Pathogens Of Respiratory Infections Research Articles

A rapid, sensitive, and high-throughput pathogen detection method and application of identifying pathogens based on multiplex PCR technology combined with capillary electrophoresis

Respiratory infections are one of the leading causes of death worldwide. Rapid and accurate detection of pathogens is crucial for timely treatment. This study established a detection method based on multiplex PCR combined with capillary electrophoresis, capable of simultaneously detecting 28 common respiratory pathogens. We used specially designed homo-tag primers, significantly reducing the formation of primer dimers and improving the specificity and sensitivity of amplification. After two rounds of PCR amplification, the products were subjected to fragment analysis using the ABI 3500XL Genetic Analyzer, enabling automated result interpretation. The detection limit of this method reaches 2.77 × 102 copies/ml, with some pathogens reaching as low as 2.77 × 10 copies/ml. The detection of 147 clinical specimens showed that the overall consistency of this method with culture, colloidal gold, fluorescent quantitative PCR, and NGS was 75.5%. The multiplex PCR detection method established in this study is rapid, sensitive, and high-throughput, can be used for routine screening of common pathogens in respiratory infections, providing an important basis for clinical diagnosis and treatment.

Analysis of the epidemic characteristics of common respiratory pathogens infection in children in a 3A special hospital

ObjectiveTo analyze the epidemic characteristics of common respiratory tract infection pathogens in children with respiratory tract infection, and provide scientific basis for the prevention and control of respiratory tract infection.MethodsA retrospective collection of clinical data was conducted on 11,538 children with respiratory tract infections at Luoyang Maternal and Child Health Hospital from December 2022 to November 2023. The types of respiratory tract infections, including upper and lower respiratory tract infections, as well as five respiratory pathogens: influenza A virus (influenza A), influenza B virus (influenza B virus, adenovirus (ADV), respiratory syncytial virus (RSV), and Mycoplasma pneumoniae (MP) infections, were analyzed and compared for different genders, ages, temperatures, and air quality in different months; And the changes of five pathogens in children with respiratory tract infections of different disease severity.ResultsFrom December 2022 to November 2023, a total of 11,538 children with respiratory infections were included in the analysis, including 6436 males and 5102 females, with an age of 4.92 ± 2.03 years. The proportion of upper respiratory tract infections is as high as 72.17%, and lower respiratory tract infections account for 27.83%. Among them, 2387 were positive for Flu A antigen, with a positive rate of 20.69%, 51 cases were positive for Flu B antigen, and the positive rate was 0.4%, 1296 cases were positive for adv antigen, with a positive rate of 11.23%, 868 cases were positive for RSV antigen, with a positive rate of 7.52%, 2481 cases were positive for MP IgM antibody or MP antigen, and the positive rate was 21.50%. Flu B in male children The infection rate of ADV and MP was higher than that of female children (p < 0.05); Among children in different age groups, the older the age, the older the Flu A The higher the infection rate of MP (p < 0.05), the higher the positive rate of RSV in children with younger age (p < 0.05). The positive rate of ADV in children aged 3–6 years and > 6 years was higher than that in children aged 0–3 years (p < 0.05); Flu A and MP are popular throughout the year, and the positive rate peaks during the period of temperature rise and air quality decline from February to March, and during the period of temperature drop and air quality index rise from August to November, The positive rate of RSV peaked after the turning point of temperature rise from March to April. The infection rate was higher during the period of sharp decline in air quality from March to May and sharp decline in temperature in November, The positive rate of ADV was higher at the turning point of temperature rise from February to March, and then the infection rate decreased. During the period of sharp temperature drop from August to November, the positive rate increased sharply, and the peak of infection occurred; As the disease worsens, The positive rates of Flu A, Flu B, RSV, MP and combined infection with more than two pathogens were all increased (p < 0.05).ConclusionAfter the new coronavirus epidemic in 2022, Flu A and MP have the highest infection rate of respiratory pathogens in children, showing a peak growth in general, with epidemic characteristics changing with environmental temperature, air quality and seasons. The main disease type is upper respiratory tract infection, MP and adv infections were mainly in male children, Flu A, MP and ADV infections are more common in older children, RSV infection was more common in younger children; Flu A, Flu B, RSV and MP infection and the co infection of more than two pathogens may more easily lead to the occurrence of severe pneumonia.

