Risk Of Pathogens Research Articles

Preparing for future public health crises by fostering a conducive environment

Abstract Vaccination is considered one of the most cost-effective public health interventions. Zoonotic diseases, which are transmitted from animals to humans, represent an escalating global health concern. Environmental degradation, wildlife trade, and intensified farming practices have disrupted natural ecosystems. This has not only heightened the risk of pathogens crossing species barriers but exacerbated the migrant crisis and deepened global inequalities, as vulnerable populations disproportionally bear the environmental and health burdens. Despite decades of awareness about these risks, the COVID-19 pandemic highlighted our lack of preparedness. At the same time, vaccination hesitancy has been revealed as an important factor in implementing universal vaccination coverage at the population level. Urgency drove innovation. Within months, new multidisciplinary and interdisciplinary approaches were implemented that enhanced our capacity to understand, treat, and protect against the virus. This led to deploying novel technologies, curbing the crisis, and even opening the door to emerging health technologies across a wide spectrum of innovation, from new medicinal products, including vaccines, to evidence synthesis tools, including for modelling and forecasting. Shifting from emergency measures to long-term management of COVID-19, there lies a critical opportunity to strengthen resilience and to increase preparedness against future health threats. The EUVABECO project seeks to harness this momentum by initiating pilot projects that test innovative vaccination tools in evidence-based selected reference practices. These pilots are planned to use suitable theoretical frameworks and consensus meetings to design and develop comprehensive implementation plans that will be shared with EU MS, thereby enhancing Europe’s preparedness and response capabilities against communicable diseases.

Microbial Dynamics and Pathogen Control During Fermentation of Distiller Grains: Effects of Fermentation Time on Feed Safety

Determining the effects of fermentation duration on the microbial ecosystem, potential pathogenic risks, and metabolite generation during the fermentation of distilled grains is essential for safeguarding the safety and enhancing the nutritional profile of animal feed. This study investigates the effect of varying fermentation times (9, 30, and 60 days) on microbial diversity, pathogenic risk, and metabolite profiles in distiller grains using 16S rDNA sequencing and LC–MS-based metabolomics. The results showed that early fermentation (9–30 days) enhanced the abundance of beneficial bacteria, such as Lactobacillus reuteri and Lactobacillus pontis (p < 0.05), while pathogenic bacteria, like Serratia marcescens and Citrobacter freundii, were significantly reduced (p < 0.05). Metabolomic analysis revealed an increase in unsaturated fatty acids and the degradation of biogenic amines during early fermentation. However, prolonged fermentation (60 days) led to a resurgence of pathogenic bacteria and reduced the synthesis of essential metabolites. These findings suggest that fermentation duration must be optimized to balance microbial safety and nutrient quality, with 30 days being the optimal period to reduce pathogenic risks and enhance feed quality.

Assessing the pig microbial health impacts of smallholder farming

The livestock industry has long been a hotspot environment for antibiotic resistance genes, with smallholder farming still holding a significant position in pig farming. However, the microbial antibiotic resistance and pathogen risks in pigs under the smallholder farming model remain unclear. We systematically analyzed the antibiotic resistance and microbial composition of pig feces from smallholder and large-scale farming models in Sichuan. The results indicated a lower abundance of antibiotic resistance genes (ARGs) and similar microbial composition in smallholder farming compared to large-scale farming. Beneficial bacteria were more abundant in small-scale farming, whereas large-scale farming exhibited more ARGs, virulence genes, and human pathogenic bacteria (HPBs), including ESBL Escherichia coli strains closely related to human strains, indicating higher zoonotic risk. The findings suggest that smallholder farming presents a relatively better microbial composition and resistance profile, highlighting its advantages over large-scale farming in terms of pig and human health. It is noteworthy that a considerable proportion of HPBs carrying ARGs still exist in the feces from smallholder farming, and given the openness of fecal handling, there remains a high risk of transmitting ARGs and pathogens to humans.

