Publications

2024

Source-to-tap investigation of the occurrence of nontuberculous mycobacteria in a full-scale chloraminated drinking water system

Dowdell KS, Potgieter SC, Olsen K, Lee S, Vedrin M, Caverly LJ, LiPuma JJ, Raskin L.

Appl Environ Microbiol. 2024 Sep 18;90(9):e0060924. doi: 10.1128/aem.00609-24

Impact of day-to-day variation in FEV1 on measures of change: A conceptual description

Magaret AS, Graham E, Caverly LJ, Cromwell EA, Paynter A, Rosenfeld M, Thornton CS, Goss CH.

J Cyst Fibros. 2024 Sep;23(5):943-946. doi: 10.1016/j.jcf.2024.07.005

Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis

Widder S, Carmody L, Opron K, Kalikin L, Caverly L, LiPuma J.

Nat Commun. 2024 Jun 7;15(1):4889. doi: 10.1038/s41467-024-49150-y

Itaconic acid inhibits nontuberculous mycobacterial growth in pH dependent manner while 4-octyl-itaconic acid enhances THP-1 clearance of nontuberculous mycobacteria in vitro

Breen P, Zimbric M, Caverly LJ.

PLoS One. 2024 May 10;19(5):e0303516. doi: 10.1371/journal.pone.0303516. eCollection 2024

From gut to lung and back again: early life microbiota in cystic fibrosis

Caverly LJ, Ross BD, Dickson RP.

Eur Respir J. 2024 May 9;63(5):2400595. doi: 10.1183/13993003.00595-2024

Prevalence and clinical impact of respiratory viral infections from the STOP2 study of cystic fibrosis pulmonary exacerbations

Thornton CS, Caverly LJ, Kalikin LM, Carmody LA, McClellan S, LeBar W, Sanders DB, West NE, Goss CH, Flume PA, Heltshe SL, VanDevanter DR, LiPuma JJ.

Ann Am Thorac Soc. 2024 Apr;21(4):595-603. doi: 10.1513/AnnalsATS.202306-576OC

Quantifying variation in home spirometry in people with cystic fibrosis during baseline health, and associations with clinical outcomes

Thornton CS, Magaret AS, Carmody LA, Kalikin LM, Simon RH, LiPuma JJ, Caverly LJ 

J Cyst Fibros. 2024 Mar;23(2):321-328. doi: 10.1016/j.jcf.2023.05.011 

Nontuberculous mycobacterial pulmonary infections in the era of elexacaftor-tezacaftor-ivacaftor

Mingora CM, Caverly LJ.

J Cyst Fibros. 2024 Jan;23(1):3-4. doi: 10.1016/j.jcf.2024.01.010

2023

Genomic analyses of longitudinal Mycobacterium abscessus isolates in a multi-center cohort reveal parallel signatures of in-host adaptation

Choi J, Keen EC, Wallace MA, Fishbein S, Prusa J, Zimbric M, Mejia-Chew CR, Mehta SB, Bailey TC, Caverly LJ, Burnham CD, Dantas G

J Infect Dis. 2023 Aug 11;228(3):321-331. doi: 10.1093/infdis/jiad187

Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis

Widder S, Opron K, Carmody LA, Kalikin LM, Caverly LJ, LiPuma JJ

bioRxiv. 2023 Jul 25:2023.07.21.550012. doi: 10.1101/2023.07.21.550012

Airway bacterial community composition in persons with advanced cystic fibrosis lung disease

Thornton CS, Carmody LA, Kalikin LM, Opron K, Caverly LJ, LiPuma JJ 

J Cyst Fibros. 2023 Jul;22(4):623-629. doi: 10.1016/j.jcf.2023.01.001

Discontinuation versus continuation of hypertonic saline or dornase alfa in modulator treated people with cystic fibrosis (SIMPLIFY): results from two parallel, multicentre, open-label, randomised, controlled, non-inferiority trials

Mayer-Hamblett N, Ratjen F, Russell R, Donaldson SH, Riekert KA, Sawicki GS, Odem-Davis K, Young JK, Rosenbluth D, Taylor-Cousar JL, Goss CH, Retsch-Bogart G, Clancy JP, Genatossio A, O'Sullivan BP, Berlinski A, Millard SL, Omlor G, Wyatt CA, Moffett K, Nichols DP, Gifford AH; SIMPLIFY Study Group

Lancet Respir Med. 2023 Apr;11(4):329-340. doi: 10.1016/S2213-2600(22)00434-9

2022

The impact of highly effective modulator therapy on cystic fibrosis microbiology and inflammation

Caverly LJ, Riquelme SA, Hisert KB

Clin Chest Med. 2022 Dec;43(4):647-665. doi: 10.1016/j.ccm.2022.06.007

Can identifying pulmonary exacerbation phenotypes guide new treatment approaches for cystic fibrosis?