Epidemiology of respiratory infection pathogens using multiplex RT-qPCR in big earthquakes Area in Turkey (2023)

IntroductionThe Kahramanmaraş earthquake, which has been classified as an earthquake with significant and destructive consequences on a global scale, has been referred to as "the disaster of the century.", occurred on February 6, 2023. A considerable number of structures were destroyed and a significant amount of damage was incurred in 11 provinces, including Kahramanmaraş. Respiratory tract infections are a serious public health problem seen in all age groups among earthquake victims living in tent and container cities. ObjectiveThe aim of the study was to determine the causative agents in respiratory tract samples taken for screening purposes from earthquake victims living in tent cities in the earthquake zone and to provide early diagnosis. MethodGaziantep Provincial Health Directorate Infectious Diseases Unit filiation teams collected nasopharyngeal swabs from earthquake victims living in tent cities around Gaziantep province between March 25 and March 30, 2023. The presence of 18 viruses and 6 bacteria that are causing respiratory tract infections were simultaneously detected by the Real-Time qPCR (RT-qPCR) technique. ResultsIn the present study, respiratory pathogens were detected in 470 (56.62 %) of a total of 830 patients. The most frequently isolated agents were rhinovirus (20 %, 94/470), S. pneumoniae (12.87 %, 60/470), RSV A/B (12.12 %, 57/470), H. influenza type b (10. 85 %, 51/470) and others. Rhinovirus was the most frequently detected pathogen in the study. The coexistence of more than one pathogen was also detected. The most common association was found between HRV and S. pneumoniae (20.93 %, 9/43). ConclusionThe results of the present study indicate that public health measures should be prioritized in natural disasters, and ıt demonstrates that infectious diseases became a significant problem in the time period after the earthquake. Early results can be obtained by screening viral and bacterial pathogen in respiratory tract samples with RT-qPCR, and an early diagnosis is ensured.

Epidemiological characteristics of common respiratory pathogens in children

Children's respiratory tract infection is a common disease affecting children's health, our purpose is to describe the epidemiological characteristics of common pathogens of children's respiratory tract infection in central Shandong, China, and compare them with those in other parts of world, so as to summarize the rules of children's respiratory tract infection in central Shandong, and provide scientific basis for health departments to prevent and treat local children's respiratory tract infection. Sputum, tracheal aspirate, alveolar lavage fluid and other samples of 4804 children admitted to wards of Zibo Maternal and Child Health Hospital for treatment of respiratory tract infection from June 2019 to December 2022 were collected, and 12 common respiratory tract pathogens were detected by PCR capillary electrophoresis fragment analysis, two bacteria (Streptococcus pneumoniae, Haemophilus influenzae), two atypical pathogens (Mycoplasma Pneumoniae, Chlamydia Pneumoniae) and eight viruses (Human rhinovirus, Respiratory Syncytial Virus, Influenza A Virus, Parainfluenza Virus, Human metapneumovirus, Human boca virus, Human coronavirus, Influenza B virus) were included, the positive detection rate of single pathogen, the proportion of each type of respiratory tract mixed infection and the positive detection rate of single pathogen in different ages and seasons were analyzed statistically. (1)Among 4804 children with respiratory tract infection, the total positive rate was 77.87% (3741/4804), the positive rate of single pathogen was 43.40% (1656/4804), Streptococcus pneumoniae, Rhinovirus and Respiratory syncytial virus were the highest, there were 2085 cases of mixed infection with two or more pathogens, the positive rate was 43.40%. (2) The positive rates of infection in infant group (0–1 years old), infant group (1–3 years old), preschool group and school age group (3 years old-) were roughly the same, the infection rates of Streptococcus pneumoniae, Respiratory syncytial virus and Parainfluenza virus in infant group, Rhinovirus in infant group, Influenza A virus, Chlamydia pneumoniae, Mycoplasma pneumoniae and Haemophilus influenzae in school age group were higher than those in other groups, the difference was statistically significant (P < 0.05). (3) The positive detection rates of spring, summer, autumn and winter groups were 43.58%, 38.64%, 33.73% and 29.27%, respectively, the positive rates of Streptococcus pneumoniae and Haemophilus influenzae in spring group, Mycoplasma pneumoniae in summer group, Rhinovirus, Respiratory syncytial virus and Influenza A virus in autumn group, Chlamydia pneumoniae, Boca virus and Influenza B virus in winter group were higher than those in other seasons, and the differences were statistically significant (P < 0.05). The pathogen detection rate of children varies with age and season, and the prevention and treatment of a certain respiratory pathogen infection must be combined with its raging season and age rule.

The Epidemiological Features and Pathogen Spectrum of Respiratory Tract Infections, Istanbul, Türkiye, from 2021 to 2023.

Respiratory tract infections (RTIs) can lead to both recurrent seasonal epidemic outbreaks and devastating pandemics. The aim of this study was to evaluate the epidemiologic characteristics and pathogen spectrum of RTIs using a multiplex RT-PCR panel. A total of 9354 cases with suspected RTIs between February 2021 and July 2023 were included in this study. A total of 11,048 nasopharyngeal and oropharyngeal samples from these patients were analyzed for 23 respiratory tract pathogens using multiplex RT-PCR. H. influenzae and S. pneumoniae were considered as colonizing bacteria. At least one pathogen was detected in 70.66% of the samples; viral pathogens were detected in 48.41% of the samples, bacterial pathogens were detected in 16.06% of the samples, and viral + bacterial pathogens were detected in 35.53% of the samples. The most frequently detected viral pathogen was rhinovirus/enterovirus (RV/EV) (19.99%). Interestingly, in 2021, respiratory syncytial virus A/B showed atypical activity and replaced RV/EV as the most prevalent pathogen. Human bocavirus, H. influenzae, and S. pneumoniae were detected at higher rates in males (p: 0.038, p: 0.042, and p: 0.035, respectively), while SARS-CoV-2 and B. pertussis were detected at higher rates in females (p < 0.001 and p: 0.033). RTIs were found at higher rates in children (p < 0.001). SARS-CoV-2 and human coronaviruses 229E were detected at higher rates in adults (p < 0.001 and p: 0.001). This comprehensive study with a large sample size investigating RTI pathogens was the first in Türkiye. Understanding the current viral circulation using multiplex RT-PCR panels enables clinicians to predict the most likely pathogens affecting patients and contributes to patient management, in addition to anticipating potential threats.

