The lung microbiome in patients with HIV complicated with community-acquired pneumonia: a cross-sectional pilot study

The lung microbiota plays a key role in respiratory health, but its composition in individuals living with HIV and diagnosed with community-acquired pneumonia (CAP) remains underexplored. A prospective cohort study in Medellín, Colombia recruited individuals with CAP and/or HIV between 2016 and 2018. Clinical and microbiological data were collected at baseline, with bronchoalveolar lavage samples obtained at baseline and induced sputum samples collected at baseline and 6-month follow-up. Microbiota composition was analyzed in these samples using Illumina MiSeq sequencing of the 16S ribosomal RNA gene. Among 248 screened participants, 64 were included: HIV and CAP (n = 27), CAP (n = 7), and HIV (n = 30); 70.3% were males, and 76.6% were between 25 and 64 years old. The HIV and CAP group had a lower proportion of receiving antiretroviral treatment and a higher prevalence of advanced immunosuppression. The most frequent micro-organisms identified by conventional methods in the HIV and CAP group were Mycobacterium tuberculosis (40.7%) and Pneumocystis jirovecii (18.5%). The dominant phyla (Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, and Actinobacteria) and genera (Streptococcus, Haemophilus, Veillonella, Neisseria, and Fusobacterium) were identified in the overall study population, including both baseline and 6-month follow-up samples. The HIV and CAP group showed changes in bacterial diversity and relative abundance over 6 months. These findings provide insights into the dynamic lung microbiota in individuals coinfected with HIV and CAP, highlighting the impact of HIV and CAP on microbial composition and diversity, which may inform future studies exploring clinical outcomes.

Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIV-positive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.

At the moment, an increase in the incidence of community-acquired pneumonia is quite an urgent problem. Its solution is based on the use of adequate antibacterial therapy, which will help significantly reduce the spread of the disease among children included in the risk group.
 Goal: Conducting a comprehensive assessment of etiological therapy tactics for community-acquired bacterial pneumonia in children and determining their compliance with modern clinical recommendations.
 Materials and methods: The study was conducted on the basis of the Voronezh Childrens Clinical Hospital of the Voronezh State Medical University named after N.N. Burdenko. A retrospective analysis of 18 case histories of patients aged 3 to 14 years who were treated from October 2021 to March 2022 with a diagnosis of community-acquired pneumonia of moderate severity was carried out.
 Results: During the analysis of the medical histories of children diagnosed with community-acquired pneumonia, it was found that the diagnosis of the patients condition was complete and sufficient in each of the cases considered, with the exception of the absence of sputum in terms of bacteriological examination, because the treatment was more empirical in nature, directed against the frequently detected pathogen determining the formation of this nosological form S. rpeimopiae.
 Conclusion: As a result of a comprehensive assessment of the tactics of etiological therapy of community-acquired bacterial pneumonia in children, it was revealed that effective antibiotic therapy was chosen for all patients in accordance with the severity of the disease and instructions for the use of antibacterial drugs, which led to the gradual elimination of clinical symptoms of community-acquired pneumonia.

Little is known about the composition and clinical implications of lung microbiome in patients with chronic obstructive pulmonary disease (COPD) and community-acquired pneumonia requiring invasive mechanical ventilation and intensive care unit admission. Therefore, this study aimed to explore the longitudinal changes in microbial airway composition and its variations between COPD patients with different weaning outcomes. Fifty-one endotracheal aspirate samples from 21 participants and 5 saline samples were collected as the patient and control group, respectively. Sequence analysis revealed significant increases and upward trends in the relative abundance of the Acinetobacter genus and Acinetobacter baumannii complex species in paired comparisons of sampling points and over time, respectively, in patients with failed weaning (p for trend = 0.012 and 0.012, respectively) but not in those with successful weaning (p for trend = 0.335 and 0.426, respectively). Furthermore, significant changes in the composition of the bacterial community were observed in paired comparisons of sampling points in patients with failed weaning compared with those with successful weaning. The alpha diversity did not differ between the patients with different weaning outcomes. These results further the understanding of longitudinal airway microbiome structure analysis and its clinical implications when managing critically ill patients with and without COPD.

The respiratory microbiome after lung transplantation: Reflection or driver of respiratory disease?

