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15 pages, 1433 KiB  
Article
A Silent Threat in Post-Tuberculosis Patients: Chronic Pulmonary Aspergillosis Survey in Multiple Regions of Indonesia (I-CHROME Study)
by Anna Rozaliyani, Findra Setianingrum, Fathiyah Isbaniah, Heidy Agustin, Raden Rara Diah Handayani, Rosamarlina Syahrir, Siti Pratiekauri, Robiatul Adawiyah, Hesti Setiastuti, Mohammad Nizam Erhamza, Retno Ariza S. Soemarwoto, Irvan Medison, Deddy Herman, Avissena Dutha Pratama, Jatu Apridasari, Jani Jane, Soedarsono Soedarsono, Tutik Kusmiati, Mufidatun Hasanah, Diah Adhyaksanti, Winda Sofvina, Ammar A. Hasyim, Chris Kosmidis and David W. Denningadd Show full author list remove Hide full author list
J. Fungi 2025, 11(5), 329; https://doi.org/10.3390/jof11050329 - 22 Apr 2025
Viewed by 795
Abstract
Background: A significant complication among post-tuberculosis patients is chronic pulmonary aspergillosis (CPA), with prevalence and outcomes varying by region. This study aimed to explore the epidemiology, clinical characteristics, and microbiological profiles of 219 post-tuberculosis patients with persistent respiratory symptoms and lung cavities in [...] Read more.
Background: A significant complication among post-tuberculosis patients is chronic pulmonary aspergillosis (CPA), with prevalence and outcomes varying by region. This study aimed to explore the epidemiology, clinical characteristics, and microbiological profiles of 219 post-tuberculosis patients with persistent respiratory symptoms and lung cavities in Indonesia. Methods: The patients were divided into CPA (n = 144) and non-CPA (n = 75) groups. This cross-sectional study diagnosed CPA in post-tuberculosis patients using ERS/ESCMID criteria, integrating clinical, radiological, and fungal assessments. Serological tests for Aspergillus-specific IgG were conducted using immunochromatographic (ICT) and ELISA on serum samples. Sputum specimens were used in parallel for fungal culture, and radiological evaluations (e.g., chest X-rays or CT scans) were performed to identify typical CPA features such as cavitation and fibrosis. Results: Persistent cough was significantly more common in CPA patients (83.3%, p = 0.015), highlighting its role as a clinical indicator for CPA. Radiological infiltrates were found in 165 patients (75.3%); critical diagnostic markers of CPA were cavitation and pericavitary fibrosis. Aspergillus-specific IgG testing demonstrated high diagnostic utility, with positivity rates of 69.4% for ICT and 63.2% for ELISA among CPA patients. Among those with infiltrates, a positive Aspergillus culture was not more common (p > 0.05), whereas Aspergillus IgG was more often raised (p = 0.037), as was a positive ICT (p = 0.021). Regional analysis revealed a higher CPA burden in Region 1 (75%) compared to Region 2 (56%, p = 0.003), with Aspergillus fumigatus and Aspergillus niger predominating in Region 1. Conclusions: These findings highlight the importance of comprehensive approaches and region-specific CPA management strategies in Indonesia. Full article
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10 pages, 356 KiB  
Article
Clinical Utility of Induced Sputum and Bronchoalveolar Lavage Cultures in Diagnosing Nontuberculous Mycobacterial Pulmonary Disease
by Maria Angela Licata, Paola Mencarini, Annelisa Mastrobattista, Serena Maria Carli, Carlotta Cerva, Silvia Mosti, Raffaella Libertone, Alberto Zolezzi, Pietro Vittozzi, Carla Nisii, Antonio Mazzarelli, Angela Cannas, Assunta Navarra, Stefania Ianniello, Rocco Trisolini, Delia Goletti, Fabrizio Palmieri and Gina Gualano
Pathogens 2024, 13(12), 1064; https://doi.org/10.3390/pathogens13121064 - 3 Dec 2024
Cited by 2 | Viewed by 1611
Abstract
Diagnosing non-tuberculous mycobacterial pulmonary disease (NTM-PD) in patients unable to produce sputum spontaneously requires invasive procedures to obtain valid respiratory specimens. In this retrospective study, we evaluated the results of microbiological tests performed on respiratory samples of 132 patients affected by NTM-PD. In [...] Read more.
