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Rukyaa J, Mushi MF, Silago V, Damiano P, Keenan K, Sabiiti W, Holden MTG, Seni J, Mshana SE. Etiology and antimicrobial susceptibility patterns of bacteria causing pneumonia among adult patients with signs and symptoms of lower respiratory tract infections during the COVID-19 pandemic in Mwanza, Tanzania: a cross-sectional study. Pneumonia (Nathan) 2024; 16:16. [PMID: 39232828 DOI: 10.1186/s41479-024-00137-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/26/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Bacterial pneumonia is among the leading causes of morbidity and mortality worldwide. The extensive misuse and overuse of antibiotics observed during the Corona Virus Disease 2019 (COVID-19) pandemic may have changed the patterns of pathogens causing bacterial pneumonia and their antibiotic susceptibility profiles. This study was designed to establish the prevalence of culture-confirmed bacterial pneumonia and describe their antimicrobial susceptibility profile in adult patients who presented with signs and symptoms of lower respiratory tract infections (LRTIs) during the COVID-19 pandemic. METHODOLOGY This hospital-based cross-sectional study was conducted from July 2021 to July 2022 at a zonal referral hospital and two district hospitals in Mwanza, Tanzania. Demographic and clinical data were collected using a standardized questionnaire. Sputum samples were processed by conventional culture followed by the identification of isolates and antibiotic susceptibility testing. Descriptive data analysis was performed using STATA version 15.0. RESULTS A total of 286 patients with a median age of 40 (IQR 29-60) years were enrolled in the study. More than half of the patients enrolled were females (52.4%, n = 150). The overall prevalence of bacterial pneumonia was 34.3% (n = 98). The majority of the bacterial pathogens isolated were Gram-negative bacteria (GNB) (61.2%, 60/98), with a predominance of Klebsiella spp., 38.8% (38/98), followed by Streptococcus pyogenes (21.4%, 21/98). Multi drug resistant (MDR) bacteria were detected in 72/98 (73.5%) of the isolates. The proportions of GNB-resistant strains were 60.0% (36/60) for ciprofloxacin, 60% (36/60) for amoxicillin, 60% (36/60) for amoxicillin, 68.3% (41/60) for trimethoprim-sulfamethoxazole and 58.3% (35/60) for ceftriaxone. CONCLUSION One-third of the patients with signs and symptoms of LRTIs had laboratory-confirmed bacterial pneumonia with a predominance of Gram negative MDR bacteria. This calls for continuous antimicrobial resistance (AMR) surveillance and antimicrobial stewardship programs in the study setting and other settings in developing countries as important strategies for tackling AMR.
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Affiliation(s)
- Johannes Rukyaa
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P. O. Box 1464, Mwanza, Tanzania.
| | - Martha F Mushi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P. O. Box 1464, Mwanza, Tanzania
| | - Vitus Silago
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P. O. Box 1464, Mwanza, Tanzania
| | - Prisca Damiano
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P. O. Box 1464, Mwanza, Tanzania
| | - Katherine Keenan
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, St. Andrews, KY16 9AL, UK
| | - Wilber Sabiiti
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, St. Andrews, KY16 9AL, UK
| | - Matthew T G Holden
- Division of Infection and Global Health, School of Medicine, University of St. Andrews, St. Andrews, KY16 9AL, UK
| | - Jeremiah Seni
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P. O. Box 1464, Mwanza, Tanzania
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P. O. Box 1464, Mwanza, Tanzania
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Bouza E, Guillen-Zabala H, Rojas A, Cañada G, Cercenado E, Sánchez-Carrillo C, Díez C, Puente L, Muñoz P, Galar A. Comparative study of the etiology of nosocomial bacteremic pneumonia in ventilated and non-ventilated patients: a 10-year experience in an institution. Microbiol Spectr 2023; 11:e0151723. [PMID: 37698391 PMCID: PMC10715084 DOI: 10.1128/spectrum.01517-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/13/2023] [Indexed: 09/13/2023] Open
Abstract
IMPORTANCE This study on bacteremic nosocomial pneumonia (bNP) demonstrates the importance of this condition both in patients undergoing and not undergoing mechanical ventilation. Staphylococcus aureus, Enterobacterales, and non-fermenting Gram-negative bacilli are all causative agents in ventilator-associated pneumonia (VAP) and hospital-acquired pneumonia (HAP), with a predominance of S. aureus in HAP and of Pseudomonas aeruginosa in VAP. Mortality in this condition is very high. Therefore, new therapeutic and preventive approaches should be sought.
