WWTPs might serve as an important source of ARGs, MDRGs, and pathogens. These observations invite further study of the origination, development, dissemination and risk assessment of industrial park WWTPs ARGs and pathogens.

Parasitic fauna of bats from Costa Rica.

Bats are important reservoirs and spreaders of pathogens, including those of zoonotic concern. Though Costa Rica hosts one of the highest bat species' diversity, no information is available about their parasites. In order to investigate the occurrence of vector-borne pathogens (VBPs) and gastrointestinal (GI) parasites of chiropterans from this neotropical area, ectoparasites (n=231) and stools (n=64) were collected from 113 bats sampled in Santa Cruz (site 1) and Talamanca (site 2). Mites, fleas and ticks were morphologically and molecularly identified, as well as pathogens transmitted by vectors (VBPs, i.e., Borrelia spp., Rickettsia spp., Bartonella spp.) and from feces, such as Giardia spp., Cryptosporidium spp. and Eimeria spp. were molecularly investigated. Overall, 21 bat species belonging to 15 genera and 5 families were identified of which 42.5% were infested by ectoparasites, with a higher percentage of mites (38.9%, i.e., Cameronieta sp. and Mitonyssoides sp.) followed by flies (2.6%, i.e., Joblingia sp.) and tick larvae (1.7%, i.e., Ornithodoros sp.). Rickettsia spp. was identified in one immature tick and phylogenetically clustered with two Rickettsia species of the Spotted Fever Group (i.e., R. massiliae and R. rhipicephali). The frequency of GI parasite infection was 14%, being 3.1% of bats infected by Giardia spp. (un-identified non-duodenalis species), 1.5% by Eimeria spp. and 9.4% by Cryptosporidium spp. (bat and rodent genotypes; one C. parvum-related human genotype). The wide range of ectoparasites collected coupled with the detection of Rickettsia sp., Giardia and Cryptosporidium in bats from Costa Rica highlight the role these mammals may play as spreaders of pathogens and the need to further investigate the pathogenic potential of these parasites.

Efeito antifúngico de óleos essenciais no controle de fitopatógenos em sementes de soja armazenadas

ABSTRACT Soybean is subject to occurrences of pathogens transmitted by seeds, requiring phytosanitary treatment, however, it can be toxic to humans and the environment. The objective of this study was to evaluate the effect of essential oils of rosemary (Rosmarinus officinalis) and eucalyptus (Corymbia citriodora) on the control of phytopathogenic fungi in stored soybean seeds. The experiment was carried out in a completely randomized design, using a 2 × 5 factorial arrangement consisted of seeds with and without fungal inoculation (Aspergillus flavus and Penicillium rubens) and five seed treatments (three essential oils, positive control, and negative control), with four replicates. Rosemary and eucalyptus essential oils and their combination were applied to soybean seeds at the rate of 4 mL kg-1, at a concentration of 700 µL mL-1. Distilled water with 2% Tween® 80 was used as negative control, and the commercial fungicide Vitavax-Thiram® 200SC was used as positive control, according to the manufacturers’ recommendations. The R. officinalis essential oil was efficient in the control of Penicillium sp. in stored soybean seeds and showed a similar effect to the positive control. The C. citriodora essential oil reduced the incidence of Aspergillus sp. Therefore, these essential oils have potential to be used as an alternative control of soybean seed pathogens.

Diversity of trematodes from the amphibian anomaly P hotspot: Role of planorbid snails.

