Infectious Disease Pathogens Research Articles

P-602. Examining the Performance of Novel Vaccines in Large Vaccine Efficacy Trials (1995-2019)

Abstract Background Vaccines are widely recognized as one of the most effective health interventions in the world. The development of novel vaccines against the world’s deadliest diseases is a global health priority. Large, randomized clinical trials are the main mechanism used to determine the efficacy of a vaccine prior to licensure. These trials are expensive and resource intensive. Given the public health importance of these trials, understanding how often they succeed vs. fail and which pathogens they are targeting is paramount to global vaccine programs. Vaccine efficacy estimates for large vaccine clinical trials against novel pathogens Vaccine efficacy Definitions: highly efficacious (lower bound vaccine efficacy 95% confidence interval ≥65%), moderately efficacious (lower bound vaccine efficacy 95% confidence interval 10-65%), possibly efficacious: lower bound of any of the 95% confidence intervals were 0-10%, and not efficacious: lower bound of any of the 95% confidence intervals were <0. Abbreviations: Enterovirus 71 (EV71), Human Papilloma Virus (HPV), Respiratory Syncytial Virus (RSV), Cytomegalovirus (CMV), Human Immunodeficiency Virus (HIV), and Herpes Simplex Virus (HSV). Methods We searched Pubmed and the International Clinical Trials Registry Platform and identified large (≥ 1000 participants), randomized, vaccine efficacy trials completed between 1995-2019 against infectious disease pathogens for which no efficacious vaccine previously existed. Summary of characteristics of large vaccine efficacy trials: Distribution by journal of publication, funding source, and pathogen Results Using the search criteria above, 3483 unique trials were identified in the International Clinical Trials Registry Platform (ICTRP) and 1867 unique citations were identified through Pubmed for a total of 5350 unique entries. During the study period, 43 trials were identified which evaluated vaccines against 18 novel pathogens. Highly efficacious vaccines were developed against EV71, Hepatitis E, and HPV (Figure 1). Moderately efficacious vaccines were developed against Dengue, H. pylori, Malaria, and RSV. A possibly efficacious vaccine was developed against Tuberculosis. Vaccine candidates against ten other novel pathogens failed: C. difficile, CMV, E. coli, HIV, HSV, Leishmania, Norovirus, Shigella, Staph aureus, and Zika. We summarized trial characteristics by journal of publication, funding type, and pathogen (Figure 2). We also performed an exploratory analysis to investigate which studies might have been underpowered and found that the trials for vaccine candidates against Norovirus and Zikavirus were possibly underpowered (Figure 3). Exploratory sub-analysis conducted to identify trials that were possibly underpowered Panel A: Trials in the upper left quadrant represent trials with high efficacy but a significantly lower than expected incidence (compared to the pre-trial estimated incidence that was used to determine the sample size needed to have sufficient power to prove efficacy). Panel B: Vaccine trials are sorted by efficacy estimate, demonstrating that there were some trials that had a high efficacy estimate but wide confidence intervals which might indicate underpowering. Conclusion The past quarter century has seen both major successes in new vaccine development and failures. The HPV vaccine has been deployed around the world and is expected to save millions of lives. The malaria vaccine became the first effective vaccine licensed against a parasite. However, many promising candidates failed. Continued efforts to predict efficacy prior to large efficacy trials are needed. Disclosures Lawrence Corey, MD, NA: HSV Antigens|The Vaccine Company: Ownership Interest|Vir Biotechnology: Ownership Interest Peter B. Gilbert, PhD, Sanofi: Advisor/Consultant|Sanofi: Dengue Vaccine research contracts

Recent developments in isothermal amplification technology for rapid detection of SARS-CoV-2.

Coronavirus disease 2019 (COVID-19), an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally, posing a significant threat to human health. Rapid and accurate detection of infectious disease pathogens is of crucial practical significance for early screening, timely intervention, and outbreak prevention. However, conventional diagnostic methods are increasingly unable to meet clinical demands. Recently developed isothermal analysis methods offer mild reaction conditions and reduce dependence on specialized instruments. These convenient, fast, and reliable methods show great promise for diagnosing infectious pathogens, especially for on-site detection in areas without laboratories or with limited resources. Among them, loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), which integrate various widely used detection techniques, stand out as rapidly advancing and relatively mature isothermal nucleic acid amplification technologies. This review outlines several representative isothermal amplification technologies and associated detection methods. We summarize the latest advancements in LAMP and RPA technologies for the rapid detection of SARS-CoV-2 and discuss the future prospects of isothermal amplification in diversified testing.