Salmonella enterica virulence databases and bioinformatic analysis tools development

Salmonella enterica, a prominent foodborne pathogen, contributes significantly to global foodborne illnesses annually. This species exhibits significant genetic diversity, potentially impacting its infectivity, disease severity, and antimicrobial resistance. Whole genome sequencing (WGS) offers comprehensive genetic insights that can be utilized for virulence assessment. However, existing bioinformatic tools for studying Salmonella virulence have notable limitations. To address this gap, a Salmonella Virulence Database with a non-redundant, comprehensive list of putative virulence factors was constructed. Two bioinformatic analysis tools, Virulence Factor Profile Assessment and Virulence Factor Profile Comparison tools, were developed. The former provides data on similarity to the reference genes, e-value, and bite score, while the latter assesses the presence/absence of virulence genes in Salmonella isolates and facilitates comparison of virulence profiles across multiple sequences. To validate the database and associated bioinformatic tools, WGS data from 43,853 Salmonella isolates spanning 14 serovars was extracted from GenBank, and WGS data previously generated in our lab was used. Overall, the Salmonella Virulence database and our bioinformatic tools effectively facilitated virulence assessment, enhancing our understanding of virulence profiles among Salmonella isolates and serovars. The public availability of these resources will empower researchers to assess Salmonella virulence comprehensively, which could inform strategies for pathogen control and risk evaluations associated with human illnesses.

Genotypic characterization of β-lactamase resistant Salmonella species isolated from different quail houses and their susceptibility to extracts of thyme and chitosan, and Saccharomyces Cerevisiae

ABSTRACT This study aimed to identify Salmonella species in two systems for quail raising (deep litter system and cages system). Determination of antibiotic susceptibility, β-lactamase resistance genes profile and susceptibility to chitosan, thyme extract and S. cerevisiae was examined. Fifteen Salmonella isolates were isolated from eighty cloacal swabs examined, with a higher incidence from those of deep litter systems than cage housing systems. Regarding the environmental samples, Salmonella was higher in the deep litter system than in cage housing. Serological identification of 27 salmonella isolates typed them into 8 Salmonella spp. including S. Tsevie, S. Infantis, S. Kentucky, S. Typhimurium, S. Larochelle, S. Molade, S. Enteritidis and S. Labadi. The profile of β-lactamase-resistance genes revealed the presence of blaTEM and blaSHV genes in S. Typhimurium and S. Infantis; blaTEM and blaCTX-M1 genes in S. Enteritidis and S. Molade, while S. Kentucky and S. Tsevie were positive for the blaCTX-M1 gene only. S. Larochelle was negative for all of them. Thyme and chitosan extract showed that S. cerevisiae had the highest inhibitory activity against the tested strains. In conclusion, farms with superior biosecurity and hygiene practices will reduce the risk of pathogens and eliminate the need for prophylactic antibiotics, thereby preventing antibiotic resistance.

Hidden pathogen risk in mature compost: Low optimal growth temperature confers pathogen survival and activity during manure composting

Livestock manure is a major reservoir for pathogens, posing significant environmental risks if used untreated. The efficacy of composting in fully inactivating pathogens remains controversial, particularly regarding the influence of their optimal growth temperature (OGT). This study investigated the composition and dynamic changes of pathogen communities and virulence factors (VFs) during the composting of chicken, bovine, ovine, and swine manure. We identified 134 pathogens across 16 composting piles, with ten pathogens exhibited increased abundance and transcriptional activity in curing phase. They included high-risk VFs-carrying pathogens, such as Mycolicibacterium thermoresistibile and Mycolicibacterium phlei, indicating the hidden pathogen risk in mature compost. Community-scale analyses revealed a linkage of these pathogens’ survival with their low OGT and an increased number of heat shock proteins (HSPs), enabling them to tolerate high temperatures and regrow. Integrating our data with prior composting studies, we found that the surviving pathogens express 42 VFs and their persistence in mature compost was a widespread issue, highlighting a greater risk of pathogen spread than previously thought. Finally, we compiled the 134 pathogens and 1009 VFs into a comprehensive Environmental Risk of Compost Pathogens (ERCP) catalog, providing a valuable resource for routine pathogen surveillance.

Plastic Polymers and Antibiotic Resistance in an Antarctic Environment (Ross Sea): Are We Revealing the Tip of an Iceberg?