Antibacterial Efficacy of Eucalyptus Essential Oil against Respiratory Infection Pathogens and Characterization of its Bioactive Compounds

Antibacterial activity of eucalyptus essential oils (EEO) against some respiratory pathogens and its mechanism of action were studied. Clinical pathogens used in the study were Enterobacter cloacae, Klebsiella pneumoniae, Staphylococcus aureus and Pseudomonas aeruginosa. Disk diffusion, macro and microbroth dilution methods were respectively used to assess antibacterial assay, minimum inhibitory concentration (MIC) and growth inhibition assay using standard antibiotics as references. Gas chromatography Mass spectrometry was used to characterize the bioactive compounds present in EEO. Scanning electron microscopy was used to determine the mode of action of EEO on test pathogens. A total of 12 compounds were found to have bioactive functions with p-Cymene having 34.07%, gamma-Terpinene (7.01%), Cyclohexasiloxane (5.30%), 2-Aminobenzoic acid (4.59%). The EEO exerts varying antibacterial effects on susceptible organisms. At 100 mg/ml concentration the EEO antibacterial activities were observed on E. cloacae with 23.0 mm mean zone of inhibition, K. pneumoniae (22.7 mm) and S. aureus (16.0 mm) while no activity was recorded on P. aeruginosa. The MIC and MBC of the EEO on susceptible organisms were E. cloacae (6.25mg/ml, 12.5mg/ml); S. aureus (25mg/ml. 50mg/ml) respectively, while both MIC and MBC of EEO on K. pneumoniae was 50mg/ml. Scanning electron microscopy displayed noticeable damages of cell morphology and ultrastructure on two most susceptible pathogens (E. cloacae and K. pneumoniae), thus increase cell permeability and subsequent cell death. This study showed EEO is a potent antibacterials against some respiratory pathogens and can be further explored in treating respiratory and other infections caused by these pathogens. The positive effect of eucalyptus essential oil on the selected respiratory infection pathogens could make it an important part of drug (ointment formation) for the treatment of such infections. Keywords Essential Oils, Bioactive Compounds, Respiratory Pathogens, Susceptibility, GCMS

In vitro Assessment of Antimicrobial potential of Siddha Polyherbal Formulation Tulasi oil against RTI pathogens

In Siddha medication, along with herbal formulations, some mineral formulations are used clinically to prevent or cure infectious diseases. The therapeutic values of some siddha formulations have been well documented earlier, but a huge number of them remain unexplored in terms of safety and efficacy. The aim of this study was to screen the antimicrobial potential of Siddha polyherbal formulation Tulasi oil (SPHTO) against respiratory tract infection (RTI) causing pathogens. The antimicrobial activity of SPHTO was examined by using the methods of agar well diffusion, Minimum inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC), Minimum Fungicidal Concentration (MFC) and Microbicidal action. Ciprofloxacin (bacteria) and Amphotericin B (fungi) were used as the positive control for this study. The potassium leakage was determined using a flame emission and atomic absorption spectroscopy. All tested concentrations gave notable antimicrobial activity against all tested pathogens. The 100mg/ml concentration showed the highest activity against E.coli followed by 200mg/ml against K. pnuemonia and C.neoformans when compared to 50 and 25mg/ml. For MIC, the highest activity was registered at 150mg/ml concentration against E. coli, while MBC/MFC was 200mg/ml concentration has shown the better activity against K. pneumonia and C. neoformans. Tulasi oil induced leakage of potassium ions from cells of E.coli and K.pneumonia suspended in glycil-glycine buffer solution and the leakage started within 10 minutes of contact of drugs with target cells. From this study, it may support the clinical claims of Tulasi oil to have potent antibacterial and antifungal activities and offer profound therapeutic benefits against respiratory tract infection.

A Path towards Timely VAP Diagnosis: Proof-of-Concept Study on Pyocyanin Sensing with Cu-Mg Doped Graphene Oxide.

