Article
Biochemistry & Molecular Biology
Mariaenrica Tine, Tommaso Neri, Davide Biondini, Nicol Bernardinello, Alvise Casara, Maria Conti, Marianna Minniti, Manuel G. Cosio, Marina Saetta, Alessandro Celi, Dario Nieri, Erica Bazzan
Summary: Cell-derived extracellular vesicles (EVs) in the circulation and body fluids can be used as biomarkers for lung and other diseases. This study compared the characteristics of EVs in bronchoalveolar lavage (BAL) and blood samples from smokers with and without COPD. The results showed that there were significant differences in macrophage-derived EVs (CD14-EVs) between nonsmokers, smokers without COPD, and COPD patients in BAL but not in plasma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Pediatrics
Jiawei Yao, Tao Ai, Wanmin Xia, Yinghong Fan, Cheng Xie, Lei Zhang
Summary: This study compared the bacterial composition and colony structure of the lower respiratory tract in infants and children with recurrent wheezing and those with a bronchial foreign body. It was found that the bacterial community in the wheezing groups was different from that in the control group, and the duration of wheezing in infants might contribute to the differences in bacterial colony structure. This suggests that recurrent wheezing in infants and children is likely due to alterations in the overall bacterial microecology and disruption of host respiration and immune homeostasis.
ITALIAN JOURNAL OF PEDIATRICS
(2022)
Article
Respiratory System
Qing Miao, Tianzhu Liang, Na Pei, Chunjiao Liu, Jue Pan, Na Li, Qingqing Wang, Yanqiong Chen, Yu Chen, Yuyan Ma, Wenting Jin, Yao Zhang, Yi Su, Yumeng Yao, Yingnan Huang, Chunmei Zhou, Rong Bao, Xiaoling Xu, Weijun Chen, Bijie Hu, Junhua Li
Summary: Clinical mNGS improves etiology diagnosis of respiratory infections but brings new challenges. This study evaluated mNGS data and assessed diagnostic strengths of different specimen types. BALF showed higher positive predictive values for diagnosing non-mycobacterium, NTM, and Aspergillus infections. Lung tissues and sputum were acceptable for diagnosing MTB. Significant taxonomy differences were found in BALF specimens and unique microbiome compositions were found in BALF specimens of tumor patients. The developed bioinformatic pipeline showed comparative diagnostic strength with clinical microbiological diagnosis.
RESPIRATORY RESEARCH
(2022)
Article
Infectious Diseases
Alexander C. Reisinger, Stefan Hatzl, Juergen Prattes, Gerald Hackl, Gernot Schilcher, Florian Eisner, Tobias Niedrist, Reinhard Raggam, Robert Krause, Philipp Eller
Summary: Serum suPAR levels were significantly higher in ARDS patients compared to those not fulfilling ARDS criteria. Serum and BALF-suPAR levels were also significantly higher in patients with evidence for invasive pulmonary aspergillosis.
Article
Multidisciplinary Sciences
Kristel S. Knudsen, Sverre Lehmann, Rune Nielsen, Solveig Tangedal, Ingvild Haaland, Pieter S. Hiemstra, Tomas M. Eagan
Summary: The study found differences in microbial diversity and antimicrobial peptide levels between idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD), and healthy controls, suggesting that changes in the microbiome of IPF may be related to microaspiration.
Article
Medicine, General & Internal
Jun Yeun Cho, Mi Yeon Kim, Ji Hyoun Kim, Eung-Gook Kim, Sun-Hyung Kim, Bumhee Yang, Hyeran Kang, Ki Man Lee, Kang Hyeon Choe, Yoon Mi Shin
Summary: Recent studies have shown that the lower airway microbiome may be important in the development and progression of interstitial lung disease (ILD). The aim of this study was to investigate the characteristics of the respiratory microbiome in ILD patients. The study found that species diversity and richness were lower in the most-affected lesions compared to the least-affected lesions, but taxonomic abundance patterns were similar. The prevalence of the Fusobacteria phylum was higher in fibrotic ILD than in nonfibrotic ILD.
