Colonization Of Respiratory Tract Research Articles

Genetic Adaptation and Acquisition of Macrolide Resistance in Haemophilus spp. during Persistent Respiratory Tract Colonization in Chronic Obstructive Pulmonary Disease (COPD) Patients Receiving Long-Term Azithromycin Treatment.

Patients with chronic obstructive pulmonary disease (COPD) benefit from the immunomodulatory effect of azithromycin, but long-term administration may alter colonizing bacteria. Our goal was to identify changes in Haemophilus influenzae and Haemophilus parainfluenzae during azithromycin treatment. Fifteen patients were followed while receiving prolonged azithromycin treatment (Hospital Universitari de Bellvitge, Spain). Four patients (P02, P08, P11, and P13) were persistently colonized by H. influenzae for at least 3 months and two (P04 and P11) by H. parainfluenzae. Isolates from these patients (53 H. influenzae and 18 H. parainfluenzae) were included to identify, by whole-genome sequencing, antimicrobial resistance changes and genetic variation accumulated during persistent colonization. All persistent lineages isolated before treatment were azithromycin-susceptible but developed resistance within the first months, apart from those belonging to P02, who discontinued the treatment. H. influenzae isolates from P08-ST107 acquired mutations in 23S rRNA, and those from P11-ST2480 and P13-ST165 had changes in L4 and L22. In H. parainfluenzae, P04 persistent isolates acquired changes in rlmC, and P11 carried genes encoding MefE/MsrD efflux pumps in an integrative conjugative element, which was also identified in H. influenzae P11-ST147. Other genetic variation occurred in genes associated with cell wall and inorganic ion metabolism. Persistent H. influenzae strains all showed changes in licA and hgpB genes. Other genes (lex1, lic3A, hgpC, and fadL) had variation in multiple lineages. Furthermore, persistent strains showed loss, acquisition, or genetic changes in prophage-associated regions. Long-term azithromycin therapy results in macrolide resistance, as well as genetic changes that likely favor bacterial adaptation during persistent respiratory colonization. IMPORTANCE The immunomodulatory properties of azithromycin reduce the frequency of exacerbations and improve the quality of life of COPD patients. However, long-term administration may alter the respiratory microbiota, such as Haemophilus influenzae, an opportunistic respiratory colonizing bacteria that play an important role in exacerbations. This study contributes to a better understanding of COPD progression by characterizing the clinical evolution of H. influenzae in a cohort of patients with prolonged azithromycin treatment. The emergence of macrolide resistance during the first months, combined with the role of Haemophilus parainfluenzae as a reservoir and source of resistance dissemination, is a cause for concern that may lead to therapeutic failure. Furthermore, genetic variations in cell wall and inorganic ion metabolism coding genes likely favor bacterial adaptation to host selective pressures. Therefore, the bacterial pathoadaptive evolution in these severe COPD patients raise our awareness of the possible spread of macrolide resistance and selection of host-adapted clones.

Pathogenic determinants of Kingella kingae disease.

Kingella kingae is an emerging pediatric pathogen and is increasingly recognized as a leading etiology of septic arthritis, osteomyelitis, and bacteremia and an occasional cause of endocarditis in young children. The pathogenesis of K. kingae disease begins with colonization of the upper respiratory tract followed by breach of the respiratory epithelial barrier and hematogenous spread to distant sites of infection, primarily the joints, bones, and endocardium. As recognition of K. kingae as a pathogen has increased, interest in defining the molecular determinants of K. kingae pathogenicity has grown. This effort has identified numerous bacterial surface factors that likely play key roles in the pathogenic process of K. kingae disease, including type IV pili and the Knh trimeric autotransporter (adherence to the host), a potent RTX-family toxin (epithelial barrier breach), and multiple surface polysaccharides (complement and neutrophil resistance). Herein, we review the current state of knowledge of each of these factors, providing insights into potential approaches to the prevention and/or treatment of K. kingae disease.

Prevalence, Antimicrobial Resistance, and Associated Factors of Streptococcus pneumoniae Colonization Rate among Old-Age Patients with Respiratory Tract Infection Attending Sheik Hassan Yebere Referral and Karamara General Hospitals, Jigjiga, Ethiopia.