Diagnosing non-tuberculous mycobacterial pulmonary disease (NTM-PD) in patients unable to produce sputum spontaneously requires invasive procedures to obtain valid respiratory specimens. In this retrospective study, we evaluated the results of microbiological tests performed on respiratory samples of 132 patients affected by NTM-PD. In the diagnostic workout, 98 patients performed both induced sputum (IS) and bronchoalveolar lavage (BAL) and were enrolled in our study. A total of 93 out of 98 BAL samples (95%) were culture-positive for mycobacteria, whereas only 67/153 (44%) induced sputum cultures were positive for NTM (p < 0.001). Molecular identification of NTM with real-time polymerase chain reaction (PCR) was positive in 48/64 BAL (75%) and in 47/139 (34%) IS samples (p < 0.001). Patients affected by nodular-bronchiectatic form were 65/98 (66%): BAL culture was positive in 95% of cases (62/65 BAL), while only 30/99 IS cultures were positive (30%; p < 0.001). PCR was positive in 76% of BAL samples examined (26/34) and in 26% of the IS samples (24 out of 91) (p < 0.001). Among 33 patients with a fibro-cavitary radiological pattern, 65% of IS (35/54) were culture-positive for NTM, whereas 94% of cases (31/33) had a positive culture for NTM from BAL (p = 0.002). PCR was positive in 73% of BAL samples tested (22/30) and 48% of IS samples tested (23/48) (p = 0.031). Our results confirm BAL mycobacterial culture as the gold standard for the diagnosis of pulmonary mycobacteriosis. FBS with BAL should be performed in every patient with a strong suspicion of NTM-PD, if other respiratory samples are repeatedly negative. Sputum induction is a useful technique to obtain valid respiratory samples when patients are unable to produce spontaneous sputum, especially in the outpatient setting. However, during the diagnostic workup of NTM-PD, we should not forget that PCR and mycobacterial culture of induced sputum have a lower yield than when performed on BAL, especially in the nodular-bronchiectatic form of the disease. Full article
(This article belongs to the Section Bacterial Pathogens)
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25 pages, 1728 KiB  
Review
Human Sputum Proteomics: Advancing Non-Invasive Diagnosis of Respiratory Diseases with Enhanced Biomarker Analysis Methods
by Norberto A. Guzman and Andrea Guzman
Int. J. Transl. Med. 2024, 4(2), 309-333; https://doi.org/10.3390/ijtm4020020 - 31 May 2024
Cited by 3 | Viewed by 3620
Abstract
Many ailments can be diagnosed while they are asymptomatic, meaning that the patient has no signs or symptoms of a progressing disease. If caught in their initial stage of formation, these disorders can be effectively treated, leading to successful outcomes; curative therapies can [...] Read more.
Many ailments can be diagnosed while they are asymptomatic, meaning that the patient has no signs or symptoms of a progressing disease. If caught in their initial stage of formation, these disorders can be effectively treated, leading to successful outcomes; curative therapies can halt illnesses from advancing, thus improving the quality of life and long-term survival of the patient. Still, cutting-edge upgrades in precision technologies are necessary for early, reliable, affordable, and rapid disease detection, but also vital for the well-being of people and the future of global public health. The emerging role and utility of non-invasive and repeatable diagnostic test approaches for the detection of health conditions have been exemplified by liquid biopsies based on genomic biomarkers. As such, biological fluids permit any measurable molecular indicator or signature (e.g., proteins) to provide valuable information on an individual’s wellness and/or disease. Among the bodily secretions used for non-invasive diagnostics is sputum, a complex viscous gel-like biopolymeric network that has gained growing recognition as a rich source of biomarkers of airway infections and pulmonary diseases, and serves as a determinant to reveal other illnesses. As per the World Health Organization, the burden of respiratory conditions is exacerbated by factors ranging from considerable subjection to air pollution and occupational contaminants to tobacco smoking and second-hand smoke, in addition to poor socio-economic status. Due to the likely increase in these determinants, respiratory tract ailments are on the rise, affecting the health of many individuals, in addition to putting stress on healthcare facilities and services worldwide. The aim of this study was to perform a narrative review of sputum constituents with an emphasis on proteins and glycoproteins assessed as possible biomarkers of lung and other organ diseases. A search was conducted using mucus, sputum proteomics, sputum biomarkers, and point-of-care testing as keywords employing Google, PubMed (MEDLINE), and Web of Science, selecting the most referenced and related papers of the last decade. We, therefore, highlight the need to use expectorated or induced sputum specimens as a routine sample source for testing valuable protein biomarkers to diagnose these chronic disorders, predict inflammation and disease progression, as well as monitor the effectiveness of treatments. Further, we discuss the urgent need for fast and reliable point-of-care methods to detect and quantify crucial protein biomarkers in sputum specimens, and the limitations faced when dealing with their complex matrices. Full article
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23 pages, 4560 KiB  
Systematic Review
The Diagnostic Performance of Various Clinical Specimens for the Detection of COVID-19: A Meta-Analysis of RT-PCR Studies
by Khaled Sadeq Ali Al-Shaibari, Haider Abdul-Lateef Mousa, Mohammed Abdullah A. Alqumber, Khaled A. Alqfail, AbdulHakim Mohammed and Khalid Bzeizi
Diagnostics 2023, 13(19), 3057; https://doi.org/10.3390/diagnostics13193057 - 26 Sep 2023
Cited by 3 | Viewed by 2764
Abstract
Background: The diagnostic performance of numerous clinical specimens to diagnose COVID-19 through RT-PCR techniques is very important, and the test result outcome is still unclear. This review aimed to analyze the diagnostic performance of clinical samples for COVID-19 detection by RT-PCR through a [...] Read more.