Article
Immunology
Yukun He, Jia Li, Wenyi Yu, Yali Zheng, Donghong Yang, Yu Xu, Lili Zhao, Xinqian Ma, Pihua Gong, Zhancheng Gao
Summary: The study found that the lower respiratory tract microbiome characteristics in patients with post-HSCT pneumonia are different from those with CAP and healthy controls, which may be associated with the patient's outcome. High abundance of Actinobacteria and low abundance of Bacteroidetes were observed in post-HSCT pneumonia samples. Pathogenic bacteria such as Pseudomonas, Acinetobacter, Burkholderia, and Mycobacterium were prominent in the pneumonia group after HSCT.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Jennifer M. Baker, Kevin J. Hinkle, Roderick A. McDonald, Christopher A. Brown, Nicole R. Falkowski, Gary B. Huffnagle, Robert P. Dickson
Summary: An ecological-based analytical approach can distinguish signal from noise in low-biomass microbiome studies, with whole lung tissue identified as the preferred specimen type for murine lung microbiome studies. It is crucial to consider potential source communities, including negative control specimens and contiguous biological sites, during sequencing, analysis, and reporting for biological interpretation of low-biomass microbiome studies.
Article
Multidisciplinary Sciences
Kotaro Iwasaki, Yasuo Matsuzawa, Hiroki Wakabayashi, Moe Shioya, Sho Hayakawa, Ichiro Tatsuno
Summary: The relationship between the lower airway microbiota and respiratory illness in humans is receiving attention. This study characterized the lower airway microbiota in Mycobacterium avium complex lung disease (MAC-LD), a subclass of nontuberculous mycobacterial lung disease (NTM-LD). Analysis revealed that Pseudomonas and MAC tended to exist exclusively in the two patient groups.
Article
Multidisciplinary Sciences
Christian Marzahl, Jenny Hill, Jason Stayt, Dorothee Bienzle, Lutz Welker, Frauke Wilm, Joern Voigt, Marc Aubreville, Andreas Maier, Robert Klopfleisch, Katharina Breininger, Christof A. Bertram
Summary: This study introduces a novel, fully annotated multi-species P-Hem dataset, and develops an annotation pipeline using deep learning and data visualization techniques. The dataset is one of the largest publicly available WSIs datasets in terms of the number of annotations, scanned area, and species covered.
Article
Biochemistry & Molecular Biology
Yasuaki Kotetsu, Toyoshi Yanagihara, Kunihiro Suzuki, Hiroyuki Ando, Daisuke Eto, Kentaro Hata, Masako Arimura-Omori, Yuzo Yamamoto, Eiji Harada, Naoki Hamada
Summary: Sarcoidosis is a systemic granulomatous disease caused by unknown immunological abnormalities, with lungs being the most vulnerable organs. Research suggests that PD-1 or TIM-3 expression on T cells in bronchoalveolar lavage fluid may serve as a prognostic factor for pulmonary lesions in sarcoidosis.
Article
Immunology
Kevin Bassler, Wataru Fujii, Theodore S. Kapellos, Erika Dudkin, Nico Reusch, Ari Horne, Benedikt Reiz, Malte D. Luecken, Collins Osei-Sarpong, Stefanie Warnat-Herresthal, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Allon Wagner, Patrick Guenther, Carmen Pizarro, Tina Schreiber, Rainer Knoll, Lisa Holsten, Charlotte Kroeger, Elena De Domenico, Matthias Becker, Kristian Haendler, Christian T. Wohnhaas, Florian Baumgartner, Meike Koehler, Heidi Theis, Michael Kraut, Marc H. Wadsworth, Travis K. Hughes, Humberto J. Ferreira, Emily Hinkley, Ines H. Kaltheuner, Matthias Geyer, Christoph Thiele, Alex K. Shalek, Andreas Feisst, Daniel Thomas, Henning Dickten, Marc Beyer, Patrick Baum, Nir Yosef, Anna C. Aschenbrenner, Thomas Ulas, Jan Hasenauer, Fabian J. Theis, Dirk Skowasch, Joachim L. Schultze
Summary: Despite the high prevalence of COPD, the cellular and molecular mechanisms of the disease remain poorly understood. This study investigates the changes in cellular and molecular compositions in the alveolar space and peripheral blood of COPD patients compared to controls. The findings suggest that myeloid cells, including invading monocytes and proliferating macrophages, are increased in COPD. Computational modeling predicts TGF-beta 1 as a major regulator of transcriptional changes in alveolar macrophages of COPD patients. Functionally, macrophages in COPD exhibit impaired immune activation.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Microbiology
Barry Linnane, Aaron M. Walsh, Calum J. Walsh, Fiona Crispie, Orla O'Sullivan, Paul D. Cotter, Michael McDermott, Julie Renwick, Paul McNally
Summary: The study thoroughly characterized the lower airway microbiome in pre-school children with CF, finding that while the CF lung microbiome is broadly similar to that in non-CF children in terms of alpha diversity at an early age, several key genera were significantly differentially abundant between the CF and non-CF groups. CF diagnosis explained only a small amount of variation between the microbiomes, and there were distinct patterns of microbial abundance changes with age in CF and non-CF populations.