Background Streptococcus pneumoniae is part of the normal flora of the upper respiratory tract of humans. Colonization of the upper respiratory tract (carriage of pneumococcus) by S. pneumoniae is considered a prerequisite for pneumococcal infection. It is the major cause of respiratory tract infection and frequent cause of physician visits, hospitalization, and death among old-aged patients because of their low immunity status. However, data on S. pneumoniae among old-aged patients in eastern Ethiopia are limited. This study was undertaken to determine the prevalence, antimicrobial resistance, and associated factor of S. pneumoniae colonization among old-aged patients. Method A health facility-based cross-sectional study was conducted from 1 March to 15 April 2020, at Sheik Hassan Yebere Referral and Karamara General Hospitals, Jigjiga, eastern Ethiopia. A total of 188 individuals greater than or equal to 60 years suspected of both upper and lower respiratory tract infections were included. Sociodemographic, behavioral, living conditions, and clinical data were collected by trained data collectors. Sputum samples were collected and examined for S. pneumoniae using the culture and biochemical tests as per the standard procedures. The Kirby–Bauer disk diffusion method was used for antimicrobial susceptibility testing. The data were entered on Epi-data version 3.1, and frequencies, crude odds ratio, and adjusted odds ratio were analyzed using SPSS version 20. Results The prevalence of S. pneumoniae colonization rate among old-aged patients was 13.8% (26/188) (95% CI: 9.6–19.1). Smoking (AOR = 3.3; 95% CI: 1.3–8.3), upper airway problems (AOR = 4.1; 95% CI: 1.1–15), and asthma disease (AOR = 3.1; 95% CI: 1.1–8.9) were the factors associated with S. pneumoniae colonization. The isolated organisms showed high antimicrobial resistance to trimethoprim-sulphamethoxazole (n = 12, 46.2%), tetracycline (n = 11, 42.3%), and ampicillin (n = 9, 34.6%). Conclusion This study showed that high prevalence of S. pneumoniae and antimicrobial resistance for trimethoprim-sulphamethoxazole, tetracycline, and ampicillin when compared to similar studies. Cigarette smoking, having upper airway problem, and asthma disease were factors associated with S. pneumoniae colonization. The provision of pneumococci conjugate vaccination and avoiding smoking are highly recommended for old aged in the community.

P183 Monitoring of candida colonization in the respiratory tract of COVID-19 cases

Poster session 2, September 22, 2022, 12:30 PM - 1:30 PMObjectivesOpportunistic yeasts potentially cause infection or colonization in the lower respiratory tract. Candida albicans is a common agent of yeast infections but other yeasts such as non-albicans Candida are important as resistant fungi to antifungal drugs. The predisposing factors for the overgrowth and invasion by Candida species include corticosteroid therapies, long-time hospitalization, antibiotic therapies, and primary infections by Mycobacterium tuberculosis and viral agents. The screening of Candida colonization in the lower respiratory tract of the cases with a history of COVID-19 was performed in this study at a great training hospital in Northwest of Iran.MethodsDuring the pandemic COVID-19, about 445 cases with severe COVID-19 hospitalized and used dexamethasone were investigated for Candida infections and colonization by the laboratory data of Medical Mycology Center, UMS University, Urmia, Iran. Our subjects were sputum, bronco-alveolar and bronchial specimens. Candida elements including pseudo-hypha and blasto-spores microscopically were investigated. Differential cultures and PCR-RFLP were used for the identification of Candida yeasts at the level of species.ResultsTotally, 54 yeast overgrowth was detected in the clinical specimens including Candida albicans 28 (51.8%), non-albicans Candida species 24 (44.4%) and a case of Pneumocystis jirovecci. All of the cases with Candida detections were Covid-19 positive. Moreover, two cases of rhino-cerebral Mucomycosis, two cases of TB, two cases of asthma, and one case of cystic fibrosis were included.ConclusionAs a conclusion, Fungi especially Candida yeasts be considered as the potential pathogens in cases with a history of severe COVID-19 and corticosteroid therapy during stay at the hospital.

COVID-19 and the Risk for Hookah Users

After two years of the pandemic, there is still concern about COVID-19, mainly among non-vaccinated and specific groups such as patients at risk, particularly, a group of young people who may or may not be vaccinated and who are hookah users. These are exposed to trachea and lung damage considering that they use the equipment in closed places with little air exchange. Studies have shown that regular hookah users share the mouthpiece exchanging saliva and its contaminants; it well describes the presence of several bacteria in shared waterpipes, revealing potential biological hazards that may contribute to respiratory tract colonization, including case reports of patients with tuberculosis due to mouthpiece exchange. Although there is no research on the presence of coronavirus in hookah waterpipes, it was already proved that the virus is present in the self-collected saliva of 91.7% of patients with COVID-19. This coincidence may contribute to a much worse perspective of the COVID-19 pandemic in those locations.