In response to the urgent requirement for rapid, precise, and cost-effective detection in intensive care units (ICUs) for ventilated patients, as well as the need to overcome the limitations of traditional detection methods, researchers have turned their attention towards advancing novel technologies. Among these, biosensors have emerged as a reliable platform for achieving accurate and early diagnoses. In this study, we explore the possibility of using Pyocyanin analysis for early detection of pathogens in ventilator-associated pneumonia (VAP) and lower respiratory tract infections in ventilated patients. To achieve this, we developed an electrochemical sensor utilizing a graphene oxide-copper oxide-doped MgO (GO - Cu - Mgo) (GCM) catalyst for Pyocyanin detection. Pyocyanin is a virulence factor in the phenazine group that is produced by Pseudomonas aeruginosa strains, leading to infections such as pneumonia, urinary tract infections, and cystic fibrosis. We additionally investigated the use of DNA aptamers for detecting Pyocyanin as a biomarker of Pseudomonas aeruginosa, a common causative agent of VAP. The results of this study indicated that electrochemical detection of Pyocyanin using a GCM catalyst shows promising potential for various applications, including clinical diagnostics and drug discovery.

Bacterial pathogens in Xpert MTB/RIF Ultra-negative sputum samples of patients with presumptive tuberculosis in a high TB burden setting: a 16S rRNA analysis.

In patients with presumptive tuberculosis (TB) in whom the diagnosis of TB was excluded, understanding the bacterial etiology of lower respiratory tract infections (LRTIs) is important for optimal patient management. A secondary analysis was performed on a cohort of 250 hospitalized patients with symptoms of TB. Bacterial DNA was extracted from sputum samples for Illumina 16S rRNA sequencing to identify bacterial species based on amplicon sequence variant level. The bacterial pathogen most likely to be responsible for the patients' LRTI could only be identified in a minority (6.0%, 13/215) of cases based on 16S rRNA amplicon sequencing: Mycoplasma pneumoniae (n = 7), Bordetella pertussis (n = 2), Acinetobacter baumanii (n = 2), and Pseudomonas aeruginosa (n = 2). Other putative pathogens were present in similar proportions of Xpert Ultra-positive and Xpert Ultra-negative sputum samples. The presence of Streptococcus (pseudo)pneumoniae appeared to increase the odds of radiological abnormalities (aOR 2.5, 95% CI 1.12-6.16) and the presence of S. (pseudo)pneumoniae (aOR 5.31, 95% CI 1.29-26.6) and Moraxella catarrhalis/nonliquefaciens (aOR 12.1, 95% CI 2.67-72.8) increased the odds of 6-month mortality, suggesting that these pathogens might have clinical relevance. M. pneumoniae, B. pertussis, and A. baumanii appeared to be the possible causes of TB-like symptoms. S. (pseudo)pneumoniae and M. catarrhalis/nonliquefaciens also appeared of clinical relevance based on 16S rRNA amplicon sequencing. Further research using tools with higher discriminatory power than 16S rRNA sequencing is required to develop optimal diagnostic and treatment strategies for this population.IMPORTANCEThe objective of this study was to identify possible bacterial lower respiratory tract infection (LRTI) pathogens in hospitalized patients who were initially suspected to have TB but later tested negative using the Xpert Ultra test. Although 16S rRNA was able to identify some less common or difficult-to-culture pathogens such as Mycoplasma pneumoniae and Bordetella pertussis, one of the main findings of the study is that, in contrast to what we had hypothesized, 16S rRNA is not a method that can be used to assist in the management of patients with presumptive TB having a negative Xpert Ultra test. Even though this could be considered a negative finding, we believe it is an important finding to report as it highlights the need for further research using different approaches.

Обнаружение возбудителей респираторных инфекций и вирусов герпеса человека в гипертрофированной аденоидной ткани у детей

Objective. Determination of nucleic acids (NA) of significant viral and bacterial pathogens of respiratory infections in the tissue of a benign hypertrophied pharyngeal tonsil (HPT) in children. Materials and methods. 27 HPT tissue samples obtained during elective adenoidectomy from patients of two age groups were studied: from 2 to 6 years 11 months (G1), n = 13, boys (B) 10/77%, girls (G) 3/23%; from 7 to 13 years (G2), n = 14 B 8/57%, G 6/43%. NC of 8 human herpes viruses (HHV), 16 respiratory viruses and 4 bacterial pathogens were determined by NA amplification using reagent kits manufactured by the Federal State Budgetary Institution of the Central Research Institute of Epidemiology of Rospotrebnadzor. The statistical analysis was carried out by the StatTech program. Results. NA of infectious agents were detected in all the studied samples. The average number of pathogens detected in one sample was 7 ± 3 microorganisms: HHV DNA and bacterial DNA were found in 100% of children; NA of respiratory viruses – in 81% (11/85% in G1, 11/79% in G2). The most frequently detected NA are: human herpes virus 6B (HHV-6B) – 96%, Epstein–Barr virus (EBV) – 89%, human herpes virus 7 (HCV-7) – 81%. EBV was detected more often in boys 18/100% and 6/67%, p = 0.029. Among bacteria, DNA of Haemophilus influenzae (HI) was detected more often than others – 59%. Rhinovirus (hRv) was the most frequent respiratory virus – 56%, bokavirus ((hBov) – the second most common detection rate of 33%, more often in G1 – 7/54% than in G2 2/14%, p = 0.046. Prognostic models have been developed showing an increase in the probability of detection of Hemophilus influenza in the presence of rhinovirus (p = 0.031) and Staphylococcus aureus in the presence of bocavirus (p = 0.012). Conclusions. Up to 12 NC pathogens of infections were found in the tissues of HPT in one patient. The most common pathogens were HCV-6B, HCV-7, EBV, hRv, hBov, HI. Key words: human herpes virus 7, human herpes virus 6 A/B, Epstein–Barr virus, adenoid hypertrophy, children, respiratory viruses, topical bacterial lysates