Biofilm as a supracellular organization of pathogenic bacteria

The high frequency of resistance to antibiotics among bacterial clinical isolates necessitates the discovery of new targets for suppressing the pathogenicity of microbes without stimulating their resistance. The studied sources suggest that this can be achieved by targeting the determinants of virulence. The search for new active substances with anti-biofilm activity based on the analysis of literature data on the structure of bacterial biofilms, mechanisms of their resistance to antimicrobial agents was the purpose of this work. An electronic search was conducted in Medline (PubMed interface), Scopus, and Web of Science between 2011 and July, 2024 using the keywords: biofilms, antibiotic resistance, Quorum sensing, persisters. 30 sources were selected, 85 were processed. The subject of the search was: microbial landscape of hospital strains of microorganisms, biofilm formation by microorganisms – pathogens of infectious diseases, regulation of virulence factors in bacterial biofilm. Studies of recent years have established that many pathogenic bacteria produce signal molecules for cellular communication. This signaling system is called Quorum sensing (QS) and it depends on the density of the bacterial population and is mediated by signaling molecules called pheromones or autoinducers (AI). Bacteria use QS to regulate activities and behavior including competence, conjugation, symbiosis, virulence, motility, sporulation, antibiotic production and biofilm formation. Researches aimed at bacterial communicative signals and suppressing QS demonstrate a fundamental approach to forming competitive microbial communication. The search, synthesis, and development of drugs based on modified autoinducers of various natures can lead to a breakthrough in the field of antibacterial therapy of infectious diseases, as well as surgical purulent postoperative complications. The pro­cessed literature describes a number of hypotheses regarding the participation of "toxin-antitoxin" systems that control the growth and metabolism of bacteria in the stimulation of the formation of persister cells. The simultaneous acquisition of resistance to many antibacterial factors, including physico-chemical ones, is suggested. Therefore, there is an increased attention of scientists to the study of the anti-biofilm effect of new compounds and drugs capable of influencing energy or metabolic processes in cells, as well as substances that do not require a metabolically active target. The review illustrates general modern approaches to the use of QS chains in pathogenic bacteria as new therapeutic targets.

Multicenter study on the detection of pathogens in primary infectious diseases of the spine using metagenomic next-generation sequencing technology

Objective: To explore the role of metagenomic next-generation sequencing (mNGS) in the diagnosis of pathogens in primary infectious diseases of the spine (IDS) and to reveal its pathogen spectrum. Methods: This is a retrospective multi-center case series study. Clinical data of 380 patients with primary IDS who were treated at four medical centers in China from December 2019 to April 2024 were retrospectively analyzed. Among them, 82 cases were from the Department of Spine Surgery at the Affiliated Hospital of Qingdao University, 129 cases were from the Orthopedics Section Ⅱ (Bone Infection), Public Health Clinical Center Affiliated to Shandong University, 112 cases were from the Department of Spine Surgery, Fuzhou Second General Hospital, and 57 cases were from the Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine. There were 238 males and 242 females, with an age of (61.4±13.1) years (range: 10 to 91 years). Specimens from the site of spinal infection were obtained for pathogen culture, pathological examination, and mNGS detection preoperatively or intraoperatively in all patients. The number, types, and positive rates of pathogens detected by the two methods were analyzed and compared using the Chi-square test. Results: Among the 380 patients, 320 had confirmed pathogenic bacteria, with the highest proportion being pyogenic bacterial infections, accounting for 76.9% (246/320). The most common pathogen was Staphylococcus aureus, accounting for 22.8% (73/320). Brucella accounted for 13.8% (44/320); Mycobacterium tuberculosis accounted for 6.3% (20/320). Fungal infections accounted for 3.4% (11/320), mainly Aspergillus and Candida. In addition, Mycoplasma was detected in 3 cases (0.9%) and Benacox body in 4 cases (1.2%). The pathogen spectrum constructed by mNGS covered 46 types of pathogens, higher than the 22 types detected by traditional methods. The positive rate of mNGS was 80.8% (308/381), significantly higher than the 27.9% (106/381) of traditional methods (χ2=182.53, P<0.01). Conclusions: mNGS improves the positive rate of pathogen diagnosis in IDS, detecting a broader spectrum of pathogens, and serves as a valuable complement to traditional diagnostic methods. Combining both methods in the diagnosis of IDS can maximize detection rates, providing robust evidence for precise anti-infective treatment.