Background: The diagnostic performance of numerous clinical specimens to diagnose COVID-19 through RT-PCR techniques is very important, and the test result outcome is still unclear. This review aimed to analyze the diagnostic performance of clinical samples for COVID-19 detection by RT-PCR through a systematic literature review process. Methodology: A compressive literature search was performed in PubMed/Medline, Scopus, Embase, and Cochrane Library from inception to November 2022. A snowball search on Google, Google Scholar, Research Gate, and MedRxiv, as well as bibliographic research, was performed to identify any other relevant articles. Observational studies that assessed the clinical usefulness of the RT-PCR technique in different human samples for the detection or screening of COVID-19 among patients or patient samples were considered for this review. The primary outcomes considered were sensitivity and specificity, while parameters such as positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient were considered secondary outcomes. Results: A total of 85 studies out of 10,213 non-duplicate records were included for the systematic review, of which 69 articles were considered for the meta-analysis. The meta-analysis indicated better pooled sensitivity with the nasopharyngeal swab (NPS) than saliva (91.06% vs. 76.70%) and was comparable with the combined NPS/oropharyngeal swab (OPS; 92%). Nevertheless, specificity was observed to be better with saliva (98.27%) than the combined NPS/OPS (98.08%) and NPS (95.57%). The other parameters were comparable among different samples. The respiratory samples and throat samples showed a promising result relative to other specimens. The sensitivity and specificity of samples such as nasopharyngeal swabs, saliva, combined nasopharyngeal/oropharyngeal, respiratory, sputum, broncho aspirate, throat swab, gargle, serum, and the mixed sample were found to be 91.06%, 76.70%, 92.00%, 99.44%, 86%, 96%, 94.4%, 95.3%, 73.63%, and above 98; and 95.57%, 98.27%, 98.08%, 100%, 37%, 100%, 100%, 97.6%, and above 97, respectively. Conclusions: NPS was observed to have relatively better sensitivity, but not specificity when compared with other clinical specimens. Head-to-head comparisons between the different samples and the time of sample collection are warranted to strengthen this evidence. Full article
(This article belongs to the Section Diagnostic Microbiology and Infectious Disease)
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14 pages, 304 KiB  
Article
The Antimicrobial Resistance (AMR) Rates of Enterobacterales in a Rural Hospital from the Eastern Region, Ghana: A Retrospective Study, 2022
by Laura Seijas-Pereda, Carlos Rescalvo-Casas, Marcos Hernando-Gozalo, Vida Angmorkie-Eshun, Eunice Agyei, Vivian Adu-Gyamfi, Isaac Sarsah, Maite Alfonso-Romero, Juan Cuadros-González, Juan Soliveri-de Carranza and Ramón Pérez-Tanoira
Antibiotics 2023, 12(8), 1321; https://doi.org/10.3390/antibiotics12081321 - 16 Aug 2023
Cited by 3 | Viewed by 2025
Abstract
Low- and middle-income countries bear a disproportionate burden of antimicrobial resistance and often lack adequate surveillance due to a paucity of microbiological studies. In this 2022 study, our goal was to contribute to a more precise antimicrobial treatment by understanding the prevalence of [...] Read more.
Low- and middle-income countries bear a disproportionate burden of antimicrobial resistance and often lack adequate surveillance due to a paucity of microbiological studies. In this 2022 study, our goal was to contribute to a more precise antimicrobial treatment by understanding the prevalence of resistance in a rural environment, promoting antibiotic stewardship, and raising awareness about antimicrobial resistance. We assessed the prevalence of Multidrug-Resistant (MDR) and Extensively Drug-Resistant (XDR) Enterobacterales in clinical samples from 2905 patients being treated at Saint Dominic’s Hospital, Akwatia, in the countryside of the Eastern Region, Ghana, in the year 2022. To this purpose, the samples were cultured on agar plates prepared in the laboratory using purified Oxoid™ Thermo Scientific™ agar (Thermo Fisher Scientific; Waltham, MA, USA). Cystine Lactose Electrolyte-Deficient (CLED) agar was used for urine samples, while blood agar, chocolate agar, and MacConkey agar were used for the rest of the specimens tested (HVS, blood, BFA, sputum). Antimicrobial susceptibility was determined on site using the disc diffusion method (Kirby-Bauer test). MDR bacteria accounted for more than half (53.7%) of all microorganisms tested for three or more antibiotics and 37.3% of these were XDR. Multivariate regression analysis was performed to identify risk factors associated with acquiring MDR/XDR bacteria. The results showed an increased likelihood of MDR acquisition linked to being male (OR 2.39, p < 0.001 for MDR and OR 1.95, p = 0.027 for XDR), higher age (OR 1.01, p = 0.049 for MDR), non-sputum samples (OR 0.32, p = 0.009 for MDR), and urine samples (OR 7.46, p < 0.001 for XDR). These findings emphasize the urgency for surveillance and control of antimicrobial resistance; to this end, making accurate diagnostics, studying the microorganism in question, and conducting susceptibility testing is of the utmost importance. Full article
(This article belongs to the Special Issue Gram-Negative Multidrug Resistant Pathogen and Its Treatment)
16 pages, 921 KiB  
Article
Community-Acquired Methicillin-Resistant Staphylococcus aureus in Hospitals: Age-Specificity and Potential Zoonotic–Zooanthroponotic Transmission Dynamics
by Ahmed Alsolami, Naif Saad ALGhasab, Mohammed S. M. Alharbi, Abdelhafiz I. Bashir, Mohd Saleem, Azharuddin Sajid Syed Khaja, Dakheel F. Aldakheel, Ehab Rakha, Jabar Aziz Alshammari, Taha E. Taha, Ziyad Melibari, Yaseer H. Alharbi, Ali A. Almutlag and Kamaleldin B. Said
Diagnostics 2023, 13(12), 2089; https://doi.org/10.3390/diagnostics13122089 - 16 Jun 2023
Cited by 7 | Viewed by 3145
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) lineages are a devastating clinical and public health issue. Data on local lineage profiles are limited. We report on the frequency of community-acquired and hospital-acquired cases (CA-MRSA, HA-MRSA). We studied 147 isolates from King Khalid tertiary care hospitals (KKH), [...] Read more.
