Chaz Langelier, MD, PhD

Associate Medical Director

The translational research in my lab bridges basic and clinical investigation by engaging genomic technologies to understand relationships between microbes, host response and clinical outcomes. We study lower respiratory tract infections, ARDS, sepsis, nosocomial infections, and emerging pathogens including SARS-CoV-2. One focus area involves developing new diagnostic techniques that combine metagenomic sequencing and machine learning to simultaneously profile both host and microbiome from clinical samples. A second focus area involves studying the host response to infections and identifying disease sub-phenotypes that correlate with outcomes. Genomic epidemiology is a third focus area, and our group carries out real-time assessment of hospital outbreaks and surveillance for emerging respiratory pathogens.

Publications:

Proteomic profiling of the local and systemic immune response to pediatric respiratory viral infections.

bioRxiv : the preprint server for biology

Lydon E, Osborne CM, Wagner BD, Ambroggio L, Harris JK, Reeder R, Carpenter TC, Maddux AB, Leroue MK, Yehya N, DeRisi JL, Hall MW, Zuppa AF, Carcillo J, Meert K, Sapru A, Pollack MM, McQuillen P, Notterman DA, Langelier CR, Mourani PM, Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediat

Fungal Lung Disease.

The European respiratory journal

Jaggi TK, Agarwal R, Tiew PY, Shah A, Lydon EC, Hage CA, Waterer GW, Langelier CR, Delhaes L, Chotirmall SH

Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.

Nature medicine

Chu VT, Glascock A, Donnell D, Grabow C, Brown CE, Ward R, Love C, Kalantar KL, Cohen SE, Cannon C, Woodworth MH, Kelley CF, Celum C, Luetkemeyer AF, Langelier CR

Pulmonary FABP4 Is an Inverse Biomarker of Pneumonia in Critically Ill Children and Adults.

American journal of respiratory and critical care medicine

Lydon EC, Phan HV, Mick E, Spottiswoode N, Calfee CS, Mourani PM, Langelier CR

Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes.

ACR open rheumatology

Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye CJ, Dall'Era M, Yazdany J, Criswell LA, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM

Immediate myeloid depot for SARS-CoV-2 in the human lung.

Science advances

Magnen M, You R, Rao AA, Davis RT, Rodriguez L, Bernard O, Simoneau CR, Hysenaj L, Hu KH, Maishan M, Conrad C, Gbenedio OM, Samad B, Consortium TUC, Love C, Woodruff PG, Erle DJ, Hendrickson CM, Calfee CS, Matthay MA, Roose JP, Sil A, Ott M, Langelier CR, Krummel MF, Looney MR

Small airway brush gene expression predicts chronic lung allograft dysfunction and mortality.

The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation

Mohanty RP, Moghbeli K, Singer JP, Calabrese DR, Hays SR, Iasella C, Lieber S, Leard LE, Shah RJ, Venado A, Kleinhenz ME, Golden JA, Martinu T, Love C, Ward R, Langelier CR, McDyer J, Greenland JR

Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19.

Nature communications

Neyton LPA, Patel RK, Sarma A, UCSF COMET Consortium, Willmore A, Haller SC, Kangelaris KN, Eckalbar WL, Erle DJ, Krummel MF, Hendrickson CM, Woodruff PG, Langelier CR, Calfee CS, Fragiadakis GK

Biological effects of corticosteroids on pneumococcal pneumonia in Mice-translational significance.

Critical care (London, England)

Taenaka H, Wick KD, Sarma A, Matsumoto S, Ghale R, Fang X, Maishan M, Gotts JE, Langelier CR, Calfee CS, Matthay MA

Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.

Research square

Langelier C, Lu D, Kalantar K, Chu V, Glascock A, Guerrero E, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones A, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani P, Pickering A, Raphenya A, Alcock B, McArthur A

Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality.

The Journal of clinical investigation

Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Haddad EK, IMPACC Network, Reed EF, Kraft M, McComsey GA, Metcalf JP, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar WL, Maecker HT, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Sekaly RP, Ehrlich LI, Fourati S, Peters B, Kleinstein SH, Guan L

Rapidly improving ARDS differs clinically and biologically from persistent ARDS.

Critical care (London, England)

Valda Toro PL, Willmore A, Wu NE, Delucchi KL, Jauregui A, Sinha P, Liu KD, Hendrickson CM, Sarma A, Neyton LPA, Leligdowicz A, Langelier CR, Zhuo H, Jones C, Kangelaris KN, Gomez AD, Matthay MA, Calfee CS

Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.

bioRxiv : the preprint server for biology

Lu D, Kalantar KL, Chu VT, Glascock AL, Guerrero ES, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones AE, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani PM, Pickering AJ, Raphenya AR, Alcock BP, McArthur AG, Langelier CR

Doxycycline post-exposure prophylaxis for sexually transmitted infections impacts the gut antimicrobial resistome.

Research square

Langelier C, Chu V, Glascock A, Donnell D, Grabow C, Brown C, Ward R, Love C, Kalantar K, Cohen S, Cannon C, Woodworth M, Kelley C, Celum C, Luetkemeyer A

Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology.

Science Translational Medicine

Phan HV, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns CB, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, IMPACC Network, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR

Host and Microbe Blood Metagenomics Reveals Key Pathways Characterizing Critical Illness Phenotypes.

American journal of respiratory and critical care medicine

Neyton LPA, Sinha P, Sarma A, Mick E, Kalantar K, Chen S, Wu N, Delucchi K, Zhuo H, Bos LDJ, Jauregui A, Gomez A, Hendrickson CM, Kangelaris KN, Leligdowicz A, Liu KD, Matthay MA, Langelier CR, Calfee CS

Molecular Phenotypes of ARDS in the ROSE Trial have Differential Outcomes and Gene Expression Patterns That Differ at Baseline and Longitudinally Over Time.

American journal of respiratory and critical care medicine

Sinha P, Neyton L, Sarma A, Wu N, Jones C, Zhuo H, Liu KD, Sanchez Guerrero E, Ghale R, Love C, Mick E, Delucchi KL, Langelier CR, Thompson BT, Matthay MA, Calfee CS, NHLBI PETAL Network

Biological Effects of Corticosteroids on Pneumococcal Pneumonia in Mice and Humans.

Research square

Taenaka H, Wick KD, Sarma A, Matsumoto S, Ghale R, Fang X, Maishan M, Gotts JE, Langelier CR, Calfee CS, Matthay MA

Host-Microbe Multiomic Profiling Reveals Age-Dependent COVID-19 Immunopathology.

medRxiv : the preprint server for health sciences

Van Phan H, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, Van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns C, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, IMPACC Network, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR

Respiratory Metagenomics: Ready for Prime Time?

American journal of respiratory and critical care medicine

Lydon E, Langelier CR

IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition.