Global trends in the application of droplet digital PCR technology in the field of infectious disease pathogen diagnosis: A bibliometric analysis from 2012 to 2023

BackgroundThis study discusses the development trends and current applications of digital droplet PCR technology in pathogen diagnostics. MethodsA bibliometric analysis was conducted by retrieving droplet digital pcr related articles published between January 1,2012 to December31, 2023, from the Web of Science Core Collection. ResultsA total of 3,513 authors from 66 countries published 508 research papers across 203 academic institutions. The keyword clustering network shows that the main advantages of ddPCR are absolute quantification, high sensitivity, and high tolerance to PCR inhibitors. The keyword timeline shows that current research hotspots include continuous pathogen nucleic acid monitoring, trace sample detection, and resistance mutation identification. ConclusionThe application of ddPCR in pathogen diagnosis is expanding, offering key advantages in absolute quantification, high sensitivity, and inhibitor tolerance, meeting emerging needs in nucleic acid monitoring and resistance detection.

Metagenomic next-generation sequencing of osteoarticular tissue for the diagnosis of suspected osteoarticular tuberculosis.

In the detection of unknown infectious disease pathogens, the overall efficacy of traditional detection methods, such as culture, is low, and traditional PCR testing is also limited to the gene sequences of known pathogenic microorganisms. Metagenomic next-generation sequencing (mNGS) performs DNA sequencing by studying the entire microbial community genome in a given sample, without the need for isolation and culture. Previous studies have shown that mNGS performs better on pulmonary and extrapulmonary samples when compared with Xpert, traditional pathogenetic tests, and even parallel diagnostics. However, it should be emphasized that only a few studies have explored the performance of mNGS in detecting Mycobacterium tuberculosis in clinical samples associated with bone and joint infections. We conducted this retrospective study to provide additional data to support the use of mNGS in the clinical setting to identify pathogens within abscesses or tissue samples associated with bone and joint infections.

NIR‐II AIEgens for Infectious Diseases Phototheranostics

AbstractPathogenic infectious diseases have persistently posed significant threats to public health. Phototheranostics, which combines the functions of diagnostic imaging and therapy, presents an extremely promising solution to block the spread of pathogens as well as the outbreak of epidemics owing to its merits of a wide‐spectrum of activity, high controllability, non‐invasiveness, and difficult to acquire resistance. Among multifarious phototheranostic agents, second near‐infrared (NIR‐II, 1000–1700 nm) aggregation‐induced emission luminogens (AIEgens) are notable by virtue of their deep penetration depth, excellent biocompatibility, balanced radiative and nonradiative decay and aggregation‐enhanced theranostic performance, making them an ideal option for combating pathogens. This minireview provides a systematical summary of the latest advancements in NIR‐II AIEgens with emphasis on the molecular design and nanoplatform formulation to fulfill high‐efficiency in treating bacterial and viral pathogens, classified by disease models. Then, the current challenges, potential opportunities, and future research directions are presented to facilitate the further progress of this emerging field.

NIR-II AIEgens for Infectious Diseases Phototheranostics.

Pathogenic infectious diseases have persistently posed significant threats to public health. Phototheranostics, which combines the functions of diagnostic imaging and therapy, presents an extremely promising solution to block the spread of pathogens as well as the outbreak of epidemics owing to its merits of a wide-spectrum of activity, high controllability, non-invasiveness, and difficult to acquire resistance. Among multifarious phototheranostic agents, second near-infrared (NIR-II, 1000-1700 nm) aggregation-induced emission luminogens (AIEgens) are notable by virtue of their deep penetration depth, excellent biocompatibility, balanced radiative and nonradiative decay and aggregation-enhanced theranostic performance, making them an ideal option for combating pathogens. This minireview provides a systematical summary of the latest advancements in NIR-II AIEgens with emphasis on the molecular design and nanoplatform formulation to fulfill high-efficiency in treating bacterial and viral pathogens, classified by disease models. Then, the current challenges, potential opportunities, and future research directions are presented to facilitate the further progress of this emerging field.