Methicillin-resistant Staphylococcus aureus (MRSA) lineages are a devastating clinical and public health issue. Data on local lineage profiles are limited. We report on the frequency of community-acquired and hospital-acquired cases (CA-MRSA, HA-MRSA). We studied 147 isolates from King Khalid tertiary care hospitals (KKH), each from a case in a patient and including 33 patients at the Maternity and Children’s Hospital (MCH). Of the 147 isolates, 87 males (59%) and 60 females (41%) were in KKH. The overwhelming majority (80%; n = 119/147) were CA-MRSA in KKH. Intriguingly, despite significant differences between males (70%) and females (53%), lineage-acquisition remained age-specific around 58–60 years in both genders. However, while CA-MRSA dominated early in life (0–20, 70% MCH), it increased with age in KKH adults; 21–50 (28%), >50 (59%) until the overall 80% (n = 144/180). Major specimens included skin-wounds, surgeries (70.3%), blood (13.5%), sputum (8.8%), very rarely urine (4.1%), and nasal (3.4%), albeit most patients showed severe enteritis and necrotizing pneumonia. Antibiograms showed high beta lactam resistances, including amoxicillin–clavulanate (83%), oxacillin (84%), cefoxitin FOX (100%), penicillin and ampicillin (~100%), as well as high resistance (82%) to carbapenem. Fortunately, high susceptibility was seen to non-beta lactams and, to a lesser extent, gentamicin, erythromycin, and fusidic acid; 33%, 34%, and 38%, respectively, in KKH. A similar pattern was seen in MCH except for a low resistance pattern to gentamicin CN, clindamycin CD, erythromycin E, and tobramycin TOB; 34%, 31%, 39%, and 41%, respectively, except for fusidic acid. These findings have significant clinical implications for MRSA patient management strategies. Clinical- and lineage-profiles imply host-selection and zoonotic–zooanthroponotic transmission dynamics. Future molecular typing, sequencing, and characterization of dominant clone(s) is imperative. Full article
(This article belongs to the Section Diagnostic Microbiology and Infectious Disease)
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12 pages, 1494 KiB  
Article
Current Trends in Antimicrobial Resistance Patterns in Bacterial Pathogens among Adult and Pediatric Patients in the Intensive Care Unit in a Tertiary Care Hospital in Kolkata, India
by Mandira Chakraborty, Sayani Sardar, Rituparna De, Malabika Biswas, Maria Teresa Mascellino, Maria Claudia Miele, Silpak Biswas and Anita Nandi Mitra
Antibiotics 2023, 12(3), 459; https://doi.org/10.3390/antibiotics12030459 - 24 Feb 2023
Cited by 14 | Viewed by 5939
Abstract
Nosocomial infections by multidrug-resistant (MDR) bacteria are among the main causes of morbidity and death in patients hospitalized in intensive care units (ICUs) worldwide. Antibiotic resistance has become a major concern for treating the patients with nosocomial infections. The aim of this study [...] Read more.