Differentiation Between Acinetobacter Baumannii Colonization and Infection and the Clinical Outcome Prediction by Infection in Lower Respiratory Tract.

PurposeAcinetobacter baumannii is the most common microorganism in sputum cultures from long-term hospitalized patients and is often the cause of hospital-acquired pneumonia (HAP), which is usually associated with poor prognosis and high mortality. It is sometimes difficult to distinguish between A. baumannii infection and colonization. This study aimed to evaluate factors that differentiate infection from colonization and predict mortality in patients with nosocomial pneumonia caused by A. baumannii.Patients and MethodsThe data used in this study were collected in our hospital between January 2018 and December 2020 from patients whose sputum cultures were positive for A. baumannii.ResultsA total of 714 patients were included, with 571 in the infection group and 143 in the colonization group. The in-hospital mortality rate in the infection group was 20.5%. Univariate and multivariate logistic regression analyses showed that age, total number of inpatient departments, absolute neutrophil count, and C-reactive protein (CRP) level helped distinguish between infection and colonization. The area under the receiver operating characteristic curve (ROC) of the identification model was 0.694. In the infection group, age, Charlson comorbidity score, neutrophil-to-lymphocyte ratio, blood urea nitrogen/albumin ratio, CRP level, presence of multidrug resistance, and clinical pulmonary infection score (≥6) ratio were associated with in-hospital mortality. The area under the ROC curve for the prediction model was 0.828. The top three drug resistance rates in the infection group were 100% (cefazolin), 98.77% (ceftriaxone), and 71.8% (cefuroxime).ConclusionThe combination of common parameters helps identify A. baumannii respiratory tract infection or colonization. Several novel predictors can be used to predict the risk of death from A. baumannii pneumonia to reduce mortality. The drug resistance of A. baumannii remains high.

Bps polysaccharide of Bordetella pertussis resists antimicrobial peptides by functioning as a dual surface shield and decoy and converts Escherichia coli into a respiratory pathogen.

Infections and disease caused by the obligate human pathogen Bordetella pertussis (Bp) are increasing, despite widespread vaccinations. The current acellular pertussis vaccines remain ineffective against nasopharyngeal colonization, carriage, and transmission. In this work, we tested the hypothesis that Bordetella polysaccharide (Bps), a member of the poly-β-1,6-N-acetyl-D-glucosamine (PNAG/PGA) family of polysaccharides promotes respiratory tract colonization of Bp by resisting killing by antimicrobial peptides (AMPs). Genetic deletion of the bpsA-D locus, as well as treatment with the specific glycoside hydrolase Dispersin B, increased susceptibility to AMP-mediated killing. Bps was found to be both cell surface-associated and released during laboratory growth and mouse infections. Addition of bacterial supernatants containing Bps and purified Bps increased B. pertussis resistance to AMPs. By utilizing ELISA, immunoblot and flow cytometry assays, we show that Bps functions as a dual surface shield and decoy. Co-inoculation of C57BL/6J mice with a Bps-proficient strain enhanced respiratory tract survival of the Bps-deficient strain. In combination, the presented results highlight the critical role of Bps as a central driver of B. pertussis pathogenesis. Heterologous production of Bps in a non-pathogenic E. coli K12 strain increased AMP resistance in vitro, and augmented bacterial survival and pathology in the mouse respiratory tract. These studies can serve as a foundation for other PNAG/PGA polysaccharides and for the development of an effective Bp vaccine that includes Bps.

COVID-19-associated pulmonary aspergillosis: an underdiagnosed or overtreated infection?

Purpose of reviewCoronavirus disease (COVID-19)-associated pulmonary aspergillosis (CAPA) may concern up to one third of intensive care unit (ICU) patients. The purpose of this review is to discuss the diagnostic criteria, the pathogenesis, the risk factors, the incidence, the impact on outcome, and the diagnostic and therapeutic management of CAPA in critically ill patients.Recent findingsThe incidence of CAPA ranges 3--28% of critically ill patients, depending on the definition used, study design, and systematic or triggered screening. COVID-19 is associated with direct damage of the respiratory epithelium, immune dysregulation, and common use of immunosuppressive drugs which might promote Aspergillus respiratory tract colonization and invasion. Positive Aspergillus tests among COVID-19 critically patients might reflect colonization rather than invasive disease. CAPA usually appears during the second week after starting invasive mechanical ventilation and is independently associated with ICU mortality.SummaryFurther studies are needed to validate CAPA case definitions, to determine the accurate incidence of CAPA in comparison to adequate controls, and its evolution during the pandemic. A pro-active diagnostic strategy, based on risk stratification, clinical assessment, and bronchoalveolar lavage could be recommended to provide early antifungal treatment in patients with high probability of CAPA and clinical deterioration.

Colonization of the newborn respiratory tract and its association with respiratory morbidity in the first 6 months of life: A prospective cohort study

ObjectivesWe aimed to determine the association between newborn bacterial colonization and infant respiratory morbidity in the first 6 months of life. MethodsThis prospective study included healthy newborn infants. Nasopharyngeal swabs performed within 72 hours of delivery were analyzed using polymerase chain reaction. We assessed cumulative respiratory morbidity of infants at 6 months. ResultsA total of 426 mother-infant pairs were recruited. In 53.3% (n = 225) of newborns, Streptococcus pneumoniae (46%) and Staphylococcus aureus (7.3%) were isolated. None had Haemophilus influenzae nor Moraxella catarrhalis. At the age of 6 months, 50.7% of infants had experienced respiratory symptoms, 25% had unscheduled doctor visits, and 10% were treated with nebulizers. Colonization with S. pneumoniae was associated with reduced risk of any respiratory symptom (adjusted odds ratio [aOR] 0.39, 95% confidence interval [CI] 0.16, 0.50), unscheduled doctor visits (aOR 0.35; 95% CI 0.18, 0.67), and nebulizer treatment (aOR 0.23, 95% CI 0.07, 0.72) at 6 months. Pregnancy-induced hypertension was also associated with increased need for nebulizer treatment (aOR 9.11, 95% CI 1.43, 58.1). ConclusionColonization of the newborn respiratory tract occurred in 53% of infants. S. pneumoniae was the most common organism, and this was associated with a reduced risk for respiratory morbidity at 6 months of life.

Air pollution induces Staphylococcus aureus USA300 respiratory tract colonization mediated by specific bacterial genetic responses involving the global virulence gene regulators Agr and Sae.

Exposure to particulate matter (PM), a major component of air pollution, is associated with exacerbation of chronic respiratory disease, and infectious diseases such as community-acquired pneumonia. Although PM can cause adverse health effects through direct damage to host cells, our previous study showed that PM can also impact bacterial behaviour by promoting in vivo colonization. In this study we describe the genetic mechanisms involved in the bacterial response to exposure to black carbon (BC), a constituent of PM found in most sources of air pollution. We show that Staphylococcus aureus strain USA300 LAC grown in BC prior to inoculation showed increased murine respiratory tract colonization and pulmonary invasion in vivo, as well as adhesion and invasion of human epithelial cells in vitro. Global transcriptional analysis showed that BC has a widespread effect on S. aureus transcriptional responses, altering the regulation of the major virulence gene regulators Sae and Agr and causing increased expression of genes encoding toxins, proteases and immune evasion factors. Together these data describe a previously unrecognized causative mechanism of air pollution-associated infection, in that exposure to BC can increase bacterial colonization and virulence factor expression by acting directly on the bacterium rather than via the host.

Clinical impact of Candida respiratory tract colonization and acute lung infections in critically ill patients with COVID-19 pneumonia

Coronavirus disease 2019 (COVID-19), which is attributable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been causing a worldwide health issue. Airways colonization by Candida spp. is prevalent among patients on automatic ventilation in intensive care units (ICUs). This research aimed to ascertain the risk factors and roles of Candida spp. respiratory tract colonization, and Candida lung infection during the progression of COVID-19 pneumonia in critically ill patients. In total, Candida spp. were recovered in 69 from 100 immunosuppressed patients with COVID-19. Bronchoscopy was used to collect the Bronchoalveolar lavage (BAL) specimens. For the identification of Candida spp. PCR sequencing was done using the ITS1 and ITS4 primers. The amplification of the HWP1 gene was conducted to identify the Candida albicans complex. The antifungal activities of fluconazole, itraconazole, voriconazole, amphotericin B and caspofungin against Candida spp. were evaluated using the Clinical and Laboratory Standards Institute M60. In 63.77% of the patients, Candida respiratory colonization at D0 and D14 had no impact on the severity of COVID-19. In comparison to C. albicans strains, Candida respiratory disorder with C. glabrata had influenced the severity of COVID-19 for critically ill patients following adjustment for the risk factors of COVID-19 (P < 0.05). Amphotericin B and caspofungin showed superior activity against all Candida spp. All antifungal agents showed 100% sensitivity against the two C. africana strains. Our observation on patients who used automatic ventilation, respiratory colonization by Candida spp. was not seen to influence the infection or death caused by COVID-19. Amphotericin B and caspofungin showed superior activity against all Candida spp. and were recommended for the treatment regime of pulmonary candidiasis associated with COVID-19 infection. Although “Candida pneumonia” is rarely being reported in critically ill patients, Candida airway colonization mainly by Candida albicans is common especially among patients with diabetes, malignancies, and kidney disorders.

Culturable Microbial Population From the Upper Respiratory Tract of 1,010 Clinically Healthy Horses in Southern Brazil

Microbiological diagnosis of equine respiratory infections is essential for disease management. However, reliable diagnosis can be a challenge due to colonization of the upper respiratory tract (URT) by a diverse microbial population, and because there is a lack of studies with samples from healthy animals. Aiming to guide adequate URT culture, this work reports culturable microbial population from the URT of 1,010 apparently healthy horses from 341 farms in Southern Brazil and identifies the putative presence of pathogenic microorganisms. Nasal swabs were cultured in 5% blood agar, and the isolates were phenotypically identified to genus level. A diverse respiratory microbial population was found, mostly composed of Gram-positive bacteria, including Staphylococcus spp., Bacillus spp., Streptococcus spp. and Corynebacterium spp. The microbiological profile from the nasal cavity of 911 horses was described, with the five most common profiles being: (1) Staphylococcus sp. + Gram-negative bacilli (12.67%), (2) Staphylococcus sp. in pure culture (12.47%), (3) Staphylococcus sp. + Bacillus sp. (10.10%), (4) Gram-negative bacilli in pure culture (6.93%), and (5) Staphylococcus sp. + Bacillus sp. + Gram-negative bacilli (6.73%). Streptococcus equi equi and Rhodococcus equi were detected in 34 horses (3.37%), demonstrating the presence of pathogenic bacteria along with commensal microorganisms in apparently healthy animals. The disclosed data may guide and facilitate microbiological diagnosis of URT infection in horses. The significant presence of Gram-negative bacilli was evidenced, as well as the occurrence of relevant pathogens, such as S. equi equi and R. equi, thus helping to improve diagnosis and antimicrobial therapy.

Cell invasion involves membrane-active and calmodulin-binding properties of the CyaA toxin translocation domain

The molecular mechanisms and forces involved in the translocation of bacterial toxins into host cells are still a matter of intense research. Bordetella pertussis, the causative agent of whooping cough, produces an adenylate cyclase (CyaA) toxin that plays an essential role in the early stages of respiratory tract colonization. CyaA displays a unique intoxication pathway of human cells via a direct translocation of its catalytic domain (AC) across the plasma membrane. Once in the cytosol, AC impairs the physiology of immune cells, leading to cell death.

Variations in infection control practices suggest a need for guidelines in primary ciliary dyskinesia patient care.

Primary ciliary dyskinesis (PCD) is an autosomal recessive disorder associated with impaired mucociliary clearance caused by defects in ciliary structure and function. The major clinical feature of PCD is recurring or persistent respiratory tract infection. Respiratory tract colonization with drug-resistant organisms impacts the frequency of infections and lung function decline. Protective gear has been employed by caregivers in an attempt to control respiratory tract bacterial spread between patients with cystic fibrosis, but use in PCD is not known. We conducted a web-based survey to investigate infection control and prevention practices of PCD centers in North America, and how practices have been influenced by the COVID-19 pandemic. The response rate was 87.0%. Before the COVID-19 pandemic, glove, gown, and mask use were variable, and only 3.7% of centers used masks during encounters with PCD outpatients. After COVID-19 mandates are lifted, 48.1% of centers plan to continue to use masks during outpatient care, while the practice regarding the use of gloves and gowns was not influenced by the current pandemic. There is no uniform practice for infection control in PCD care indicating the need for practice guidelines. Mitigation of respiratory virus transmission learned during the COVID-19 pandemic may impact future infection control approaches used for patients with PCD and other lung diseases.

Experimental infection of specific-pathogen-free domestic lambs with Mycoplasma ovipneumoniae causes asymptomatic colonization of the upper airways that is resistant to antibiotic treatment

Mycoplasma ovipneumoniae (M. ovipneumoniae) is a respiratory pathogen associated with mild to moderate respiratory disease in domestic lambs and severe pneumonia outbreaks in wild ruminants such as bighorn sheep. However, whether M. ovipneumoniae by itself causes clinical respiratory disease in domestic sheep in the absence of secondary bacterial pathogens is still unclear. The goal of our study was to better understand the role of M. ovipneumoniae as a respiratory pathogen in domestic sheep and to explore potential antibiotic treatment approaches. Therefore, we inoculated four 4-month-old, specific-pathogen-free lambs with fresh nasal wash fluids from M. ovipneumoniae-infected sheep. The lambs were monitored for M. ovipneumoniae colonization, M. ovipneumoniae-specific antibodies, clinical signs, and cellular and molecular correlates of lung inflammation for eight weeks. All lambs then were treated with gamithromycin and observed for an additional four weeks. M. ovipneumoniae inoculation resulted in stable colonization of the upper respiratory tract in all M. ovipneumoniae-inoculated, but in none of the four mock-infected control lambs. All M. ovipneumoniae-infected lambs developed a robust antibody response to M. ovipneumoniae within 2 weeks. However, we did not observe significant signs of respiratory disease, evidence of lung damage or inflammation in any of the infected lambs. Interestingly, treatment with gamithromycin, which blocked growth of the M. ovipneumoniae in vitro, failed to reduce M. ovipneumoniae colonization. These observations indicate that, in the absence of co-infections, M. ovipneumoniae caused asymptomatic colonization of the upper respiratory tract that was resistant to clearance by the host immune response and by gamithromycin treatment.

Invasive pulmonary aspergillosis among intubated patients with SARS-CoV-2 or influenza pneumonia: a European multicenter comparative cohort study

BackgroundRecent multicenter studies identified COVID-19 as a risk factor for invasive pulmonary aspergillosis (IPA). However, no large multicenter study has compared the incidence of IPA between COVID-19 and influenza patients.ObjectivesTo determine the incidence of putative IPA in critically ill SARS-CoV-2 patients, compared with influenza patients.MethodsThis study was a planned ancillary analysis of the coVAPid multicenter retrospective European cohort. Consecutive adult patients requiring invasive mechanical ventilation for > 48 h for SARS-CoV-2 pneumonia or influenza pneumonia were included. The 28-day cumulative incidence of putative IPA, based on Blot definition, was the primary outcome. IPA incidence was estimated using the Kalbfleisch and Prentice method, considering extubation (dead or alive) within 28 days as competing event.ResultsA total of 1047 patients were included (566 in the SARS-CoV-2 group and 481 in the influenza group). The incidence of putative IPA was lower in SARS-CoV-2 pneumonia group (14, 2.5%) than in influenza pneumonia group (29, 6%), adjusted cause-specific hazard ratio (cHR) 3.29 (95% CI 1.53–7.02, p = 0.0006). When putative IPA and Aspergillus respiratory tract colonization were combined, the incidence was also significantly lower in the SARS-CoV-2 group, as compared to influenza group (4.1% vs. 10.2%), adjusted cHR 3.21 (95% CI 1.88–5.46, p < 0.0001). In the whole study population, putative IPA was associated with significant increase in 28-day mortality rate, and length of ICU stay, compared with colonized patients, or those with no IPA or Aspergillus colonization.ConclusionsOverall, the incidence of putative IPA was low. Its incidence was significantly lower in patients with SARS-CoV-2 pneumonia than in those with influenza pneumonia.Clinical trial registration The study was registered at ClinicalTrials.gov, number NCT04359693.

Microbiota in the pathogenesis of COPD and its impact on the course of the disease

Chronic obstructive pulmonary disease (COPD) is a serious problem for global health. Infectious agents play a main role in the development of COPD exacerbations. Bacterial colonization of the lower respiratory tract is common in patients with stable COPD. The role of microbiota and host immune response to potential pathogens is not well studied. Microbiota composition disorders in respiratory tract are found in patients with COPD and associated with maladaptive changes in the immune system of the lungs and increased level of inflammation. This review investigates role of microbiota in the pathogenesis of COPD and its impact on the course of the disease. Some important issues such as pneumococcal vaccination and antimicrobial resistance of respiratory pathogens are also discussed.

Cord factor producer Mycobacterium abscessus subsp. bolletii in asymptomatic immunocompetent host sputa samples

We report a case of Mycobacterium abscessus subsp. bolletii colonization in upper respiratory tract of an immunocompetent patient, who was misdiagnosed as tuberculosis by Acid Fast Bacilli (AFB) and cord factor formation observed directly from the sputa culture in liquid medium. This fact reflected a significant impact on the individual case’s life and showed the importance to identify the mycobacteria isolated from clinical sample at species level, and to determine the true implication of nontuberculous mycobacteria (NTM) detected in clinical samples.

Порушення мікробіоти дихальних шляхів у дітей з респіраторними захворюваннями (літературний огляд)

У статті наведено дані вітчизняної та зарубіжної літератури про мікробіоценози організму людини у нормі та патології. Розглянуто етапи заселення респіраторного тракту мікрофлорою у різні періоди дитячого віку. Представлені дані численних досліджень мікробіоти легень порівняно з мікробіоценозом верхніх дихальних шляхів. Наведені експериментальні дані, що підтверджують наявність мікрофлори у легенях здорової людини та прямий взаємозв’язок між мікробіотою верхніх і нижніх дихальних шляхів. Одним із найважливіших факторів, що визначають стан мікробіоти легень, є мікроаспірація. Показано значення мікробіоценозів відкритих порожнин організму для формування мукозального імунітету. Викладено наукову концепцію щодо алгоритму функціонування колонізаційної резистентності слизових організму. Розглянуто методику оцінки мікробіоценозу носоглотки та визначення ступеня дисбіозу. Особливу увагу приділено стану мікробіоти верхніх і нижніх відділів респіраторного тракту у дітей, які часто хворіють, а також дітей із рецидивуючими та хронічними захворюваннями органів дихання. Показано, що виявлення збудника в посіві матеріалу з верхніх і нижніх дихальних шляхів не обов’язково свідчить про його роль як збудника гострого бронхолегеневого захворювання. Необхідна оцінка ступеня вираженості дисбіозу. Однак тривала персистенція інфекційного збудника у пацієнтів з гострими бронхолегеневими захворюваннями може привести до дисбалансу імунної реактивності і формування хронічного бронхолегеневого запального процесу. Підвищена колонізація дихальних шляхів у пацієнтів з хронічними респіраторними захворюваннями є істотним чинником ризику, що сприяє розвитку загострень. Відзначено, що моніторинг етіологічно значущих штамів мікроорганізмів у пацієнтів з гострою та хронічною бронхолегеневою патологією є необхідним для удосконалення патогенетичної тактики лікування та профілактики формування хронічних станів.

Comparison of microbial composition of cough swabs and sputum for pathogen detection in patients with cystic fibrosis

BackgroundWith the continued advancement of CFTR modulator therapies there is likely to be a burgeoning population of adult cystic fibrosis (CF) patients unable to expectorate sputum. Consequently, the detection and surveillance of pulmonary colonisation, previously reliant on sputum culture, needs re-examining. We hypothesised that cough swabs analysed with culture-independent analysis of the 16S gene could serve as a surrogate for colonisation of the lower airways. MethodsCough swabs and sputum samples were prospectively collected from consecutive adults and children with CF across two sites at regular outpatient appointments. Conventional culture analysis and next generation sequencing were used to compare paired same day samples. ResultsTwenty-two adults and 8 paediatric patients provided 75 paired cough swabs and sputum samples. Alpha diversity measures showed increased bacterial richness in sputum, while evenness and Simpson's diveristy index were higher in cough swabs. Within each sampling technique, microbial composition showed greater similarity when considering intra-patient variation. Poor concordance was observed between culture independent cough swabs and culture dependent/independent sputum analysis for specific pathogens, with cough swabs unable to accurately identify commonly associated CF pathogens (AUROCC range: 0.51 to 0.64). ConclusionCulture independent analysis of cough swabs provides an inaccurate diagnosis of lower respiratory tract colonisation and should not be used as a diagnostic test in patients with CF.