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1.
Russian Journal of Infection & Immunity ; 12(4):713-725, 2022.
Article in Russian | Academic Search Complete | ID: covidwho-2040487

ABSTRACT

Objective of the research — to specify respiratory tract bacterial microflora in patients suffering from community-acquired pneumonia (CAP) during initial and repeat examination. To determine local factors affecting microflora in the cohort examined. Materials and methods. Surveillance subject — 241 patients with CAP differed by their status and age who stayed in two healthcare facilities of the Khabarovsk city. Examination of respiratory smears was performed. Results. Indices of Gram-negative enterobacteria (30.8% [22.6–39.7%]) and Gram-negative nonfermentable bacteria (14.5% [8.6–21.7%]), isolated from patients hospitalized in healthcare institution No. 1 and mostly comprised of the elderly (aged over 61 years — 82.0%;74.3–88.6%) with more severe disease state including patients at the ICU, were higher compared to data obtained from healthcare institution No. 2 (19.8% (13.4–27.0);6.1% (2.7–10.8) respectively). Prevalent pathogen was Klebsiella pneumoniae — 13.6% (7.8–20.6) and 10.7% (6.0–16.5). Identification of Acinetobacter baumannii complex — 6.4% (2.6–11.7) and 3.1% (0.8–6.7) — should be also noted. A high percentage of drug-resistant bacterial variants was observed and for Klebsiella pneumoniae totaled 66.7% (41.8–87.4) and 57.1% (32.2–80.2) at the healthcare institutions No. 1 and No. 2, respectively. A. baumannii complex drug resistant variants were found in 85.7% (52.7–99.97) at healthcare institution No. 1. All isolates of A. baumannii complex at the healthcare institution No. 2 were drug resistant. High prevalence of Candida spp. was revealed in both healthcare institutions reaching 54.5% (45.2–63.7) and 58.0% (49.5–66.3), respectively, with minimal detection rate of classic pathogens such as S. pneumoniae — 5.4% (2.0–10.4) and 5.3% (2.1–9.8) and H. influenzae — 3.6% (0.9–7.9) and 3.8% (1.2–7.7), respectively. Repeat examination of 122 patients conducted 7–10 days later showed diverse changes in microflora spectrum regardless of the healthcare institution that was manifested as loss or emergence of drug-resistant variants as well as simultaneous presence of different variants of the same pathogen. Conclusion. The results obtained evidence about complexity and variety of mechanisms underlying microorganism community formation during the course of infectious process in patients. Local factors influencing microflora characteristics of patients at the two healthcare institutions were revealed. (English) [ FROM AUTHOR] Цель исследования — определить бактериальную микрофлору респираторного тракта больных внебольничной пневмонией (ВП) при их первичном и повторном обследовании, выявить локальные факторы, влияющие на показатели микрофлоры у наблюдаемого контингента. Объект наблюдения — 241 больной ВП из двух лечебных учреждений г. Хабаровска, различающихся по статусу и возрастному составу пациентов. Исследованы респираторные мазки. В ЛПУ № 1, в котором сосредоточены пациенты старше 61 года — 82,0% (74,3–88,6) с более тяжелым течением болезни, в том числе пациенты РАО, показатели выявления грамотрицательных энтеробактерий — 30,8% (22,6–39,7) и неферментирующих грамотрицательных бактерий — 14,5% (8,6–21,7) были выше по сравнению с ЛПУ № 2 — 19,8% (13,4–27,0) и 6,1% (2,7–10,8) соответственно группам возбудителей. Ведущий возбудитель в обоих ЛПУ — Klebsiella pneumoniae — 13,6% (7,8–20,6) и 10,7% (6,0–16,5). Следует отметить регистрацию Acinetobacter baumannii complex — 6,4% (2,6–11,7) и 3,1% (0,8–6,7). Характерна высокая доля участия лекарственноустойчивых вариантов — 66,7% (41,8–87,4) и 57,1% (32,2–80,2) для K. pneumoniae, в ЛПУ № 1 и ЛПУ № 2 соответственно, и для A. baumannii complex — в ЛПУ № 1 их вклад составил 85,7% (52,7–99,97), в ЛПУ № 2 все изоляты имели лекарственную устойчивость. В обоих ЛПУ у больных отмечены высокие показатели выявления грибов рода Candida — 54,5% (45,2–63,7) и 58,0% (49,5–66,3) соответственно, и минимальные уровни классических возбудителей: S. pneumoniae — 5,4% (2,0–10,4) и 5,3% (2,1–9,8) и H. influenzae — 3,6% (0,9–7,9) и 3,8% (1,2–7,7) соответственно. Через 7–10 дней при повторном обследовании 122 больных отмечено разнонаправленное из менение микрофлоры, независимое от статуса ЛПУ, и проявляющееся как по линии утраты лекарственноустойчивых вариантов, так и в приобретении их или одновременном присутствии разных вариантов одного возбудителя. Полученные результаты свидетельствуют о сложности и множественности механизмов формирования популяции микроорганизмов в динамике инфекционного процесса у больного. Выявлены локальные факторы, влияющие на показатели микрофлоры больных в двух лечебных учреждениях. (Russian) [ FROM AUTHOR] Copyright of Russian Journal of Infection & Immunity is the property of National Electronic-Information Consortium and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

2.
Medical News of North Caucasus ; 17(2):202-204, 2022.
Article in English | EMBASE | ID: covidwho-2033430

ABSTRACT

The study determined the etiological structure and sensitivity to antibacterial agents of pathogens of uncomplicated and complicated forms of pneumonia in children treated in a multidisciplinary hospital. According to the study, that timely bacteriological diagnosis in the treatment of pneumonia in childhood with an adequate selection of effective antibacterial agents helps reduce hospitalizations and the development of complicated forms of pneumonia.