Trematode infection of the second intermediate hosts can lead to changes in their fitness and, as a result, a change in the invasion rate of animal communities. It is especially pronounced during the invasion of parasite species that reduce activity due to the manipulation of hosts through the changes of their morphology and physiology. One of these cases is an anomaly P syndrome hotspot found in some populations of water frogs and toads in Europe caused by the trematode Strigea robusta metacercariae. The occurrence of pathogen and their participation in ecosystems are intrigues questions in the anomaly P phenomenon, as well as the role of planorbid snails that serve as the first intermediate hosts for many trematode species. Herein, we focused on trematodes spectra from planorbid snails and amphibians from the anomaly P hosts with the aim to undetected interactions between the pathways of parasites. Emerging cercariae of 6802 planorbid snails of dominant species (Planorbarius corneus, Planorbis planorbis, and Anisus spp.) were detected by both morphological and molecular methods in seven waterbodies in Privolzhskaya Lesostep Nature Reserve (Russia). A total of 95 sequences of 18 species were received, and 48 sequences were unique and did not present in any genetic databases. The 18 species of trematodes from snails and 14 species of trematodes from amphibian hosts (Pelophylax ridibundus; Ranidae; Anura) were detected. Three species (Echinostoma nasincovae, Tylodelphys circibuteonis and Australapatemon burti) was new for the trematode fauna of the Middle Volga River region and Russia as a whole. Eleven species of parasitic flatworms have amphibians in their life cycles and nine species used amphibians as metacercariae hosts: Echinostoma nasincovae, E. miyagawai, Echinoparyphium recurvatum, Tylodelphys circibuteonis, Neodiplostomum spathula, Paralepoderma cloacicola, Macrodera longicollis, Strigea robusta, and Strigea strigis. The occurrence of trematode species from planorbid mollusks and frogs were compared.

Trends in Bacterial Pathogens of Bats: Global Distribution and Knowledge Gaps

Bats have received considerable recent attention for infectious disease research because of their potential to host and transmit viruses, including Ebola, Hendra, Nipah, and multiple coronaviruses. These pathogens are occasionally transmitted from bats to wildlife, livestock, and to humans, directly or through other bridging (intermediate) hosts. Due to their public health relevance, zoonotic viruses are a primary focus of research attention. In contrast, other emerging pathogens of bats, such as bacteria, are vastly understudied despite their ubiquity and diversity. Here, we describe the currently known host ranges and geographic distributional patterns of potentially zoonotic bacterial genera in bats, using published presence-absence data of pathogen occurrence. We identify apparent gaps in our understanding of the distribution of these pathogens on a global scale. The most frequently detected bacterial genera in bats are Bartonella, Leptospira, and Mycoplasma. However, a wide variety of other potentially zoonotic bacterial genera are also occasionally found in bats, such as Anaplasma, Brucella, Borrelia, Coxiella, Ehrlichia, Francisella, Neorickettsia, and Rickettsia. The bat families Phyllostomidae, Vespertilionidae, and Pteropodidae are most frequently reported as hosts of bacterial pathogens; however, the presence of at least one bacterial genus was confirmed in all 15 bat families tested. On a spatial scale, molecular diagnostics of samples from 58 countries and four overseas departments and island states (French Guiana, Mayotte, New Caledonia, and Réunion Island) reported testing for at least one bacterial pathogen in bats. We also identified geographical areas that have been mostly neglected during bacterial pathogen research in bats, such as the Afrotropical region and Southern Asia. Current knowledge on the distribution of potentially zoonotic bacterial genera in bats is strongly biased by research effort towards certain taxonomic groups and geographic regions. Identifying these biases can guide future surveillance efforts, contributing to a better understanding of the ecoepidemiology of zoonotic pathogens in bats.

The mycobiota associated with the weed water hyacinth Pontederia crassipes in Kolkata, India, with emphasis on biological control of the macrophyte

