A Caltech Library Service

Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum

Kopf, Sebastian H. and Sessions, Alex L. and Cowley, Elise S. and Reyes, Carmen and Van Sambeek, Lindsey and Hu, Yang and Orphan, Victoria J. and Kato, Roberta M. and Newman, Dianne K. (2016) Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum. Proceedings of the National Academy of Sciences of the United States of America, 113 (2). E110-E116. ISSN 0027-8424. PMCID PMC4720290. doi:10.1073/pnas.1512057112.

[img] PDF - Published Version
See Usage Policy.

[img] PDF - Supplemental Material
See Usage Policy.


Use this Persistent URL to link to this item:


Effective treatment for chronic infections is undermined by a significant gap in understanding of the physiological state of pathogens at the site of infection. Chronic pulmonary infections are responsible for the morbidity and mortality of millions of immunocompromised individuals worldwide, yet drugs that are successful in laboratory culture are far less effective against pathogen populations persisting in vivo. Laboratory models, upon which preclinical development of new drugs is based, can only replicate host conditions when we understand the metabolic state of the pathogens and the degree of heterogeneity within the population. In this study, we measured the anabolic activity of the pathogen Staphylococcus aureus directly in the sputum of pediatric patients with cystic fibrosis (CF), by combining the high sensitivity of isotope ratio mass spectrometry with a heavy water labeling approach to capture the full range of in situ growth rates. Our results reveal S. aureus generation times with a median of 2.1 d, with extensive growth rate heterogeneity at the single-cell level. These growth rates are far below the detection limit of previous estimates of CF pathogen growth rates, and the rates are slowest in acutely sick patients undergoing pulmonary exacerbations; nevertheless, they are accessible to experimental replication within laboratory models. Treatment regimens that include specific antibiotics (vancomycin, piperacillin/tazobactam, tobramycin) further appear to correlate with slow growth of S. aureus on average, but follow-up longitudinal studies must be performed to determine whether this effect holds for individual patients.

Item Type:Article
Related URLs:
URLURL TypeDescription Information CentralArticle
Kopf, Sebastian H.0000-0002-2044-0201
Sessions, Alex L.0000-0001-6120-2763
Van Sambeek, Lindsey0000-0002-7206-7410
Orphan, Victoria J.0000-0002-5374-6178
Newman, Dianne K.0000-0003-1647-1918
Additional Information:© 2015 National Academy of Sciences. Published online before print December 29, 2015. We are grateful to Shawn McGlynn, Ryan Hunter, Abigail Green-Saxena, Yunbin Guan, Alejandro LaRiviere, Ian Booth, Nathan Dalleska, Fadi Asfour, Douglas Li, Kyle McCallin, Sally Ward, Thomas Keens, and patients of the Pulmonary CF Clinic at CHLA for supporting this study. We thank the editor and reviewers for constructive criticism that improved the manuscript. This research was supported by grants from the NIH (Grant 5R01HL117328-03) and the Howard Hughes Medical Institute (HHMI) (to D.K.N.). S.H.K. was an HHMI International Research Scholar, and D.K.N. is an HHMI Investigator. Author contributions: S.H.K., A.L.S., and D.K.N. designed research; S.H.K., E.S.C., and Y.H. performed research; S.H.K., A.L.S., E.S.C., C.R., L.V., V.J.O., R.K., and D.K.N. analyzed data; S.H.K. and D.K.N. wrote the paper; and C.R., L.V., and R.K. provided clinical advice and assistance. The authors declare no conflict of interest. This article is a PNAS Direct Submission. This article contains supporting information online at
Funding AgencyGrant Number
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Subject Keywords:slow growth infectious disease metabolic heterogeneity cystic fibrosis hydrogen isotope labeling
Issue or Number:2
PubMed Central ID:PMC4720290
Record Number:CaltechAUTHORS:20160104-065151473
Persistent URL:
Official Citation:Sebastian H. Kopf, Alex L. Sessions, Elise S. Cowley, Carmen Reyes, Lindsey Van Sambeek, Yang Hu, Victoria J. Orphan, Roberta Kato, and Dianne K. Newman Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum PNAS 2016 113 (2) E110-E116; published ahead of print December 29, 2015, doi:10.1073/pnas.1512057112
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:63308
Deposited On:04 Jan 2016 19:19
Last Modified:13 May 2022 00:28

Repository Staff Only: item control page