3.
Journal of Clinical Medicine ; 11(17):5214, 2022.
Article in English | ProQuest Central | ID: covidwho-2023805

ABSTRACT

In older adults, community-acquired pneumonia (CAP) is often aspiration-related. However, as aspiration pneumonia (AP) lacks clear diagnostic criteria, the reported prevalence and clinical management vary greatly. We investigated what clinical factors appeared to influence the diagnosis of AP and non-AP in a clinical setting and reconsidered a more clinically relevant approach. Medical records of patients aged ≥75 years admitted with CAP were reviewed retrospectively. A total of 803 patients (134 APs and 669 non-APs) were included. The AP group had significantly higher rates of frailty, had higher SARC-F scores, resided in institutions, had neurologic conditions, previous pneumonia diagnoses, known dysphagia, and were more likely to present with vomiting or coughing on food. Nil by mouth orders, speech therapist referrals, and broad-spectrum antibiotics were significantly more common, while computed tomography scans and blood cultures were rarely performed;alternative diagnoses, such as cancer and pulmonary embolism, were detected significantly less. AP is diagnosed more commonly in frail patients, while aspiration is the underlying aetiology in most types of pneumonia. A presumptive diagnosis of AP may deny patients necessary investigation and management. We suggest a paradigm shift in the way we approach older patients with CAP;rather than trying to differentiate AP and non-AP, it would be more clinically relevant to recognise all pneumonia as just pneumonia, and assess their swallowing functions, causative organisms, and investigate alternative diagnoses or underlying causes of dysphagia. This will enable appropriate clinical management.

4.
Frontiers in Microbiology ; 13, 2022.
Article in English | Scopus | ID: covidwho-2022791

ABSTRACT

Persistent infection and prolonged shedding of human bocavirus 1 (HBoV1) in children have been reported, and the role of HBoV1 as a sole causative pathogen in acute respiratory infection (ARI) is yet to be established. While the reported prevalence of HBoV infection varies due to different detection methods and sampling criteria, determining the viral and bacterial etiology of HBoV infection using multiplex real-time PCR is yet to be reported. Herein, we aimed to further explore the pathogenicity of HBoV in patients with ARI by screening the viral and bacterial infections in children with ARI in Qingdao and comparing the epidemiological, clinical characteristics, and etiological results. Human bocavirus was identified in 28.1% of the samples, and further sequencing analysis of the detected HBoV confirmed 96.4% as HBoV1. The rate of HBoV as a single viral infection was 75%, and the rate of coinfection with bacteria was 66.1%, suggesting the need for continued monitoring of HBoV in children with ARIs. Clinical characterization suggested that HBoV infection may affect the function of organs, such as the liver, kidney, and heart, and the blood acid–base balance. Additionally, it is essential to promote awareness about the importance of disinfection and sterilization of the hospital environment and standardizing operations. The interactions between HBoV and other pathogens remain to be investigated in further detail in the future. Copyright © 2022 Wang, Guan, Liu, Zhang, Sun, Liu, Shi, Su, Liang, Hao, Wang and Liu.