Assessing changes in the pattern of healthcare-associated infectious agents in intensive care units during a novel coronavirus infection pandemic (COVID-19)

Introduction. The novel coronavirus infection (COVID-19) pandemic has been a major challenge to the global healthcare system, affecting more than 32 million patients worldwide. Unprecedented anti-epidemic measures carried out in hospitals allowed clinicians to hope for a decrease of hospital infection, however, the pandemic exacerbated the problem of the spread and circulation of multidrug-resistant bacteria in hospitals. The goal of study to conduct a comparative assessment of changes in the microbial landscape and the level of antibiotic resistance of the main pathogens of lower respiratory tract infections in ICU patients who were in different epidemiological conditions during the COVID-19 pandemic in comparison with the “pre-Covid” period. Materials and methods. A multicenter retrospective observational cohort study was conducted, which included the ICU of 4 hospitals in Yekaterinburg, which were in different epidemiological situations during the COVID-19 pandemic, as well as a comparative analysis of the length of stay of patients in the ICU, the frequency and duration of mechanical ventilation, the resuscitation mortality rate, and also the results of microbiological examination of sputum with an assessment of the structure of pathogens and the level of their antibiotic resistance. Results. The structure of pathogens in sputum in ICU patients of the “green zone” has not fundamentally changed. In the “red zone” there was an increase in the number of documented infections of the lower respiratory tract and blood flow, while hospitals showed differences in changes in the microbial landscape. The microbiological situation in the ICU of the “red zone” was characterized by a decrease in the number of isolated strains of Enterobacterales and non-fermenting Gram-negative bacteria by the end of the pandemic, as well as a significant increase fungi in sputum. In hospitals, where there was an alternation of periods of work in the “red” and “green” zones, there was a decrease of Enterobacterales, an increase in non-fermenting Gram-negative bacteria and a fungi. Among the microflora isolated by bacteriological methods in patients with COVID-19, gram-negative bacteria and fungi predominated, mainly Klebsiella pneumonia, Acinetobacter baumanii and fungi of the Candida spp. A significant increase in the proportion of fungi in sputum was noted in ICU patients in infectious diseases hospitals during the pandemic period. An increase in the level of antibiotic resistance of the main pathogens of lower respiratory tract infections was revealed with the appearance of multi-resistant and extremely resistant strains of Klebsiella pneumoniae and Acinetobacter baumanii. Discussion. Changes in the microbial landscape may indirectly reflect the features of immune damage in patients with a new coronavirus infection COVID-19, which, combined with the severity of the disease and the characteristics of its therapy, led to an increase in complications in the form of a secondary bacterial infection. The reasons for the increase in HAI cases include: an increase in the number of patients with severe comorbidities in an artificial closed ecosystem - the “red zone”; features of the methods of treatment (glucocorticosteroids, genetically engineered biological products - IL-6 inhibitors, etc.); high frequency of unreasonable use of antibacterial drugs; increase in the duration ofuse of various invasive devices and mechanical ventilation; changing the structure and practice of staffing hospitals, increasing the number of inexperienced medical workers and volunteers; inadequate hand hygiene, use of unsuitable individual protection means with a lack of developed methods for their processing in the new conditions. Conclusion. The results obtained indicate the importance of the work of a multidisciplinary with a microbiologist, epidemiologist, clinical pharmacologist in order to improve the quality of care for patients, especially in a difficult epidemiological situation. Surveillance over the spread of HAI pathogens should be attributed to the most progressive form of anti-epidemic activity. Microbiological monitoring and its results can serve as the basis for making managerial decisions to combat and prevent hospital infections. It is the main method for assessing the etiology, phenotype, mechanisms of resistance to antimicrobial drugs, allows you to identify epidemiological relationships between diseases, reasonably prescribe antibiotic therapy, and conduct targeted purchases of drugs (antibiotics) for the needs of this hospital.