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Affiliation(s)
- Emilio Bouza
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBERES (CB06/06/0058), CIBER Enfermedades Respiratorias, Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Helmuth Guillen-Zabala
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Adriana Rojas
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Gabriela Cañada
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Emilia Cercenado
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBERES (CB06/06/0058), CIBER Enfermedades Respiratorias, Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Carlos Sánchez-Carrillo
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Cristina Díez
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Luis Puente
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
- Department of Pneumology, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Patricia Muñoz
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBERES (CB06/06/0058), CIBER Enfermedades Respiratorias, Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Alicia Galar
- Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
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Seid A, Girma Y, Abebe A, Dereb E, Kassa M, Berhane N. Characteristics of TB/HIV Co-Infection and Patterns of Multidrug-Resistance Tuberculosis in the Northwest Amhara, Ethiopia. Infect Drug Resist 2023; 16:3829-3845. [PMID: 37346368 PMCID: PMC10281285 DOI: 10.2147/idr.s412951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023] Open
Abstract
Background Multidrug-resistant tuberculosis (MDR-TB) has continued to be a serious public health threat and significantly challenges global TB control and prevention efforts, where the TB/HIV co-infection epidemic makes the situation much worse. The aim of the study was to determine the determinant factors associated with patterns of MDR-TB among pulmonary TB patients in the Northwest Amhara, Ethiopia. Methods A hospital-based cross-sectional study was conducted from May 2022 to February 2023 in the Northwest Amhara, Ethiopia. Data on the participants' socio-demographics and clinical characteristics were obtained using a pre-tested checklist. Phenotypic susceptibility testing to first-line anti-TB drugs was performed on 180 isolates by automated BD BACTEC MGIT 960 system. Logistic regression analysis was performed to determine the association of risk factors with patterns of MDR-TB. A p-value ≤0.05 was considered statistically significant. Results The overall proportion of TB with HIV co-infected cases was 19.8% (50/252). Culture positivity was confirmed in 203/252 (80.6%) of sputum samples. Among 168 isolates, the DST showed that 119 (70.8%) isolates were pan-susceptible to all first-line drugs and prevalence of any resistance to first-line drugs was 49,168 (29.2%). Among the resistant isolates, 28 (16.7%) were any mono-resistance and 12 (7.1%) were determined to be resistant to MDR-TB. TB with a previous TB treatment (aOR = 6.73, 95% CI: 1.78-25.47, p = 0.005) and HIV co-infected (aOR = 0.252, 95% CI: 0.73-0.875, p = 0.03) were significantly associated with MDR-TB. Conclusion Higher prevalence of TB and MDR-TB was examined among TB patients in the study area. In the study, history of previous TB treatment was the strongest risk factor MDR-TB infection followed by TB with HIV co-infected cases. Therefore, there is a need of strengthening TB control and prevention programs to reduce the increase of TB incidence, further emergence and transmission of a public health threat of MDR-TB cases.
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Affiliation(s)
- Aynias Seid
- Department of Biology, College of Natural and Computational Science, Debre-Tabor University, Debre-Tabor, Ethiopia
- Department of Medical Biotechnology, Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Yilak Girma
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Ayenesh Abebe
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Eseye Dereb
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Meseret Kassa
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Nega Berhane
- Department of Medical Biotechnology, Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
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Gram Stain and Culture of Sputum Samples Detect Only Few Pathogens in Community-Acquired Lower Respiratory Tract Infections: Secondary Analysis of a Randomized Controlled Trial. Diagnostics (Basel) 2023; 13:diagnostics13040628. [PMID: 36832116 PMCID: PMC9955084 DOI: 10.3390/diagnostics13040628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/05/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Identification of the bacterial etiology of lower respiratory tract infections (LRTI) is crucial to ensure a narrow-spectrum, targeted antibiotic treatment. However, Gram stain and culture results are often difficult to interpret as they depend strongly on sputum sample quality. We aimed to investigate the diagnostic yield of Gram stain and culture from respiratory samples collected by tracheal suction and expiratory technique from adults admitted with suspected community-acquired LRTI (CA-LRTI). In this secondary analysis of a randomized controlled trial, 177 (62%) samples were collected by tracheal suction, and 108 (38%) by expiratory technique. We detected few pathogenic microorganisms, and regardless of sputum quality, there were no significant differences between the sample types. Common pathogens of CA-LRTI were identified by culture in 19 (7%) samples, with a significant difference between patients with or without prior antibiotic treatment (p = 0.007). The clinical value of sputum Gram stain and culture in CA-LRTI is therefore questionable, especially in patients treated with antibiotics.
