Separating putative pathogens from background contamination with principal orthogonal decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome

Steven J. Schiff, Julius Kiwanuka, Gina Riggio, Lan Nguyen, Kevin Mu, Emily Sproul, Joel Bazira, Juliet Mwanga-Amumpaire, Dickson Tumusiime, Eunice Nyesigire, Nkangi Lwanga, Kaleb T. Bogale, Vivek Kapur, James R. Broach, Sarah U. Morton, Benjamin C. Warf, Mary Poss

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Neonatal sepsis (NS) is responsible for over 1 million yearly deaths worldwide. In the developing world, NS is often treated without an identified microbial pathogen. Amplicon sequencing of the bacterial 16S rRNA gene can be used to identify organisms that are difficult to detect by routine microbiological methods. However, contaminating bacteria are ubiquitous in both hospital settings and research reagents and must be accounted for to make effective use of these data. In this study, we sequenced the bacterial 16S rRNA gene obtained from blood and cerebrospinal fluid (CSF) of 80 neonates presenting with NS to the Mbarara Regional Hospital in Uganda. Assuming that patterns of background contamination would be independent of pathogenic microorganism DNA, we applied a novel quantitative approach using principal orthogonal decomposition to separate background contamination from potential pathogens in sequencing data. We designed our quantitative approach contrasting blood, CSF, and control specimens and employed a variety of statistical random matrix bootstrap hypotheses to estimate statistical significance. These analyses demonstrate that Leptospira appears present in some infants presenting within 48 h of birth, indicative of infection in utero, and up to 28 days of age, suggesting environmental exposure. This organism cannot be cultured in routine bacteriological settings and is enzootic in the cattle that often live in close proximity to the rural peoples of western Uganda. Our findings demonstrate that statistical approaches to remove background organisms common in 16S sequence data can reveal putative pathogens in small volume biological samples from newborns. This computational analysis thus reveals an important medical finding that has the potential to alter therapy and prevention efforts in a critically ill population.

Original languageEnglish (US)
Article number22
JournalFrontiers in Medicine
Volume3
Issue numberJUN
DOIs
StatePublished - Jan 1 2016

Fingerprint

Leptospira
Uganda
rRNA Genes
Cerebrospinal Fluid
Newborn Infant
Environmental Exposure
Critical Illness
Parturition
Bacteria
DNA
Infection
Research
Population
Neonatal Sepsis
Therapeutics

All Science Journal Classification (ASJC) codes

  • Medicine(all)

Cite this

Schiff, Steven J. ; Kiwanuka, Julius ; Riggio, Gina ; Nguyen, Lan ; Mu, Kevin ; Sproul, Emily ; Bazira, Joel ; Mwanga-Amumpaire, Juliet ; Tumusiime, Dickson ; Nyesigire, Eunice ; Lwanga, Nkangi ; Bogale, Kaleb T. ; Kapur, Vivek ; Broach, James R. ; Morton, Sarah U. ; Warf, Benjamin C. ; Poss, Mary. / Separating putative pathogens from background contamination with principal orthogonal decomposition : Evidence for Leptospira in the Ugandan Neonatal Septisome. In: Frontiers in Medicine. 2016 ; Vol. 3, No. JUN.
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abstract = "Neonatal sepsis (NS) is responsible for over 1 million yearly deaths worldwide. In the developing world, NS is often treated without an identified microbial pathogen. Amplicon sequencing of the bacterial 16S rRNA gene can be used to identify organisms that are difficult to detect by routine microbiological methods. However, contaminating bacteria are ubiquitous in both hospital settings and research reagents and must be accounted for to make effective use of these data. In this study, we sequenced the bacterial 16S rRNA gene obtained from blood and cerebrospinal fluid (CSF) of 80 neonates presenting with NS to the Mbarara Regional Hospital in Uganda. Assuming that patterns of background contamination would be independent of pathogenic microorganism DNA, we applied a novel quantitative approach using principal orthogonal decomposition to separate background contamination from potential pathogens in sequencing data. We designed our quantitative approach contrasting blood, CSF, and control specimens and employed a variety of statistical random matrix bootstrap hypotheses to estimate statistical significance. These analyses demonstrate that Leptospira appears present in some infants presenting within 48 h of birth, indicative of infection in utero, and up to 28 days of age, suggesting environmental exposure. This organism cannot be cultured in routine bacteriological settings and is enzootic in the cattle that often live in close proximity to the rural peoples of western Uganda. Our findings demonstrate that statistical approaches to remove background organisms common in 16S sequence data can reveal putative pathogens in small volume biological samples from newborns. This computational analysis thus reveals an important medical finding that has the potential to alter therapy and prevention efforts in a critically ill population.",
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Schiff, SJ, Kiwanuka, J, Riggio, G, Nguyen, L, Mu, K, Sproul, E, Bazira, J, Mwanga-Amumpaire, J, Tumusiime, D, Nyesigire, E, Lwanga, N, Bogale, KT, Kapur, V, Broach, JR, Morton, SU, Warf, BC & Poss, M 2016, 'Separating putative pathogens from background contamination with principal orthogonal decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome', Frontiers in Medicine, vol. 3, no. JUN, 22. https://doi.org/10.3389/fmed.2016.00022