Article
Microbiology
Jinghua Cui, Yuanyuan Zhang, Hanqing Zhao, Xuemei Sun, Zhen Chen, Qun Zhang, Chao Yan, Guanhua Xue, Shaoli Li, Yanling Feng, Han Liu, Xianghui Xie, Jing Yuan
Summary: The study found a correlation between the lower respiratory tract microbiome in children and allergic respiratory diseases, with significant differences in microbial composition and distribution, and some bacteria showing correlations with clinical indices.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Respiratory System
Qian He, Ming Zhang, Chunlai Feng
Summary: In this study, it was found that plasma and BALF levels of PTX3 were significantly higher in COPD patients with IPA. The sensitivity of PTX3 for diagnosing IPA in patients with COPD was superior to that of GM, and the combination of GM and PTX3 was useful for the diagnosis of IPA in these patients.
BMC PULMONARY MEDICINE
(2021)
Article
Infectious Diseases
D. S. Wenger, M. Triplette, S. Shahrir, K. M. Akgun, C. Wongtrakool, S. T. Brown, J. W. Kim, G. W. Soo Hoo, M. C. Rodriguez-Barradas, L. Huang, L. C. Feemster, J. Zifodya, K. Crothers
Summary: This study found that marijuana smoking in people living with HIV was associated with higher lung volumes and potentially radiographic emphysema, but the associations were not statistically significant in participants without HIV. Overall, no consistently negative associations were observed between marijuana use and measures of chronic lung health.
Article
Microbiology
Amanda J. Meyer, Emmanuel Ochom, Patricia Turimumahoro, Patrick Byanyima, Ingvar Sanyu, Rejani Lalitha, Sylvia Kaswabuli, Alfred Andama, Nicholas D. Walter, Achilles Katamba, Adithya Cattamanchi, William Worodria, Laurence Huang, Christina Yoon, J. Lucian Davis
Summary: The study aimed to evaluate the diagnostic performance of serum C-reactive protein (CRP) as a triage test for tuberculosis (TB) among HIV-seronegative inpatients in a national referral hospital in Kampala, Uganda. Results showed that CRP testing fell below the target thresholds for sensitivity and specificity in diagnosing TB among HIV-seronegative inpatients. Additional studies are needed to assess the utility of CRP for TB screening in clinics and community settings, as its performance varied across different thresholds and illness severity levels.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Review
Respiratory System
Katerina Byanova, Ken M. Kunisaki, Joshua Vasquez, Laurence Huang
Summary: COPD is more prevalent in people with HIV, leading to increased morbidity and mortality. The mechanisms behind COPD development and progression in PWH are not fully understood, with a lack of specific management guidelines for this population. Further research is needed to explore the pathophysiology of the interaction between HIV and COPD and evaluate specific therapies for this vulnerable patient group.