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Teklemariam AD, Hashem AM, Saber SH, Almuhayawi MS, Haque S, Abujamel TS, Harakeh S. Bacterial co-infections and antimicrobial resistance associated with the Coronavirus Disease 2019 infection. Biotechnol Genet Eng Rev 2022:1-22. [PMID: 36123822 DOI: 10.1080/02648725.2022.2122297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
Bacterial co-infections are typically associated with viral respiratory tract infections and pose a significant public health problem around the world. COVID-19 infection damages tissues lining the respiratory track and regulates immune cells/cytokines leading to microbiome dysbiosis and facilitating the area to be colonized by pathogenic bacterial agents. There have been reports of different types of bacterial co-infection in COVID-19 patients. Some of these reports showed despite geographical differences and differences in hospital settings, bacterial co-infections are a major cause of morbidity and mortality in COVID-19 patients. The inappropriate use of antibiotics for bacterial infections, particularly broad-spectrum antibiotics, can also further complicate the infection process, often leading to multi drug resistance, clinical deterioration, poor prognosis, and eventually death. To this end, researchers must establish a new therapeutic approach to control SARS-CoV-2 and the associated microbial coinfections. Hence, the aim of this review is to highlight the bacterial co-infection that has been recorded in COVID-19 patients and the status of antimicrobial resistance associated with the dual infections.
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Affiliation(s)
- Addisu D Teklemariam
- Department of Biology, Faculty of sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Vaccines and immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saber H Saber
- Molecular Cell Biology Laboratory, Department of Zoology, Faculty of Science, Assiut University, Asyut, Egypt
| | - Mohammed S Almuhayawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Turki S Abujamel
- Vaccines and immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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Lapa SA, Miftakhov RA, Klochikhina ES, Ammur YI, Blagodatskikh SA, Shershov VE, Zasedatelev AS, Chudinov AV. Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens. Mol Biol 2021; 55:828-838. [PMID: 34955557 PMCID: PMC8682033 DOI: 10.1134/s0026893321040063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/23/2022]
Abstract
A prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, which significantly reduces the background signal and increases the sensitivity of the analysis. The use of a specialized detector makes it possible to read the signals of elongated primers directly through the transparent cover film of the reaction chamber. This solution is designed to prevent cross-contamination and is suitable for simultaneous testing of a large number of test samples. The proposed platform is able to detect the presence of several pathogens of pneumonia in a sample and has an open architecture that allows expansion of the range of pathogenic bacteria and viruses that can be detected.
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Affiliation(s)
- S A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - R A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E S Klochikhina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Yu I Ammur
- Mechnikov Institute of Vaccines and Serums, 105064 Moscow, Russia
| | - S A Blagodatskikh
- Scientific Center of Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - V E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Sirohi M, Lall M, Yenishetti S, Panat L, Kumar A. Development of a Machine learning image segmentation-based algorithm for the determination of the adequacy of Gram-stained sputum smear images. Med J Armed Forces India 2021; 78:339-344. [DOI: 10.1016/j.mjafi.2021.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022] Open
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Mardian Y, Menur Naysilla A, Lokida D, Farida H, Aman AT, Karyana M, Lukman N, Kosasih H, Kline A, Lau CY. Approach to Identifying Causative Pathogens of Community-Acquired Pneumonia in Children Using Culture, Molecular, and Serology Tests. Front Pediatr 2021; 9:629318. [PMID: 34123961 PMCID: PMC8193353 DOI: 10.3389/fped.2021.629318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/04/2021] [Indexed: 01/29/2023] Open
Abstract
Determining the causative pathogen(s) of community-acquired pneumonia (CAP) in children remains a challenge despite advances in diagnostic methods. Currently available guidelines generally recommend empiric antimicrobial therapy when the specific etiology is unknown. However, shifts in epidemiology, emergence of new pathogens, and increasing antimicrobial resistance underscore the importance of identifying causative pathogen(s). Although viral CAP among children is increasingly recognized, distinguishing viral from bacterial etiologies remains difficult. Obtaining high quality samples from infected lung tissue is typically the limiting factor. Additionally, interpretation of results from routinely collected specimens (blood, sputum, and nasopharyngeal swabs) is complicated by bacterial colonization and prolonged shedding of incidental respiratory viruses. Using current literature on assessment of CAP causes in children, we developed an approach for identifying the most likely causative pathogen(s) using blood and sputum culture, polymerase chain reaction (PCR), and paired serology. Our proposed rules do not rely on carriage prevalence data from controls. We herein share our perspective in order to help clinicians and researchers classify and manage childhood pneumonia.