Caverly LJ

Ann Am Thorac Soc. 2022 Nov;19(11):1799-1801. doi: 10.1513/AnnalsATS.202208-703ED

Considerations for CF airway infection sampling and impact of CFTR modulators

Caverly LJ 

J Cyst Fibros. 2022 Nov;21(6):906-907. doi: 10.1016/j.jcf.2022.09.004

The elusive role of airway infection in cystic fibrosis exacerbation.

Caverly LJ, VanDevanter DR 

J Pediatric Infect Dis Soc. 2022 Sep 7;11(Supplement_2):S40-S45. doi: 10.1093/jpids/piac062

Changes in airway bacterial communities occur soon after initiation of antibiotic treatment of pulmonary exacerbations in cystic fibrosis

Carmody LA, Kalikin LM, VanDevanter DR, Li G, Opron K, Simon RH, Caverly LJ, LiPuma JJ

J Cyst Fibros. 2022 Sep;21(5):766-768. doi: 10.1016/j.jcf.2022.05.011

Sputum metabolites associated with nontuberculous mycobacterial infection in cystic fibrosis

Breen P, Zimbric M, Opron K, Caverly LJ

mSphere. 2022 Jun 29;7(3):e0010422. doi: 10.1128/msphere.00104-22

Testing the effects of combining azithromycin with inhaled tobramycin for P. aeruginosa in cystic fibrosis: a randomised, controlled clinical trial

Nichols DP, Singh PK, Baines A, Caverly LJ, Chmiel JF, GIbson RL, Lascano J, Morgan SJ, Retsch-Bogart G, Saiman L, Sadeghi H, Billings JL, Heltshe SL, Kirby S, Kong A, Nick JA, Mayer-Hamblett N; TEACH Study Group

Thorax. 2022 Jun;77(6):581-588. doi: 10.1136/thoraxjnl-2021-217782

Coming up for air: The role of anaerobes in cystic fibrosis

Thornton CS, Caverly LJ, LiPuma JJ 

Ann Am Thorac Soc. 2022 May;19(5):713-716. doi: 10.1513/AnnalsATS.202110-1142PS

Tenets of a holistic approach to drinking water-associated pathogen research, management, and communication

Proctor C, Garner E, Hamilton KA, Ashbolt NJ, Caverly LJ, Falkinham JO 3rd, Haas CN, Prevost M, Prevots DR, Pruden A, Raskin L, Stout J, Haig SJ 

Water Res. 2022 Mar 1;211:117997. doi: 10.1016/j.watres.2021.117997

2021

Aminoglycoside dosing and monitoring for Pseudomonas aeruginosa during acute pulmonary exacerbations in cystic fibrosis

Ochs MA, Dillman NO, Caverly LJ, Chaffee VD 

Pediatr Pulmonol. 2021 Dec;56(12):3634-3643. doi: 10.1002/ppul.25441

Outcomes of cystic fibrosis pulmonary exacerbations treated with antibiotics with activity against anaerobic bacteria

Castner LM, Zimbric M, Cahalan S, Powell C, Caverly LJ 

J Cyst Fibros. 2021 Nov;20(6):926-931. doi: 10.1016/j.jcf.2021.02.001

Comparative genomics of Mycobacterium avium complex reveals signatures of environment-specific adaptation and community acquisition

Keen EC, Choi J, Wallace MA, Azar M, Mejia-Chew CR, Mehta SB, Bailey TC, Caverly LJ, Burnham CD, Dantas G

mSystems. 2021 Oct 26;6(5):e0119421. doi: 10.1128/mSystems.01194-21

Cystic fibrosis airway microbiota associated with outcomes of nontuberculous mycobacterial infection