Nature communications

Haslund-Gourley BS, Woloszczuk K, Hou J, Connors J, Cusimano G, Bell M, Taramangalam B, Fourati S, Mege N, Bernui M, Altman MC, Krammer F, van Bakel H, IMPACC Network, Maecker HT, Rouphael N, Diray-Arce J, Wigdahl B, Kutzler MA, Cairns CB, Haddad EK, Comunale MA

Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study.

Nature communications

Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, Dandekar R, Shannon CP, Sekaly RP, Ehrlich LIR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, van Bakel H, Kim-Schulze S, Hafler DA, Levy O, Kraft M, Bime C, Haddad EK, Calfee CS, Erle DJ, Langelier CR, Eckalbar W, Bosinger SE, IMPACC Network, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Maecker HT, Altman MC, Montgomery RR, Becker PM, Rouphael N

The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients.

Nature communications

Chu VT, Tsitsiklis A, Mick E, Ambroggio L, Kalantar KL, Glascock A, Osborne CM, Wagner BD, Matthay MA, DeRisi JL, Calfee CS, Mourani PM, Langelier CR

Host-Microbe Multi-omic Profiling Identifies a Unique Program of COVID-19 Inflammatory Dysregulation in Solid Organ Transplant Recipients.

Research square

Langelier C, Pickering H, Schaenman J, Phan H, Maguire C, Tsitsiklis A, Rouphael N, Higuita N, Atkinson M, Breckenridge S, Fung M, Messer W, Network I, Salehi-Rad R, Altman M, Becker P, Bosinger S, Eckalbar W, Hoch A, Jayavelu N, Kim-Schulze S, Jenkins M, Kleinstein S, Krammer F, Maecker H, Ozonoff A, Diray-Arce J, Shaw A, Baden L, Levy O, Reed E

Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes.

bioRxiv : the preprint server for biology

Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye C, Dall'Era M, Yazdany J, Criswell L, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM

Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants.

bioRxiv : the preprint server for biology

Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Network I, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf J, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Augustine AD, Sekaly RP, Ehrlich LIR, Fourati S, Peters B, Kleinstein SH, Guan L

Viral Detection by Reverse Transcriptase Polymerase Chain Reaction in Upper Respiratory Tract and Metagenomic RNA Sequencing in Lower Respiratory Tract in Critically Ill Children With Suspected Lower Respiratory Tract Infection.

Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies

Osborne CM, Langelier C, Kamm J, Williamson K, Ambroggio L, Reeder RW, Locandro C, Kirk Harris J, Wagner BD, Maddux AB, Caldera S, Lyden A, Soesanto V, Simões EAF, Leroue MK, Carpenter TC, Hall MW, Zuppa AF, Carcillo JA, Meert KL, Pollack MM, McQuillen PS, Notterman DA, DeRisi J, Mourani PM, National Institute for Child Health and Human Development Collaborative Pediatric Critical Care Rese

The antibiotic resistance reservoir of the lung microbiome expands with age.

Research square

Langelier C, Chu V, Tsitsiklis A, Mick E, Ambroggio L, Kalantar K, Glascock A, Osborne C, Wagner B, Matthay M, DeRisi J, Calfee C, Mourani P

A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling.

iScience

Hackney JA, Shivram H, Vander Heiden J, Overall C, Orozco L, Gao X, Kim E, West N, Qamra A, Chang D, Chakrabarti A, Choy DF, Combes AJ, Courau T, Fragiadakis GK, Rao AA, Ray A, Tsui J, Hu K, Kuhn NF, Krummel MF, Erle DJ, Kangelaris K, Sarma A, Lyon Z, Calfee CS, Woodruff PG, Ghale R, Mick E, Byrne A, Zha BS, Langelier C, Hendrickson CM, van der Wijst MGP, Hartoularos GC, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Ye CJ, UCSF COMET Consortium, Ramalingam T, McBride JM, Cai F, Teterina A, Bao M, Tsai L, Rosas IO, Regev A, Kapadia SB, Bauer RN, Rosenberger CM

In host evolution of beta lactam resistance during active treatment for Pseudomonas aeruginosa bacteremia.

Frontiers in cellular and infection microbiology

Spottiswoode N, Hao S, Sanchez-Guerrero E, Detweiler AM, Mekonen H, Neff N, Macmillan H, Schwartz BS, Engel J, DeRisi JL, Miller SA, Langelier CR

Identifying molecular phenotypes in sepsis: an analysis of two prospective observational cohorts and secondary analysis of two randomised controlled trials.

The Lancet. Respiratory medicine

Sinha P, Kerchberger VE, Willmore A, Chambers J, Zhuo H, Abbott J, Jones C, Wickersham N, Wu N, Neyton L, Langelier CR, Mick E, He J, Jauregui A, Churpek MM, Gomez AD, Hendrickson CM, Kangelaris KN, Sarma A, Leligdowicz A, Delucchi KL, Liu KD, Russell JA, Matthay MA, Walley KR, Ware LB, Calfee CS

Posttransfusion Sepsis Attributable to Bacterial Contamination in Platelet Collection Set Manufacturing Facility, United States.

Emerging infectious diseases

Kracalik I, Kent AG, Villa CH, Gable P, Annambhotla P, McAllister G, Yokoe D, Langelier CR, Oakeson K, Noble-Wang J, Illoh O, Halpin AL, Eder AF, Basavaraju SV

Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19.

Research square

Fragiadakis G, Neyton L, Patel R, Sarma A, Consortium UC, Willmore A, Haller SC, Kangelaris K, Eckalbar W, Erle D, Krummel M, Hendrickson C, Woodruff P, Langelier C, Calfee C

Clinical and biological heterogeneity of multisystem inflammatory syndrome in adults following SARS-CoV-2 infection: a case series.

Frontiers in medicine

Barth KE, Spottiswoode N, Hurabielle C, Subbaraj L, COMET Consortium, Calfee CS, Matthay MA, French S, Connolly A, Hewitt SM, Vannella KM, Barnett C, Langelier CR, Patterson S

Whole-genome sequencing rule-out of suspected hospital-onset Rhizopus outbreaks.

Infection control and hospital epidemiology

Chu VT, Nafees S, Waltari E, McNeil N, Caughell C, Sanchez-Guerrero E, Wang L, Stanley K, Cunningham G, Wong J, Phelps M, Tato CM, Miller S, DeRisi JL, Yokoe DS, Ramirez-Avila L, Langelier CR

Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients.

Cell reports. Medicine

Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K, IMPACC Network, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH

Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children.

The Journal of clinical investigation

Mick E, Tsitsiklis A, Kamm J, Kalantar KL, Caldera S, Lyden A, Tan M, Detweiler AM, Neff N, Osborne CM, Williamson KM, Soesanto V, Leroue M, Maddux AB, Sim?es EA, Carpenter TC, Wagner BD, DeRisi JL, Ambroggio L, Mourani PM, Langelier CR

Metagenomic Sequencing in the ICU for Precision Diagnosis of Critical Infectious Illnesses.

Critical care (London, England)

Neyton LPA, Langelier CR, Calfee CS

Aerosolized nicotine from e-cigarettes alters gene expression, increases lung protein permeability, and impairs viral clearance in murine influenza infection.