Dual-modal detection of antimicrobial susceptibility in pathogenic bacteria based on the high-throughput microfluidic platform

For pathogenic bacterial infectious diseases such as sepsis, accurate and rapid antimicrobial susceptibility testing (AST) plays an important role in improving antimicrobial screening and clinical outcomes. Traditional culture-based AST assays have the limitations of time-consuming, labor-intensive, expensive, and consuming reagents. In this work, a simple, fast, high-throughput microfluidic platform integrated with isolation, identification, and detection functions was designed for antibiotic susceptibility analysis in pathogenic bacteria. For the above purpose, MnO2@ZIF-90 nanoprobes with dual functions of nanozyme and fluorescence were prepared for visual eye or RGB analysis through a smartphone APP. More importantly, the redox activity of bacterial membrane in active pathogenic bacteria could decompose the MnO2 of MnO2@ZIF-90 nanoprobes and reduce the enzyme-like activity, which weakens the colorimetric signal of Timebox. Meanwhile, the ATP released from active pathogenic bacteria further triggered the breakdown of the inner ZIF-90 layer, generating a fluorescence signal. Therefore, a dual detection combining colorimetric and fluorescence was used to perform more accurate and reliable antibiotic susceptibility analysis of pathogenic bacteria. With the proposed microfluidic platform, a low detection of 10 CFU mL−1 bacteria and fast AST results were achieved within 5 min. The clinical applicability of the platform was further demonstrated through the analysis of clinical samples. This work provides a low-cost, easy-to-operation, fast-response, and high-throughput platform for the AST assays in pathogenic bacterial infectious diseases such as sepsis.

Magnetic Fe3O4@MOF@aptamer-mediated entropy-driven fluorescence biosensor for multiplexed and DNA extraction- and amplification-free detection of pathogenic bacteria

Rapid and early identification of pathogenic bacteria in food and clinical samples is critical for infectious disease control and precision medicine. In this study, we present a novel Magnetic Fe3O4@metal–organic framework (MOF)@Aptamer-based Entropy-driven fluorescence biosensor combined with mesophilic Clostridium butyricumArgonaute (CbAgo) for multiplexed and DNA extraction- and amplification-free detection of pathogenic bacteria, termed the MAEA biosensor. In this study, magnetic zirconium-based MOF nanoparticles were modified with a phosphorylated aptamer as an efficient signal converter, which recognized the pathogens and released the complementary DNA to activate the entropy-driven circuit reaction. The highly efficient catalytic DNA circuit and isothermal enzyme-free format produce large amounts of guide DNA. CbAgo exerts precise and highly efficient endonuclease activity under the guidance of guide DNA, which makes the MAEA biosensor useful for multiplexed and DNA extraction- and amplification-free detection of pathogenic bacteria with high sensitivity (<102 CFU/mL). This study demonstrates a highly selective and reliable magnetic Fe3O4@MOF@aptamer-based biosensor using CbAgo for simultaneously detecting multiple pathogenic bacteria, providing a potential tool for other infectious disease pathogens with convenient operation and high sensitivity.

HRS Facilitates Newcastle Disease Virus Replication in Tumor Cells by Promoting Viral Budding.

Newcastle disease virus (NDV) is a highly pathogenic avian infectious disease agent and also a promising oncolytic virus with broad application prospects. The Endosomal Sorting Complex Required for Transport (ESCRT) machinery has been increasingly recognized for its crucial role in the life cycles of enveloped viruses, influencing processes such as viral entry, replication, and budding. In this study, we employed an RNA interference screening approach to identify key ESCRT components that regulate NDV replication in tumor cells. qPCR, immunofluorescence, and Western blot assays demonstrated that knockdown of HRS, CHMP4A, CHMP4B, and CHMP4C significantly impaired NDV replication in HeLa cells, with HRS exhibiting the most pronounced inhibitory effect. Additionally, HRS knockout significantly inhibited viral budding and suppressed NDV-induced cell death in HeLa cells. Notably, NDV infection was shown to significantly upregulate HRS gene and protein expression in a time-dependent manner. In conclusion, this study systematically identifies critical ESCRT components involved in NDV replication within tumor cells, with a particular focus on the role of HRS in promoting NDV's replication by promoting viral budding, offering new insights for the development of NDV-based oncolytic therapies.