Microbial colonization of plastic polymers in Antarctic environments is an under-investigated issue. While several studies are documenting the spread of plastic pollution in the Ross Sea, whether the formation of a plastisphere (namely the complex microbial assemblage colonizing plastics) may favor the spread of antibiotic-resistant bacteria (ARB) in this marine environment is unknown yet. A colonization experiment was performed in this ecosystem, aiming at exploring the potential role of plastic polymers as a reservoir of antibiotic resistance. To this end, the biofilm-producing activity and the antibiotic susceptibility profiles of bacterial strains isolated from biofilms colonizing submerged polyvinylchloride and polyethylene panels were screened. The colonization experiment was carried out at two different sites of the Ross Sea, namely Road Bay and Tethys Bay. Most of bacterial isolates were able to produce biofilm; several multidrug resistances were detected in the bacterial members of biofilms associated to PVC and PE (also named as the plastisphere), as well as in the bacterial strains isolated from the surrounding water. The lowest percentage of ARB was found in the PE-associated plastisphere from the not-impacted (control) Punta Stocchino station, whereas the highest one was detected in the PVC-associated plastisphere from the Tethys Bay station. However, no selective enrichment of ARB in relation to the study sites or to either type of plastic material was observed, suggesting that resistance to antibiotics was a generalized widespread phenomenon. Resistance against to all the three classes of antibiotics assayed in this study (i.e., cell wall antibiotics, nucleic acids, and protein synthesis inhibitors) was observed. The high percentage of bacterial isolates showing resistance in remote environments like Antarctic ones, suffering increasing anthropic pressure, points out an emerging threat with a potential pathogenic risk that needs further deepening studies.

Domesticating the wild through escapees of two iconic mediterranean farmed fish species

Extractive fisheries and marine aquaculture share space and target species. Several regional-scale examples exist of escapees entering wild fisheries landings, yet no study has assessed the influence of aquaculture on landings at an ecosystem scale. We examined the effects of farmed fish escapes on fisheries using FAO data and published escape rates for Gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax). Seabream landings were significantly correlated with the estimated biomass of escaped seabream entering the wild. There was a similar pattern for seabass until 2005, but the overall relationship between landings and escapes was not significant due to the dramatic drop in catches in recent years. We argue that seabass escapees’ relatively high mortality, lower capturability, and minor ‘leaking’ from farms may obscure their influence on landings. Significant positive fisheries regime shifts were detected for both species, matching the onset of aquaculture in the Mediterranean and the period when escapees from aquaculture surpassed landings. Our results suggest that fish escapes of these two iconic species may mask wild stock overexploitation, confound stock assessments, alter genetic diversity, increase the risk of spreading pathogens and parasites, and compete with wild conspecifics while boosting fisheries landings.

Enrichment Characteristics and Ecological Risk Prediction of Pathogens on Typical Microplastic Biofilms

As an emerging niche colonized by microorganisms, microplastics may selectively enrich pathogens, resulting in crucial ecological risks and potential threats to public health in aquatic environments. However, the enrichment characteristics and ecological risks of pathogens on different microplastic biofilms remain unclear. In this study, 16S rRNA high-throughput sequencing technology was used to investigate the differences in the bacterial community structure, occurrence characteristics of pathogens, and prediction of ecological risks on five typical microplastic biofilms of polyethylene （PE）, polypropylene （PP）, polystyrene （PS）, polyethylene terephthalate （PET）, and polyvinyl chloride （PVC） through a field in-situ incubation experiment. The results showed that after 28 d of in situ incubation, the macroscopic biofilms were formed on the surface of all microplastics, and the diversity and richness of the bacterial community on all microplastic biofilms were higher than in the surrounding water, indicating that the microorganisms in the surrounding water were selectively enriched on microplastics. Each type of microplastic biofilm had formed a unique bacterial community structure； in particular, PVC microplastics were more inclined to selectively enrich the members of Proteobacteria. A total of 47 human pathogens were identified using the HPB database, including six antibiotic resistance pathogens belonging to the lists of critical priority control. The number and total abundance of human pathogens detected on microplastic biofilm were higher than those in the surrounding water, and the dominant pathogens such as Bartonella, Burkholderia, and Brucella were selectively enriched on microplastic biofilms. Microbial phenotype prediction results based on BugBase showed that three functional phenotypes including biofilm formation, mobile element contained, and potentially pathogenic on microplastic biofilms had significantly increased by 2.38%-5.57%, 0.82%-7.13%, and 3.04%-8.30%, respectively, which were mainly contributed by α-Proteobacteria and γ-Proteobacteria. These results not only indicate that the selective enrichment of opportunistic pathogens on microplastic biofilms may lead to the increased risk of pathogenicity and antibiotic resistance co-spread but also provide reference for the accurate assessment of ecological risks caused by microplastic pollution in aquatic environments.