Frontiers in immunology

Maishan M, Sarma A, Chun LF, Caldera S, Fang X, Abbott J, Christenson SA, Langelier CR, Calfee CS, Gotts JE, Matthay MA

SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants.

Stem cell reports

Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP

Tobacco smoke exposure, the lower airways microbiome and outcomes of ventilated children.

Pediatric research

Leroue MK, Williamson KM, Curtin PC, Sontag MK, Wagner BD, Ambroggio L, Bixby M, Busgang SA, Murphy SE, Peterson LA, Vevang KR, Sipe CJ, Kirk Harris J, Reeder RW, Locandro C, Carpenter TC, Maddux AB, Sim?es EAF, Osborne CM, Robertson CE, Langelier C, Carcillo JA, Meert KL, Pollack MM, McQuillen PS, Mourani PM

Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries.

Global health action

Perier C, Nasinghe E, Charles I, Ssetaba LJ, Ahyong V, Bangs D, Beatty PR, Czudnochowski N, Diallo A, Dugan E, Fabius JM, Fong Baker H, Gardner J, Isaacs S, Joanah B, Kalantar K, Kateete D, Knight M, Krasilnikov M, Krogan NJ, Langelier C, Lee E, Li LM, Licht D, Lien K, Lyons Z, Mboowa G, Mwebaza I, Mwesigwa S, Nalwadda G, Nichols R, Penaranda ME, Petnic S, Phelps M, Popper SJ, Rape M, Reingold A, Robbins R, Rosenberg OS, Savage DF, Schildhauer S, Settles ML, Sserwadda I, Stanley S, Tato CM, Tsitsiklis A, Van Dis E, Vanaerschot M, Vinden J, Cox JS, Joloba ML, Schaletzky J

NKG2D receptor activation drives primary graft dysfunction severity and poor lung transplantation outcomes.

JCI insight

Calabrese DR, Tsao T, Magnen M, Valet C, Gao Y, Mallavia B, Tian JJ, Aminian EA, Wang KM, Shemesh A, Punzalan EB, Sarma A, Calfee CS, Christenson SA, Langelier CR, Hays SR, Golden JA, Leard LE, Kleinhenz ME, Kolaitis NA, Shah RJ, Venado A, Lanier LL, Greenland JR, Sayah DM, Ardehali A, Kukreja J, Weigt SS, Belperio JA, Singer JP, Looney MR

Prevalence of type-1 interferon autoantibodies in adults with non-COVID-19 acute respiratory failure.

Respiratory research

Ghale R, Spottiswoode N, Anderson MS, Mitchell A, Wang G, Calfee CS, DeRisi JL, Langelier CR

A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants.

mSystems

Albright J, Mick E, Sanchez-Guerrero E, Kamm J, Mitchell A, Detweiler AM, Neff N, Tsitsiklis A, Hayakawa Serpa P, Ratnasiri K, Havlir D, Kistler A, DeRisi JL, Pisco AO, Langelier CR

Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults.

Nature microbiology

Kalantar KL, Neyton L, Abdelghany M, Mick E, Jauregui A, Caldera S, Serpa PH, Ghale R, Albright J, Sarma A, Tsitsiklis A, Leligdowicz A, Christenson SA, Liu K, Kangelaris KN, Hendrickson C, Sinha P, Gomez A, Neff N, Pisco A, Doernberg SB, Derisi JL, Matthay MA, Calfee CS, Langelier CR

COVID-19-Associated Lung Microvascular Endotheliopathy: A "From the Bench" Perspective.

American journal of respiratory and critical care medicine

Joffre J, Rodriguez L, Matthay ZA, Lloyd E, Fields AT, Bainton RJ, Kurien P, Sil A, Calfee CS, Woodruff PG, Erle DJ, Hendrickson C, Krummel MF, Langelier CR, Matthay MA, Kornblith LZ, Hellman J, COMET consortium and the Co-ACIT Study Group

Plasma SARS-CoV-2 nucleocapsid antigen levels are associated with progression to severe disease in hospitalized COVID-19.

Critical care (London, England)

Wick KD, Leligdowicz A, Willmore A, Carrillo SA, Ghale R, Jauregui A, Chak SS, Nguyen V, Lee D, Jones C, Dewar R, Lane HC, Kangelaris KN, Hendrickson CM, Liu KD, Sinha P, Erle DJ, Langelier CR, Krummell MF, Woodruff PG, Calfee CS, Matthay MA, COMET Consortium

COVID-19 in Vaccinated Versus Unvaccinated Hematologic Malignancy Patients.

Transplant infectious disease : an official journal of the Transplantation Society

DeVoe C, Pandey S, Shariff D, Arora S, Henrich TJ, Yokoe DS, Langelier CR, Servellita V, Chiu C, Miller S, Babik JM, Chin-Hong P, Fung M

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections.

Genome medicine

Serpa PH, Deng X, Abdelghany M, Crawford E, Malcolm K, Caldera S, Fung M, McGeever A, Kalantar KL, Lyden A, Ghale R, Deiss T, Neff N, Miller SA, Doernberg SB, Chiu CY, DeRisi JL, Calfee CS, Langelier CR

Upper airway gene expression shows a more robust adaptive immune response to SARS-CoV-2 in children.

Nature communications

Mick E, Tsitsiklis A, Spottiswoode N, Caldera S, Serpa PH, Detweiler AM, Neff N, Pisco AO, Li LM, Retallack H, Ratnasiri K, Williamson KM, Soesanto V, Simões EAF, Smith C, Abuogi L, Kistler A, Wagner BD, DeRisi JL, Ambroggio L, Mourani PM, Langelier CR

Physical Activity Associates with Lower Systemic Inflammatory Gene Expression in Rheumatoid Arthritis.

The Journal of rheumatology

Patterson SL, Sun S, Rychkov D, Katz P, Tsitsiklis A, Nakamura MC, Serpa PH, Langelier CR, Sirota M

Impact of e-cigarette aerosol on primary human alveolar epithelial type 2 cells.

American journal of physiology. Lung cellular and molecular physiology

Wick KD, Fang X, Maishan M, Matsumoto S, Spottiswoode N, Sarma A, Simoneau C, Khakoo M, Langelier C, Calfee CS, Gotts JE, Matthay MA

Mass cytometry reveals a conserved immune trajectory of recovery in hospitalized COVID-19 patients.

Immunity

Burnett CE, Okholm TLH, Tenvooren I, Marquez DM, Tamaki S, Munoz Sandoval P, Willmore A, UCSF COMET Consortium, Hendrickson CM, Kangelaris KN, Langelier CR, Krummel MF, Woodruff PG, Calfee CS, Erle DJ, Ansel KM, Spitzer MH

Immediate myeloid depot for SARS-CoV-2 in the human lung.