ABSTRACT The invasive macrophyte water hyacinth, Pontederia crassipes (Mart.) Solms (Pontederiaceae), was first introduced in India at the Acharya Jagadish Chandra Bose Indian Botanic Garden, near Kolkata in 1889 from where they spread throughout the sub-continent. An extensive systematic survey of water bodies in and around Kolkata, India, was done for the first time to assess the natural occurrence of indigenous phytopathogenic fungi of the weed between 2014 and 2019. The study brings into light several species, along with some first reports, of naturally occurring native phytopathogenic fungi and their evolutionary-related lineages. The occurrence and frequency of pathogens varied from site to site. Around 150 fungal pathogens isolated from water hyacinth were evaluated for their disease-causing potential against the weed. The isolated fungi were identified using morphological and molecular techniques. Fusarium Link followed by Alternaria Nees were the highest and most consistently isolated genera. Seven potential fungi that caused more than 90% disease in whole plant pathogenicity bioassay were subjected to host-range evaluation against 67 plant species selected based on ecological nearness or economic significance. Among these Fusarium oxysporum f. sp. lycopersici (WHK-59) was found to have a narrow host range and be effective against water hyacinth. With further studies on their impact assessment, environmental viability and tolerance, few of them, especially F. oxysporum (WHK- 26, 106) may effectively reduce population growth of water hyacinth by themselves or in conjunction with other introduced biocontrol agents, including insects and other plant pathogens.

Strengthening the One Health Approach in the Eastern Mediterranean Region

One Health aims to use a multidisciplinary approach to combat health threats at animal, human, and environmental health interfaces. Among its broad focus areas are issues related to food safety, the control of zoonoses, laboratory services, neglected tropical diseases, environmental health, biosafety and biosecurity, and combatting antimicrobial resistance. A roundtable session was conducted on November 18, 2021, as part of the Eastern Mediterranean Public Health Network's (EMPHNET) seventh regional conference to highlight what role Global Health Development (GHD)|EMPHNET can play to strengthen the One Health approach. This viewpoint summarizes the findings of the roundtable discussion to highlight the experts' viewpoints on strengthening the One Health approach, including the extent of zoonotic diseases and the dynamics of pathogens and emerging diseases; the occurrence of antimicrobial-resistant pathogens as a silent pandemic; issues surrounding the globalization of trade and food safety; the importance of integrated solutions as a new norm; issues around the institutionalization and governance toward effective operationalization of the One Health approach in the region; and how the One Health approach can be operationalized at global, regional, and local levels. The panel concluded that One Health is an integrated unifying approach that aims to sustainably balance and optimize the health of people, animals, and ecosystems, and provided recommendations to strengthen the One Health approach. It also discussed how GHD|EMPHNET can play its role in transferring the concept of One Health from theory to practice via a solid operationalization road map guide at the Eastern Mediterranean region level. The five broad priority areas of this operational guide include (1) establishing and strengthening a governance architecture, legal framework, and policy and advocacy structure for One Health operationalization in the region; (2) fostering coordination, communication, and collaboration for One Health actions across the region and beyond; (3) building the workforce capacity for effective One Health operationalization in the region; (4) supporting regional platforms for timely, effective, and efficient data sharing and exchange on all One Health-related issues; and (5) supporting risk communication, behavior change communication, and community engagement efforts in the region.

Fine-Scale Landscape Epidemiology: Sarcoptic Mange in Bare-Nosed Wombats (Vombatus ursinus)

Landscape epidemiology provides a valuable framework to interpret, predict, and manage spatiotemporal patterns of disease. Yet, owing to the difficulty of detecting pathogen occurrence in free-ranging wildlife, disentangling the factors driving disease dynamics remains a considerable challenge, particularly at fine spatial scales. Here, we investigated the fine-scale landscape epidemiology of sarcoptic mange—a visually apparent disease caused by the mite Sarcoptes scabiei—in bare-nosed wombats (Vombatus ursinus), by: (1) characterizing the distribution and density of wombats within the landscape and (2) examining the effect of environmental variation on the occurrence and apparent prevalence of mange. Wombats were heterogeneously distributed over 19.4 km of transect space (0.096–1.39 wombats ha−1) and seven months of time (increasing by a factor of 1.76). Wombat density was negatively associated with distance to vegetation cover, supporting a general propensity for wombats to occur and burrow near vegetation (native and exotic, excluding pasture). The apparent prevalence of mange varied spatially (3.1–37.5%), with the probability of disease greater in wombats with minimal vegetation and low-lying pans in their estimated home range. We observed trends of increased prevalence in areas with more burrows available per wombat and in individuals occurring near vegetation cover (although not within their home range). Wombat density and active burrow density did not influence the prevalence of mange. This research emphasizes the fine scale at which spatiotemporal patterns of disease can manifest and is the first to investigate the influence of host density for any species with indirect transmission of S. scabiei. Collectively, our results suggest that individuals inhabiting less optimal habitat (pasture) may be at greater risk of disease, or that diseased wombats may be competitively excluded from more optimal habitat (vegetated areas). We discuss implications for understanding and managing mange in wombats and cross-applicability to other mange-affected species with environmental transmission.