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Affiliation(s)
- Yan Mardian
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia
| | | | - Dewi Lokida
- Tangerang District Hospital, Tangerang, Indonesia
| | - Helmia Farida
- Dr. Kariadi Hospital/Diponegoro University, Semarang, Indonesia
| | - Abu Tholib Aman
- Dr. Sardjito Hospital/Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Muhammad Karyana
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia
- National Institute of Health Research and Development, Ministry of Health, Republic of Indonesia, Jakarta, Indonesia
| | - Nurhayati Lukman
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia
| | - Herman Kosasih
- Indonesia Research Partnership on Infectious Disease, Jakarta, Indonesia
| | - Ahnika Kline
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Chuen-Yen Lau
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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Abstract
PURPOSE OF REVIEW Nosocomial pneumonia represents a significant burden even for the most resilient healthcare systems. Timely and reliable diagnosis is critical but remains a deficient field. This review critically revises the latest literature on the diagnosis of nosocomial pneumonia, including advances in imaging techniques, as well as the utility of rapid microbiological tests in establishing the etiological diagnosis. RECENT FINDINGS Studies on low radiation computed tomography (CT) and lung ultrasound (LUS) have shown promising results for early nosocomial pneumonia diagnosis; however, further data on their sensitivity and specificity are needed, especially for picking up subtle and nonspecific radiographic findings. Moreover, data supporting their superiority in pneumonia diagnosis is still limited. As for microbiological diagnosis, several culture-independent molecular diagnostic techniques have been developed, identifying both causative microorganisms as well as determinants of antimicrobial resistance, but more studies are needed to delineate their role in nosocomial pneumonia diagnosis. SUMMARY The development of nonculture dependent tests has launched a new era in microbiological nosocomial pneumonia diagnosis. These modalities along with the use of LUS and/or low radiation CT might improve the sensitivity and specificity of nosocomial pneumonia diagnosis, enhance early detection and guide the antimicrobial therapy but more studies are needed to further evaluate them and determine their role for the routine clinical practice.
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Oriano M, Gramegna A, Terranova L, Sotgiu G, Sulaiman I, Ruggiero L, Saderi L, Wu B, Chalmers JD, Segal LN, Marchisio P, Blasi F, Aliberti S. Sputum neutrophil elastase associates with microbiota and Pseudomonas aeruginosa in bronchiectasis. Eur Respir J 2020; 56:13993003.00769-2020. [PMID: 32499333 DOI: 10.1183/13993003.00769-2020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/19/2020] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Neutrophilic inflammation is a major driver of bronchiectasis pathophysiology, and neutrophil elastase activity is the most promising biomarker evaluated in sputum to date. How active neutrophil elastase correlates with the lung microbiome in bronchiectasis is still unexplored. We aimed to understand whether active neutrophil elastase is associated with low microbial diversity and distinct microbiome characteristics. METHODS An observational, cross-sectional study was conducted at the bronchiectasis programme of the Policlinico Hospital in Milan, Italy, where adults with bronchiectasis were enrolled between March 2017 and March 2019. Active neutrophil elastase was measured on sputum collected during stable state, microbiota analysed through 16S rRNA gene sequencing, molecular assessment of respiratory pathogens carried out through real-time PCR and clinical data collected. RESULTS Among 185 patients enrolled, decreasing α-diversity, evaluated through the Shannon entropy (ρ -0.37, p<0.00001) and Pielou's evenness (ρ -0.36, p<0.00001) and richness (ρ -0.33, p<0.00001), was significantly correlated with increasing elastase. A significant difference in median levels of Shannon entropy as detected between patients with neutrophil elastase ≥20 µg·mL-1 (median 3.82, interquartile range 2.20-4.96) versus neutrophil elastase <20 µg·mL-1 (4.88, 3.68-5.80; p<0.0001). A distinct microbiome was found in these two groups, mainly characterised by enrichment with Pseudomonas in the high-elastase group and with Streptococcus in the low-elastase group. Further confirmation of the association of Pseudomonas aeruginosa with elevated active neutrophil elastase was found based on standard culture and targeted real-time PCR. CONCLUSIONS High levels of active neutrophil elastase are associated to low microbiome diversity and specifically to P. aeruginosa infection.