EXPERT REVIEW OF RESPIRATORY MEDICINE
(2021)
Article
Immunology
Amanda K. Jan, Julia Moore, Richard J. Wang, Maggie Mcging, Carly K. Farr, Daniela Moisi, Marlena Hartman-Filson, Robert Kerruish, Diane Jeon, Eula Lewis, Kristina Crothers, Michael M. Lederman, Peter W. Hunt, Laurence Huang
Summary: Studies have shown that individuals with HIV may have an increased risk for chronic lung diseases and abnormalities in lung function, potentially linked to immune activation. Different markers of immune activation and inflammation are associated with FEV1% predicted, DLco% predicted, and iso down arrow DLco among people with HIV, suggesting unique pathways of chronic lung diseases.
Article
Immunology
Mark H. Kuniholm, Mariam Bramah-Lawani, Meghan Fitzpatrick, Mehdi Nouraie, Shulin Qin, Laurence Huang, Abbe N. Vallejo, Alan L. Landay, Alison Morris
Summary: The expression of CD11b(+) on classical monocytes is positively associated with the FEV1/FVC ratio in people living with HIV, especially in those with good CD4 T-cell recovery. This suggests that this specific monocyte subset may play a role in preserving pulmonary function in PLWH.
JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES
(2021)
Editorial Material
Biochemistry & Molecular Biology
Lucy van Dorp, Muki S. Shey, Elodie Ghedin, Franziska Michor, Eugene V. Koonin, Katie Hampson
Article
Immunology
Deepti G. Singhvi, Mehdi Nouraie, Cathy Kessinger, Deborah K. McMahon, Renee Weinman, Kristina Crothers, Laurence Huang, Jessica Bon, Alison Morris, Jessica Merlin
Summary: In people with HIV, pain is common and associated with airflow obstruction, dyspnea, and sleep disturbance.
JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES
(2021)
Article
Multidisciplinary Sciences
Nicholas D. Walter, Sarah E. M. Born, Gregory T. Robertson, Matthew Reichlen, Christian Dide-Agossou, Victoria A. Ektnitphong, Karen Rossmassler, Michelle E. Ramey, Allison A. Bauman, Victor Ozols, Shelby C. Bearrows, Gary Schoolnik, Gregory Dolganov, Benjamin Garcia, Emmanuel Musisi, William Worodria, Laurence Huang, J. Lucian Davis, Nhung V. Nguyen, Hung V. Nguyen, Anh T. V. Nguyen, Ha Phan, Carol Wilusz, Brendan K. Podell, N' Dira Sanoussi, Bouke C. de Jong, Corinne S. Merle, Dissou Affolabi, Helen McIlleron, Maria Garcia-Cremades, Ekaterina Maidji, Franceen Eshun-Wilson, Brandon Aguilar-Rodriguez, Dhuvarakesh Karthikeyan, Khisimuzi Mdluli, Cathy Bansbach, Anne J. Lenaerts, Radojka M. Savic, Payam Nahid, Joshua J. Vasquez, Martin I. Voskuil
Summary: The study demonstrates that sterilizing drugs and highly effective drug regimens profoundly suppress Mycobacterium tuberculosis rRNA synthesis, while non-sterilizing drugs and weaker regimens do not. Utilizing the rRNA synthesis ratio as a metric of drug activity may accelerate the development of shorter tuberculosis treatment regimens.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Virology
Arthur H. Totten, Jung-Ho Youn, Allison Roder, Elodie Ghedin, Tara N. Palmore, Karen M. Frank, Sanchita Das, Adrian M. Zelazny
JOURNAL OF CLINICAL VIROLOGY
(2021)
Article
Microbiology
Imran Sulaiman, Matthew Chung, Luis Angel, Jun-Chieh J. Tsay, Benjamin G. Wu, Stephen T. Yeung, Kelsey Krolikowski, Yonghua Li, Ralf Duerr, Rosemary Schluger, Sara A. Thannickal, Akiko Koide, Samaan Rafeq, Clea Barnett, Radu Postelnicu, Chang Wang, Stephanie Banakis, Lizzette Perez-Perez, Guomiao Shen, George Jour, Peter Meyn, Joseph Carpenito, Xiuxiu Liu, Kun Ji, Destiny Collazo, Anthony Labarbiera, Nancy Amoroso, Shari Brosnahan, Vikramjit Mukherjee, David Kaufman, Jan Bakker, Anthony Lubinsky, Deepak Pradhan, Daniel H. Sterman, Michael Weiden, Adriana Hegu, Laura Evans, Timothy M. Uyeki, Jose C. Clemente, Emmie de Wit, Ann Marie Schmidt, Bo Shopsin, Ludovic Desvignes, Chan Wang, Huilin Li, Bin Zhang, Christian Forst, Shohei Koide, Kenneth A. Stapleford, Kamal M. Khanna, Elodie Ghedin, Leopoldo N. Segal
Summary: Analysis of lower respiratory tract microbiome of mechanically ventilated COVID-19 patients rules out a role for secondary respiratory infections as drivers of increased mortality. Mortality is more likely associated with viral replication levels, host immune response, and enrichment of specific microbes.