Microbial community characteristics and pathogens detection in Rhipicephalus sanguineus and Haemaphysalis hystricis from Hainan Island, China.

Microbial communities significantly influence the vector capacity of ticks, which, along with tick-borne diseases, pose an increasing global threat. Due to the substantial individual variability caused by various factors, it is essential to assess tick microbial communities and vectorial capacities under different environmental conditions. However, there is a relative scarcity of research on the microbial communities and pathogen transmission of ticks in different physiological states and environmental conditions, especially in Hainan Island, southern China. From 2021 to 2022, we collected 4,167 tick samples, grouping them by blood meal status, developmental stage, sex, time, geographical location, and tick species. We selected 128 samples for full-length 16S rRNA sequencing to describe microbial community characteristics and identify potential biomarkers. Seven hundred seventy-two samples were tested for seven tick-borne pathogens (Rickettsia, Borrelia burgdorferi, Ehrlichia, Anaplasma, Theileria, Babesia, and Hepatozoon), and sera from 208 residents of Hainan Island were tested for IgG antibodies against Rickettsia and B. burgdorferi. Blood meal status, developmental stage, sex, time, geographical location, and tick species significantly influenced the microbial communities of ticks. We observed distinct microbial community characteristics across different states. We noted the non-random replacement of stable and transient species, with functional differences between parasitic and engorged ticks mainly driven by transient species. Functionally, we observed three distinct response patterns: driven by stable species, transient species, and both together in response to the six factors. We identified 273 potential biomarkers (200 robust core species and 73 robust differential species). Six genera and eight species of pathogens were detected in ticks, with an overall positivity rate of 12.44% (96/772). Among humans, 18.27% (38/208) of serum samples were positive for at least one tick-borne pathogen IgG. Our findings indicate that these six factors significantly influence both tick microbial communities and vectorial capacity, with varying effects on vector competence for different pathogens and inconsistent impacts on microbial communities under different conditions. This study supplemented the understanding of tick microbial communities on Hainan Island, assessed the relatively high risk of tick-borne pathogens in the region, and evaluated the impact of these factors on both microbial communities and vectorial capacity.

A new protein source for pet food: cultivated meat

Cultivated meat is an alternative protein source developed to address the sustainability, public health and animal welfare concerns of conventional meat production. Hundreds of startups and academic institutions worldwide are working to make cultivated meat a cost-effective protein source for humans. However, cultivated meat could also be used to feed dogs and cats, contributing to solving the meat supply issues that the growing pet food market has been facing in recent years. The advantages of using cultivated meat as a protein source for pets would include a reduction of the environmental impact of pets' diets, decreased farm animal suffering and several benefits in the One Health framework, as cultivated meat-based pet food would significantly decrease the risk of spreading food safety pathogens, zoonotic diseases and resistant bacteria. The antibiotic-free manufacturing process and the aseptic conditions the cells require to grow in the bioreactors lead to these public health advantages. However, cultivated meat has never been produced at scale for human or pet consumption. Several technical challenges need to be overcome to make cultivated meat-based pet food prices accessible to consumers. As a novel ingredient, there is also no evidence of the effect of feeding cultivated meat to dogs and cats. In principle, cultivated meat can be both safe to be consumed long-term and nutritionally adequate – and with several possibilities for nutritional enhancement, potentially even superior to its conventional counterpart. However, the safety and nutritional soundness of cultivated meat-based products must be demonstrated by manufacturers to gain regulatory approval and favour consumer adoption. Veterinarians, veterinary nurses and technicians will play a critical role in the development of this new ingredient in many aspects, including product development, assessing safety and nutrition, conducting research and informing consumers. This review summarises the benefits and challenges of using cultivated meat as a pet food ingredient.