Occurrence of antibiotic resistance genes and potentially pathogenic bacteria in the Yangtze River tributary (Nanjing section) and their correlation with environmental factors

Freshwater environments are vulnerable to emerging contaminants such as Antibiotic resistance genes (ARGs), and their occurrence is gaining more attention. However, the occurrence of ARGs along with potential pathogens is less explored. The current study aimed to evaluate the abundance of ARGs and explore bacterial communities for the presence of potential bacterial pathogens in water samples collected from a tributary to the Yangtze River in Nanjing. Twelve physico-chemical parameters were analyzed, followed by quantifying 10 ARGs targeting sulfonamide (sul1, sul2), tetracycline (tetG, tetM, tetQ), erythromycin (ermB), vancomycin (vanA, vanR), and streptomycin (strA, strB) using real-time PCR and bacterial diversity characterization using high-throughput 16 S rRNA sequencing. The results indicated poor water quality and high-level eutrophication in most sampling locations. sul1, sul2, and strB were dominant in the study area with average concentrations of 6.8, 7.1, and 6.5 Log10 gene copies/100 ml, respectively. Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria were the main phyla detected in the study area, and genus-level analysis revealed the presence of eight potential pathogenic and ten fecal-associated bacterial genera at several locations in the study area. The distance-based Redundancy analysis indicated that total phosphorus, electrical conductivity, dissolved oxygen, total dissolved solids, ammonium-N (NH4 +-N), and chlorophyll a had significantly influenced the bacterial community composition in the monitored locations. Correlation analysis demonstrated that water temperature, pH, NH4 +-N, and total organic carbon were positively correlated with sul2, tetG, and vanR genes, indicating that these environmental parameters significantly affected the ARGs distribution pattern. Overall, our results provide valuable information regarding the occurrence of ARGs and potential bacterial pathogens in the study area; however, their co-existence highlights increased human health risks.

The Soaring Increase of Resistant Microorganisms Demands Immediate Action Solutions are Available

Clinical environments provide an ideal reservoir for the growth, proliferation, and transmission of pathogenic organisms. Surfaces in hospitals e.g. hospital furniture, ECG lead wires and other cables, push buttons of infusion pumps, control knobs of ventilation machines, textiles as well as implantable biomaterials like central venous catheters, urologic catheters, endotracheal tubes are contaminated increasingly frequent with multiresistant microorganisms. These microorganisms are distributed by the hands of the nursing personnel throughout the hospital with serious, life threatening consequences. 1.8 million patients suffer from a nosocomial infection per year in Europe; approximately 180,000 deaths are attributed to these infections. The Centers for Disease Control (CDC) estimates that 2 million U.S. patients per year acquire a hospital-related infection. These infections cause 90,000 deaths each year and cost an average of $47,000 per patient to treat. The added cost to hospitals is $4.8 billion anually for extended care treatment. Microorganisms show an increasing rate of resistance against the majority of antibiotics including carbapenems as last available antibiotic. 700,000 deaths have been rеρorted worldwide, 30 000 deaths alone in Europe during the last year due to infections where no effective antimicrobial substance was available. The use of disinfectants is ostensibly intended to remove/kill pathogens on surfaces. However studies have shown that more than one-half the time, surfaces are not adequately cleaned or are re-contaminated within minutes. Much emphasis has been put therefore on hand disinfection. However there are also rеρorts of the emergence of alcohol tolerant/insensitive microorganisms e.g., vancomycin resistant enterococci. This phenomenon has the potential to undermine the effectiveness of alcohol based disinfectant standard precautions. The reason for this dramatic development of resistant microorganisms is still in debate. The indiscriminate use of antibiotics for prevention of a bacterial superinfections e.g. sinusitis, otitis media after a viral infections is frequently incriminated, however this seems to have little impact on the occurrence of multi-resistant hospital pathogens in general. However individual patients are seriously affected by the selection of multi-resistant pathogens. In contrast there is increasing evidence that the widespread use of disinfectants is responsible: disinfectants - analogous to antibiotics - must be incorporated into the metabolism of microorganisms. This is inevitably associated with induction of resistance by transfer of resistance plasmids e.g. induction of efflux pumps. 10 167 рublications (PUBMed Jan. 2023) are available in the international literature which document the resistance of microorganisms against disinfectants; 649 рublications describe the cross resistance with antibiotics, at the same time there are 11 237 publications on the toxicity of disinfectants.