Nosocomial infections by multidrug-resistant (MDR) bacteria are among the main causes of morbidity and death in patients hospitalized in intensive care units (ICUs) worldwide. Antibiotic resistance has become a major concern for treating the patients with nosocomial infections. The aim of this study was to describe the antibiotic resistance patterns of pathogens causing infections in adult and pediatric patients in the ICUs of a tertiary care hospital in Kolkata, India. A cross-sectional, retrospective study was conducted from January 2022 to October 2022 on a total of 139 adult and 146 pediatric patients. Depending on clinical symptoms of the patients, samples were collected and subjected to antibiotic sensitivity testing. The culture and sensitivity pattern of clinical isolates from blood, urine, sputum, endotracheal tube (ET) aspirate, and central line catheter insertion site swabs were analyzed. A total of 695 and 556 specimens were obtained from adult and pediatric ICU, respectively. Culture positivity rate among adults and pediatric patients were 37% and 40%, respectively. The most commonly isolated organisms were Gram-negative Enterobacterales and non-fermenters. Most of the bacterial isolates showed very high resistance against multiple antibiotics. Escherichia coli from adult and pediatricpatients were found to be resistant to second generation cephalosporins (95% and 96%, respectively), beta-lactams (95% and 63%, respectively), fluoroquinolones (95% and 81%, respectively), and cotrimoxazole (85% and 78%, respectively). Klebsiella spp. from adult patients were found to be resistant to aminoglycosides (75%), second generation cephalosporins (100%), beta-lactams (94%), fluoroquinolones (92%), carbapenems (88%), and cotrimoxazole (83%). Proteus spp., Acinetobacter baumannii, and Pseudomonas spp. werefound to be resistant to multiple antibiotics. Enterococcus spp. from ICUs showed more than 90% resistance against ampicillin and more than 75% resistance against fluoroquinolones. MDR bacterial infections are increasing in both adult and pediatric ICUs, leading to significant therapeutic challenges. A frequent study of antimicrobial resistance patterns is imperative for antibiotic stewardshipin combatting the deadly effect of the MDR bacteria in critically ill patients. Full article
(This article belongs to the Special Issue Multi-Drug Resistant Gram-Negative Microorganisms, 2nd Edition)
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9 pages, 1622 KiB  
Article
Comparison of Analytical Sensitivity (Limit of Detection) of Xpert MTB/RIF and Xpert MTB/RIF Ultra for Non-Sputum Specimens
by Marisa C. Nielsen, Paula Clarner, Ruchi Paroha, Sunhee Lee, Phyu M. Thwe and Ping Ren
Pathogens 2023, 12(2), 157; https://doi.org/10.3390/pathogens12020157 - 18 Jan 2023
Cited by 4 | Viewed by 3504
Abstract
Tuberculosis (TB) is a significant public health threat and has remained a leading cause of death in many parts of the world. Rapid and accurate testing and timely diagnosis can improve treatment efficacy and reduce new exposures. The Cepheid Xpert® MTB/RIF tests have [...] Read more.
Tuberculosis (TB) is a significant public health threat and has remained a leading cause of death in many parts of the world. Rapid and accurate testing and timely diagnosis can improve treatment efficacy and reduce new exposures. The Cepheid Xpert® MTB/RIF tests have two marketed products (US-IVD and Ultra) that are widely accepted for diagnosis of TB but have not yet been approved for non-sputum specimens. Despite numerous studies in the literature, no data for the analytical sensitivity of these two products on the non-sputum samples are available to date. This is the first study that systematically determined the analytical sensitivities of both US-IVD and Ultra tests on cerebrospinal fluid (CSF), tissue, and bronchoalveolar lavage (BAL). The limits of detection (LoDs) on the US-IVD test for both Mycobacterium tuberculosis and rifampin resistance in CFU/mL, respectively, were as follows: CSF (3.3 and 4.6), tissue (15 and 23), and bronchoalveolar lavage (BAL) (45 and 60), and on the Ultra test: CSF (0.16 and 2.7), tissue (0.11 and 12), and BAL (0.65, and 7.5). Overall, the analytical sensitivities of the Ultra test were substantially better than US-IVD for all sample types tested. This study provided a foundation for using either the US-IVD or Ultra test for the early detection of both pulmonary and extrapulmonary (EP) TB. Furthermore, using Ultra could result in higher TB case detection rates in subjects with paucibacillary TB and EP TB, positively impacting WHO goals to eradicate TB. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Emerging Pathogens)
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9 pages, 668 KiB  
Brief Report
Pulmonary Granulomas and Mycobacterial Infection: Concordance between the Results of Special Stains Performed on Lung Tissue Sections and Tissue Cultures
by Hisham F. Bahmad, Roshanak Azimi, Ekim Kilinc, Claudio Tuda and Cristina Vincentelli
Diseases 2022, 10(4), 96; https://doi.org/10.3390/diseases10040096 - 1 Nov 2022
Cited by 1 | Viewed by 3084
Abstract
Background: The most common cause of infectious pulmonary granulomas worldwide is Mycobacterium tuberculosis. The diagnosis is based on clinical presentation, histopathologic findings, detection of acid-fast bacilli (AFB) in tissue or sputum using special stains, and/or isolation of mycobacteria in cultures or via [...] Read more.