Research square

Looney M, Magnen M, You R, Rao A, Davis R, Rodriguez L, Simoneau C, Hysenaj L, Hu K, Love C, Woodruff P, Erle D, Hendrickson C, Calfee C, Matthay M, Roose J, Sil A, Ott M, Langelier C, Krummel M

Immediate myeloid depot for SARS-CoV-2 in the human lung.

bioRxiv : the preprint server for biology

Magnen M, You R, Rao AA, Davis RT, Rodriguez L, Simoneau CR, Hysenaj L, Hu KH, UCSF COMET Consortium, Love C, Woodruff PG, Erle DJ, Hendrickson CM, Calfee CS, Matthay MA, Roose JP, Sil A, Ott M, Langelier CR, Krummel MF, Looney MR

Etiology of Lower Respiratory Tract Infections in Children Requiring Mechanical Ventilation: A Multicenter Prospective Surveillance Study Incorporating Airway Metagenomics

Lancet Microbe.

• Tsitsiklis A, Osborne CM, Kamm J, Williamson K, Kalantar KL, Dudas G, Caldera S, Lyden A, Tan M, Neff, N, Soesanto V, Harris JK, Ambroggio L, Maddux AB, Carpenter, TC, Sontag MK, Reeder RW, Locandro C, Simões, E, Leroue MK, Hall MW, Zuppa AF, Carcillo J, Meert KL, Sapru A, Pollack MM, McQuillen P Notterman DA, Dean JM, Zinter M, Wagner BD, DeRisi JL, Mourani PM, Langelier C.

Pneumonia Surveillance in Ugandans with HIV Through the Lens of Culture-Independent Metatranscriptomics: A Cross Sectional Study

Lancet Microbe

Spottiswoode N, Bloomstein J, Caldera S, Sessolo A, Byanyima P, Zawedde J, Kalantar K, Kaswabuli S, Rutishauser RL, Davis L, Jan A, Moore J, Iwai S, Shenoy M, Sanyu I, DeRisi JL, Lynch SV, Worodria W. Huang L, Langelier C

Integrating central nervous system metagenomics and host response for diagnosis of tuberculosis meningitis and its mimics.

Nature communications

Ramachandran PS, Ramesh A, Creswell FV, Wapniarski A, Narendra R, Quinn CM, Tran EB, Rutakingirwa MK, Bangdiwala AS, Kagimu E, Kandole KT, Zorn KC, Tugume L, Kasibante J, Ssebambulidde K, Okirwoth M, Bahr NC, Musubire A, Skipper CP, Fouassier C, Lyden A, Serpa P, Castaneda G, Caldera S, Ahyong V, DeRisi JL, Langelier C, Crawford ED, Boulware DR, Meya DB, Wilson MR

Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study.

The Lancet. Microbe

Spottiswoode N, Bloomstein JD, Caldera S, Sessolo A, McCauley K, Byanyima P, Zawedde J, Kalantar K, Kaswabuli S, Rutishauser RL, Lieng MK, Davis JL, Moore J, Jan A, Iwai S, Shenoy M, Sanyu I, DeRisi JL, Lynch SV, Worodria W, Huang L, Langelier CR

Prolonged silent carriage, genomic virulence potential and transmission between staff and patients characterize a neonatal intensive care unit (NICU) outbreak of methicillin-resistant Staphylococcus aureus (MRSA).

Infection control and hospital epidemiology

Madera S, McNeil N, Serpa PH, Kamm J, Pak C, Caughell C, Nichols A, Dynerman D, Li LM, Sanchez-Guerrero E, Phelps MS, Detweiler AM, Neff N, Reyes H, Miller SA, Yokoe DS, DeRisi JL, Ramirez-Avila L, Langelier CR

A conserved immune trajectory of recovery in hospitalized COVID-19 patients.

bioRxiv : the preprint server for biology

Burnett CE, Hauge Okholm TL, Tenvooren I, Marquez DM, Tamaki S, Sandoval PM, UCSF COMET Consortium, Calfee CS, Hendrickson CM, Kangelaris KN, Langelier CR, Krummel MF, Woodruff PG, Erle DJ, Ansel KM, Spitzer MH

Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics.

The Lancet. Microbe

Tsitsiklis A, Osborne CM, Kamm J, Williamson K, Kalantar K, Dudas G, Caldera S, Lyden A, Tan M, Neff N, Soesanto V, Harris JK, Ambroggio L, Maddux AB, Carpenter TC, Reeder RW, Locandro C, Simões EAF, Leroue MK, Hall MW, Zuppa AF, Carcillo J, Meert KL, Sapru A, Pollack MM, McQuillen PS, Notterman DA, Dean JM, Zinter MS, Wagner BD, DeRisi JL, Mourani PM, Langelier CR

Functional Transcriptomic Studies of Immune Responses and Endotoxin Tolerance In early Human Sepsis.

Shock (Augusta, Ga.)

Leligdowicz A, Kamm J, Kalantar K, Jauregui A, Vessel K, Caldera S, Serpa PH, Abbott J, Fang X, Tian X, Prakash A, Kangelaris KN, Liu KD, Calfee CS, Langelier C, Matthay MA

Impaired antibacterial immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.

medRxiv : the preprint server for health sciences

Tsitsiklis A, Zha BS, Byrne A, Devoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay MA, Lynch SV, DeRisi JL, COMET Consortium+ , Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, Langelier CR

Cerebrospinal fluid pterins, pterin-dependent neurotransmitters, and mortality in pediatric cerebral malaria.

The Journal of infectious diseases

Rubach MP, Mukemba JP, Florence SM, Lopansri BK, Hyland K, Simmons RA, Langelier C, Nakielny S, DeRisi JL, Yeo TW, Anstey NM, Weinberg JB, Mwaikambo ED, Granger DL

Increased rates of secondary bacterial infections, including Enterococcus bacteremia, in patients hospitalized with coronavirus disease 2019 (COVID-19).

Infection control and hospital epidemiology

DeVoe C, Segal MR, Wang L, Stanley K, Madera S, Fan J, Schouest J, Graham-Ojo R, Nichols A, Prasad PA, Ghale R, Love C, Abe-Jones Y, Kangelaris KN, Patterson SL, Yokoe DS, Langelier CR

Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01.

EClinicalMedicine

Weiner J, Suwalski P, Holtgrewe M, Rakitko A, Thibeault C, Müller M, Patriki D, Quedenau C, Krüger U, Ilinsky V, Popov I, Balnis J, Jaitovich A, Helbig ET, Lippert LJ, Stubbemann P, Real LM, Macías J, Pineda JA, Fernandez-Fuertes M, Wang X, Karadeniz Z, Saccomanno J, Doehn JM, Hübner RH, Hinzmann B, Salvo M, Blueher A, Siemann S, Jurisic S, Beer JH, Rutishauser J, Wiggli B, Schmid H, Danninger K, Binder R, Corman VM, Mühlemann B, Arjun Arkal R, Fragiadakis GK, Mick E, Comet C, Calfee CS, Erle DJ, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Langelier CR, Venkataramani U, García F, Zyla J, Drosten C, Alice B, Jones TC, Suttorp N, Witzenrath M, Hippenstiel S, Zemojtel T, Skurk C, Wolfgang P, Borodina T, Pa-Covid SG, Ripke S, Sander LE, Beule D, Landmesser U, Guettouche T, Kurth F, Heidecker B

Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS.