Limited information is available regarding the impact of prior outpatient use of systemic corticosteroids (SCS) in patients subsequently developing community-acquired pneumonia (CAP). We investigate the effects of prior SCS on severity of illness, microbiology and clinical outcomes for patients hospitalized with CAP. A retrospective cohort study of subjects with CAP (according to International Classification of Diseases, 9th edition codes) was conducted over a 3-year period at two tertiary teaching hospitals. Subjects were considered to be SCS users if they received oral corticosteroids prior to admission. Primary outcomes were severity of illness, microbiology and 30-day mortality. Data were abstracted on 698 patients [prior SCS users, 75 (10.7%) versus prior non-SCS users 623 (89.3%)]. Prior SCS users were more likely to have chronic obstructive pulmonary disease. No differences were found in severity of disease at admission, microbiological etiology including opportunistic and drug-resistant pathogens and clinical outcomes, including 30-day mortality, intensive care unit admission, length of hospital stay, need for mechanical ventilation and need for vasopressors. Prior SCS use is not associated with increased 30-day mortality for patients hospitalized with CAP. In addition, no differences were found in either the severity of the disease at the time of presentation or in the presence of the resistant or opportunistic pathogens among groups.

ObjectiveTo determine the prevalence and factors associated with left ventricular diastolic dysfunction in children with HIV/AIDS.MethodEchocardiographic studies were carried out in 90 children/adolescents aged 18 months to 14 years.with HIV/AIDS and a healthy control group of 90 age and gender matched.Results47.8% of the HIV/AIDS patients (subjects) had LVDD. This was more pronounced in the AIDS group (100%). The E/A ratio was 1.9 ± 0.56 in the HIV group, 2.09 ± 0.04 in the AIDS group, and 1.20 ± 0.39 in the control group (p = 0.04). The mean Left ventricular isovolumic relaxation time (IVRT) was 79.4 ± 20.12 in the HIV group, 110.4 ± 10.12 in the AIDS group and 89.22 ± 25.76 in the control group. (p = 0.04). Deceleration time (DT) was also lower in HIV carrier group compared to AIDS group, p = 0.02. A restrictive filling pattern was the most described; with 27 (36.5%) in the HIV group, 16 (100.0%) in the AIDS group and 2 (2.2%) in the control group. (p = 0.02). The impaired relaxation pattern, 3 (4.0%) seen in the HIV group only. Positive correlation exists between body surface area (BSA) and LVDD. Body surface area and younger age were the significant predictors (BSA: r = 0.425, p = 0.038 in HIV and r = 0.827, p = 0.042) of LVDD in the AIDS group.ConclusionThis study showed a high prevalence of LVDD in Nigerian children with HIV and AIDS. This justifies inclusion of echocardiographic studies in the policy care of children with HIV/AIDS in sub-Sahara Africa region.

The study of the secretory leukocyte protease inhibitor (SLPI) level in children with pneumonia is important because it may indicate protease-antiprotease imbalance and predict local regulation of proteolytic activity at different degrees of pneumonia in children. The aim of the study was to assess the level of SLPI as a marker of proinflammatory response in the serum of young children, depending on the severity of pneumonia, including the presence or absence of lesions of the hepatobiliary system. The study investigated the SLPI as a marker of the inflammatory response in children with community-acquired pneumonia, depending on the severity of the disease, lesions of the hepatobiliary system, age and sex. The level of SLPI in the serum was determined by enzyme-linked immunosorbent assay using a diagnostic test system from “IMMUNOTECH” (France). “IBM SPSS Statistica” Version 12 (20) was used for statistical processing of the results. It was found that the course of community-acquired pneumonia is accompanied by an increase in the serum level of SLPI in children in parallel with the severity of the disease. The development of a lesion from the GBS reduces the level of a protease inhibitor in the blood serum of children with pneumonia, which indicates a decrease in the body's defense systems. In children 1-12 months, the level of SLPI is higher than in children 13-36 months, which indicates more significant protective capabilities of the body of children in the first year of life. It has been shown that an increase in the level of SLPI correlates with an increase in the level of inflammatory cytokines, which indicates a unidirectional change in the formation of local immunity in response to damage to the lung tissue. At the same time, a negative correlation was found between the level of SLPI and the activities of AST, GGT and CRP (rxy= -0.054; rxy= -0.215; rxy= -0.215, respectively), which indicates a violation of liver function during the development of an infectious-inflammatory process in the body. Studies of the nature of the effects of cytokines and protease inhibitors (protective factors) on the development and maintenance of inflammatory process in the lungs in young children with community-acquired pneumonia with lesions of the hepatobiliary system may be the basis for predicting its course.