Збудники інфекційних хвороб людини і тварин та їх розповсюдження в Європі іксодовим кліщем Dermacentor reticulatus

Due to climate change, the possibility of human infective diseases caused by pathogens from the genera Borelia, Anaplasma, Rickettsia, Babesia, Bartonella, Coxiella, etc. is increasing in Europe. Generally, these pathogens are directly related to arthropod vectors, in particular, to Ixodes ticks. The aim of the study was to determine the current trends in the spread of tick-borne infections transmitted by Dermacentor reticulatus ticks in some European countries, including Ukraine, based on the analysis of literature. Over the past 10 years, in the vast majority of countries, including Europe, the situation with the defeat of farm and wild animals, as well as humans, by pathogens of severe infectious diseases from the genera Borrelia, Anaplasma, Rickettsia, Babesia, Theileria, Coxiella, Bartonella, Francisella, etc. has been aggravated. Representatives of these genera lead to severe diseases, such as tick-borne borreliosis, which are accompanied by damage to the central nervous system, joints, skin, and cardiovascular system. Members of the Rickettsiales genus cause a variety of feverish conditions in animals and humans. Species of the genus Babesia cause babesiosis, a disease caused by damage to red blood cells and the appearance of anti-erythrocyte antibodies, and representatives of the genus Toxoplasma cause toxoplasmosis, accompanied by damage to the nervous, lymphatic, and cardiovascular systems. Q fever is caused by species of the genus Coxiella. Severe human diseases are caused by tick-borne encephalitis viruses. Various PCR test systems have been developed and used to detect these pathogens. For example, in Poland, PCR for Borrelia burgdorferi s.l. was performed using the B. burgdorferi s.l. PCR kit (GeneProof, Czech Republic) for in vitro diagnosis. Anaplasma PCR kits (Blirt-DNA Gdańsk, Poland) were used to detect Anaplasma phagocytophilum DNA. For the detection of Babesia spp., a fragment of the 18S rDNA gene encoding a small ribosomal subunit localized in the conserved region V4 was used. To detect Bartonella spp., the tests Hum PCR Bartonella, Hum PCR Coxiella burnetii, and Vet PCR Rickettsia kit (BioIngenTech, Chile), Coxiella burnetii and Rickettsia spp. were used. In the Laboratory for the Study of Ticks and Tick-Borne Infections of Ternopil National Medical University (Ukraine), pathogens were identified using several test systems, namely DNA A. phagocytophilum, / DNA E. muris, / DNA E. chaffeensis, DNA B. burgdorferi s.l., DNA B. myamotoi; DNA Babesia sp., and RNA Ticks borne of encephalitis viruses (MolGen, Italy), which allow real-time determination on anamplifier "ROTOR Gene 6000" by Corbett Research. Studies in many European countries have shown infection of the Dermacentor reticulatus tick with the pathogens B. burgdorferi s.l. in the range from 1.6 to 49.8 %; A. phagocytophilum – 0.1–2.2 %; Babesia sрp. – 9.8–43.8 %; Coxiella spр. – 0.1–0.2%; Francisella spp. – 0.7–95%; Toxoplasma spр. – 3.2–16.7 %; and ticks borne of encephalitis viruses 8.5–16.6 %. Some Ukrainian scientists presented data on D. reticulatus infection, in particular B. burgdorferi s. l. – 10.1–22.1 %; A. phagocytophilum – 3–25.36 %; Babesia spр. – 1–41.2 %; Rickettsia sp. – 28 %; Bartonella spp. – 5 %; Coxiella spр. – 5.1 %, and tick-borne f encephalitis viruses – 11.9–71 %. The spread of many infectious agents is largely correlated with the spread of their vectors, including ticks of the D. reticulatus species. According to many scientists, this species is widespread in Europe, in particular, two metapopulations are currently distinguished as the western one, which includes the territories of France, Belgium, Slovakia, the Czech Republic, the Netherlands, and Germany, and the eastern one, which covers Lithuania, Latvia, Belarus, eastern and central Poland, and west of the Vistula River up to the Ural Mountains. In the Czech Republic, this species is found in all regions, more often in the southeastern and northwestern regions. In the UK, ticks have been found in West Wales, Devon, and Essex. In Romania, D. reticulatus was found in 17 counties, and in Moldova – in the Lower Dniester region. In Ukraine, this species is widespread from the Carpathians and Prykarpattia, Polissya, and Forest-Steppe, to the southeastern regions and Crimea.