Nature communications

Sarma A, Christenson SA, Byrne A, Mick E, Pisco AO, DeVoe C, Deiss T, Ghale R, Zha BS, Tsitsiklis A, Jauregui A, Moazed F, Detweiler AM, Spottiswoode N, Sinha P, Neff N, Tan M, Serpa PH, Willmore A, Ansel KM, Wilson JG, Leligdowicz A, Siegel ER, Sirota M, DeRisi JL, Matthay MA, COMET Consortium , Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Calfee CS, Langelier CR

Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults.

Research square

Mick E, Tsitsiklis A, Spottiswoode N, Caldera S, Serpa P, Detweiler A, Neff N, Pisco AO, Li L, Retallack H, Ratnasiri K, Williamson K, Soesanto V, Simões E, Kistler A, Wagner B, DeRisi J, Ambroggio L, Mourani P, Langelier C

Type I interferon autoantibodies are associated with systemic immune alterations in patients with COVID-19.

Science Translational Medicine

van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Le Voyer T, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ, UCSF COMET consortium

Metagenomic characterization of swine slurry in a North American swine farm operation.

Scientific reports

Ramesh A, Bailey ES, Ahyong V, Langelier C, Phelps M, Neff N, Sit R, Tato C, DeRisi JL, Greer AG, Gray GC

Host-Microbe Metagenomics: a Lens To Refocus Our Perspective on Infectious and Inflammatory Diseases.

mSystems

Kalantar KL, Langelier CR

Publisher Correction: Global absence and targeting of protective immune states in severe COVID-19.

Nature

Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Chew NW, Cleary SJ, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Im KW, Serwas NK, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, UCSF COMET Consortium , Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF

The sputum transcriptome better predicts COPD exacerbations after the withdrawal of inhaled corticosteroids than sputum eosinophils.

ERJ open research

Ditz B, Sarma A, Kerstjens HAM, Liesker JJW, Bathoorn E, Vonk JM, Bernal V, Horvatovich P, Guryev V, Caldera S, Langelier C, Faiz A, Christenson SA, van den Berge M

SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator.

bioRxiv : the preprint server for biology

Hysenaj L, Little S, Kulhanek K, Gbenedio OM, Rodriguez L, Shen A, Lone JC, Lupin-Jimenez LC, Bonser LR, Serwas NK, Bahl K, Mick E, Li JZ, Ding VW, Matsumoto S, Maishan M, Simoneau C, Fragiadakis G, Jablons DM, Langelier CR, Matthay M, Ott M, Krummel M, Combes AJ, Sil A, Erle DJ, Kratz JR, Roose JP

Intestinal Infection Is Associated With Impaired Lung Innate Immunity to Secondary Respiratory Infection.

Open forum infectious diseases

Trivedi S, Grossmann AH, Jensen O, Cody MJ, Wahlig TA, Hayakawa Serpa P, Langelier C, Warren KJ, Yost CC, Leung DT

Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.

Research square

Tsitsiklis A, Zha B, Byrne A, DeVoe C, Levan S, Rackaityte E, Sunshine S, Mick E, Ghale R, Jauregui A, Neff N, Sarma A, Serpa P, Deiss T, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Jones N, Wu B, Darmanis S, Matthay M, Lynch S, DeRisi J, Consortium C, Hendrickson C, Kangelaris K, Krummel M, Woodruff P, Erle D, Rosenberg O, Calfee C, Langelier C

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium.

Genome medicine

Temporal airway microbiome changes related to ventilator associated pneumonia in children.

The European respiratory journal

Mourani PM, Sontag MK, Williamson KM, Harris JK, Reeder R, Locandro C, Carpenter TC, Maddux AB, Ziegler K, Simões EAF, Osborne CM, Ambroggio L, Leroue MK, Robertson CE, Langelier C, DeRisi JL, Kamm J, Hall MW, Zuppa AF, Carcillo J, Meert K, Sapru A, Pollack MM, McQuillen P, Notterman DA, Dean JM, Wagner BD

Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19.

bioRxiv : the preprint server for biology

van der Wijst MGP, Vazquez SE, Hartoularos GC, Bastard P, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Mann SA, Lynch KL, Yun C, Havlir DV, Chamie G, Marquez C, Greenhouse B, Lionakis MS, Norris PJ, Dumont LJ, Kelly K, Zhang P, Zhang Q, Gervais A, Voyer TL, Whatley A, Si Y, Byrne A, Combes AJ, Rao AA, Song YS, UCSF COMET consortium , Fragiadakis GK, Kangelaris K, Calfee CS, Erle DJ, Hendrickson C, Krummel MF, Woodruff PG, Langelier CR, Casanova JL, Derisi JL, Anderson MS, Ye CJ

Nasopharyngeal SARS-CoV-2 viral loads in young children do not differ significantly from those in older children and adults.

Scientific reports

Madera S, Crawford E, Langelier C, Tran NK, Thornborrow E, Miller S, DeRisi JL

Global absence and targeting of protective immune states in severe COVID-19.

Nature

Antibiotic-Selected Gene Amplification Heightens Metal Resistance.

mBio

Hufnagel DA, Choby JE, Hao S, Johnson AF, Burd EM, Langelier C, Weiss DS

COVID-19 ARDS is characterized by a dysregulated host response that differs from cytokine storm and is modified by dexamethasone.

Research square

Sarma A, Christenson S, Mick E, Deiss T, DeVoe C, Pisco A, Ghale R, Jauregui A, Byrne A, Moazed F, Spottiswoode N, Sinha P, Zha B, Neff N, Tan M, Serpa PH, Ansel KM, Wilson J, Leligdowicz A, Seigel E, Sirota M, DeRisi J, Matthay M, Consortium C, Hendrickson C, Kangelaris K, Krummel M, Woodruff P, Erle D, Calfee C, Langelier C

Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.

Cell

Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M

Dose-Dependent Pulmonary Toxicity of Aerosolized Vitamin E Acetate.

American journal of respiratory cell and molecular biology

Matsumoto S, Fang X, Traber MG, Jones KD, Langelier C, Hayakawa Serpa P, Calfee CS, Matthay MA, Gotts JE

Type-1 Immunity and Endogenous Immune Regulators Predominate in the Airway Transcriptome during Chronic Lung Allograft Dysfunction.

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons

Iasella CJ, Hoji A, Popescu I, Wei J, Snyder M, Zhang Y, Xu W, Iouchmanov V, Koshy R, Brown M, Fung M, Langelier C, Lendermon EA, Dugger D, Shah R, Lee J, Johnson B, Golden J, Leard LE, Kleinhenz ME, Kilaru S, Hays SR, Singer JP, Sanchez PG, Morrell MR, Pilewski JM, Greenland JR, Chen K, McDyer JF

Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses.