Community-acquired pneumonia (CAP) is one of the leading reasons for background prescribing antibacterial therapy (ABT) in pediatric practice. In 2015, the Russian Pediatric Respiratory Society published a guideline on CAP in children. Objective. To assess compliance with the recommendations of starting ABT for CAP of pediatric inpatients in various regions of the Russia. Materials and methods. We reviewed the medical records of pediatric patients with CAP who were hospitalized in 2017–2018. The study was in 6 regions of the Russia. A total of 793 cases of CAP were studied in children aged 1 month to 16 years. We analyzed data from patients, such as demographic indicators, severity of the disease, the presence and nature of complications, and starting ABT. Results. The patient’s age ranged from 1 month to 16 years (average – 4.33 years). The amount of cases of severe CAP was 5.55%, in the remaining 94.45% of cases there was a moderate CAP. Complications were present among 3.91% of patients. The overwhelming majority of patients received parenteral ABT (more than 89%). In the majority of cases, third-generation cephalosporins (65.2%) were used as starting therapy. Amoxicillin was prescribed in only 4.04% of patients. The combination therapy was used in 13.27% of cases (beta-lactam with macrolides or aminoglycosides used most often). We found a significant discrepancy between the actual practice of the recommendations: excessive use of parenteral and combined ABT, private prescription of 3rd generation cephalosporins and rare prescription of amoxicillin, the use of aminoglycosides (including as monotherapy). Conclusion. The use of antibiotics for CAP in children in Russia is often incorrect, which can reduce the effectiveness of treatment and contribute to an increase in antimicrobial resistance. Increased education of pediatricians in ABT and the introduction of antibiotic control is required to address this problem. Key words: children, community-acquired pneumonia, antibiotic therapy

The treatment of community-acquired pneumonia (CAP) in children is empirical, being based on the knowledge of the etiology of CAP at different ages. As a result of currently available methods in everyday clinical practice, a microbe-specific diagnosis is not realistic in the majority of patients. Even the differentiation between viral, 'atypical' bacterial (Mycoplasma pneumoniae or Chlamydia pneumoniae) and 'typical' bacterial (Streptococcus pneumoniae) CAP is often not possible. Moreover, up to one-third of CAP cases seem to be mixed viral-bacterial or dual bacterial infections. Recent serologic studies have confirmed that S. pneumoniae is an important causative agent of CAP at all ages. M. pneumoniae is common from the age of 5 years onwards, and C. pneumoniae is common from the age of 10 years onwards. In addition to age, the etiology and treatment of CAP are dependent on the severity of the disease. Pneumococcal infections are predominant in children treated in hospital, and mycoplasmal infections are predominant in children treated at home.In ambulatory patients with CAP, amoxicillin (or penicillin V [phenoxymethylpenicillin]) is the drug of choice from the age of 4 months to 4 years, and at all ages if S. pneumoniae is the presumptive causative organism. Macrolides, preferably clarithromycin or azithromycin, are the first-line drugs from the age of 5 years onwards. In hospitalized patients who need parenteral therapy for CAP, cefuroxime (or penicillin G [benzylpenicillin]) is the drug of choice. Macrolides should be administered concomitantly if M. pneumoniae or C. pneumoniae infection is suspected. Radiologic findings and C-reactive protein (CRP) levels offer limited help for the selection of antibacterials; alveolar infiltrations and high CRP levels indicate pneumococcal pneumonia, but the lack of these findings does not rule out bacterial CAP. Most guidelines recommend antibacterials for 7-10 days (except azithromycin, which has a recommended treatment duration of 5 days). If no improvement takes place within 2 days, therapy must be reviewed.