5.
Indian Journal of Critical Care Medicine ; 26:S27-S28, 2022.
Article in English | EMBASE | ID: covidwho-2006332

ABSTRACT

Foreword: Pneumonia remains an important medical and social problem at the beginning of the 21st century as well. This is due to its high prevalence, fairly high rates of disability and mortality, as well as significant economic expenditures for treatment. The incidence of pneumonia in different regions of the world ranges from 3.5 to 15 cases per 1 thousand population. The mortality rate from pneumonia in different countries of the world ranges from 2-3 to 25%. Pneumonia takes the first place among the causes of lethality and mortality from infectious diseases and the sixth one - among all the causes of death and the fourth - among causes of death in patients older than 65 years. Objective of research: Find out the peculiarities of correlation indicators of the hemostasis system and leukocytic index of intoxication in patients with out-of-hospital pneumonia on the background of COVID-19. Materials and methods of research: Based on NMMCC MMCH, a retrospective review analyzed 66 maps of inpatients with out-of-hospital pneumonia associated with COVID-19. The average age of the patients included in the study was 38.9 ± 0.7 years for males [66% (n = 37)] and 39.3 ± 0.83 for females [44% (n = 29)]. The leukocyte intoxication index (LII) was calculated and the severity of pneumonia was assessed according to the PSI scale (Pneumonia Severity Index, 2004). Results of the personal research: After dividing the patients according to the level of LII and PSI stratification class, we identified three groups of patients: with mild intoxication (n = 30, LII - 2.13 ± 0.09), which corresponded to class II on PSI (61.5 ± 6, 5);with intoxication of moderate severity (n = 31, LII - 4.83 ± 0.29), which corresponded to class III for PSI (79.4 ± 7.4);with severe intoxication (n = 5, LII - 10.11 ± 0.53), which corresponded to class IV PSI (110.4 ± 11.4). Assessing the severity of pneumonia on the PSI and LII scale [in the first group (LII - 2.13 ± 0.09, PSI - 61.5 ± 6.5), in the second group (LII - 4.83 ± 0.29, PSI - 79.4 ± 7.4), and in the third group (LII - 10.11 ± 0.53, PSI - 110.4 ± 11.4)], we found a direct strong credible Pearson's correlation (r = 0.56;p < 0.05) between the level of leukocyte intoxication index and the level of PSI. In addition, it was found that the increasing degree of intoxication significantly increases the value of LII (p < 0.05). When assessing changes in the coagulogram of patients depending on LII (in the first group of LII - 2.13 ± 0.09, PI,% - 91.3 ± 0.86, APTT, c - 33.38 ± 0.2, fibrinogen A, g\L - 3.37 ± 0.08, fibrinogen B, qualitatively - 1.6 ± 0.14, activated plasma recalcification time, c - 84.5 ± 1.64, in the second group of LII - 4.83 ± 0.29, PI,% - 84.6 ± 0.98, APTT, c - 31.96 ± 0.19, fibrinogen A, g\L - 3.69 ± 0.05, fibrinogen B, qualitatively - 2.48 ± 0.13, activated plasma recalcification time, c - 94.19 ± 1.31, in the third group LII - 10.11 ± 0.53, PI,% - 83 ± 2.0, APTT, c - 31, 42 ± 0.26, fibrinogen A, g\L - 3.93 ± 0.11, fibrinogen B, qualitatively - 3.0 ± 0.31, activated plasma recalcification time, c - 97.0 ± 4.63), it was found that with increasing degree of intoxication PI and APTT indicators decreased, while levels of fibrinogen A and B raised, as well as the rate of activated plasma recalcification (a significant difference between the data of groups I and II with p < 0.01;I and II with p < 0.001;I and III with p < 0.05;I and III with p < 0.001 was defined). Conclusion: (1) In assessment, the severity of pneumonia on the PSI scales and leukocyte intoxication index, we found a direct strong veracious correlation by Pearson's method (r = 0.56;p <0.05) between the level of leukocyte intoxication index and the level of PSI. (2) Characteristic features of changes in the leukocyte index of intoxication in patients with community-acquired pneumonia are the following: with increasing degree of intoxication, the value of leukocyte index of intoxication increases significantly (p < 0.05). (3) When assessing changes in the coagulogram depending on LII and PSI scale, it was found that with increasing degree of intoxication PI and APTT indicators decreased but the levels of fibrinogen A and B increased, as well as the rate of the activated plasma recalcification.

6.
Indian Journal of Critical Care Medicine ; 26:S1, 2022.
Article in English | EMBASE | ID: covidwho-2006312

ABSTRACT

Aim and background: Approximately 50% of the COVID-19 patients require intensive care due to pneumonia and respiratory failure. The CURB-65,3 CRB-654, A-DROP5 score, and Pneumonia Severity Index (PSI) scoring systems are established prognostic tools for community-acquired pneumonia (CAP). Similarly, the qSOFA score is a prognostic tool for critically ill patients. However, the utility of these scoring systems in the context of COVID-19 is yet to be established as a predictive tool for triage by means of rapid decision-making and preventive measures to combat the ongoing pandemic. Materials and methods: This observational, retrospective cohort study was conducted AIIMS, New Delhi during May to June, 2021 after obtaining institutional ethical committee approval (IEC-860/4.9.2020). Only the RT-PCR-proven patients >18 years among the institutionalized patients with severe acute respiratory infections (SARI) were included. Results: Out of the 235 included patients, 27.2% of patients required mechanical ventilation, and the overall period of hospital stay was 9 (5-13) days. While the SMART COP score with an AUC of 0.812 (95% CI 0.752-0.871), the PSI score with an AUC of 0.819 (95% CI 0.762- 0.877) obtained significant results for mortality, the A drop score with an AUC of 0.92 (0.897-0.954), and both the PSI (AUC of 0.964;95% CI 0.928-1.000), and the SMART COP (AUC of 0.925;95% CI 0.887-0.962) acquired the best result for intubation and thereby requirement of mechanical ventilation. Conclusion: Although the outcome of COVID-19 depends upon multiple factors the SMART COP, PSI, and A-drop scoring systems seem to be promising predictive tools for morbidity and mortality.