Advancing Zebrafish Husbandry: Takeaways From the 2024 Husbandry Workshop and Husbandry Summit.

The 2024 Zebrafish Husbandry Workshop and Summit held during the World Aquaculture Society Meeting in San Antonio focused on key areas for improving zebrafish husbandry research. Discussions highlighted the need for comprehensive literature on husbandry, better communication and collaboration between researchers and facility staff, and the adoption of a standardized reference diet. Current literature lacks comprehensive data and often overlooks crucial factors such as housing density and space requirements for fish development. Collaborative efforts between researchers and facility managers are essential for acquiring accurate husbandry data and minimizing pathogen risks. Standardizing descriptive language and parameter lists in publications and enhancing communication between facilities can improve research quality. Action items proposed include better communication of incoming fish information, standardization of pathogen monitors, transparency in husbandry practices, and fostering a spirit of collaboration among organizations. The summit emphasized the importance of increased PI awareness about husbandry, testing existing standardized diets, forming consortia to oversee diet standardization, creating unified repositories and forums, and conducting evidence-based husbandry studies.

A Review of Pathogen Removal from Municipal Wastewater using Advanced Oxidation Processes: Agricultural Application, Regrowth Risks, and New Perspectives

Pathogen removal in wastewater offers a chance to recover water and nutrients for crop production, reducing environmental contamination and public health risks. However, the risk of pathogens regrowing in treated effluents can endanger public health if reused in agriculture, attracting stringent reuse standards. While advanced oxidation processes (AOPs) promise to reduce pathogens, eliminating regrowth potential in AOP-treated effluents requires further scrutiny. This review aimed to summarize the available evidence on understanding pathogen reduction and regrowth potential in AOP-treated effluents, following best practices for scoping reviews like the preferred reporting items for systematic reviews and meta-analysis (PRISMA). It covers recent pathogen studies under AOPs, current AOP investigations, the impact of AOP dosage and retention time on pathogen control, and challenges in reusing AOP-treated effluents for crop production. Additionally, it identifies areas needing improvement or complementary treatments for pathogen-free effluents with no regrowth potential. The review concludes by summarizing key findings and suggesting research areas for further exploration.

Analysis of pathogenic bacteria and risk factors of neonatal ventilator-associated pneumonia

Analysis of pathogenic bacteria and risk factors of neonatal ventilator-associated pneumonia

Microbiota profile in organs of the horseflies (Diptera: Tabanidae) in Northeastern China.

Tabanids, commonly known as horseflies and belonging to the family Tabanidae, are blood-feeding arthropods (BFA) found worldwide. They are known for their ability to mechanically and biologically transmit various animal pathogens. Tabanids are potential vectors for diseases such as Francisella tularensis, Anaplasma marginale, Theileria spp., and contributors to lumpy skin diseases. Despite their involvement in common BFA studies, tabanids have not been extensively explored in microbiome research. In this study, the microbiota structure and composition in various organs of four distinct genera of tabanids: Atylotus, Haematopota, Tabanus, and Hybomitra were examined. High-throughput sequencing of the bacterial 16S rRNA gene was performed to gain insights into the microbial communities associated with the different tabanid species. Result display that microbiota composition and diversity, including Firmicutes, Proteobacteria, and Bacteroidetes, varied significantly among the different organs, with the ovaries exhibiting significantly higher diversity. Apart from the Haematopota genus, Tenericutes were enriched in the midgut of other tabanid species, whereas the Malpighian tubules exhibited a higher abundance of Bacteroides. Notably, the ovarian microbiota structure was conserved among the four tabanid species, indicating its potential association with reproductive development. Evaluation of the potential pathogen risk revealed putative pathogens in over 100 genera associated with these tabanid commensal organisms. Twenty genera were annotated as zoonotic agents with a high abundance of Citrobacter and Brucella, highlighting the presence of this important group of zoonotic pathogens. Functional predictions of vector-microbiota interactions indicate that microbiota significantly affects vector biological traits and can influence pathogen transmission via direct interactions or by regulating host immunity and nutrition. For the first time, the distribution characteristics and functions of four genera of horsefly microbiota were analyzed, revealing the presence of multiple potential pathogenic microorganisms. These findings provide valuable insights for future research and the development of symbiotic-based strategies to control insect-borne diseases among tabanids.