The evolutionary features and roles of single nucleotide variants and charged amino acid mutations in influenza outbreaks during NPI period

The epidemic and outbreaks of influenza B Victoria lineage (Bv) during 2019–2022 led to an analysis of genetic, epitopes, charged amino acids and Bv outbreaks. Based on the National Influenza Surveillance Network (NISN), the Bv 72 strains isolated during 2019–2022 were selected by spatio-temporal sampling, then were sequenced. Using the Compare Means, Correlate and Cluster, the outbreak data were analyzed, including the single nucleotide variant (SNV), amino acid (AA), epitope, evolutionary rate (ER), Shannon entropy value (SV), charged amino acid and outbreak. With the emergence of COVID-19, the non-pharmaceutical interventions (NPIs) made Less distant transmission and only Bv outbreak. The 2021–2022 strains in the HA genes were located in the same subset, but were distinct from the 2019–2020 strains (P < 0.001). The codon G → A transition in nucleotide was in the highest ratio but the transversion of C → A and T → A made the most significant contribution to the outbreaks, while the increase in amino acid mutations characterized by polar, acidic and basic signatures played a key role in the Bv epidemic in 2021–2022. Both ER and SV were positively correlated in HA genes (R = 0.690) and NA genes (R = 0.711), respectively, however, the number of mutations in the HA genes was 1.59 times higher than that of the NA gene (2.15/1.36) from the beginning of 2020 to 2022. The positively selective sites 174, 199, 214 and 563 in HA genes and the sites 73 and 384 in NA genes were evolutionarily selected in the 2021–2022 influenza outbreaks. Overall, the prevalent factors related to 2021–2022 influenza outbreaks included epidemic timing, Tv, Ts, Tv/Ts, P137 (B → P), P148 (B → P), P199 (P → A), P212 (P → A), P214 (H → P) and P563 (B → P). The preference of amino acid mutations for charge/pH could influence the epidemic/outbreak trends of infectious diseases. Here was a good model of the evolution of infectious disease pathogens. This study, on account of further exploration of virology, genetics, bioinformatics and outbreak information, might facilitate further understanding of their deep interaction mechanisms in the spread of infectious diseases.

Ectozoans of dogs and cats

The purpose of the study is to analyze the species composition and distribution of ectoparasites of dogs and cats on the territory of the Russian Federation. Research objectives: to study the epizootic situation regarding ectoparasites of dogs and cats on the territory of the Russian Federation. Ectoparasites of dogs and cats are widespread in the Russian Federation and pose the greatest danger as carriers of pathogens of infectious and invasive diseases. Depending on the region, the species composition and abundance of ectoparasites varies significantly. Thus, in Moscow, aphanipterosis (46–62%), otodectosis in cats (34–38%) and demodicosis in dogs (39%) were more often recorded. When examining dogs in Tyumen with diseases of the skin and hair, skin diseases of parasitic etiology were recorded in 33.86% of all examined animals. Aphanipteriosis was detected more often – 28.55%, otodectosis – 21.9%, flea allergic dermatitis – 14.65%, cheyletiosis – 13.2%, demodicosis – 12.6%, sarcoptic mange – 9.1%. A study of dogs and cats in Novosibirsk identified 6 types of parasites: Ctenocephalides canis, Otodectes cynotis, Demodex canis, Notoedres cati, Sarcoptes canis and Cheyletiella jascuri. Among cats and dogs. the most common were: aphanipterosis 4.8%, otodectosis 1.9%, demodicosis 0.23%, notoedrosis 0.14%, sarcoptic mange 0.09% and cheyletiellosis 0.3%. In the Nizhny Novgorod region, dogs and cats were diagnosed with infestation of two types of fleas (Ctenocephalides felis, C. canis), one type of lice-eater (Trichodectes canis), in addition, the following were found on the animals’ bodies: dog louse (Linognathus setosus), ixodid ticks Dermacentor reticulates, D. marginatus and I. ricinus. Thus, aphanipterosis (4.78–62.0%) and demodicosis (2.52–39.0%) are more often recorded in dogs; trichodectosis (0.64–4.2%) and ixodid ticks (9.75%) are less common. –18.0%), sarcoptic mange (1.0–9.1%), otodectosis (0.17–1.94%), and in cats – otodectosis (34–63%), notoedrosis (0.31–8.9%) and cheyletiellosis (0.27%).

Occurrence of pathogenic Mycobacteria avium and Pseudomonas aeruginosa in outdoor decorative fountain water and the associated microbial community.