2588. Burden of Mortality and Antimicrobial Resistance of Bacterial Pathogens Associated with Lower Respiratory Tract and Other Thorax Infection in United States in 2019: A Systematic Analysis

Abstract Background Detailed information about the impact of bacterial antimicrobial resistance (AMR) on Lower Respiratory Tract and other thorax Infections (LRTIs) is currently unavailable. It is important to have precise data on bacterial AMR to develop effective programs and policies for controlling AMR and to use antibiotics prudently for optimal treatment of LRTI patients. The primary objective of this research is to present extensive estimates of the mortality due to "bacterial pathogens" and its "AMR" of LRTIs in the United States in 2019. Methods Mortality data associated with bacterial antimicrobial resistance and lower respiratory tract infection (LRTI) pathogens were acquired from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) in 2019. Results In United States, there were 88089 deaths (95% uncertainty interval [UI]: 66909-117145) due to bacterial pathogens in LRIT in 2019. Highest number of deaths observed due to Staphylococcus aureus (34.04%), followed by Streptococcus pneumoniae (18.30%), Pseudomonas aeruginosa (12.48%) in LRTI in 2019. There were 10984 deaths attributed to and 46482 deaths associated with bacterial AMR in LRTI in 2019. Conclusion Bacterial pathogens causing LRTIs are a significant cause of mortality in the United States. Moreover, antimicrobial resistance (AMR) among these pathogens has become a growing concern, exacerbating the burden of LRTI-related deaths. The implementation of such measures, along with the promotion of antimicrobial stewardship, can help to mitigate the impact of LRTI-associated deaths and preserve the effectiveness of available antimicrobial agents for the future. Disclosures All Authors: No reported disclosures

ANTIBIOTIC RESISTANCE OF BACTERIAL PATHOGENS IN LOWER RESPIRATORY TRACT INFECTIONS

This article provides an overview of scientific studies on the problem of microbial resistance to antibiotics. It summarizes current concepts of antibiotic resistance, the division of microorganisms into sensitive and resistant to antibiotics, and explains the concept of minimal inhibitory concentration from a modern perspective. The main mechanisms of the development of antibiotic resistance, vectors, and genes responsible for the transmission of resistance are revealed. Microorganism resistance to antibacterial agents can be innate or acquired. The bacterial pathogens of respiratory infections, such as Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, and other gram-positive and gram-negative bacteria, are described. Non-hereditary resistance mechanisms are shown, including changes in metabolic activity, phenotypic plasticity, and biofilm formation. The factors involved in the acquisition and transmission of antibiotic resistance, as well as the evolution of antibiotic resistance, which goes through several key stages, are discussed. One of the vectors in studying the evolution of antibiotic resistance should be the analysis of bacterial communities forming biofilms rather than isolated bacterial strains, as microorganisms in biofilms exhibit low sensitivity to various antibiotics due to phenotypic resistance mechanisms.The methods of combating antibiotic resistance include several approaches: rational use of antibiotics, development of new antibiotics, and vaccination

Multicenter evaluation of the Acaruiter Respiratory Panel for diagnosis of respiratory tract infections in Chinese children.

Respiratory tract infection represents the most frequent infectious disease afflicting children worldwide. This study was to evaluate the performance of Acaruiter Respiratory Panel (fluorescent PCR) in the detection of respiratory tract infection pathogens in children. Clinical trials were conducted in three representative pediatric hospitals in Shanghai, Chengdu, and Beijing. With reference to another widely used multiplex assay and first-generation sequencing, the sensitivity, specificity, accuracy, and consistency coefficient kappa (κ) value of the assay were evaluated to verify the accuracy and effectiveness in the detection of clinical respiratory pathogens, so as to objectively evaluate the clinical performance and application value of Acaruiter Respiratory Panel (fluorescent PCR). A total of 1,540 samples were screened in this clinical trial project, of which 1,404 were valid samples. Based on the comprehensive analysis of the clinical trial data of 1,404 effective samples, the detection ability of Acaruiter Respiratory Panel (fluorescent PCR) for various pathogens compared with the results of clinical diagnosis, the positive percent agreement was 97.04%-100%, the negative percent agreement was 99.31%-100%, the total percent agreement was 99.36%-100%, and the kappa value was 0.982-1.000, which had good consistency and high accuracy.IMPORTANCECompared to multiplex PCR assays that are available in the Chinese market, the Acaruiter Respiratory Panel (fluorescent PCR) covers a wider range of pathogens including eight viruses, five bacteria, Mycoplasma pneumoniae and Chlamydia pneumoniae, and has high accuracy and effectiveness in the detection of pathogens. This is the first study to evaluate the performance of the Acaruiter Respiratory Panel. This regent may be a promising assay for comprehensive testing for respiratory pathogens from nasopharyngeal swab specimens in Chinese children.

Pharynx infectious and inflammatory diseases local etiotropic therapy efficacy comprehensive assessment in preschool and primary school-age children