7.
Journal of General Internal Medicine ; 37:S453, 2022.
Article in English | EMBASE | ID: covidwho-1995835

ABSTRACT

CASE: 66yo woman with a past medical history of hypertension and monoclonal gammopathy of undetermined significance was sent from clinic in winter for 4 days of worsening fevers and sinus congestion unrelieved by over-the- counter medications. COVID and flu negative. Patient has had no sick contacts or recent travel and has pet cats but no recent scratches. Initial chest x-ray showed no acute processes, but patient was continuing to have fevers up to 103 with mild dyspnea and chills so a CT chest was completed which showed ground glass opacities in the right middle lobe. Blood and sputum cultures were obtained, and patient was started on ceftriaxone and azithromycin for community acquired pneumonia. Urine strep and legionella antigens were also acquired, both negative. Over the next two days, she continued to have high fevers and chills at nights with leukocytosis, thrombocytopenia, hyponatremia, and notable worsening of mild elevation of liver enzymes on admission. Cultures were negative and patient had no other indication of an infection aside from the cyclical fevers therefore empiric doxycycline was added for coverage of atypical infections. Over the next two days, she continued to have nightly fevers up to 103 so ID was consulted for fever of unknown origin. On repeat exposure assessment, patient revealed that she lived with multiple animals including cats, dogs, parakeets, chickens, geese and a pony. Patient was continued on doxycycline while additional lab tests were sent for atypical infections including Rickettsia typhi, Coxiella brunetti (Q fever), and Brucella spp given patient's history of exposure to multiple animals at home. Patient was discharged on doxycycline after being afebrile for 48hrs with declining white count and liver enzymes. Lab results confirmed the diagnosis with high titers for Rickettsia typhi IgG and IgM. IMPACT/DISCUSSION: This case illustrates an atypical presentation of murine typhus with pneumonia in winter. There are several key teaching points in this case: 1. Ricketssia typhi infections have largely nonspecific symptoms therefore it should should be included in differential diagnoses of febrile illnesses with thrombocytopenia and elevated liver enzymes 2. Although a complete history is acquired on admission, it is important to revisit and review information again when a clinical diagnosis has not been established 3. Defeverscence after starting doxycycline can take anywhere from 4 to 66hrs so fevers during this timeframe is not an indication of failure of therapy CONCLUSION: Murine typhus presents with non-specific symptoms so it should be included in the differential diagnosis of patients with fevers of unknown origin with potential exposure to flea-bearing animals. The optimal therapy is doxycycline 100mg twice a day for seven days. Patients should also be advised to treat their animals for fleas to prevent recurrent infections.

8.
Journal of General Internal Medicine ; 37:S487, 2022.
Article in English | EMBASE | ID: covidwho-1995703

ABSTRACT

CASE: Patient is a 21-year-old Guatemalan female with no significant past medical history was hospitalized with worsening productive cough for the last 4 weeks, with greenish sputum associated with pleuritic chest pain, shortness of breath and low appetite. Patient denies any fever, night sweating, weight loss. She states that she came from Guatemala around 3 years ago. Denies any nausea, vomiting, diarrhea, abdominal pain, falls or injuries. She works in the poultry industry. No sick contact. No recent travel. She denies any family members with similar symptoms. No reported history of TB in the family. On admission, she was alert, vitals were stable except for mild tachycardia, and was saturating well on room air. Physical examination revealed dullness on percussion, diffuse crackles, and decreasing breath sound bilaterally. Cell blood count with white blood cells 8.6G/L (72.4% neutrophil and 15% lymphocyte) and hemoglobin ad hematocrit 10.5/34.7 and mildly elevated liver transaminase level were recorded. Chest X-ray showed, Severe bilateral basilar pneumonitis worse on left. Moderate-sized left pleural effusion and the first contrast-enhanced chest computed tomography (CT)revealed severe multifocal necrotizing pneumonia with bilateral pleural effusions. The left pleural effusion raised the question of a loculated infected pleural effusion, and she also developed small apical hydropneumothorax. Patient was started on broadspectrum antibiotic coverage as well as pigtail placement on the left for drainage of pleural effusion. Fungal serologies, QuantiFERON gold assay, pleural fluid studies and sputum series for AFB stain were sent. COVID PCR negative. Cryptococcal negative. HIV negative. Sputum culture showing gram- negative rods Serratia marcescens and positive acid-fast bacilli for mycobacterium tuberculosis, pleural fluid is strongly exudative and sputum AFB smear showed positive PCR for Mycobacterium tuberculosis complex. She started on Rifampin, INH, Pyrazinamide and Ethambutol. IMPACT/DISCUSSION: Necrotizing pneumonia is a serious complication of community acquired Pneumonia, it's a rare but severe condition of lung parenchyma destruction commonly caused by bacterial pathogens. Necrotizing Pneumonia with M.tuberculosis have been reported in children and several cases of pulmonary gangrene in adults but very few cases of necrotizing pneumonia have been reported.The destruction of pulmonary parenchyma induced by M. tuberculosis usually develops from months to years but there are a few cases (necrotizing pneumonia and pulmonary gangrene) in which this destruction may progress rapidly causing severe respiratory failure. The pathogenic mechanism can be explained by the intensive tuberculous inflammation causing the widespread vascular thrombosis and arteritis. CONCLUSION: Our case report highlights the rarity of Mycobacterium tuberculosis causing necrotizing pneumonia and physicians should be aware of this rare presentation which develops rapidly causing severe respiratory failure.

9.
3rd International Conference on Computer Vision, Image and Deep Learning and International Conference on Computer Engineering and Applications, CVIDL and ICCEA 2022 ; : 15-20, 2022.
Article in English | Scopus | ID: covidwho-1992587

ABSTRACT

Since the outbreak of novel coronavirus pneumonia (COVID-19) in 2019, normal learning and living have been severely affected, and human life and health have been seriously threatened. Therefore, it is crucial to diagnose the novel coronavirus pneumonia rapidly and efficiently. In this study, based on the classical image classification neural network model, a novel deep convolutional neural network model based on the attention mechanism is proposed and named the LACNN_CBAM model. The accuracy Acc, precision Pre, recall Rec and F-1 scores of the model in the public dataset collated from published papers are 0.989, 0.992, 0.992, and 0.992, which are respectively higher than existing learning models. The model determines whether a patient has COVID-19 and community-acquired pneumonia by patient's CT images. The effectiveness of the model was demonstrated by experimental results on a clinical dataset. We believe that the model proposed in this paper can help physicians to diagnose COVID-19 and community-acquired pneumonia efficiently and accurately in reality. © 2022 IEEE.