Outcomes in Pediatric Central Line-associated Bloodstream Infections Treated With Antimicrobial Locks: A 14-Year Retrospective Analysis.

Central line-associated bloodstream infections (CLABSI) are the most common healthcare-associated infection in children. Antimicrobial lock therapy (ALT) is a recommended component of CLABSI treatment; however, studies characterizing pediatric ALT-based CLABSI therapy are few. All CLABSI treated with ALT at a single tertiary-care pediatric hospital for years 2004-2018 were identified by retrospective chart review and demographic, clinical, microbiological and pharmacy data were extracted. Three clinical outcomes were defined: CLABSI clearance, central venous catheter (CVC) removal and infection recurrence. Factors associated with these outcomes were examined and patterns in pathogen occurrence were described. During the study period, 1188 CLABSI treated with ALT were identified. In all, 969 (85%) CLABSI initially cleared. In the CLABSI with initial clearance, CVCs were retained a median of 63 days after infection onset, and 20% recurred. Skin-colonizing microbes ( Staphylococcus aureus , coagulase-negative Staphylococci) were more likely to produce monomicrobial infections, whereas bowel-colonizing microbes ( Escherichia coli , Enterococci) were more associated with polymicrobial infections. In a multivariate model, infection history, resistant pathogens and CVC type were strongly correlated with infection recurrence, whereas bone marrow transplant status, neutrophil count and line type were correlated with CVC removal. Optimal therapeutic approaches to pediatric CLABSI remain uncertain, including the utility of ALT. Prior reports of ALT use in children have been smaller in size and largely described hematology-oncology or hemodialysis populations. We describe trends in pediatric CLABSI, including efficacy among solid organ transplant recipients and children with short-gut syndrome. These data provide guidance on selecting CLABSI for optimal ALT use.

Incidence of Invasive Fungal Infections in Liver Transplant Recipients under Targeted Echinocandin Prophylaxis