Background. The oropharyngeal microbiota is important in maintaining resistance, eliminating viruses and regulating local protective reactions in response to inflammation in acute respiratory infections.&#x0D; Aim. To evaluate of the effect of topical etiotropic therapy on clinical manifestations, elimination of viruses and on oropharyngeal microbiota in the treatment of acute infectious inflammation of the throat that occurred as part of acute respiratory infections in children aged 510 years.&#x0D; Materials and methods. 120 outpatient patients randomized into 3 equal groups were treated for 7 days: in Group 1 0.2% hexethidine-containing aerosol, in Group 2 0.03 mg combined spray gramicidin S and 0.1 mg cetylpyridinium chloride, in Group 3 0.01% topical solution containing benzyldimethyl-myristoylamino-propylammonium. Changes in the severity of clinical manifestations were compared (integral indicator modified Tonsillopharyngitis Severity Score TSSm for children, the severity of the "sore throat" symptom on the WongBaker scale, the severity of local signs of inflammation according to pharyngoscopy data) in groups at Visit 2 (day 51) and Visit 3 (day 121) compared with the Visit 1. The elimination of acute respiratory infection pathogens was evaluated: polymerase chain reaction (PCR) of oropharyngeal smears obtained on days 1, 3 and 5 (1) PCR-1, PCR-2, PCR-3 respectively, with the detection of 12 respiratory viruses, including SARS-CoV-2. The state of the microbiota was assessed by sequencing the full-size 16S gene in samples obtained before and after treatment 1st and 12th (1) days, and compared with 19 indicators in healthy.&#x0D; Results. By Visit 3, the decrease in TSSm indicators was: 4.01.07 in Group 1; 5.01.48 in Group 2 and 4.01.02 in Group 3. The intergroup differences between Group 2 and 1, Group 2 and 3 were statistically significant (p0.05). The severity of sore throat by Visit 3 decreased in groups 1, 2 and 3 respectively by 2.00.90, 2.50.61 and 2.10.60, intergroup differences between groups 2 and 1, 2 and 3 had statistical significance at p0.05. The time to achieve complete relief of the disease according to the TSSm indicator was (day, MSE): 16.61.47 in Group 1; 11.91.13 in Group 2 and 12.41.38 in Group 3, intergroup differences (groups 1 and 2) are significant, p0.05. The time of complete relief from sore throat for groups 13 was 12.60.96, 8.00.87 and 9.41.01 respectively, intergroup differences (groups 1 and 2) were significant, p0.05. By Visit 2, the proportion of patients with a negative PCR result increased in Group 1 by 25%, in Group 2 by 43% and in Group 3 by 38%, which corresponded to the elimination of 81, 92 and 74% of viruses detected in groups according to PCR-1 and PCR-2. The microbiota of participants in all groups before treatment differed from the microbiota of healthy in terms of alpha and beta diversity, as well as in terms of indicators obtained by the NearesBalance method. After completion of treatment, changes in the microbiota in terms of beta diversity were observed in all groups compared to the initial state. In contrast to groups 1 and 3, in Group 2 there were statistically significant changes in species-level balances between groups of microbes that distinguish between sick and healthy, towards indicators of healthy.&#x0D; Conclusion. Topical etiotropic medications provide rapid relief of complaints and local signs of inflammation in the treatment of patients aged 510 years with sore throat in acute respiratory infections and contribute to the rapid elimination of pathogens of acute respiratory infections. A combined preparation containing an antiseptic and a bacteriocin-like antimicrobial peptide gramicidin S provides a more pronounced therapeutic effect at an earlier time and the elimination of 90% of all respiratory viruses, including SARS-CoV-2, by the fifth day of therapy, and also has the most sparing effect on the oropharyngeal microbiota compared to antiseptic monopreparations, which may explain its more pronounced anti-inflammatory effect.

The CD19+ B cell as a marker for the febrile children infected with influenza A and Omicron variant.

H3N2 and Omicron are common pathogens of respiratory infections in children. This study aimed to explore dynamic changes of lymphocyte subsets and the diagnostic value of CD19+ B cell in children infected with influenza A and Omicron. One hundred and sixty-five in-patients with H3N2, 175 in-patients with Omicron variant, and 50 age-matched healthy children from Children's Hospital of Soochow University were included in this study. The participants underwent 13 respiratory pathogens by DNA polymerase chain reaction (PCR), sputum culture, severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) DNA PCR, routine blood, and lymphocyte subset assays within 24 h of admission. The neutrophils, neutrophil-to-lymphocyte ratio, and monocyte-to-lymphocyte ratio in the H3N2 and Omicron groups were significantly higher than in the control groups (p < 0.05). However, the lymphocytes and eosinophils in the H3N2 and Omicron groups were lower than the control groups (p < 0.05). The CD3+ T cell, CD3+ CD4+ T cell, CD3+ CD8+ T cell, CD3- CD19+ B cell, and natural killer cell were lower in the H3N2 and Omicron groups than in the control group (p < 0.05). The CD3- CD19+ cell in the Omicron group was higher than that in the H3N2 group but lower than that in the control group (p < 0.05). In addition, CD3- CD19+ cell had good diagnostic value for H3N2 (area under the receiver operating characteristic curve = 0.902, p < 0.05). The children with H3N2 were more likely to have lower lymphocytes than children with Omicron. Additionally, B-cell count had good diagnostic value for H3N2.