10.
Problemy Osobo Opasnykh Infektsii ; - (1):130-136, 2022.
Article in Russian | Scopus | ID: covidwho-1988791

ABSTRACT

The aim of the work was to summarize the experience of the Rostov-on-Don Research Anti-Plague Institute in the organizational and functional response aimed at ensuring the implementation of a complex of on-going and scheduled anti-epidemic (preventive) measures at different territorial levels in the context of COVID-19 pandemic. Stage-wise reassignment of scientific and operational subdivisions of the facility was carried out in a timely manner in a flexible mode for a prompt response to the challenges that arose from community transmission of the new coronavirus infection in the territory of the Russian Federation. It allowed an effective distribution of the forces and assets without damage for specialized functioning in the main areas of scientific and practical activities. Realized was an effective interdepartmental interaction with territorial scientific and practical institutions of the Rospotrebnadzor and specialized medical organizations. Practical, methodological and advisory assistance was provided to personnel of specialized medical institutions within the framework of conversing in-patient facilities into hospitals for the treatment of patients with COVID-19. Priority research to study the level of the humoral and cellular immune response to SARS-CoV-2 among the population of the Rostov Region, the etiological spectrum of the causative agents of community-acquired pneumonia associated with COVID-19, full genome sequencing of SARS-CoV-2 isolates was carried out. Specialists of the task forces reinforced human resources of individual laboratory facilities in Moscow city, the Republic of Crimea and the Rostov Region. Complex objective of effective functioning has been implemented: in an operational mode – participation in anti-epidemic (preventive) measures in the face of changes in the dynamics and intensity of the epidemic manifestations of new coronavirus infection;in scheduled mode – the implementation of activities in the main areas of the scientific work of the organization. © 2022 Russian Research Anti-Plague Institute. All rights reserved.

11.
J Infect Chemother ; 28(10): 1353-1357, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-1983462

ABSTRACT

Legionella pneumophila is a major causative pathogen of community-acquired pneumonia (CAP), but recently the novel coronavirus disease 2019 (COVID-19) became the most common causative pathogen of CAP. Because L. pneumophila CAP is clinically distinct from bacterial CAPs, the Japan Society for Chemotherapy (JSC) developed a simple scoring system, the Legionella Score, using six parameters for the presumptive diagnosis of L. pneumophila pneumonia. We investigated the clinical and laboratory differences of L. pneumophila CAP and COVID-19 CAP and validated the Legionella Score in both CAP groups. We analyzed 102 patients with L. pneumophila CAP and 956 patients with COVID-19 CAP. Dyspnea and psychiatric symptoms were more frequently observed and cough was less frequently observed in patients with L. pneumophila CAP than those with COVID-19 CAP. Loss of taste and anosmia were observed in patients with COVID-19 CAP but not observed in those with L. pneumophila CAP. C-reactive protein and lactate dehydrogenase levels in L. pneumophila CAP group were significantly higher than in the COVID-19 CAP group. In contrast, sodium level in the L. pneumophila CAP group was significantly lower than in the COVID-19 CAP group. The median Legionella Score was significantly higher in the L. pneumophila CAP group than the COVID-19 CAP group (score 4 vs 2, p < 0.001). Our results demonstrated that the JSC Legionella Score had good diagnostic ability during the COVID-19 pandemic. However, physicians should consider COVID-19 CAP when loss of taste and/or anosmia are observed regardless of the Legionella Score.


Subject(s)
Ageusia , COVID-19 , Community-Acquired Infections , Legionella pneumophila , Legionella , Legionnaires' Disease , Pneumonia , Anosmia , COVID-19/diagnosis , Community-Acquired Infections/drug therapy , Humans , Legionnaires' Disease/microbiology , Pandemics , Pneumonia/microbiology
12.
Indian Journal of Critical Care Medicine ; 26(8):920-929, 2022.
Article in English | EMBASE | ID: covidwho-1979533

ABSTRACT

Background: Diagnosing pneumonia is challenging because of multiple differential diagnosis. Bedside lung ultrasound (BLUS) is a safe, portable, rapid and inexpensive new modality to diagnose pneumonia. This study was aimed to evaluate the sensitivity of BLUS vs chest X-ray (CXR) to diagnose community-acquired pneumonia (CAP) using computed tomography (CT) scans as the gold standard. Patients and methods: An observational cross-sectional study was conducted in selected intensive care units (ICUs). Eligible 85 adult patients with symptoms suggestive of pneumonia as per 2007 Infectious Disease Society of America (IDSA), American Thoracic Society (ATS) criteria, and 2D echocardiography were enrolled consecutively by using convenient sampling technique. Real-time reverse transcription-polymerase chain reaction (RT-PCR) assay for SARS-associated coronavirus was sent with in 1 hour followed by BLUS and CXR within 24 hours of ICU admission. The final confirmation of CAP was done by a thoracic CT scan. Results: Bedside lung ultrasound vs CXR could detect 74 vs 58 cases out of 84 confirmed cases. Sensitivity and specificity of BLUS vs CXR was 88.1% vs 67.8% and 100% vs 0%, respectively. Moreover, LR+ and LR− for BLUS was found to be 0 and 0.12 in comparison to 0.68 and 0 for CXR. The area under receiver operator characteristics (ROC) curve for BLUS vs CXR was 0.94 (95% CI 0.0–1.0) with p = 0.13 and 0.66 (95% CI 0.12–1.0) with p = 0.58. There was a significant agreement between diagnostic accuracy of BLUS and CT scan [kappa value (κ) = 0.14, p = 0.009], whereas CXR could not establish its diagnostic efficiency (κ = −0.023, p = 0.493). Sonographic features of pneumonia were B-lines, shred, and hepatization signs. Conclusion: It is observed that BLUS showed higher sensitivity, specificity, and diagnostic accuracy as compared to CXR to diagnose pneumonia.