Background: The most common cause of infectious pulmonary granulomas worldwide is Mycobacterium tuberculosis. The diagnosis is based on clinical presentation, histopathologic findings, detection of acid-fast bacilli (AFB) in tissue or sputum using special stains, and/or isolation of mycobacteria in cultures or via PCR-based methods. Different studies have shown that high levels of discrepancy exist between these diagnostic approaches in lung tissue specimens. Objective: To assess the degree of concordance between the results of special stains and cultures on lung tissue specimens in the diagnosis of mycobacterial infections. Methodology: Eighty-seven patients with a diagnosis of granulomas (necrotizing and non-necrotizing) on lung tissue specimens were identified. Cohen’s kappa was used to measure the general concordance between the results of the histopathological examination (special stains) and bacteriological tissue cultures. Results: With Kinyoun acid-fast stains, 8/48 (16.7%) cases were positive for AFB. With FITE stains, 10/57 (17.5%) cases were positive for AFB. There was strong agreement between Kinyoun acid-fast and FITE stains (Kappa = 0.806; p-value < 0.001). Tissue cultures were performed on 38/87 cases (43.7%), and 10/38 (26.3%) of the cultures were positive for mycobacteria. There was no concordance between Kinyoun acid-fast stains or FITE stains and tissue cultures results. Conclusion: Our observations represent an initial step in the process of reviewing the two methods used at our institution to diagnose mycobacterial infections on lung tissue specimens and highlight the need of incorporating more advanced diagnostic methods such as PCR to confirm mycobacterial infections and improve patient management. Importantly, species-level identification of mycobacteria is necessary to guide treatment. Full article
(This article belongs to the Section Infectious Disease)
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10 pages, 2447 KiB  
Article
Nontuberculous Mycobacterial Lung Disease in the Patients with Cystic Fibrosis—A Challenging Diagnostic Problem
by Dorota Wyrostkiewicz, Lucyna Opoka, Dorota Filipczak, Ewa Jankowska, Wojciech Skorupa, Ewa Augustynowicz-Kopeć and Monika Szturmowicz
Diagnostics 2022, 12(7), 1514; https://doi.org/10.3390/diagnostics12071514 - 21 Jun 2022
Cited by 6 | Viewed by 2772
Abstract
Background: Cystic fibrosis (CF) is an autosomal, recessive genetic disorder, caused by a mutation in the cystic fibrosis transmembrane conductance receptor regulator (CFTR) gene. Dysregulated mucous production, and decreased bronchial mucociliary clearance, results in increased susceptibility to bacterial and fungal infections. Recently, nontuberculous [...] Read more.
Background: Cystic fibrosis (CF) is an autosomal, recessive genetic disorder, caused by a mutation in the cystic fibrosis transmembrane conductance receptor regulator (CFTR) gene. Dysregulated mucous production, and decreased bronchial mucociliary clearance, results in increased susceptibility to bacterial and fungal infections. Recently, nontuberculous mycobacteria (NTM) infections were identified as an emerging clinical problem in CF patients. Aim: The aim of the present study was to assess the frequency of NTM isolations in CF patients hospitalized in the pulmonary department, serving as a hospital CF center, and to describe challenges concerning the recognition of NTMLD (nontuberculous mycobacterial lung disease) in those patients. Methods: Consecutive CF patients, who were hospitalized due to pulmonary exacerbations (PEX), in a single CF center, between 2010 and 2020, were retrospectively assessed for the presence of NTM in respiratory specimens. Clinical and radiological data were retrospectively reviewed. Results: Positive respiratory specimen cultures for NTM were obtained in 11 out of 151 patients (7%), mean age—35.7 years, mean BMI—20.2 kg/m2, mean FEV1—58.6% pred. Cultures and phenotyping revealed the presence of Mycobacterium avium (M. avium)—in six patients, Mycobacterium chimaera (M. chimaera) in two, Mycobacterium kansasii (M. kansasii)—in one, Mycobacterium abscessus (M. abscessus)—in one, Mycobacterium lentifavum (M. lentiflavum)—in one. Simultaneously, respiratory cultures were positive for fungi in 91% of patients: Candida albicans (C. albicans)—in 82%, Aspergillus fumigatus (A. fumigatus)—in 45%. Clinical signs of NTMLD were non—specific, chest CT indicated NTMLD in five patients only. Conclusion: Due to non-specific clinical presentation, frequent sputum cultures for NTM and analysis of serial chest CT examinations are crucial for NTMLD recognition in CF patients. Further studies concerning the predictive role of fungal pathogens for NTMLD development in CF patients are needed. Full article
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10 pages, 3610 KiB  
Brief Report
Preliminary Results of NGS Gene Panel Test Using NSCLC Sputum Cytology and Therapeutic Effect Using Corresponding Molecular-Targeted Drugs
by Kei Morikawa, Kohei Kinoshita, Hirotaka Kida, Takeo Inoue and Masamichi Mineshita
Genes 2022, 13(5), 812; https://doi.org/10.3390/genes13050812 - 2 May 2022
Cited by 9 | Viewed by 3038
Abstract
As more molecular-targeted drugs for advanced non-small cell lung cancer are brought to market, batch tests for the identification of gene mutations are needed at initial diagnosis. However, since current gene panel tests require a sufficient amount of tissue sample, there are many [...] Read more.