Nature communications

Mick E, Kamm J, Pisco AO, Ratnasiri K, Babik JM, Castañeda G, DeRisi JL, Detweiler AM, Hao SL, Kangelaris KN, Kumar GR, Li LM, Mann SA, Neff N, Prasad PA, Serpa PH, Shah SJ, Spottiswoode N, Tan M, Calfee CS, Christenson SA, Kistler A, Langelier C

Global Absence and Targeting of Protective Immune States in Severe COVID-19.

bioRxiv : the preprint server for biology

Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Cleary SJ, Chew NW, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF

Global Absence and Targeting of Protective Immune States in Severe COVID-19.

Research square

Krummel M, Combes A, Courau T, Kuhn N, Hu K, Ray A, Chen W, Cleary S, Chew N, Kushnoor D, Reeder G, Shen A, Tsui J, Hiam K, Sandoval PM, Zhu W, Lee D, Sun Y, You R, Magnen M, Rodriguez L, Leligdowicz A, Zamecnik C, Loudermilk R, Wilson M, Ye C, Fragiadakis G, Looney M, Chan V, Ward A, Carrillo S, Matthay M, Erle D, Woodruff P, Langelier C, Kangelaris K, Hendrickson C, Calfee C, Rao A

Rapid deployment of SARS-CoV-2 testing: The CLIAHUB.

PLoS pathogens

Crawford ED, Acosta I, Ahyong V, Anderson EC, Arevalo S, Asarnow D, Axelrod S, Ayscue P, Azimi CS, Azumaya CM, Bachl S, Bachmutsky I, Bhaduri A, Brown JB, Batson J, Behnert A, Boileau RM, Bollam SR, Bonny AR, Booth D, Borja MJB, Brown D, Buie B, Burnett CE, Byrnes LE, Cabral KA, Cabrera JP, Caldera S, Canales G, Castañeda GR, Chan AP, Chang CR, Charles-Orszag A, Cheung C, Chio U, Chow ED, Citron YR, Cohen A, Cohn LB, Chiu C, Cole MA, Conrad DN, Constantino A, Cote A, Crayton-Hall T, Darmanis S, Detweiler AM, Dial RL, Dong S, Duarte EM, Dynerman D, Egger R, Fanton A, Frumm SM, Fu BXH, Garcia VE, Garcia J, Gladkova C, Goldman M, Gomez-Sjoberg R, Gordon MG, Grove JCR, Gupta S, Haddjeri-Hopkins A, Hadley P, Haliburton J, Hao SL, Hartoularos G, Herrera N, Hilberg M, Ho KYE, Hoppe N, Hosseinzadeh S, Howard CJ, Hussmann JA, Hwang E, Ingebrigtsen D, Jackson JR, Jowhar ZM, Kain D, Kim JYS, Kistler A, Kreutzfeld O, Kulsuptrakul J, Kung AF, Langelier C, Laurie MT, Lee L, Leng K, Leon KE, Leonetti MD, Levan SR, Li S, Li AW, Liu J, Lubin HS, Lyden A, Mann J, Mann S, Margulis G, Marquez DM, Marsh BP, Martyn C, McCarthy EE, McGeever A, Merriman AF, Meyer LK, Miller S, Moore MK, Mowery CT, Mukhtar T, Mwakibete LL, Narez N, Neff NF, Osso LA, Oviedo D, Peng S, Phelps M, Phong K, Picard P, Pieper LM, Pincha N, Pisco AO, Pogson A, Pourmal S, Puccinelli RR, Puschnik AS, Rackaityte E, Raghavan P, Raghavan M, Reese J, Replogle JM, Retallack H, Reyes H, Rose D, Rosenberg MF, Sanchez-Guerrero E, Sattler SM, Savy L, See SK, Sellers KK, Serpa PH, Sheehy M, Sheu J, Silas S, Streithorst JA, Strickland J, Stryke D, Sunshine S, Suslow P, Sutanto R, Tamura S, Tan M, Tan J, Tang A, Tato CM, Taylor JC, Tenvooren I, Thompson EM, Thornborrow EC, Tse E, Tung T, Turner ML, Turner VS, Turnham RE, Turocy MJ, Vaidyanathan TV, Vainchtein ID, Vanaerschot M, Vazquez SE, Wandler AM, Wapniarski A, Webber JT, Weinberg ZY, Westbrook A, Wong AW, Wong E, Worthington G, Xie F, Xu A, Yamamoto T, Yang Y, Yarza F, Zaltsman Y, Zheng T, DeRisi JL

Chronic lung allograft dysfunction small airways reveal a lymphocytic inflammation gene signature.

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons

Dugger DT, Fung M, Hays SR, Singer JP, Kleinhenz ME, Leard LE, Golden JA, Shah RJ, Lee JS, Deiter F, Greenland NY, Jones KD, Langelier CR, Greenland JR

Genomic Profiling of Evolving Daptomycin Resistance in a Patient with Recurrent Staphylococcus argenteus Sepsis.

Antimicrobial agents and chemotherapy

Hao S, Abdelghany M, Lyden A, Sit R, Tan M, Tato CM, DeRisi JL, Miller S, Doernberg SB, Langelier C

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19.

EClinicalMedicine

Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Kangelaris KN, Langelier C, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Castaneda G

Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Crawford E, Kamm J, Miller S, Li LM, Caldera S, Lyden A, Yokoe D, Nichols A, Tran NK, Barnard SE, Conner PM, Nambiar A, Zinter MS, Moayeri M, Serpa PH, Prince BC, Quan J, Sit R, Tan M, Phelps M, DeRisi JL, Tato CM, Langelier C

Sepsis from an apheresis platelet contaminated with Acinetobacter calcoaceticus/baumannii complex bacteria and Staphylococcus saprophyticus after pathogen reduction.

Transfusion

Fridey JL, Stramer SL, Nambiar A, Moayeri M, Bakkour S, Langelier C, Crawford E, Lu T, Lanteri MC, Kamm J, Miller S, Wagner SJ, Benjamin RJ, Busch MP

Draft Genome Sequence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Strain from a Returned Traveler from Pakistan.

Microbiology resource announcements

Hao S, Veuthey T, Caldera S, Serpa PH, Haller B, Tan M, Neff N, Madera S, Langelier C

Cystic Fibrosis Lung Transplant Recipients Have Suppressed Airway Interferon Responses during Pseudomonas Infection.

Cell reports. Medicine

Dugger DT, Fung M, Zlock L, Caldera S, Sharp L, Hays SR, Singer JP, Leard LE, Golden JA, Shah RJ, Kukreja J, Gordon E, Finkbeiner W, Kleinhenz ME, Langelier C, Greenland JR

Clinical Outcomes and Serologic Response in Solid Organ Transplant Recipients with COVID-19: A Case Series from the United States.