13.
European Journal of Neurology ; 29:71, 2022.
Article in English | EMBASE | ID: covidwho-1978447

ABSTRACT

Background and aims: Two years after onset of the pandemic, the precise nature and temporal evolution of the effects of COVID-19 on neurologic disorders remain uncharacterized. Studies have established an association with neurological syndromes, including anosmia, encephalopathy, and ischemic stroke, but it is unknown whether COVID-19 also influences the incidence of specific neurologic diseases and whether it differs from other respiratory infections. Methods: Using population-based electronic health records we investigated the association between COVID-19 and specific central and peripheral neurologic diseases. We compared patients with COVID-19 to individuals without, and to patients with influenza A/B and community-acquired bacterial pneumonia. We assessed the incidence of neurologic disease one, three, six, and twelve months after positive test results. Results: We identified 42,535 people with COVID-19, 8,329 with influenza, 1,566 with pneumonia, and 2,392,400 without COVID-19. Compared to individuals without COVID-19, patients with COVID-19 had increased relative risk (RR) of developing Guillain Barré syndrome (RR=3.1;95% CI=1.5-6.7), multiple sclerosis (RR=1.4;95% CI=1.2-1.7), narcolepsy (RR=3.2;95% CI=1.6-6.2), Parkinson's disease (RR=2.8;95% CI=2.4-3.2), Alzheimer's disease (RR=4.9;95% CI=4.0-6.0), dementia of any type (RR=5.2;95% CI=4.5-6.1), and ischemic stroke (RR=2.3;95% CI=2.1-2.5). However, compared to patients hospitalized with influenza, patients hospitalized with COVID-19 only had an increased risk of ischemic stroke at one (RR=1.9;95% CI=1.3-2.8), three (RR=1.8;95% CI=1.3-2.5) and six months (RR=1.9, 95% CI=1.3-2.7). Compared to patients hospitalized with pneumonia, the risk of neurologic diseases was not increased. Conclusion: COVID-19 increases the risk of a broad range of neurological disorders. However, except for ischemic stroke, there is no excess risk compared to influenza A/B and community-acquired pneumonia.

14.
Lancet Reg Health Eur ; 21: 100473, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-1977612

ABSTRACT

Background: The emergence of COVID-19 and public health measures implemented to reduce SARS-CoV-2 infections have both affected acute lower respiratory tract disease (aLRTD) epidemiology and incidence trends. The severity of COVID-19 and non-SARS-CoV-2 aLRTD during this period have not been compared in detail. Methods: We conducted a prospective cohort study of adults age ≥18 years admitted to either of two acute care hospitals in Bristol, UK, from August 2020 to November 2021. Patients were included if they presented with signs or symptoms of aLRTD (e.g., cough, pleurisy), or a clinical or radiological aLRTD diagnosis. Findings: 12,557 adult aLRTD hospitalisations occurred: 10,087 were associated with infection (pneumonia or non-pneumonic lower respiratory tract infection [NP-LRTI]), 2161 with no infective cause, with 306 providing a minimal surveillance dataset. Confirmed SARS-CoV-2 infection accounted for 32% (3178/10,087) of respiratory infections. Annual incidences of overall, COVID-19, and non- SARS-CoV-2 pneumonia were 714.1, 264.2, and 449.9, and NP-LRTI were 346.2, 43.8, and 302.4 per 100,000 adults, respectively. Weekly incidence trends in COVID-19 aLRTD showed large surges (median 6.5 [IQR 0.7-10.2] admissions per 100,000 adults per week), while other infective aLRTD events were more stable (median 14.3 [IQR 12.8-16.4] admissions per 100,000 adults per week) as were non-infective aLRTD events (median 4.4 [IQR 3.5-5.5] admissions per 100,000 adults per week). Interpretation: While COVID-19 disease was a large component of total aLRTD during this pandemic period, non- SARS-CoV-2 infection still caused the majority of respiratory infection hospitalisations. COVID-19 disease showed significant temporal fluctuations in frequency, which were less apparent in non-SARS-CoV-2 infection. Despite public health interventions to reduce respiratory infection, disease incidence remains high. Funding: AvonCAP is an investigator-led project funded under a collaborative agreement by Pfizer.