As more molecular-targeted drugs for advanced non-small cell lung cancer are brought to market, batch tests for the identification of gene mutations are needed at initial diagnosis. However, since current gene panel tests require a sufficient amount of tissue sample, there are many instances where panel tests cannot be performed. Therefore, we have developed a highly sensitive next generation sequencing (NGS) panel test to facilitate cytological specimens. Herein, we describe three cases positive for epidermal growth factor receptor (EGFR) exon 19 deletion, MET exon 14 skipping, and KRAS G12A using NGS analysis from sputum. In each case, genetic information was consistent with companion diagnostic analysis obtained from tissue samples collected under bronchoscopy. In cases of EGFR and MET mutations, the corresponding tyrosine kinase inhibitors were highly effective. This is the first report to demonstrate that a novel panel test could detect gene mutations in sputum samples in clinical practice and compare the gene allele ratio with the sample directly collected from the lesion. Full article
(This article belongs to the Section Genetic Diagnosis)
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17 pages, 896 KiB  
Review
Towards Accurate Point-of-Care Tests for Tuberculosis in Children
by Nina Vaezipour, Nora Fritschi, Noé Brasier, Sabine Bélard, José Domínguez, Marc Tebruegge, Damien Portevin and Nicole Ritz
Pathogens 2022, 11(3), 327; https://doi.org/10.3390/pathogens11030327 - 8 Mar 2022
Cited by 18 | Viewed by 11212
Abstract
In childhood tuberculosis (TB), with an estimated 69% of missed cases in children under 5 years of age, the case detection gap is larger than in other age groups, mainly due to its paucibacillary nature and children’s difficulties in delivering sputum specimens. Accurate [...] Read more.
In childhood tuberculosis (TB), with an estimated 69% of missed cases in children under 5 years of age, the case detection gap is larger than in other age groups, mainly due to its paucibacillary nature and children’s difficulties in delivering sputum specimens. Accurate and accessible point-of-care tests (POCTs) are needed to detect TB disease in children and, in turn, reduce TB-related morbidity and mortality in this vulnerable population. In recent years, several POCTs for TB have been developed. These include new tools to improve the detection of TB in respiratory and gastric samples, such as molecular detection of Mycobacterium tuberculosis using loop-mediated isothermal amplification (LAMP) and portable polymerase chain reaction (PCR)-based GeneXpert. In addition, the urine-based detection of lipoarabinomannan (LAM), as well as imaging modalities through point-of-care ultrasonography (POCUS), are currently the POCTs in use. Further to this, artificial intelligence-based interpretation of ultrasound imaging and radiography is now integrated into computer-aided detection products. In the future, portable radiography may become more widely available, and robotics-supported ultrasound imaging is currently being trialed. Finally, novel blood-based tests evaluating the immune response using “omic-“techniques are underway. This approach, including transcriptomics, metabolomic, proteomics, lipidomics and genomics, is still distant from being translated into POCT formats, but the digital development may rapidly enhance innovation in this field. Despite these significant advances, TB-POCT development and implementation remains challenged by the lack of standard ways to access non-sputum-based samples, the need to differentiate TB infection from disease and to gain acceptance for novel testing strategies specific to the conditions and settings of use. Full article
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14 pages, 1101 KiB  
Review
Transcending Blood—Opportunities for Alternate Liquid Biopsies in Oncology
by Bonnita Werner, Kristina Warton and Caroline E. Ford
Cancers 2022, 14(5), 1309; https://doi.org/10.3390/cancers14051309 - 3 Mar 2022
Cited by 16 | Viewed by 3316
Abstract
Cell-free DNA (cfDNA) is a useful molecular biomarker in oncology research and treatment, but while research into its properties in blood has flourished, there remains much to be discovered about cfDNA in other body fluids. The cfDNA from saliva, sputum, cerebrospinal fluid, urine, [...] Read more.
Cell-free DNA (cfDNA) is a useful molecular biomarker in oncology research and treatment, but while research into its properties in blood has flourished, there remains much to be discovered about cfDNA in other body fluids. The cfDNA from saliva, sputum, cerebrospinal fluid, urine, faeces, pleural effusions, and ascites has unique advantages over blood, and has potential as an alternative ‘liquid biopsy’ template. This review summarises the state of current knowledge and identifies the gaps in our understanding of non-blood liquid biopsies; where their advantages lie, where caution is needed, where they might fit clinically, and where research should focus in order to accelerate clinical implementation. An emphasis is placed on ascites and pleural effusions, being pathological fluids directly associated with cancer. We conclude that non-blood fluids are viable sources of cfDNA in situations where solid tissue biopsies are inaccessible, or only accessible from dated archived specimens. In addition, we show that due to the abundance of cfDNA in non-blood fluids, they can outperform blood in many circumstances. We demonstrate multiple instances in which DNA from various sources can provide additional information, and thus we advocate for analysing non-blood sources as a complement to blood and/or tissue. Further research into these fluids will highlight opportunities to improve patient outcomes across cancer types. Full article
(This article belongs to the Special Issue Cell-Free DNA as Prognostic and Predictive Biomarker in Solid Cancers)
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11 pages, 1392 KiB  
Article
Correlation between Carbapenem Consumption and Carbapenems Susceptibility Profiles of Acinetobacter baumannii and Pseudomonas aeruginosa in an Academic Medical Center in Thailand
by Taniya Paiboonvong, Phatchareeporn Tedtaisong, Preecha Montakantikul, Sarun Gorsanan and Woraphot Tantisiriwat
Antibiotics 2022, 11(2), 143; https://doi.org/10.3390/antibiotics11020143 - 23 Jan 2022
Cited by 11 | Viewed by 3533
Abstract
The emergent issue of carbapenem-resistant Acinetobacter baumannii (A. baumannii) and Pseudomonas aeruginosa (P. aeruginosa) is a major problem in Thailand. The wide use of carbapenems can increase selective pressure of bacterial resistance. The objective of this study [...] Read more.