This study was performed to determine the type of periodontal pathology found in a group of HIV+ patients and its relation to serum levels of CD4. The sample consisted of 101 individuals: intravenous drug users (84%), homosexuals (7%), and heterosexuals (10%). Each patient was examined clinically and radiographically. Periodontal clinical parameters included gingival index and probing depth and loss of attachment on four sites per tooth. Severity of disease was defined as the most severe lesion found: gingivitis, or early, moderate, or advanced periodontitis. CD4 counts were determined on 64 of these patients. Associations between severity of the disease and gender and CD4 counts were analyzed using the Mantel Haenszel chi square test, while associations between severity and age and CD4/CD8 ratio were analyzed using the Kruskal-Wallis test. No disease was found in 14.8% of the sample, gingivitis was found in 21.8%, early periodontitis in 43.6%, moderate periodontitis in 10.9%, and advanced periodontitis in 8.9%. Linear gingival erythema (LGE) was seen in 17.8% of all patients and necrotizing periodontitis (NUP) in 4.9%. No statistically significant differences were observed between the severity of the disease and CD4 counts.

Microbial metabolic efficiency and community stability in high and low fertility soils following wheat residue addition

The influence of wet-to-dry season shifts on the microbial community stability and nitrogen cycle in the Poyang Lake sediment

Community-acquired pneumonia (CAP) is one of the most common acute infectious diseases. To date, the incidence of CAP among children was decreased significantly worldwide, mainly due to increasing use of effective preventive measures. Nevertheless, CAP remains a common cause of childhood morbidity and mortality. Pneumonia may develop at any age, but most often it occurs in young children, who are more likely to have a more severe course of pneumonia. Currently, early diagnosis and prognosis of the disease severity in children is an urgent issue. It was found that, in most cases, a panel of conventional biomarkers, including the number of leukocytes, procalcitonin, CRP is not sufficient for the diagnosis of pediatric CAP. There is a demand for new biological markers which, along with clinical evaluation, may significantly improve diagnostics and management of CAP in children, thus reducing the risk of adverse outcomes associated with this disease. Such markers could be found among the cytokines, which are active participants in the CAP pathogenesis. The aim of this study was to determine the level of several cytokines in blood serum of children with CAP and to assess changes in the cytokine profile depending on the patient’s age and severity of the disease. The study included 117 children aged 1 to 18 years with a diagnosis of CAP confirmed by X-ray examination. The comparison group included 28 healthy children who did not have CAP or other signs of acute respiratory viral infection at the time of examination, being free of any chronic pathology requiring outpatient observation. A number of cytokines were determined quantitatively in blood serum, i.e., IL-1β, IFNγ, IL-2, IL-4, IL-6, IL-10, TNFα, IFNλ2 (IL-28A), IFNλ3 (IL-28B), IL-8, MCP-1, IL-17AF, GM-CSF using test systems based on the “sandwich” method of solid-phase ELISA using peroxidase labeling. As a result, it was found that the content of IL-6, IL-17AF, IL-1β, IFNγ, MCP-1, IFNλ2 (IL-28A), IFNλ3 (IL-28B), GM-CSF was significantly higher in the group of children with severe community-acquired pneumonia. The levels of certain cytokines, e.g., IL-6, IFNλ2 (IL-28A), IFNλ3 (IL-28B), GM-CSF varied depending on the age of patients, thus, probably, reflecting the degree of immune system activation in the children of different age groups.

The treatment of community-acquired pneumonia (CAP) in children is empirical, being based on the knowledge of the etiology of CAP at different ages. As a result of currently available methods in everyday clinical practice, a microbe-specific diagnosis is not realistic in the majority of patients. Even the differentiation between viral, ‘atypical’ bacterial (Mycoplasma pneumoniae or Chlamydia pneumoniae) and ‘typical’ bacterial (Streptococcus pneumoniae) CAP is often not possible. Moreover, up to one-third of CAP cases seem to be mixed viral-bacterial or dual bacterial infections. Recent serologic studies have confirmed that S. pneumoniae is an important causative agent of CAP at all ages. M. pneumoniae is common from the age of 5 years onwards, and C. pneumoniae is common from the age of 10 years onwards. In addition to age, the etiology and treatment of CAP are dependent on the severity of the disease. Pneumococcal infections are predominant in children treated in hospital, and mycoplasmal infections are predominant in children treated at home.