Outdoor decorative fountains usually attract residents to visit. However, opportunistic pathogens (OPs) can proliferate and grow in the stagnant fountain water, posing potential health risks to visitors due to the inhalation of spaying aerosols. In this study, the abundance of selected OPs and associated microbial communities in three large outdoor decorative fountain waters were investigated using quantitative PCR and 16S rRNA sequencing. The results indicated that Mycobacteria avium and Pseudomonas aeruginosa were consistently detected in all decorative fountain waters throughout the year. Redundancy analysis showed that OPs abundance was negatively correlated with water temperature but positively correlated with nutrient concentrations. The gene copy numbers of M. avium varied between 2.4 and 3.9 log10 (gene copies/mL), which were significantly lower than P. aeruginosa by several orders of magnitude, reaching 6.5-7.1 log10 (gene copies/mL) during winter. The analysis of taxonomic composition and prediction of functional potential also revealed pathogenic microorganisms and infectious disease metabolic pathways associated with microbial communities in different decorative fountain waters. This study provided a deeper understanding of the pathogenic conditions of the outdoor decorative fountain water, and future works should focus on accurately assessing the health risks posed by OPs in aerosols.

RESP2: An uncertainty aware multi-target multi-property optimization AI pipeline for antibody discovery.

Discovery of therapeutic antibodies against infectious disease pathogens presents distinct challenges. Ideal candidates must possess not only the properties required for any therapeutic antibody (e.g. specificity, low immunogenicity) but also high affinity to many mutants of the target antigen. Here we present RESP2, an enhanced version of our RESP pipeline, designed for the discovery of antibodies against diverse antigens with simultaneously optimized developability properties. RESP2 provides a suite of methods to estimate the uncertainty of predictions including a new model combining neural network and Gaussian process with great flexibility to model protein engineering data, which accelerates in silico directed evolution to identify tight binders even those not present in the original screening library. An interpretable model is then exploited to assess antibody humanness to minimize immunogenicity risk of the selected candidates. To demonstrate the power of this pipeline, we use the receptor binding domain (RBD) of the COVID-19 spike protein as a case study, and discover a highly human antibody with broad (mid to high-affinity) binding to at least 8 different variants of the RBD. These results illustrate the advantages of this pipeline for antibody discovery against a challenging target. The code needed to reproduce the experiments in this paper is available at https://github.com/Wang-lab-UCSD/RESP2.

Crystal structures of NAD(P)H nitroreductases from Klebsiella pneumoniae.

Klebsiella pneumoniae (Kp) is an infectious disease pathogen that poses a significant global health threat due to its potential to cause severe infections andits tendency to exhibit multidrug resistance. Understanding the enzymatic mechanisms of the oxygen-insensitive nitroreductases (Kp-NRs) from Kp is crucial for the development of effective nitrofuran drugs, such as nitrofurantoin, that can be activated as antibiotics. In this paper, three crystal structures of two Kp-NRs (PDB entries 7tmf/7tmg and 8dor) are presented, and an analysis of their crystal structures and their flavin mononucleotide (FMN)-binding mode is provided. The structures with PDB codes 7tmf (Kp-NR1a), 7tmg (Kp-NR1b) and 8dor (Kp-NR2) were determined at resolutions of 1.97, 1.90 and 1.35 Å, respectively. The Kp-NR1a and Kp-NR1b structures adopt an αβ fold, in which four-stranded antiparallel β-sheets are surrounded by five helices. With domain swapping, the β-sheet was expanded with a β-strand from the other molecule of the dimer. The difference between the structures lies in the loop spanning Leu173-Ala185: in Kp-NR1a the loop is disordered, whereas the loop adopts multiple conformations in Kp-NR1b. The FMN interactions within Kp-NR1/NR2 involve hydrogen-bond and π-stacking interactions. Kp-NR2 contains four-stranded antiparallel β-sheets surrounded by eight helices with two short helices and one β-sheet. Structural and sequence alignments show that Kp-NR1a/b and Kp-NR2 are homologs of the Escherichia coli oxygen-insensitive NRs YdjA and NfnB and of Enterobacter cloacae NR, respectively. By homology inference from E. coli, Kp-NR1a/b and Kp-NR2 may detoxify polynitroaromatic compounds and Kp-NR2 may activate nitrofuran drugs to cause bactericidal activity through a ping-pong bi-bi mechanism, respectively.

A novel vaccine construct against Zika virus fever: insights from epitope-based vaccine discovery through molecular modeling and immunoinformatics approaches.