Caverly LJ, Zimbric M, Azar M, Opron K, LiPuma JJ

ERJ Open Res. 2021 Apr 19;7(2):00578-2020. doi: 10.1183/23120541.00578-2020

Clinical characteristics and outcomes associated with Inquilinus infection in cystic fibrosis

Lenhart-Pendergrass PM, Caverly LJ, Wagner BD, Sagel SD, Nick JA, LiPuma JJ, Martiniano SL 

J Cyst Fibros. 2021 Mar;20(2):310-315. doi: 10.1016/j.jcf.2020.07.011

Liquid chromatography mass spectrometry detection of antibiotic agents in sputum from persons with cystic fibrosis

Gallagher T, Riedel S, Kapcia J, Caverly LJ, Carmody L, Kalikin LM, Lu J, Phan J, Gargus M, Kagawa M, Leemans SW, Rothman JA, Grun F, LiPuma JJ, Whiteson KL 

Antimicrob Agents Chemother. 2021 Jan 20;65(2):e00927-20. doi: 10.1128/AAC.00927-20

2020

Quality improvement initiative to improve pulmonary function in pediatric cystic fibrosis patients

Filbrun AG, Enochs C, Caverly L, Rajala K, Powell C, Merrick E, Nasr SZ 

Pediatr Pulmonol. 2020 Nov;55(11):3039-3045. doi: 10.1002/ppul.25017

Parallel analysis of cystic fibrosis sputum and saliva reveals overlapping communities and an opportunity for sample decontamination

Lu J, Carmody LA, Opron K, Simon RH, Kalikin LM, Caverly LJ, LiPuma JJ

mSystems. 2020 Jul 7;5(4):e00296-20. doi: 10.1128/mSystems.00296-20

Distribution and outcomes of infection of Mycobacterium avium complex species in cystic fibrosis

Azar M, Zimbric M, Shedden K, Caverly LJ

J Cyst Fibros. 2020 Mar;19(2):232-235. doi: 10.1016/j.jcf.2019.07.007

Challenging scenarios in nontuberculous mycobacterial infection in cystic fibrosis

Martiniano SL, Esther CR, Haworth CS, Kasperbauer SH, Zemanick ET, Caverly LJ 

Pediatr Pulmonol. 2020 Feb;55(2):521-525. doi: 10.1002/ppul.24604

2019

In vitro activities of β-lactam-β-lactamase inhibitor antimicrobial agents against cystic fibrosis respiratory pathogens

Caverly LJ, Spilker T, Kalikin LM, Stillwell T, Young C, Huang DB, LiPuma JJ

Antimicrob Agents Chemother. 2019 Dec 20;64(1):e01595-19. doi: 10.1128/AAC.01595-19

Measures of cystic fibrosis airway microbiota during periods of clinical stability

Caverly LJ, Lu J, Carmody LA, Kalikin LM, Shedden K, Opron K, Azar M, Cahalan S, Foster B, VanDevanter DR, Simon RH, LiPuma JJ

Ann Am Thorac Soc. 2019 Dec;16(12):1534-1542. doi: 10.1513/AnnalsATS.201903-270OC

Past, present, and future research on the lung microbiome in inflammatory airway disease

Caverly LJ, Huang YJ, Sze MA 

Chest. 2019 Aug;156(2):376-382. doi: 10.1016/j.chest.2019.05.011

Retrospective analysis of nontuberculous mycobacterial infection and monochloramine disinfection of municipal drinking water in Michigan

Kotlarz N, Raskin L, Zimbric M, Errickson J, LiPuma JJ, Caverly LJ 

mSphere. 2019 Jul 3;4(4):e00160-19. doi: 10.1128/mSphere.00160-19

Nontuberculous mycobacteria in drinking water systems - the challenges of characterization and risk mitigation

Dowdell K, Haig SJ, Caverly LJ, Shen Y, LiPuma JJ, Raskin L 

Curr Opin Biotechnol. 2019 Jun;57:127-136. doi: 10.1016/j.copbio.2019.03.010

2018

Cystic fibrosis respiratory microbiota: unraveling complexity to inform clinical practice

Caverly LJ, LiPuma JJ 

Expert Rev Respir Med. 2018 Oct;12(10):857-865. doi: 10.1080/17476348.2018.1513331