NATURE MICROBIOLOGY
(2021)
Article
Immunology
Veronique Nussenblatt, Allison E. Roder, Sanchita Das, Emmie de Wit, Jung-Ho Youn, Stephanie Banakis, Alexandra Mushegian, Christopher Mederos, Wei Wang, Matthew Chung, Lizzette Perez-Perez, Tara Palmore, Jennifer N. Brudno, James N. Kochenderfer, Elodie Ghedin
Summary: B-cell-depleting therapies can result in prolonged disease and viral shedding in SARS-CoV-2-infected individuals, raising concerns for viral evolution. This study sequenced early and late samples from a 335-day infection in an immunocompromised patient and identified unique viral mutations, highlighting the importance of analyzing viral evolution in prolonged infections, especially in immunosuppressed hosts.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Shaohuan Wu, Ted M. Ross, Michael A. Carlock, Elodie Ghedin, Hyungwon Choi, Christine Vogel
Summary: The study identifies determinants of influenza vaccine efficacy, with prior vaccination history, baseline titer level, and age being major factors. Other factors such as BMI, comorbidities, vaccine dose, and race have negligible effects. Models can accurately predict categorical responses in most cases, and generate a new seroconversion score corrected for these factors, facilitating future biomarker identification.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Chang Wang, Lauren P. Lashua, Chalise E. Carter, Scott K. Johnson, Minghui Wang, Ted M. Ross, Elodie Ghedin, Bin Zhang, Christian V. Forst
Summary: In this study, a network-based approach was used to analyze the blood transcriptome of female and male ferrets infected with influenza A virus. Significant differences in the temporal dynamics and regulation of immune responses between females and males were identified. The results provide molecular insights into sex differences in the transcriptional regulation of immune responses and contribute to a better understanding of sex biases in influenza pathogenesis.
Article
Respiratory System
Ioannis Konstantinidis, Shulin Qin, Meghan Fitzpatrick, Cathy Kessinger, Heather Gentry, Deborah McMahon, R. Dawn Weinman, Phyllis Tien, Laurence Huang, Meredith McCormack, Igor Barjaktarevic, Divya Reddy, Robert Foronjy, Deepa Lazarous, Mardge H. Cohen, Heather McKay, Adaora A. Adimora, Caitlin Moran, Margaret A. Fischl, Jodie Dionne-Odom, Valentina Stosor, M. Bradley Drummond, Sushma K. Cribbs, Ken Kunisaki, Charles Rinaldo, Alison Morris, S. Mehdi Nouraie
Summary: This study identified distinct longitudinal pulmonary function phenotypes in HIV patients and investigated their determinants and outcomes. The findings showed significant differences in characteristics and outcomes among different pulmonary function phenotypes, highlighting the importance of monitoring lung dysfunction over time in people with HIV.
ANNALS OF THE AMERICAN THORACIC SOCIETY
(2022)
Article
Virology
Margarita Rangel, Nicholas Catanzaro, Sara A. Thannickal, Kelly A. Crotty, Maria G. Noval, Katherine E. E. Johnson, Elodie Ghedin, Helen M. Lazear, Kenneth A. Stapleford
Summary: This study identifies structurally conserved residues in class II fusion glycoproteins of alphaviruses and flaviviruses that contribute to common mechanisms of viral entry, dissemination, and infectious-virion production.
JOURNAL OF VIROLOGY
(2022)