The emergent issue of carbapenem-resistant Acinetobacter baumannii (A. baumannii) and Pseudomonas aeruginosa (P. aeruginosa) is a major problem in Thailand. The wide use of carbapenems can increase selective pressure of bacterial resistance. The objective of this study was to determine the relationship between carbapenem consumption and the susceptibility rates of A. baumannii and P. aeruginosa, including multi-drug resistance (MDR) strains. This was a retrospective study. Carbapenem consumption and susceptibility profiles were collected from 2007 to 2013 at the Her Royal Highness Princess Maha Chakri Sirindhorn Medical Center, Thailand. We found that the susceptibility rate of A. baumannii to imipenem and meropenem from the sputum and the bronchoalveolar lavage (BAL) specimens was significantly decreased during the study period, but no significant change was found in the P. aeruginosa data. The relationship between carbapenem consumption and the susceptibility rate of A. baumannii had a clear association with the use of ertapenem. We found a statistically significant negative correlation between ertapenem consumption and the susceptibility rate of A. baumannii to imipenem (r = −0.91; p = 0.004) and meropenem (r = −0.97; p = 0.000) in the data from the non-ICU wards. In addition, imipenem use had a moderate negative correlation with the MDR P. aeruginosa data but no statistical significance (r = −0.714; p > 0.05). In conclusion, our study suggested there is an association between carbapenem use and the susceptibility of A. baumannii and P. aeruginosa. Notwithstanding this, information on ecological factors should be considered for further study. These findings showed the need to optimize the carbapenem prescription policy. Avoiding carbapenem overuse and rethinking the appropriate initial therapy might decrease the rate of resistant organisms. Full article
(This article belongs to the Section Antibiotics Use and Antimicrobial Stewardship)
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15 pages, 1807 KiB  
Article
Biofilm Formation and Phenotypic Detection of ESBL, MBL, KPC and AmpC Enzymes and Their Coexistence in Klebsiella spp. Isolated at the National Reference Laboratory, Kathmandu, Nepal
by Susmita Kuinkel, Jyoti Acharya, Binod Dhungel, Sanjib Adhikari, Nabaraj Adhikari, Upendra Thapa Shrestha, Megha Raj Banjara, Komal Raj Rijal and Prakash Ghimire
Microbiol. Res. 2021, 12(3), 683-697; https://doi.org/10.3390/microbiolres12030049 - 18 Aug 2021
Cited by 21 | Viewed by 7707
Abstract
Klebsiella spp. are associated with several nosocomial and opportunistic infections. Increasing antimicrobial resistance of Klebsiella species is aggravated by a number of intrinsic and extrinsic factors. The main aim of this study is to determine antimicrobial resistance due to production of β-lactamase enzymes, [...] Read more.
Klebsiella spp. are associated with several nosocomial and opportunistic infections. Increasing antimicrobial resistance of Klebsiella species is aggravated by a number of intrinsic and extrinsic factors. The main aim of this study is to determine antimicrobial resistance due to production of β-lactamase enzymes, extended spectrum beta-lactamase (ESBL), metallo-beta-lactamase (MBL) and AmpC and Klebsiella pneumoniae carbapenemase (KPC) and biofilm formation in Klebsiella isolates. A total of 2197 non-duplicate specimens of urine, sputum and pus were obtained from the National Public Health Laboratory (NPHL), Kathmandu, Nepal, between February and August 2019. Klebsiella species were isolated, identified and screened for antimicrobial susceptibility testing with the disk diffusion method. Phenotypic detection of ESBL, MBL, KPC and AmpC production was observed and biofilm production was detected by the microtiter plate method. Out of a total of 2197 clinical specimens, bacterial growth was detected in 8% (175/2197) of the specimens. Of the total isolates, 86.3% (151/175) were Gram-negative bacteria and 37.7% (57/151) were Klebsiella spp. Of the total Klebsiella spp., 56% (32/57) were multi drug resistant (MDR), 16% (9/57) were ESBL, 26% (15/57) were MBL, 4% (2/57) were KPC (class A carbapenemase), 16% (9/57) were AmpC producers and 95% (54/57) were biofilm producers. Gentamicin was the most effective antibiotic, followed by cotrimoxazole, as 68% (39/57) and 47% (27/57) of the Klebsiella isolates were susceptible towards these drugs, respectively. The study results show evidence of β-lactamase production, high prevalence of MDR and biofilm producing Klebsiella species. Integrating the test parameters for phenotypic confirmation of ESBL, MBL, AmpC β lactamase and KPC in routine diagnostic procedures can help in the early detection and management of these resistant strains. Full article
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