15.
Front Bioeng Biotechnol ; 10: 903426, 2022.
Article in English | MEDLINE | ID: covidwho-1968989

ABSTRACT

Background: The ability to assess adverse outcomes in patients with community-acquired pneumonia (CAP) could improve clinical decision-making to enhance clinical practice, but the studies remain insufficient, and similarly, few machine learning (ML) models have been developed. Objective: We aimed to explore the effectiveness of predicting adverse outcomes in CAP through ML models. Methods: A total of 2,302 adults with CAP who were prospectively recruited between January 2012 and March 2015 across three cities in South America were extracted from DryadData. After a 70:30 training set: test set split of the data, nine ML algorithms were executed and their diagnostic accuracy was measured mainly by the area under the curve (AUC). The nine ML algorithms included decision trees, random forests, extreme gradient boosting (XGBoost), support vector machines, Naïve Bayes, K-nearest neighbors, ridge regression, logistic regression without regularization, and neural networks. The adverse outcomes included hospital admission, mortality, ICU admission, and one-year post-enrollment status. Results: The XGBoost algorithm had the best performance in predicting hospital admission. Its AUC reached 0.921, and accuracy, precision, recall, and F1-score were better than those of other models. In the prediction of ICU admission, a model trained with the XGBoost algorithm showed the best performance with AUC 0.801. XGBoost algorithm also did a good job at predicting one-year post-enrollment status. The results of AUC, accuracy, precision, recall, and F1-score indicated the algorithm had high accuracy and precision. In addition, the best performance was seen by the neural network algorithm when predicting death (AUC 0.831). Conclusions: ML algorithms, particularly the XGBoost algorithm, were feasible and effective in predicting adverse outcomes of CAP patients. The ML models based on available common clinical features had great potential to guide individual treatment and subsequent clinical decisions.

16.
Russian Journal of Infection and Immunity ; 12(3):563-568, 2022.
Article in Russian | EMBASE | ID: covidwho-1969869

ABSTRACT

Multidrug-resistant K. pneumoniae bacterial strains producing extended range of beta-lactamases or carbapenemases are of serious clinical concern. The aim of the study was to determine the resistance factors of K. pneumoniae strains isolated from the lower respiratory tract of patients diagnosed with community-acquired pneumonia during the COVID-19 pandemic. Materials and methods. The study of resistance to antimicrobial drugs included 138 strains of K. pneumoniae isolated from the sputum of patients treated in infectious diseases monohospitals in the city of Tyumen and the Tyumen region within the period from May 2020 to June 2021. Among the strains examined, 51.4% of them were isolated from SARS-CoV-2 positive patients. The presence of resistance genes was determined by PCR in 71 strains of K. pneumoniae (34 strains from COVID-19-positive and 37 strains from COVID-19-negative patients). Identification of isolated bacterial strains was carried out according to the protein spectra by using a desktop time-of-flight mass spectrometer with matrix laser desorption MALDI-TOF MS (Bruker, Germany). The belonging of the strains to the hypermucoid phenotype was determined using the string test. Sensitivity to antimicrobial drugs was assessed in the disk diffusion method on Muller-Hinton medium. The sensitivity of culture strains to bacteriophage preparations was determined by the drop method (spot-test). In the study, we used “Polyvalent Sextaphage Pyobacteriophage” and “Purified Polyvalent Klebsiella Bacteriophage”, JSC NPO Microgen, Russia. Detection of resistance genes to beta-lactam antibiotics by real-time PCR was carried out using the BakRezista kit (OOO DNA-technology, Russia). The results of the study evidence that K. pneumoniae bacteria isolated from COVID-19-positive and COVID-19-negative patients diagnosed with community-acquired pneumonia displayed a high resistance to antimicrobial drugs and commercial phage-containing drugs. Resistance of K. pneumoniae strains was recorded from 50% (to aminoglycosides and carbapenems) to 90% (to inhibitor-protected penicillins). Sensitivity to bacteriophages was noted on average in no more than 20% of strains. It is important to emphasize that strains isolated from COVID-19-positive patients more often showed a hypermucoid phenotype, suggesting a high bacterial virulence, and also showed greater resistance to all groups of antibacterial drugs examined in the study, which is confirmed by the presence of resistance genes of the ESBL group and carbapenemase. The results of the study suggest that the high level of resistance of K. pneumoniae strains isolated from COVID-19-positive patients is associated with immunosuppression provoked by the SARS-CoV-2 virus, which contributes to their colonization by more virulent strains.

17.
Russian Journal of Infection and Immunity ; 12(3):535-542, 2022.
Article in Russian | EMBASE | ID: covidwho-1969865

ABSTRACT

Microbiological monitoring after infectious diseases in the system of epidemiological surveillance implies simultaneous pathogen identification both among patients and in hospital environment. Our aim is to assess potential hospital environmental hazard for the two in-patient infectious disease hospitals of the Khabarovsk city by using bacteriological and epidemiological analysis during new coronavirus disease pandemic. Materials and methods. Bacteriological assessment of nasopharyngeal microflora in 241 patients suffering from community-acquired pneumonia that were hospitalized in the two prevention and treatment facilities of the Khabarovsk city was performed. Sanitary-bacteriological control of hospital environment (428 hospital environment samples and 91 air samples) was carried out in parallel. Bacteriological assessment was performed with classical methods. Identification of isolated bacteriological pathogens and evaluation of drug-resistant strains were carried out by utilizing bacteriological analyzer Vitek 2 Compact. Results. Nine different pathogens (Pseudomonas aeruginosa, Pseudomonas stutzeri, Acinetobacter baumannii, Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Pantoea, Enterococcus faecium, Staphylococcus haemolyticus) were isolated in 20 out of 428 samples — 4.7% [2.7–6.7]. Half of isolated agents — 2.3% [0.9–3.8] — were represented by drug-resistant isolates (10 out of 20 isolates) including 5 carbapenem-resistant isolates (Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae) and 5 isolates with multiple drug resistance (Enterobacter cloacae, Pantoea, Enterococcus faecium, Staphylococcus haemolyticus). Air samples contained pathogenic biological agents found in 6 out of 91 samples — 6.6% [1.5–11.7], and half of them — 3.3% [0.6–7.9] — were identified as drug-resistant variants, including S. aureus и S. haemolyticus. One of the surveyed hospitals was recognized as more hazardous due to microflora isolated from intensive care unit (A. baumannii and P. aeruginosa were resistant to 3rd–4th generation cephalosporins and carbapenems). Conclusion. Revealed circulation of wide range of microorganisms isolated from environment of two in-patient hospitals indicates high risk of healthcare-associated infections formation. Intensive care units can serve as a reservoir of healthcare-associated infections due to high percentage of patients with severe disease cases (“main reservoir” of drug-resistant strains).