Invasive fungal infections (IFIs) are one of the most important infectious complications after liver transplantation, determining morbidity and mortality. Antimycotic prophylaxis may impede IFI, but a consensus on indication, agent, or duration is still missing. Therefore, this study aimed to investigate the incidence of IFIs under targeted echinocandin antimycotic prophylaxis in adult high-risk liver transplant recipients. We retrospectively reviewed all patients undergoing a deceased donor liver transplantation at the Medical University of Innsbruck in the period from 2017 to 2020. Of 299 patients, 224 met the inclusion criteria. We defined patients as being at high risk for IFI if they had two or more prespecified risk factors and these patients received prophylaxis. In total, 85% (190/224) of the patients were correctly classified according to the developed algorithm, being able to predict an IFI with a sensitivity of 89%. Although 83% (90/109) so defined high-risk recipients received echinocandin prophylaxis, 21% (23/109) still developed an IFI. The multivariate analysis identified the age of the recipient (hazard ratio-HR = 0.97, p = 0.027), split liver transplantation (HR = 5.18, p = 0.014), massive intraoperative blood transfusion (HR = 24.08, p = 0.004), donor-derived infection (HR = 9.70, p < 0.001), and relaparotomy (HR = 4.62, p = 0.003) as variables with increased hazard ratios for an IFI within 90 days. The fungal colonization at baseline, high-urgency transplantation, posttransplant dialysis, bile leak, and early transplantation showed significance only in a univariate model. Notably, 57% (12/21) of the invasive Candida infections were caused by a non-albicans species, entailing a markedly reduced one-year survival. The attributable 90-day mortality rate of an IFI after a liver transplant was 53% (9/17). None of the patients with invasive aspergillosis survived. Despite targeted echinocandin prophylaxis, there is still a notable risk for IFI. Consequently, the prophylactic use of echinocandins must be critically questioned regarding the high rate of breakthrough infections, the increased occurrence of fluconazole-resistant pathogens, and the higher mortality rate in non-albicans Candida species. Adherence to the internal prophylaxis algorithms is of immense importance, bearing in mind the high IFI rates in case algorithms are not followed.

Research Progress in Superhydrophobic Titanium-Based Implants for Antibacterial Applications

Titanium and its alloys have been extensively used as implant materials in clinic settings. However, implant-associated bacterial infection or inflammation remains a primary cause of implantation failure, which threatens human health, and has already become a global issue. Recently, a superhydrophobic surface endowed with a water contact angle higher than 150° has attracted widespread attention in antibacterial applications for their self-cleaning and low-adhesion properties, which has emerged as an important path in preventing biofilm formation. This review first describes the basic theories of wettability. In the second section, we explain biofilm formation, which is a primary pathogenic occurrence in the development of infection in implants. In the last and most important section, we summarize the progress of superhydrophobic titanium-based implants and recent antibacterial applications. This review will attract great interest from both research scientists and clinicians, which will help to rapidly expand superhydrophobic titanium-based implants for antibacterial applications.

Low to Zero Concentrations of Airborne Bacterial Pathogens and Indicator E. coli in Proximity to Beef Cattle Feedlots in Imperial Valley, California.

This study characterized the effect of distance from beef cattle feedlots, environmental factors, and climate on the occurrence of airborne bacterial indicators and pathogens. Three hundred air samples were collected over 6 months from five feedlots, with each air sample comprising 6000 L of air. Air samples were processed onto TSB-enriched air filters, qPCR-screened, and then qPCR-confirmed for suspect positive colonies of E. coli O157, non-O157-Shiga-toxin-producing E. coli (STEC), Salmonella, and E. coli. Direct enumeration of E. coli was also collected. Although no bacterial pathogens were qPCR-confirmed for the 300 samples, E. coli was detected in 16.7% (50/300) of samples, with an overall mean concentration of 0.17 CFU/6000 L air. Logistic regression analyses revealed a higher odds of E. coli for samples in close proximity compared to >610 m (2000 ft) distance from feedlots, along with significant associations with meteorological factors, sampling hour of day, and the presence of a dust-generating activity such as plowing a field or nearby vehicular traffic. The lack of bacterial pathogen detection suggests airborne deposition from nearby feedlots may not be a significant mechanism of leafy green bacterial pathogen contamination; the result of our study provides data to inform future revisions of produce-safety guidance.

Prevalence of honey bee pathogens and parasites in South Korea: A five-year surveillance study from 2017 to 2021