The Zika virus (ZIKV) is an emerging virus associated with the Flaviviridae family that mainly causes infection in pregnant women and leads to several abnormalities during pregnancy. This virus has unique properties that may lead to pathological diseases. As the virus has the ability to evade immune response, a crucial effort is required to deal with ZIKV. Vaccines are a safe means to control different pathogenic infectious diseases. In the current research, a multi-epitope-based vaccination against ZIKV is being designed using in silico methods. For the epitope prediction and prioritization phase, ZIKV polyprotein (YP_002790881.1) and flavivirus polyprotein (>YP_009428568.1) were targeted. The predicted B-cell epitopes were used for MHC-I and MHC-II epitope prediction. Afterward, several immunoinformatics filters were applied and nine (REDLWCGSL, MQDLWLLRR, YKKSGITEV, TYTDRRWCF, RDAFPDSNS, KPSLGLINR, ELIGRARVS, AITQGKREE, and EARRSRRAV) epitopes were found to be probably antigenic in nature, non-allergenic, non-toxic, and water soluble without any toxins. Selected epitopes were joined using a particular GPGPG linker to create the base vaccination for epitopes, and an extra EAAAK linker was used to link the adjuvant. A total of 312 amino acids with a molecular weight (MW) of 31.62762 and an instability value of 34.06 were computed in the physicochemical characteristic analysis, indicating that the vaccine design is stable. The molecular docking analysis predicted a binding energy of -329.46 (kcal/mol) for TLR-3 and -358.54 (kcal/mol) for TLR-2. Moreover, the molecular dynamics simulation analysis predicted that the vaccine and receptor molecules have stable binding interactions in a dynamic environment. The C-immune simulation analysis predicted that the vaccine has the ability to generate both humoral and cellular immune responses. Based on the design, the vaccine construct has the best efficacy to evoke immune response in theory, but experimental analysis is required to validate the in silico base approach and ensure its safety.

Comprehensive profiling of social mixing patterns in resource poor countries: A mixed methods research protocol.

Low-and-middle-income countries (LMICs) bear a disproportionate burden of communicable diseases. Social interaction data inform infectious disease models and disease prevention strategies. The variations in demographics and contact patterns across ages, cultures, and locations significantly impact infectious disease dynamics and pathogen transmission. LMICs lack sufficient social interaction data for infectious disease modeling. To address this gap, we will collect qualitative and quantitative data from eight study sites (encompassing both rural and urban settings) across Guatemala, India, Pakistan, and Mozambique. We will conduct focus group discussions and cognitive interviews to assess the feasibility and acceptability of our data collection tools at each site. Thematic and rapid analyses will help to identify key themes and categories through coding, guiding the design of quantitative data collection tools (enrollment survey, contact diaries, exit survey, and wearable proximity sensors) and the implementation of study procedures. We will create three age-specific contact matrices (physical, nonphysical, and both) at each study site using data from standardized contact diaries to characterize the patterns of social mixing. Regression analysis will be conducted to identify key drivers of contacts. We will comprehensively profile the frequency, duration, and intensity of infants' interactions with household members using high resolution data from the proximity sensors and calculating infants' proximity score (fraction of time spent by each household member in proximity with the infant, over the total infant contact time) for each household member. Our qualitative data yielded insights into the perceptions and acceptability of contact diaries and wearable proximity sensors for collecting social mixing data in LMICs. The quantitative data will allow a more accurate representation of human interactions that lead to the transmission of pathogens through close contact in LMICs. Our findings will provide more appropriate social mixing data for parameterizing mathematical models of LMIC populations. Our study tools could be adapted for other studies.

The role of microbiological monitoring in the prevention and control of antibiotic resistance

The article deals with the problem of antibiotic resistance of opportunistic microorganisms. The aim of the study is to determine the predominant microflora of a medical organization and to develop protocols for empirical antibacterial therapy in infectious and inflammatory processes. The main groups of infectious agents in the departments for the treatment of patients with new coronavirus infection of the Oryol region «Botkin City Hospital» for 2020–2022 are analyzed. Isolation, identification and determination of antibiotic sensitivity were carried out using standard methods. The results of the study made it possible to identify priority microorganisms and assess their antibiotic resistance. The growth of resistance to carbapenems of microorganisms isolated from patients in 2020–2021 was revealed. The effect obtained from the correction of antibiotic therapy has been shown, which has significantly reduced the resistance of isolated strains to carbapenems. To ensure effective epidemiological surveillance of clinically significant microorganisms and curb the growth of antimicrobial resistance in medical organizations of the Orel region, it is important to consider the possibility of maintaining a regional medical information system in order to monitor the prevalence of potential pathogens of infectious diseases, including those related to the provision of medical care resistant to antimicrobial drugs.