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons

Fung M, Chiu CY, DeVoe C, Doernberg SB, Schwartz BS, Langelier C, Henrich TJ, Yokoe D, Davis J, Hays SR, Chandran S, Kukreja J, Ng D, Prostko J, Taylor R, Reyes K, Bainbridge E, Bond A, Chin-Hong P, Babik JM

The ex vivo perfused human lung is resistant to injury by high-dose S. pneumoniae bacteremia.

American journal of physiology. Lung cellular and molecular physiology

Ross JT, Nesseler N, Leligdowicz A, Zemans RL, Mahida RY, Minus E, Langelier C, Gotts JE, Matthay MA

The gut microbiome's role in the development, maintenance, and outcomes of sepsis.

Critical care (London, England)

Adelman MW, Woodworth MH, Langelier C, Busch LM, Kempker JA, Kraft CS, Martin GS

Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2.

medRxiv : the preprint server for health sciences

Mick E, Kamm J, Pisco AO, Ratnasiri K, Babik JM, Calfee CS, Castaneda G, DeRisi JL, Detweiler AM, Hao S, Kangelaris KN, Kumar GR, Li LM, Mann SA, Neff N, Prasad PA, Serpa PH, Shah SJ, Spottiswoode N, Tan M, Christenson SA, Kistler A, Langelier C

Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19.

medRxiv : the preprint server for health sciences

Shah SJ, Barish PN, Prasad PA, Kistler AL, Neff N, Kamm J, Li LM, Chiu CY, Babick JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Davis JM, Castenada GD, Consortium C, Dadasovich RM, Deng X, DeRisi JL, Detweiler AM, Federman S, Haliburton JR, Hao SL, Kerkhoff AD, Kumar R, Malcolm K, Mann SA, Martinez SP, Marya R, Mick E, Mwakibete LL, Najafi N, Peluso MJ, Phelps MS, Pisco AO, Ratnasiri K, Rubio LA, Sellas AB, Sherwood KD, Sheu J, Spottiswoode N, Tan M, Yu G, Kangelaris KN, Langelier C

Central Nervous System Virus Infection in African Children with Cerebral Malaria.

The American journal of tropical medicine and hygiene

Postels DG, Osei-Tutu L, Seydel KB, Xu Q, Li C, Taylor TE, John CC, Mallewa M, Solomon T, Agbenyega T, Ansong D, Opoka RO, Khan LM, Leon KE, DeRisi JL, Langelier C, Wilson MR

Genomic and serologic characterization of enterovirus A71 brainstem encephalitis.

Neurology(R) neuroimmunology & neuroinflammation

Leon KE, Schubert RD, Casas-Alba D, Hawes IA, Ramachandran PS, Ramesh A, Pak JE, Wu W, Cheung CK, Crawford ED, Khan LM, Launes C, Sample HA, Zorn KC, Cabrerizo M, Valero-Rello A, Langelier C, Muñoz-Almagro C, DeRisi JL, Wilson MR

Detection of Pneumonia Pathogens from Plasma Cell-Free DNA.

American journal of respiratory and critical care medicine

Langelier C, Fung M, Caldera S, Deiss T, Lyden A, Prince BC, Hayakawa Serpa P, Moazed F, Chin-Hong P, DeRisi JL, Calfee CS

Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens.

mBio

Saha S, Ramesh A, Kalantar K, Malaker R, Hasanuzzaman M, Khan LM, Mayday MY, Sajib MSI, Li LM, Langelier C, Rahman H, Crawford ED, Tato CM, Islam M, Juan YF, de Bourcy C, Dimitrov B, Wang J, Tang J, Sheu J, Egger R, De Carvalho TR, Wilson MR, Saha SK, DeRisi JL

FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences.

Nucleic acids research

Quan J, Langelier C, Kuchta A, Batson J, Teyssier N, Lyden A, Caldera S, McGeever A, Dimitrov B, King R, Wilheim J, Murphy M, Ares LP, Travisano KA, Sit R, Amato R, Mumbengegwi DR, Smith JL, Bennett A, Gosling R, Mourani PM, Calfee CS, Neff NF, Chow ED, Kim PS, Greenhouse B, DeRisi JL, Crawford ED

Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers.

Emerging infectious diseases

Langelier C, Graves M, Kalantar K, Caldera S, Durrant R, Fisher M, Backman R, Tanner W, DeRisi JL, Leung DT

Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda.

PloS one

Ramesh A, Nakielny S, Hsu J, Kyohere M, Byaruhanga O, de Bourcy C, Egger R, Dimitrov B, Juan YF, Sheu J, Wang J, Kalantar K, Langelier C, Ruel T, Mpimbaza A, Wilson MR, Rosenthal PJ, DeRisi JL

Sepsis Attributed to Bacterial Contamination of Platelets Associated with a Potential Common Source - Multiple States, 2018.

MMWR. Morbidity and mortality weekly report

Jones SA, Jones JM, Leung V, Nakashima AK, Oakeson KF, Smith AR, Hunter R, Kim JJ, Cumming M, McHale E, Young PP, Fridey JL, Kelley WE, Stramer SL, Wagner SJ, West FB, Herron R, Snyder E, Hendrickson JE, Peaper DR, Gundlapalli AV, Langelier C, Miller S, Nambiar A, Moayeri M, Kamm J, Moulton-Meissner H, Annambhotla P, Gable P, McAllister GA, Breaker E, Sula E, Halpin AL, Basavaraju SV

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.

The New England journal of medicine

Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, Federman S, Stryke D, Briggs B, Langelier C, Berger A, Douglas V, Josephson SA, Chow FC, Fulton BD, DeRisi JL, Gelfand JM, Naccache SN, Bender J, Dien Bard J, Murkey J, Carlson M, Vespa PM, Vijayan T, Allyn PR, Campeau S, Humphries RM, Klausner JD, Ganzon CD, Memar F, Ocampo NA, Zimmermann LL, Cohen SH, Polage CR, DeBiasi RL, Haller B, Dallas R, Maron G, Hayden R, Messacar K, Dominguez SR, Miller S, Chiu CY

Sentinel Case of Candida auris in the Western United States Following Prolonged Occult Colonization in a Returned Traveler from India.

Microbial drug resistance (Larchmont, N.Y.)

Woodworth MH, Dynerman D, Crawford ED, Doernberg SB, Ramirez-Avila L, Serpa PH, Nichols A, Li LM, Lyden A, Tato CM, Miller S, Derisi JL, Langelier C

Detection of Cryptococcus DNA by metagenomic next-generation sequencing in symptomatic cryptococcal antigenemia.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Ramachandran PS, Cresswell FV, Meya DB, Crawford ED, DeRisi JL, Boulware DR, Wilson MR

Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Zinter MS, Dvorak CC, Mayday MY, Iwanaga K, Ly NP, McGarry ME, Church GD, Faricy LE, Rowan CM, Hume JR, Steiner ME, Crawford ED, Langelier C, Kalantar K, Chow ED, Miller S, Shimano K, Melton A, Yanik GA, Sapru A, DeRisi JL

Bergeyella cardium: Clinical Characteristics and Draft Genome of an Emerging Pathogen in Native and Prosthetic Valve Endocarditis.