Honey bees play an important role in the pollination of crops and wild plants and provide important products to humans. Pathogens and parasites are the main factors that threaten beekeeping in South Korea. Therefore, a nationwide detection of 14 honey bee pathogens, including parasites (phorid flies, Nosema ceranae, and Acarapis woodi mites), viruses, bacteria, and fungal pathogens, was conducted from 2017 to 2021 in the country. The infection rate and the trend of detection of each pathogenic agent were determined. A total of 830 honey bee samples from Apis cerana (n = 357) and A. mellifera (n = 473) were examined. N. ceranae (35.53%), deformed wing virus (52.63%), sacbrood virus (SBV) (52.63%), and black queen cell virus (55.26%) were the most prevalent honey bee pathogens, and their prevalence rapidly increased from 2017 to 2021. The prevalence of Paenibacillus larvae, Israeli acute paralysis virus, Ascosphaera apis, A. woodi, Melissococcus plutonius, and chronic bee paralysis virus remained stable during the surveillance period, with infection rates ranging from 5.26% to 16.45% in 2021. Other pathogens, including acute bee paralysis virus, phorid flies, Kashmir bee virus, and Aspergillus flavus, had low infection rates that gradually declined during the detection period. The occurrence of honeybee pathogens peaked in July. SBV was the most common pathogen in A. cerana, whereas N. ceranae was predominant in A. mellifera. This study provides information regarding the current status of honey bee pathogens and presents the trend of the occurrence of each pathogen in South Korea. These data are important for predicting outbreaks of honey bee diseases in the country.

Metagenomic analysis characterizes resistomes of an acidic, multimetal(loid)-enriched coal source mine drainage treatment system

Heavy metal(loid) contaminations caused by mine activities are potential hot spots of antibiotic resistance genes (ARGs) because of heavy metal(loid)-induced co-selection of ARGs and heavy metal(loid) resistance genes (MRGs). This study used high-throughput metagenomic sequencing to analyze the resistome characteristics of a coal source acid mine drainage passive treatment system. The multidrug efflux mechanism dominated the antibiotic resistome, and a highly diverse heavy metal(loid) resistome was dominated by mercury-, iron-, and arsenic--associated resistance. Correlation analysis indicated that mobile gene elements had a greater influence on the dynamic of MRGs than ARGs. Among the metagenome-assembled genomes, six potential pathogens carrying multiple resistance genes resistant to several antibiotics and heavy metal(loid)s were recovered. Pseudomonas spp. contained the highest numbers of resistance genes, with resistance to two types of antibiotics and 12 types of heavy metal(loid)s. Thus, high contents of heavy metal(loid)s drove the co-selection of ARGs and MRGs. The occurrence of potential pathogens containing multiple resistance genes might increase the risk of ARG dissemination in the environment.

Fungal trunk diseases of fruit trees in Europe: pathogens, spread and future directions

Production from crops of pome, stone fruit, nut, berry fruit, citrus, grapevine, and olive is increasingly threatened by fungal trunk diseases (FTD). These diseases and the consequent production losses are major problems. Many fungi (including Botryosphaeriaceae, Calosphaeriaceae, Diaporthaceae, Diatrypaceae, Nectriaceae, Phaeomoniellaceae, Pleosporaceae, Togniniaceae, Valsaceae) infect host wood, mainly through wounds and subsequent colonization of woody tissues, causing symptoms such as cankers, gummosis, wood rotting, blight and dieback. Propagative plant material, seedlings and fruit play a significant role in pathogen spread. Several abiotic factors (e.g. shifts in cultural practices and climate change) are involved in the disease development. This paper reviews recent literature on FTD of fruit crops, particularly focusing on the European status of pathogen occurrence. Case studies are described related to diseases of apple, citrus, grapevine, berry, nut and stone fruit, and olive trees. Aspects related to epidemiology and the increase in disease incidence along with the future perspectives on the FTD research are also discussed.