Relating Wildlife Camera Trap Data to Tick Abundance: Testing the Relationship in Different Habitats.

The increase in acarological risk of tick bites is significantly driven by profound changes in landscape, which alter the density and distribution of wildlife that support tick populations. As a result of habitat shifts and land abandonment, which create environments conducive to tick proliferation, the risk of disease transmission to humans and animals is increasing. In this context, it is important to explore tick ecology by applying a comprehensive methodology. In this study, we examined the relationship between wildlife temporal occupancy and tick abundance in two distinct regions: an alpine hunting district and a natural park in the Apennines. For each sampling point, we calculated wildlife temporal occupancy from camera trap pictures and estimated ticks' abundance from dragging transects in the area immediately surrounding camera traps. In modelling the relationship between those two variables, we included abiotic factors such as saturation deficit, normalized difference vegetation index, and altitude. Results show the importance of altitude and wildlife temporal occupancy (itself related to different habitat and land management characteristics) on the ecology of questing ticks. If employed in management decisions for natural environments, such information is useful to modulate the acarological risk and thus the risk of tick-borne pathogens' transmission.

Survey of the invasive alien pink salmon (Oncorhynchus gorbuscha) for infective agents in the Fennoscandian Rivers Tana and Neiden

Pink salmon (Oncorhynchus gorbuscha, Walbaum 1792) is an invasive alien species in the Fennoscandian rivers, and its growing populations cause concern for their impact on the native salmonids and river ecosystems. One of the major concerns is fish diseases and the potential ability of pink salmon to transmit pathogens to the native salmonid species. In this study, pink salmon were sampled during their spawning migration in the Rivers Tana and Neiden in northern Norway and Finland in 2021. The fish were surveyed for viral hemorrhagic septicemia virus (VHSV), infectious pancreatic necrosis virus (IPNV), infectious salmon anemia virus (ISAV), salmonid alphavirus (SAV), piscine orthoreovirus (PRV), Renibacterium salmoninarum, and Gyrodactylus salaris. No viral diseases or infections with R. salmoninarum or G. salaris were detected. However, 23 % of the fish were found infected with a parasitic roundworm, Hysterothylacium aduncum. Additionally, external anomalies, such as hemorrhages or lesions in the skin, were observed in 35 % of the fish studied, and some of the fish exhibited degenerative myopathy. Based on this study, pink salmon appears not to pose a high infection risk to the native salmonid fish populations in the Rivers Tana and Neiden. Nevertheless, the results demonstrate that pink salmon have the potential to carry salmonid pathogens. More information on the susceptibility of pink salmon to different pathogens and on the overall effect this invasive species has on native fish species is needed. As the number of migrating pink salmon in the Fennoscandian rivers appears to increase, the potential risk of parasites and other pathogens spreading between fish species will also rise.

Extreme trophic tales: deciphering bacterial diversity and potential functions in oligotrophic and hypereutrophic lakes