Good cop, bad cop: anaerobes in cystic fibrosis airways

Caverly LJ, LiPuma JJ 

Eur Respir J. 2018 Jul 11;52(1):1801146. doi: 10.1183/13993003.01146-2018

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis

Carmody LA, Caverly LJ, Foster BK, Rogers MAM, Kalikin LM, Simon RH, VanDevanter DR, LiPuma JJ 

PLoS One. 2018 Mar 9;13(3):e0194060. doi: 10.1371/journal.pone.0194060

2016

Complete genome sequences of 17 rapidly growing nontuberculous mycobacterial strains

Caverly LJ, Spilker T, LiPuma JJ

Genome Announc. 2016 Sep 22;4(5):e01009-16. doi: 10.1128/genomeA.01009-16

Episodic oral antibiotic use in CF: Discordance between the electronic medical record and self-report

Caverly LJ, Caverly TJ, Kalikin LM, Foster BK, Simon RH, LiPuma JJ

J Cyst Fibros. 2016 Sep;15(5):630-3. doi: 10.1016/j.jcf.2016.04.009

Complete genome sequence of Mycobacterium abscessus subsp. bolletii

Caverly LJ, Spilker T, LiPuma JJ 

Genome Announc. 2016 Jun 9;4(3):e00543-16. doi: 10.1128/genomeA.00543-16

Culture-independent identification of nontuberculous mycobacteria in cystic fibrosis respiratory samples 

Caverly LJ, Carmody LA, Haig SJ, Kotlarz N, Kalikin LM, Raskin L, LiPuma JJ 

PLoS One. 2016 Apr 19;11(4):e0153876. doi: 10.1371/journal.pone.0153876

2015

Cystic fibrosis lung microbiome: opportunities to reconsider management of airway infection

Caverly LJ, Zhao J, LiPuma JJ

Pediatr Pulmonol. 2015 Oct;50 Suppl 40:S31-8. doi: 10.1002/ppul.23243

Mycobacterium abscessus morphotype comparison in a murine model

Caverly LJ, Caceres SM, Fratelli C, Happoldt C, Kidwell KM, Malcolm KC, Nick JA, Nichols DP

PLoS One. 2015 Feb 12;10(2):e0117657. doi: 10.1371/journal.pone.0117657

2014

Differential responses to rhinovirus- and influenza-associated pulmonary exacerbations in patients with cystic fibrosis

Ramirez IA, Caverly LJ, Kalikin LM, Goldsmith AM, Lewis TC, Burke DT, LiPuma JJ, Sajjan US, Hershenson MB

Ann Am Thorac Soc. 2014 May;11(4):554-61. doi: 10.1513/AnnalsATS.201310-346OC

2013

Effects of azithromycin in Pseudomonas aeruginosa burn wound infection

Nichols DP, Caceres S, Caverly L, Fratelli C, Kim SH, Malcolm K, Poch KR, Saavedra M, Solomon G, Taylor-Cousar J, Moskowitz S, Nick JA

J Surg Res. 2013 Aug;183(2):767-76. doi: 10.1016/j.jss.2013.02.003

Mycobacterium abscessus induces a limited pattern of neutrophil activation that promotes pathogen survival

Malcolm KC, Nichols EM, Caceres SM, Kret JE, Martiniano SL, Sagel SD, Chan ED, Caverly L, Solomon GM, Reynolds P, Bratton DL, Taylor-Cousar JL, Nichols DP, Saavedra MT, Nick JA

PLoS One. 2013;8(2):e57402. doi: 10.1371/journal.pone.0057402

2010

Octreotide treatment of chylothorax in pediatric patients following cardiothoracic surgery

Caverly L, Rausch CM, da Cruz E, Kaufman J

Congenit Heart Dis. 2010 Nov-Dec;5(6):573-8. doi: 10.1111/j.1747-0803.2010.00464.x

2007

Brief report: Post-traumatic stress during emerging adulthood in survivors of pediatric cancer

Gerhardt CA, Yopp JM, Leininger (Caverly) L, Valerius KS, Correll J, Vannatta K, Noll RB

J Pediatr Psychol. 2007 Sep;32(8):1018-23. doi: 10.1093/jpepsy/jsm038