18.
Fundamental and Clinical Pharmacology ; 36:17, 2022.
Article in English | EMBASE | ID: covidwho-1968103

ABSTRACT

Introduction: The urgency of finding effective treatments for severe forms of COVID-19 has necessitated adaptations to clinical trial designs. Almost all of the initial randomized trials had to be open-label and placebo-free. We were able to seize the opportunity to conduct a double-blind placebo-controlled trial by integrating ourselves into an ongoing trial and offer here some lessons from this experience. Material and methods: The CAPE-COD trial (NCT 02517489) sought to show a decrease in day 28 mortality in patients admitted to critical care with community-acquired pneumonia and receiving hydrocortisone compared with placebo. The inclusion of patients with COVID-19 was possible but required urgent responses to several problems: i) choose between subgroup analysis or segregation of COVID patients from others;ii) simultaneously include in both trials or discontinue the parent trial;iii) adapt methods to achieve a rapid response, including changing the primary endpoint;iv) define the maximum size and stopping boundaries of a sequential trial in the absence of solid data on disease progression;v) quickly obtain ethical and regulatory approvals and funding;vi) conduct the trial in overcrowded centers;vii) not jeopardize the rigor of the parent trial despite an interruption in its recruitment [1]. These elements will be discussed orally. Results: 150 patients were included before the DSMB suggested that inclusions be stopped due to the pre-publication of RECOVERY. Hydrocortisone did not significantly reduce the primary endpoint, treatment failure (defined as death or persistent respiratory support) at day 21, but a post-hoc analysis showed that relative mortality at day 21 was 46% lower (14.7 vs. 27.4%) with hydrocortisone compared to placebo, a non-significant difference (p = 0.057) but with an effect size comparable to that observed in RECOVERY. Tolerance was good [2]. Discussion/Conclusion: The rapid response to many methodological problems allowed a trial with low risk of bias to be conducted despite the pandemic pressure.

19.
Pediatr Pulmonol ; 57(1): 253-263, 2022 01.
Article in English | MEDLINE | ID: covidwho-1966091

ABSTRACT

OBJECTIVES: To describe the etiology of community-acquired pneumonia (CAP) in hospitalized children in Spain and analyze the predictors of the etiology. HYPOTHESIS: The different etiological groups of pediatric CAP are associated with different clinical, radiographic, and analytical data. DESIGN: Observational, multicenter, and prospective study. PATIENT SELECTION: This study included children aged 1 month to 17 years with CAP, who were hospitalized between April 2012 and May 2019. METHODS: An extensive microbiological workup was performed. The clinical, radiographic, and analytical parameters were analyzed for three etiological groups. RESULTS: Among the 495 children included, at least one causative pathogen was identified in 262 (52.9%): pathogenic viruses in 155/262 (59.2%); atypical bacteria (AB), mainly Mycoplasma pneumonia, in 84/262 (32.1%); and typical bacteria (TyB) in 40/262 (15.3%). Consolidation was observed in 89/138 (64.5%) patients with viral CAP, 74/84 (88.1%) with CAP caused by AB, and 40/40 (100%) with CAP caused by TyB. Para-pneumonic pleural effusion (PPE) was observed in 112/495 (22.6%) patients, of which 61/112 (54.5%) presented a likely causative pathogen: viruses in 12/61 (19.7%); AB in 23/61 (37.7%); and TyB in 26/61 (42.6%). Viral etiology was significantly frequent in young patients and in those with low oxygen saturation, wheezing, no consolidation, and high lymphocyte counts. CAP patients with AB as the etiological agent had a significantly longer and less serious course as compared to those with other causative pathogens. CONCLUSIONS: Viruses and M. pneumoniae are the main causes of pediatric CAP in Spain. Wheezing, young age, and no consolidation on radiographs are indicative of viral etiology. Viruses and AB can also cause PPE. Since only a few cases can be directly attributed to TyB, the indications for antibiotics must be carefully considered in each patient.


Subject(s)
Community-Acquired Infections , Pneumonia, Mycoplasma , Viruses , Child , Community-Acquired Infections/epidemiology , Humans , Mycoplasma pneumoniae , Pneumonia, Mycoplasma/complications , Pneumonia, Mycoplasma/epidemiology , Prospective Studies , Spain/epidemiology
20.
Open Respiratory Archives ; 4(3), 2022.
Article in English | EMBASE | ID: covidwho-1966975
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