BackgroundOligotrophy and hypereutrophy represent the two extremes of lake trophic states, and understanding the distribution of bacterial communities across these contrasting conditions is crucial for advancing aquatic microbial research. Despite the significance of these extreme trophic states, bacterial community characteristics and co-occurrence patterns in such environments have been scarcely interpreted. To bridge this knowledge gap, we collected 60 water samples from Lake Fuxian (oligotrophic) and Lake Xingyun (hypereutrophic) during different hydrological periods.ResultsEmploying 16S rRNA gene sequencing, our findings revealed distinct community structures and metabolic potentials in bacterial communities of hypereutrophic and oligotrophic lake ecosystems. The hypereutrophic ecosystem exhibited higher bacterial α- and β-diversity compared to the oligotrophic ecosystem. Actinobacteria dominated the oligotrophic Lake Fuxian, while Cyanobacteria, Proteobacteria, and Bacteroidetes were more prevalent in the hypereutrophic Lake Xingyun. Functions associated with methanol oxidation, methylotrophy, fermentation, aromatic compound degradation, nitrogen/nitrate respiration, and nitrogen/nitrate denitrification were enriched in the oligotrophic lake, underscoring the vital role of bacteria in carbon and nitrogen cycling. In contrast, functions related to ureolysis, human pathogens, animal parasites or symbionts, and phototrophy were enriched in the hypereutrophic lake, highlighting human activity-related disturbances and potential pathogenic risks. Co-occurrence network analysis unveiled a more complex and stable bacterial network in the hypereutrophic lake compared to the oligotrophic lake.ConclusionOur study provides insights into the intricate relationships between trophic states and bacterial community structure, emphasizing significant differences in diversity, community composition, and network characteristics between extreme states of oligotrophy and hypereutrophy. Additionally, it explores the nuanced responses of bacterial communities to environmental conditions in these two contrasting trophic states.

Pathogenic organism and risk factors of infection after acute ischemic stroke during the COVID-19 pandemic

This study aims to determine the pathogen organisms’ profile and risk factors for infection after acute ischemic stroke (AIS) during the COVID-19 pandemic because of few studies. We conducted a retrospective cross-sectional study using the medical records of AIS inpatients at the National Brain Center Hospital Prof. Dr. dr. Mahar Mardjono, Jakarta, Indonesia, from 2020-2021. We found the species of pathogen organisms based on the positive growth of microbiological cultures of various specimens. Among 479 AIS patients, the infection prevalence was 12.3%. This study found the common pathogenic organisms were Gram-negative bacteria, and there were drug-resistant strains in <i>S. aureus, S. epidermidis, K. pneumoniae,</i> and <i>E. coli. </i>The risk factors for infection in COVID-19-infected patients were pneumonia (OR 6.89, 95% CI 1.49-31.79, <i>p </i>= 0.013) and intensive care stay (OR 0.13, 95% CI 0.05-0.36, <i>p </i>< 0.001); meanwhile, in non-COVID-19 patients were HIV comorbidity (OR 1.55, 95% CI 1.18-2.06, <i>p </i>= 0.002), leukocytosis (OR 0.07, 95% CI 0.01-0.43, <i>p </i>= 0.004), use of CVC (OR 0.29, 95% CI 0.12-0.68, <i>p </i>= 0.005), use of steroids (OR 0.21, 95% CI 0.06-0.70, <i>p </i>= 0.011), and tracheostomy (OR 0.17, 95% CI 0.05-0.62, <i>p </i>= 0.007). To sum up, the growth of pathogenic organisms indicated that the prevalence of infections after AIS during the COVID-19 pandemic did not increase. The risk factor for infections depends on the characteristics of patients, whether they have COVID-19 or have not been infected.

Nosocomial pneumonia

Nosocomial pneumonia is defined as pneumonia occurring ≥ 48 h after hospital admission in apatient without severe immunosuppression. It can occur in spontaneously breathing patients or with noninvasive ventilation (NIV) and mechanically ventilated patients. In patients with suspected ventilator-associated pneumonia (VAP) (semi)quantitative cultures of tracheobronchial aspirates or bronchoalveolar lavage fluid should be perfomed. The initial empirical antimicrobial treatment is determined by the risk for multidrug-resistant pathogens (MDRP). The advantage of combination treatment increases with the prevalence of MDRPs. The antibiotic treatment should be adapted when the microbiological results are available. After 72 h astandardized re-evaluation including the response to treatment and also checking of the suspected diagnosis of pneumonia in astructured form is mandatory. Treatment failure can occur as aprimary or secondary failure and in the case of primary progression necessitates another comprehensive diagnostic work-up before any further antibiotic treatment.