Smart-Plexer: a breakthrough workflow for hybrid development of multiplex PCR assays

Developing multiplex PCR assays requires extensive experimental testing, the number of which exponentially increases by the number of multiplexed targets. Dedicated efforts must be devoted to the design of optimal multiplex assays ensuring specific and sensitive identification of multiple analytes in a single well reaction. Inspired by data-driven approaches, we reinvent the process of developing and designing multiplex assays using a hybrid, simple workflow, named Smart-Plexer, which couples empirical testing of singleplex assays and computer simulation to develop optimised multiplex combinations. The Smart-Plexer analyses kinetic inter-target distances between amplification curves to generate optimal multiplex PCR primer sets for accurate multi-pathogen identification. In this study, the Smart-Plexer method is applied and evaluated for seven respiratory infection target detection using an optimised multiplexed PCR assay. Single-channel multiplex assays, together with the recently published data-driven methodology, Amplification Curve Analysis (ACA), were demonstrated to be capable of classifying the presence of desired targets in a single test for seven common respiratory infection pathogens.

Molecular Epidemiology and Genetic Diversity of Human Respiratory Syncytial Virus in Sicily during Pre- and Post-COVID-19 Surveillance Seasons.

Human respiratory syncytial virus (hRSV) is an important pathogen of acute respiratory tract infection of global significance. In this study, we investigated the molecular epidemiology and the genetic variability of hRSV over seven surveillance seasons between 2015 and 2023 in Sicily, Italy. hRSV subgroups co-circulated through every season, although hRSV-B mostly prevailed. After the considerable reduction in the circulation of hRSV due to the widespread implementation of non-pharmaceutical preventive measures during the COVID-19 pandemic, hRSV rapidly re-emerged at a high intensity in 2022-2023. The G gene was sequenced for genotyping and analysis of deduced amino acids. A total of 128 hRSV-A and 179 hRSV-B G gene sequences were obtained. The phylogenetic analysis revealed that the GA2.3.5a (ON1) and GB5.0.5a (BA9) genotypes were responsible for the hRSV epidemics in Sicily.; only one strain belonged to the genotype GB5.0.4a. No differences were observed in the circulating genotypes during pre- and post-pandemic years. Amino acid sequence alignment revealed the continuous evolution of the G gene, with a combination of amino acid changes specifically appearing in 2022-2023. The predicted N-glycosylation sites were relatively conserved in ON1 and BA9 genotype strains. Our findings augment the understanding and prediction of the seasonal evolution of hRSV at the local level and its implication in the monitoring of novel variants worth considering in better design of candidate vaccines.

Whole genome sequencing and evolution analyses of Human metapneumovirus.

Human metapneumovirus (HMPV) is a major pathogen of acute respiratory tract infections (ARTIs) in children. Whole genome sequence analyses could help understand the evolution and transmission events of this virus. In this study, we sequenced HMPV whole genomes to improve the identification of molecular epidemiology in Beijing, China. Nasopharyngeal aspirates of hospitalized children aged < 14years old with ARTIs were screened for HMPV infection using qPCR. Fourteen pairs of overlapping primers were used to amplify whole genome sequences of HMPV from positive samples with high viral loads. The epidemiology of HMPV was analysed and 27 HMPV whole genome sequences were obtained. Sequence identity and the positional entropy analyses showed that most regions of HMPV genome are conserved, whereas the G gene contained many variations. Phylogenetic analysis identified 25 HMPV sequences that belonged to a newly defined subtype A2b1; G gene sequences from 24 of these contained a 111-nucleotide duplication. HMPV is an important respiratory pathogen in paediatric patients. The new subtype A2b1 with a 111-nucleotide duplication has become predominate in Beijing, China.

The effectiveness of a polyvalent antigenic complex including bacterial lysates in the treatment and prevention of rhinosinusitis against the background of acute respiratory viral infections and COVID-19 (clinical description)

One of the urgent tasks of the Ministry of Health of the Russian Federation, noted in the State report on the state of sanitary and epidemiological welfare of the population, is the improvement and implementation of diagnostic and treatment and prevention technologies. First of all, this concerns the continued growth of respiratory viral infections, seasonal influenza epidemics, where SARS-CoV-2 coronavirus infection occupies a special place, which often cause various otorhinolaryngological complications – acute and exacerbations of chronic tonsillopharyngitis, rhinosinusitis, tubotitis, purulent otitis media. In the treatment of bacterial sinusitis, in accordance with clinical recommendations, intranasal corticosteroids, elimination therapy, herbal remedies, and antibacterial drugs are used. Due to the period of the SARS-CoV-2 pandemic, a significant proportion of patients took large doses of antibacterial drugs, which caused an increase in the resistance of microorganisms to them. In this regard, it is possible to use immunostimulating drugs that stimulate cellular and humoral immunity, promote the development of a specific immune response and activate nonspecific defense factors such as lysozyme, mucin, lactoferrin and normalize mucociliary clearance. As a rule, the identification of a viral agent is carried out in case of a severe clinical course of the disease or complications from the ORL and other organs, and the use of immunostimulating agents in complex therapy is necessary at the earliest possible time of the disease. In this context, the use of immunostimulants containing polyvalent antigenic complexes, including bacterial lysates, the most common pathogens of respiratory infections, is justified. It is preferable in these cases to use lysates of bacteria obtained by mechanical destruction of bacterial cells, since they have a more pronounced non-specific immunostimulatory and specific vaccinating effect.