A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

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Hawkey, Jane
Vezina, Ben
Monk, Jonathan M
Judd, Louise M
Harshegyi, Taylor
Lopez-Fernandez, Sebastian
Rodrigues, