scholarly journals Microbiota of the lower respiratory tract in community-acquired pneumonia, including cases associated with SARS-CoV-2

2021 ◽  
Vol 98 (5) ◽  
pp. 528-537
Author(s):  
L. V. Kataeva ◽  
A. A. Vakarina ◽  
T. F. Stepanova ◽  
K. B. Stepanova

Introduction. Many aspects of the pathogenesis and pathomorphology of pneumonia associated with novel coronavirus require a comprehensive study using modern diagnostic methods.The aim of the study was to study the microbiota of the lower respiratory tract in community-acquired pneumonia associated with SARS-CoV-2, to assess the antibiotic and phage resistance of circulating strains of microorganisms.Materials and methods. The analysis of biosamples from 486 patients undergoing inpatient treatment in five mono-hospitals in Tyumen and Tyumen region with a diagnosis of moderate and severe community-acquired pneumonia was carried out. In almost 90% of cases patients received oxygen therapy, about 8% of patients were connected to ventilators. The inoculation of the cultures with clinical samples was carried out for six months (from April to October 2020). The isolated bacterial strains were identified by mass spectrometry. The resistance to antimicrobial drugs and bacteriophages was assessed for identified isolated.Results. Gram-positive cocci, mainly opportunistic microorganisms of the genus Streptococcus and Candida fungi predominated in the microbiota of the lower respiratory tract of patients diagnosed with community-acquired pneumonia associated with SARS-CoV-2. At the same time, bacteria of the Enterobacteriaceae family and nonfermenting gram-negative bacteria were less common compared to patients without coronavirus infection. In the structure of pathogens, the leading position was occupied by the bacteria K. pneumoniae and Acinetobacter spp. The analysis of the sensitivity of microorganisms to antimicrobial drugs showed the highest resistance rates in strains of Acinetobacter spp., Enterococcus spp., Coagulase-negative Staphylococcus. It has been established that in the group of patients with community-acquired pneumonia associated with SARS-CoV-2, the risk of infection with Streptococcus spp. with high level of antibiotic resistance was 1.5 times higher, and taking into account the 95% confidence interval, the value of this indicator ranged from 1.1 to 2.1 times.Conclusion. The data obtained indicate that the microbiota of the lower respiratory tract in community-acquired pneumonia associated with SARS-CoV-2 is represented mainly by bacteria of the genus Streptococcus, which have a high level of resistance to antimicrobial drugs.

2021 ◽  
Vol 13 (4) ◽  
pp. 5-13
Author(s):  
I. V. Babachenko ◽  
E. A. Kozyrev ◽  
E. V. Sharipova ◽  
E. D. Orlova ◽  
N. S. Tian

The sharp increase in viral pneumonia against the background of the pandemic of the new coronavirus infection SARS-CoV-2 requires more attention to the study of the role of viruses in damage to the lower respiratory tract, including their etiological significance in the development of community-acquired pneumonia. Modern possibilities of laboratory diagnostics make it possible not only to identify and study respiratory viruses, but also to help differentiate active viral infections as a cause of lower respiratory tract disease from virus carriers. The review describes the epidemiological and clinical features of the most relevant or less studied pneumotropic viral infections in children (respiratory syncytial, adenovirus, bocavirus, metapneumovirus), including their role in the etiology of pneumonia in children. Understanding the viral etiology of pneumonia in children will reduce the antibacterial load, which will help to reduce the side effects of chemotherapy and slow the emergence of antimicrobialresistant bacterial strains.


2020 ◽  
Vol 19 (2) ◽  
pp. 14-18
Author(s):  
E. V. Sharipova ◽  
I. V. Babachenko ◽  
M. A. Shcherbatyh

Long time the main pathogens associated with the development of community-acquired pneumonia were bacteria. However, in recent years in the Russian Federation, like all over the world, the view of the damage of lower respiratory tract changed, including a unique approach to community-acquired pneumonia as a bacterial infection, and respiratory viruses have become seen as a direct cause of lower respiratory tract damage, or as part of a viral-bacterial co-infection. These studies became possible since the widespread introduction of PCR techniques in the clinical setting, identification of respiratory viruses has increased and new microorganisms such, one as human bocavirus have been discovered. Objective: to study the features of respiratory tract damage in acute bocavirus infection in children of different ages. Materials and methods: A retrospective analysis of 97 medical hospital documentation of children with acute bocavirus infection, detected confirmed by PCR in nasopharyngeal aspirate. Results: In this work, it was shown that human bocavirus spread throughout the year with an increase in the incidence of clinically significant forms in the autumnwinter period, including during the period of an increase in the incidence of influenza. HBoV infection requiring hospitals is most significant in the first three years of life. In 74.2% of hospitalized children, bocavirus infection occurs with lower respiratory tract infections in the form of bronchitis — 77.8%, pneumonia — 28.9% and rarely bronchiolitis and is complicated by the development of respiratory failure in 28.9% of cases. Changes in the blood test are non-specific, and the level of C-reactive protein in children with various clinical manifestations of HBoV infection generally does not exceed 50 mg / l. An x-ray of the chest organs does not objectively reflect the existing volume and nature of the inflammatory process in the lungs.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Niina Haiminen ◽  
Filippo Utro ◽  
Ed Seabolt ◽  
Laxmi Parida

AbstractIn response to the ongoing global pandemic, characterizing the molecular-level host interactions of the new coronavirus SARS-CoV-2 responsible for COVID-19 has been at the center of unprecedented scientific focus. However, when the virus enters the body it also interacts with the micro-organisms already inhabiting the host. Understanding the virus-host-microbiome interactions can yield additional insights into the biological processes perturbed by viral invasion. Alterations in the gut microbiome species and metabolites have been noted during respiratory viral infections, possibly impacting the lungs via gut-lung microbiome crosstalk. To better characterize microbial functions in the lower respiratory tract during COVID-19 infection, we carry out a functional analysis of previously published metatranscriptome sequencing data of bronchoalveolar lavage fluid from eight COVID-19 cases, twenty-five community-acquired pneumonia patients, and twenty healthy controls. The functional profiles resulting from comparing the sequences against annotated microbial protein domains clearly separate the cohorts. By examining the associated metabolic pathways, distinguishing functional signatures in COVID-19 respiratory tract microbiomes are identified, including decreased potential for lipid metabolism and glycan biosynthesis and metabolism pathways, and increased potential for carbohydrate metabolism pathways. The results include overlap between previous studies on COVID-19 microbiomes, including decrease in the glycosaminoglycan degradation pathway and increase in carbohydrate metabolism. The results also suggest novel connections to consider, possibly specific to the lower respiratory tract microbiome, calling for further research on microbial functions and host-microbiome interactions during SARS-CoV-2 infection.


Author(s):  
Timothy J.J. Inglis ◽  
Dionne B. Rolim ◽  
Jorge L.N. Rodriguez

Melioidosis is an emerging infection in Brazil and neighbouring South American countries. The wide range of clinical presentations include severe community-acquired pneumonia, septicaemia, central nervous system infection and less severe soft tissue infection. Diagnosis depends heavily on the clinical microbiology laboratory for culture. Burkholderia pseudomallei, the bacterial cause of melioidosis, is easily cultured from blood, sputum and other clinical samples. However, B. pseudomallei can be difficult to identify reliably, and can be confused with closely related bacteria, some of which may be dismissed as insignificant culture contaminants. Serological tests can help to support a diagnosis of melioidosis, but by themselves do not provide a definitive diagnosis. The use of a laboratory discovery pathway can help reduce the risk of missing atypical B. pseudomallei isolates. Recommended antibiotic treatment for severe infection is either intravenous Ceftazidime or Meropenem for several weeks, followed by up to 20 weeks oral treatment with a combination of trimethoprim-sulphamethoxazole and doxycycline. Consistent use of diagnostic microbiology to confirm the diagnosis, and rigorous treatment of severe infection with the correct antibiotics in two stages; acute and eradication, will contribute to a reduction in mortality from melioidosis.


2020 ◽  
Vol 7 (7) ◽  
Author(s):  
Eric J Chow ◽  
Melissa A Rolfes ◽  
Ruth L Carrico ◽  
Stephen Furmanek ◽  
Julio A Ramirez ◽  
...  

Abstract Background Preventing severe complications of influenza such as hospitalization is a public health priority; however, estimates of influenza vaccine effectiveness (VE) against influenza-associated acute lower respiratory tract infection (LRTI) hospitalizations are limited. We examined influenza VE against influenza-associated LRTIs in hospitalized adult patients. Methods We retrospectively analyzed data from a randomized trial of oseltamivir treatment in adults hospitalized with LRTI in Louisville, Kentucky, from 2010 to 2013. Patients were systematically tested for influenza at the time of enrollment. We estimated VE as 1 – the adjusted odds ratio (aOR) of antecedent vaccination in influenza-positives vs negatives × 100%. Vaccination status was obtained by patient self-report. Using logistic regression adjusting for age, sex, season, timing of illness, history of chronic lung disease, and activities of daily living, we estimated VE against hospitalized influenza-associated LRTIs and community-acquired pneumonia (CAP) with radiographic findings of infiltrate. Results Of 810 patients with LRTI (median age, 62 years), 184 (23%) were influenza-positive and 57% had radiographically confirmed CAP. Among influenza-positives and -negatives, respectively, 61% and 69% were vaccinated. Overall, 29% were hospitalized in the prior 90 days and >80% had comorbidities. Influenza-negatives were more likely to have a history of chronic obstructive pulmonary disease than influenza-positives (59% vs 48%; P = .01), but baseline medical conditions were otherwise similar. Overall, VE was 35% (95% CI, 4% to 56%) against influenza-associated LRTI and 51% (95% CI, 13% to 72%) against influenza-associated radiographically confirmed CAP. Conclusions Vaccination reduced the risk of hospitalization for influenza-associated LRTI and radiographically confirmed CAP. Clinicians should maintain high rates of influenza vaccination to prevent severe influenza-associated complications.


2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S624-S624
Author(s):  
Sandra Rajme-López ◽  
María F Gonzalez-Lara ◽  
Andrea Rangel-Cordero ◽  
Alfredo Ponce de Leon

Abstract Background Geotrichum spp has been recognized as an emergent pathogen that causes invasive infection in immunosuppressed hosts. There is no data in Latin America about invasive Geotrichum spp. infections. Our objective was to describe the epidemiology, clinical characteristics, and outcomes of patients with this infection. Methods We conducted a retrospective survey from 2001 to 2018, of all the Geotrichum spp. isolated from clinical samples at our institution. Data on demographic, clinical, laboratory findings, and imaging studies were obtained from medical records. All cases classified as proven or probable invasive fungal infections (IFI) according to the EORTC/MSG criteria were included. Isolates with unavailable clinical information were excluded. Descriptive analysis was made. Results We found 18 patients with a proven/probable Geotrichum spp. IFI. The mean age was 48.5 years and 55.5% were male. The most common predisposing condition was hematological malignancy (55.5%), autoimmune diseases (22.2%) and HIV, chronic granulomatous disease, and solid-organ malignancy in 1 case, respectively. Fifteen (83.3%) received immunosuppressors (cancer chemotherapy or steroids); 27.7% had neutropenia at the time of diagnosis. The most common clinical syndromes were lower respiratory tract infection and persistent fever (83.3%). Chest abnormalities were present in 15/16 CT scans, pulmonary nodules were the most common finding (62.5%). Geotrichum spp. was isolated from bronchoalveolar lavage, 77.7%; blood culture, 22.2%; and peritoneal dyalisis fluid, 5.6%. Seven patients were coinfected with other pathogens: 4 Aspergillus spp., 1 H. parainfluenzae, 1 P. aeruginosa, and 1 E. coli. Fifteen patients received antifungal treatment: 7 amphotericin B, 8 voriconazole, and 1 itraconazole. Among survivors (11), 72.7% received antifungal therapy at discharge: 4 voriconazole and 4 itraconazole. Three patients did not receive any antifungal: 1 was diagnosed postmortem and 2 were considered colonization (both were alive at 30 days). Overall mortality was 38.8%. Conclusion Eighteen cases of Geotrichum spp. were found. The majority had lower respiratory tract infection. Despite antifungal therapy 38.8% died. Geotrichum spp. should be recognized as an emerging pathogen in immunosuppressed hosts. Disclosures All authors: No reported disclosures.


2021 ◽  
Vol 38 (4) ◽  
pp. 471-473
Author(s):  
Fahriye EKŞİ ◽  
Mehmet ERİNMEZ

Acinetobacter baumannii is an opportunistic pathogen which colonize inpatients and cause severe infections, septic shock and death. With emergence of multi-drug resistant gramnegative species and being effective in A. baumannii infections, colistin becomes a treatment option again. N-acetylcysteine (NAC), is a mucolitic agent which used commonly in lower respiratory tract infections especially patients who have cronic respiratory disorders like Chronic obstructive pulmonary disease, cystic fibrosis and bronchiectasis. In this study we aim to investigate the effect of NAC, which commonly added in lower respiratory tract infections tratment regime, on MIC values colistin used in A. baumanni tratment. Fifty A.baumannii isolates were included in the study. The isolates were identified by automated identification system. With broth microdilution method, we investigated and compared the MIC (minimum inhibitory concentration) values of colistin and NAC+Colistin combination. Colistin MIC50 value is 0.25 μg/mL and MİK90 value is 1 μg/mL, NAC+Colistin combination MIC50 value is 0.25 μg/mL and MİK90 value is 1 μg/mL. The screening for the effectiveness of clinical drugs may provide clinical strategy to improve treatment outcomes of A. baumannii and reduce hospitalization days.


2020 ◽  
pp. 14-21
Author(s):  
Ye.P. Ortemenka ◽  
◽  
S.I. Tarnavska ◽  
T.V. Krasnova ◽  
◽  
...  

Diagnosis of acute infectious-inflammatory processes of the lower respiratory tract with a respect to justify etiotropic therapy is often based on evaluation of the activity of blood inflammatory markers and data of lungs' X-ray examination, but scientific evidence of their informativity in the differential diagnosis of community-acquired pneumonia and acute bronchitis is conflicting. Purpose — to study the predictor role of some paraclinical indices in the verification of infectious and inflammatory diseases of the lower respiratory tract (community-acquired pneumonia and acute obstructive bronchitis) in children of different ages in order to optimize the treatment. Materials and methods. To achieve the goal of the study, a cohort of patients with acute infectious-inflammatory pathology of children with different ages (75 patients) who received inpatient treatment at the pulmonology department of the Regional Children's Clinical Hospital in Chernivtsi has been formed by the method of simple random sampling. The first (I) clinical group was formed by 51 patients with a verified diagnosis of community-acquired pneumonia (CAP), acute course, and the second (II) clinical group included 24 children, in which the infiltrative acute process in the lungs was excluded, but who had broncho-obstructive syndrome. According to the main clinical characteristics, the comparison groups have been comparable. The results of the study have been analyzed by parametric («P», Student's criterion) and non-parametric («Рϕ», Fisher's angular transform method) calculation methods, and methods of clinical epidemiology with an evaluation of the diagnostic value of the tests has been performed taking into account their sensitivity (Se) and specificity (Sp), as well as attributive (AR) and relative (RR) risks, and the odd ratio (OR) of the event, taking into account their 95% confidence intervals (95% CI). Results. The analysis of the obtained dada has showed that in the patients with CAP such common inflammatory blood markers (leukocytosis, relative neutrophilosis, shift of leukocyte formula to the left, elevation of erythrocyte sedimentation rate (ESR) or high level of CRP — С-reactive protein) are characterized by low sensitivity (Se in range between 11% and 63%) indicating that they are inadvisable for use as the screening tests for the verification of pneumonia. At the same time, it has been shown that these inflammatory blood markers are characterized by sufficient specificity (in the range from 75% to 93%) in the verification of pneumonia only under their significant increase (total leukocyte count >15.0x109, ESR>10 mm/h and CRP level in blood >6 mg/ml), indicating that they are enough, but only for confirming inflammation of the lung parenchyma. From the standpoint of clinical epidemiology, it has been proved that the asymmetry of findings at lung radiographs (asymmetry of pulmonary enhancement, asymmetric changes of lung roots and, especially, the presence of infiltrative changes at lung parenchyma) are the most informative diagnostic tests in pneumonia verification (ST=90–95%) and have a statistically significant predictor role in the final diagnosis (OR=11.6–150). When assessing the hemogram in children of the II clinical group it has been found that only the relative number of band neutrophils <5%, as a diagnostic test, had an insignificant amount (16%) of false-positive results, which allows to use this marker in confirming the diagnosis of acute obstructive bronchitis, but not as its predictor (OR=2.21; 95% CI: 0.69–7.06) or screening test (Se=29%). At the same time, a significant diagnostic and predictor role of the chest X-ray examination in the differential diagnosis of acute BOS with pneumonia has been established. Namely, symmetrical alteration of the lung root architecture at chest radiographs in the absence of infiltrative changes in the pulmonary fields was characterized by few false-negative results (10%), which allow the use of this feature as a screening pattern in the diagnosis of acute obstructive bronchitis. The absence of changes of pulmonary at chest radiographs should be used to confirm the diagnosis of acute obstructive bronchitis (Sp=98%), but not as a screening sign due to the significant number of negative results in the presence of the disease (Se=48%). Conclusions. In general, the low diagnostic and predicting role of the common blood inflammatory markers for the diagnosis of acute inflammation of the lung parenchyma in children of different ages, as well as in the differential diagnosis of pneumonia and acute obstructive bronchitis have been confirmed. At the same time, it has been found that such radiological features as asymmetry of pulmonary pattern enhancement and the presence of asymmetric infiltrative changes of the lung parenchyma are the most informative diagnostic tests in the verification of pneumonia (Se=80–88% and Sp=90–95%), and have a statistically significant predictor role in the final diagnosis (OR=38.95–150). It has been shown that symmetrical changes of lung roots (their deformation, widening or infiltration) at chest radiographs in the absence of infiltrations in the pulmonary fields, as well as the absence of changes in the pulmonary pattern, have a statistically significant predictor role in the diagnosis of acute obstructive bronchitis (OR=20,78–55,0). The study was carried out in accordance with the principles of the Helsinki Declaration. The study protocol was approved by the Local Ethics Committee of the institution specified in the work. Informed consent was obtained from the parents of the children for the research. The authors declare no conflicts of interest. Key words: community-acquired pneumonia, obstructive bronchitis, children, diagnostic value, predictors.


1998 ◽  
Vol 9 (suppl e) ◽  
pp. 30E-34E
Author(s):  
Alasdair P MacGowan ◽  
Tracey Halladay ◽  
Andrew M Lovering

A number of national guidelines have been published to aid the antimicrobial management of community-acquired pneumonia. However, data on prescriptions for lower respiratory tract infection (LRTI) indicate considerable variation in the choice of first-line and subsequent therapy at national and local levels. Outcomes research in LRTI, whether based on clinical, economic or patient-focused criteria, is still evolving. Clinical outcomes are best studied for both pneumonia and exacerbation of chronic obstructive pulmonary disease. Economic evaluations often do not encompass all of the costs, for example, time off from work or the economic impact of antibacterial resistance. Duration of hospital stay is a good marker of costs for hospital providers and may be affected by age. marital status and comorbidities. Antibiotic choice may have an impact on the duration of hospital stay by increasing side effects, predisposing patients to hospitalacquired infection or reduced clinical efficacy. Patient expectation is largely unstudied in pulmonary infection.


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