Open forum infectious diseases

Mulliken JS, Langelier C, Budak JZ, Miller S, Dynerman D, Hao S, Li LM, Crawford E, Lyden A, Woodworth MH, DeRisi JL, Desmond E, Browne C, Luu A, Grandis DJ, Grossman W, Deuse T, Melcher GP

A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota.

American journal of physiology. Lung cellular and molecular physiology

Kalantar KL, Moazed F, Christenson SC, Wilson J, Deiss T, Belzer A, Vessel K, Caldera S, Jauregui A, Bolourchi S, DeRisi JL, Calfee CS, Langelier C

A high five for TB screening

Science Translational Medicine

Langelier, C.

Malaria and the microbiome: a systematic review.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Ippolito MM, Denny JE, Langelier C, Sears CL, Schmidt NW

Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.

Proceedings of the National Academy of Sciences of the United States of America

Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, Jauregui A, Malcolm K, Lyden A, Khan L, Vessel K, Quan J, Zinter M, Chiu CY, Chow ED, Wilson J, Miller S, Matthay MA, Pollard KS, Christenson S, Calfee CS, DeRisi JL

Breakthrough Invasive Fungal Infections on Isavuconazole Prophylaxis and Treatment: What is Happening in the Real-world Setting?

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Fung M, Schwartz BS, Doernberg SB, Langelier C, Lo M, Graff L, Tan M, Logan AC, Chin-Hong P, Babik JM

The resistance potential of a quintessential commensal

Science Translational Medicine

Langelier, Chaz

Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing.

JAMA neurology

Wilson MR, O'Donovan BD, Gelfand JM, Sample HA, Chow FC, Betjemann JP, Shah MP, Richie MB, Gorman MP, Hajj-Ali RA, Calabrese LH, Zorn KC, Chow ED, Greenlee JE, Blum JH, Green G, Khan LM, Banerji D, Langelier C, Bryson-Cahn C, Harrington W, Lingappa JR, Shanbhag NM, Green AJ, Brew BJ, Soldatos A, Strnad L, Doernberg SB, Jay CA, Douglas V, Josephson SA, DeRisi JL

A molecular warning system for invasive pneumococcus

Science Translational Medicine

Chaz Langelier

A firsthand view of how secondhand smoke disrupts airway immunity

Science Translational Medicine

Chaz Langelier

Lung Microbiota is Related to Smoking Status and to Development of ARDS in Critically Ill Trauma Patients.

American journal of respiratory and critical care medicine

Panzer AR, Lynch SV, Langelier C, Christie JD, McCauley K, Nelson M, Cheung CK, Benowitz NL, Cohen MJ, Calfee CS

A proactive charcoal approach shields the gut microbiome from systemic antibiotics

Science Translational Medicine

Chaz Langelier

Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients.

American journal of respiratory and critical care medicine

Langelier C, Zinter MS, Kalantar K, Yanik GA, Christenson S, O'Donovan B, White C, Wilson M, Sapru A, Dvorak CC, Miller S, Chiu CY, DeRisi JL

IFN-stimulated Gene Expression, Type 2 Inflammation, and Endoplasmic Reticulum Stress in Asthma.

American journal of respiratory and critical care medicine

Bhakta NR, Christenson SA, Nerella S, Solberg OD, Nguyen CP, Choy DF, Jung KL, Garudadri S, Bonser LR, Pollack JL, Zlock LT, Erle DJ, Langelier C, Derisi JL, Arron JR, Fahy JV, Woodruff PG

Transcriptomic profiling reveals gene expression kinetics in patients with hypoxia and high altitude pulmonary edema.

Gene

Yuhong L, Tana W, Zhengzhong B, Feng T, Qin G, Yingzhong Y, Wei G, Yaping W, Langelier C, Rondina MT, Ge RL

Complete Genome Sequence of a Divergent Human Rhinovirus C Isolate from an Infant with Severe Community-Acquired Pneumonia in Colorado, USA.

Genome announcements

Langelier C, White CV, Sontag MK, Mourani PM, DeRisi JL

Use of isavuconazole in a patient with voriconazole-induced QTc prolongation.

Transplant infectious disease : an official journal of the Transplantation Society

Trang TP, Hanretty AM, Langelier C, Yang K

Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater.

PloS one

Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL

Antimicrobial Resistance: A Call to Action!

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Brown L, Langelier C, Reid MJ, Rutishauser RL, Strnad L

Raccoon Roundworm Infection Associated with Central Nervous System Disease and Ocular Disease - Six States, 2013-2015.

MMWR. Morbidity and mortality weekly report

Sircar AD, Abanyie F, Blumberg D, Chin-Hong P, Coulter KS, Cunningham D, Huskins WC, Langelier C, Reid M, Scott BJ, Shirley DA, Babik JM, Belova A, Sapp SG, McAuliffe I, Rivera HN, Yabsley MJ, Montgomery SP

Baylisascaris procyonis-Associated Meningoencephalitis in a Previously Healthy Adult, California, USA.

Emerging infectious diseases

Langelier C, Reid MJ, Halabi C, Witek N, LaRiviere A, Shah M, Wilson MR, Chin-Hong P, Douglas V, Kazacos KR, Babik JM

Monocyte polarization in children with falciparum malaria: relationship to nitric oxide insufficiency and disease severity.

Scientific reports

Weinberg JB, Volkheimer AD, Rubach MP, Florence SM, Mukemba JP, Kalingonji AR, Langelier C, Chen Y, Bush M, Yeo TW, Granger DL, Anstey NM, Mwaikambo ED

An Expression of Clinical Significance: Exploring the Human Genome to Understand the Variable Response to Rhinovirus.

American journal of respiratory and critical care medicine

Langelier C, Christenson SA

Two Rapidly Growing Mycobacterial Species Isolated from a Brain Abscess: First Whole-Genome Sequences of Mycobacterium immunogenum and Mycobacterium llatzerense.

Journal of clinical microbiology

Greninger AL, Langelier C, Cunningham G, Keh C, Melgar M, Chiu CY, Miller S

Beyond the superficial: Coccidioides immitis fungaemia in a man with fever, fatigue and skin nodules: a case of an emerging and evolving pathogen.

BMJ case reports

Langelier C, Baxi SM, Iribarne D, Chin-Hong P

Clinical, genomic, and metagenomic characterization of oral tongue squamous cell carcinoma in patients who do not smoke.

Head & neck

Li R, Faden DL, Fakhry C, Langelier C, Jiao Y, Wang Y, Wilkerson MD, Pedamallu CS, Old M, Lang J, Loyo M, Ahn SM, Tan M, Gooi Z, Chan J, Richmon J, Wood LD, Hruban RH, Bishop J, Westra WH, Chung CH, Califano J, Gourin CG, Bettegowda C, Meyerson M, Papadopoulos N, Kinzler KW, Vogelstein B, DeRisi JL, Koch WM, Agrawal N