Separating putative pathogens from background contamination with principal orthogonal decomposition : Evidence for Leptospira in the Ugandan Neonatal Septisome. / Schiff, Steven J.; Kiwanuka, Julius; Riggio, Gina; Nguyen, Lan; Mu, Kevin; Sproul, Emily; Bazira, Joel; Mwanga-Amumpaire, Juliet; Tumusiime, Dickson; Nyesigire, Eunice; Lwanga, Nkangi; Bogale, Kaleb T.; Kapur, Vivek; Broach, James R.; Morton, Sarah U.; Warf, Benjamin C.; Poss, Mary.

In: Frontiers in Medicine, Vol. 3, No. JUN, 22, 01.01.2016.

Research output: Contribution to journalArticle

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T1 - Separating putative pathogens from background contamination with principal orthogonal decomposition

T2 - Evidence for Leptospira in the Ugandan Neonatal Septisome

AU - Schiff, Steven J.

AU - Kiwanuka, Julius

AU - Riggio, Gina

AU - Nguyen, Lan

AU - Mu, Kevin

AU - Sproul, Emily

AU - Bazira, Joel

AU - Mwanga-Amumpaire, Juliet

AU - Tumusiime, Dickson

AU - Nyesigire, Eunice

AU - Lwanga, Nkangi

AU - Bogale, Kaleb T.

AU - Kapur, Vivek

AU - Broach, James R.

AU - Morton, Sarah U.

AU - Warf, Benjamin C.

AU - Poss, Mary

PY - 2016/1/1

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N2 - Neonatal sepsis (NS) is responsible for over 1 million yearly deaths worldwide. In the developing world, NS is often treated without an identified microbial pathogen. Amplicon sequencing of the bacterial 16S rRNA gene can be used to identify organisms that are difficult to detect by routine microbiological methods. However, contaminating bacteria are ubiquitous in both hospital settings and research reagents and must be accounted for to make effective use of these data. In this study, we sequenced the bacterial 16S rRNA gene obtained from blood and cerebrospinal fluid (CSF) of 80 neonates presenting with NS to the Mbarara Regional Hospital in Uganda. Assuming that patterns of background contamination would be independent of pathogenic microorganism DNA, we applied a novel quantitative approach using principal orthogonal decomposition to separate background contamination from potential pathogens in sequencing data. We designed our quantitative approach contrasting blood, CSF, and control specimens and employed a variety of statistical random matrix bootstrap hypotheses to estimate statistical significance. These analyses demonstrate that Leptospira appears present in some infants presenting within 48 h of birth, indicative of infection in utero, and up to 28 days of age, suggesting environmental exposure. This organism cannot be cultured in routine bacteriological settings and is enzootic in the cattle that often live in close proximity to the rural peoples of western Uganda. Our findings demonstrate that statistical approaches to remove background organisms common in 16S sequence data can reveal putative pathogens in small volume biological samples from newborns. This computational analysis thus reveals an important medical finding that has the potential to alter therapy and prevention efforts in a critically ill population.

AB - Neonatal sepsis (NS) is responsible for over 1 million yearly deaths worldwide. In the developing world, NS is often treated without an identified microbial pathogen. Amplicon sequencing of the bacterial 16S rRNA gene can be used to identify organisms that are difficult to detect by routine microbiological methods. However, contaminating bacteria are ubiquitous in both hospital settings and research reagents and must be accounted for to make effective use of these data. In this study, we sequenced the bacterial 16S rRNA gene obtained from blood and cerebrospinal fluid (CSF) of 80 neonates presenting with NS to the Mbarara Regional Hospital in Uganda. Assuming that patterns of background contamination would be independent of pathogenic microorganism DNA, we applied a novel quantitative approach using principal orthogonal decomposition to separate background contamination from potential pathogens in sequencing data. We designed our quantitative approach contrasting blood, CSF, and control specimens and employed a variety of statistical random matrix bootstrap hypotheses to estimate statistical significance. These analyses demonstrate that Leptospira appears present in some infants presenting within 48 h of birth, indicative of infection in utero, and up to 28 days of age, suggesting environmental exposure. This organism cannot be cultured in routine bacteriological settings and is enzootic in the cattle that often live in close proximity to the rural peoples of western Uganda. Our findings demonstrate that statistical approaches to remove background organisms common in 16S sequence data can reveal putative pathogens in small volume biological samples from newborns. This computational analysis thus reveals an important medical finding that has the potential to alter therapy and prevention efforts in a critically ill population.

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