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Affiliation(s)
- Martina Oriano
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy.,Dept of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Andrea Gramegna
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
| | - Leonardo Terranova
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
| | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Dept of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Luca Ruggiero
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Milan, Italy
| | - Laura Saderi
- Clinical Epidemiology and Medical Statistics Unit, Dept of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Benjamin Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - James D Chalmers
- University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Paola Marchisio
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Paediatric Highly Intensive Care Unit, Milan, Italy
| | - Francesco Blasi
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
| | - Stefano Aliberti
- University of Milan, Dept of Pathophysiology and Transplantation, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Internal Medicine Dept, Respiratory Unit and Adult Cystic Fibrosis Center, Milan, Italy
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Chen X, Liao B, Cheng L, Peng X, Xu X, Li Y, Hu T, Li J, Zhou X, Ren B. The microbial coinfection in COVID-19. Appl Microbiol Biotechnol 2020; 104:7777-7785. [PMID: 32780290 PMCID: PMC7417782 DOI: 10.1007/s00253-020-10814-6] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/07/2020] [Accepted: 08/02/2020] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel β-coronavirus, is the main pathogenic agent of the rapidly spreading pneumonia called coronavirus disease 2019 (COVID-19). SARS-CoV-2 infects much more people, especially the elder population, around the world than other coronavirus, such as SARS-CoV and MERS-CoV, which is challenging current global public health system. Beyond the pathogenesis of SARS-CoV-2, microbial coinfection plays an important role in the occurrence and development of SARS-CoV-2 infection by raising the difficulties of diagnosis, treatment, prognosis of COVID-19, and even increasing the disease symptom and mortality. We summarize the coinfection of virus, bacteria and fungi with SARS-CoV-2, their effects on COVID-19, the reasons of coinfection, and the diagnosis to emphasize the importance of microbial coinfection in COVID-19. KEY POINTS: • Microbial coinfection is a nonnegligible factor in COVID-19. • Microbial coinfection exacerbates the processes of the occurrence, development and prognosis of COVID-19, and the difficulties of clinical diagnosis and treatment. • Different virus, bacteria, and fungi contributed to the coinfection with SARS-CoV-2.
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Affiliation(s)
- Xi Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Binyou Liao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
| | - Xin Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
| | - Tao Hu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Jiyao Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China.
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Biao Ren
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China.
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Traditional Herbal Remedies with a Multifunctional Therapeutic Approach as an Implication in COVID-19 Associated Co-Infections. COATINGS 2020. [DOI: 10.3390/coatings10080761] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Co-infection in patients with viral infection as a predisposing factor is less focused on during epidemic outbreaks, resulting in increased morbidity and mortality. Recent studies showed that patients with coronavirus disease 2019 (COVID-19) often have both bacterial and fungal co-infections. In this study, sputum samples of 120 OPD (outdoor patients) suffering from respiratory tract infection (RTI) but negative for tuberculosis infection were collected with informed consent. Morphological, biochemical, and resistance criteria were used to classify isolates and to distinguish multidrug resistant (MDR) isolates, which were further classified on a molecular basis. We found that the isolates, including MDR strains, showed remarkable sensitivity against acetone and methanol extracts of Moringa oleifera, Adhatoda vasica, and Cassia fistula. The results strongly confirmed that multifactorial infections can produce MDR characteristics against antimicrobial drugs, which gave insight into the use of herbal drugs with their age-old traditional importance as having antiviral, antibacterial, antifungal, anti-inflammatory, and immunomodulatory effects. We conclude that apart from this, the anti-infective potential of these plants can be used in the future in the form of products such as cosmetics, pharmaceutical coatings, surface coatings, drug delivery vehicle coatings, and other bioengineered coatings for public use. Future studies are required to assess therapeutics for co-infective resistant strains and nosocomial infections with immune-enhancing effects, thereby promoting their function in holistic treatment and therapy of COVID-19 patients.
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