Health risk posed by direct ingestion of yeasts from polluted river water

River water is an essential human resource that may be contaminated with hazardous microorganisms. However, the risk of yeast infection through river water exposure is unclear because it is highly dependant on individual susceptibility and has therefore not been well-studied, to date. To evaluate this undefined risk, we analysed the fungal communities in less polluted (LP) and highly polluted (HP) river water, as determined using principal coordinate analysis of pollution indicators. We enumerated culturable yeasts using a thermally selective isolation procedure (37 °C) and thus promoted the growth of potentially opportunistic species. Yeast species identified as clinically relevant were then tested for antifungal resistance. In addition, we propose a quantitative microbial risk assessment (QMRA) framework to quantitatively assess the potential risk of yeast infection. Our results indicated that pollution levels significantly altered fungal communities (p = 0.007) and that genera representing opportunistic and pathogenic members were significantly more abundant in HP waters (p = 0.038). Additionally, the yeast species Candida glabrata and Clavispora lusitaniae positively correlated with other pollution indicators, demonstrating the species’ indicator potential. Our QMRA results further indicate that higher risk of infection is associated with increased water pollution levels (considering both physicochemical and bacterial indicators). Furthermore, yeast species with higher pathogenic potential present an increased risk of infection despite lower observed concentrations in the river water. Interestingly, the bloom of Meyerozyma guilliermondii during the wet season suggests that other environmental factors, such as dissolved oxygen levels and water turbulence, might affect growth characteristics of yeasts in river water, which consequently affects the distribution of annual infection risks. The presence of antifungal resistant yeasts, observed in this study, could further contribute to variation in risk distribution. Research on the ecophysiology of yeasts in these environments is therefore necessary to ameliorate the uncertainty and sensitivity of the proposed QMRA model. In addition to the vital knowledge on opportunistic and pathogenic yeast occurrence in river water and their observed association with pollution, this study provides valuable methods and insights to initiate future QMRAs of yeast infections.

Contemporary Evaluation of Tebipenem In Vitro Activity against Enterobacterales Clinical Isolates Causing Urinary Tract Infections in US Medical Centers (2019-2020).

Tebipenem pivoxil is an oral broad-spectrum carbapenem. This study evaluated the activity of tebipenem and comparators against UTI Enterobacterales from US hospitals (2019-2020). 3,576 Enterobacterales causing UTI in 52 centers in 9 US Census Divisions were included. Susceptibility testing followed the CLSI broth microdilution method. Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis with an MIC of ≥2 μg/mL for ceftazidime, ceftriaxone, and/or aztreonam were designated ESBL. Isolates were also grouped based on MDR phenotype. Tebipenem, meropenem, and ertapenem had MIC90 against Enterobacterales of 0.06 μg/mL, 0.06 μg/mL and 0.03 μg/mL, respectively. Low susceptibility results for aztreonam (87.1% susceptible), cefazidime (88.1%), ceftriaxone (84.8%), and other agents were observed. Tebipenem and ertapenem were equally potent (MIC90, 0.015 to 0.03 μg/mL) against E. coli and K. pneumoniae, whereas ertapenem showed an MIC 8-fold lower than tebipenem against P. mirabilis. Oral agents, such as amoxicillin-clavulanate, levofloxacin, and trimethoprim-sulfamethoxazole, showed elevated nonsusceptibility rates in the Middle Atlantic region (26, 45, 47, and 41%, respectively). ESBL prevalence varied from 7% to 16%, except in the Middle Atlantic region (42%). The carbapenems were active against ESBL and MDR isolates (93.7 to 96.8% susceptible). Elevated rates of ESBL in UTI pathogens in US hospitals were noted as well as a uniform in vitro potency (MIC90) of tebipenem and the intravenous carbapenems, regardless of phenotype. IMPORTANCE The occurrence of urinary-tract Enterobacterales pathogens producing ESBL enzymes in community and nosocomial settings continues to increase, as does the coresistance to fluoroquinolones, trimethoprim-sulfamethoxazole and nitrofurantoin often exhibited by these pathogens. This scenario complicates the clinical empirical and guided management of UTI by precluding the use of oral and many intravenous options. Oral options appear compromised even among some ESBL-negative isolates, against which the use of parenteral agents may be required. In addition, the interregional variability of susceptibility results of US UTI pathogens provides a less predictable susceptibility pattern to inform empirical treatment decisions. This study evaluated the in vitro activity of tebipenem against contemporary uropathogens, including those resistant to currently available oral options.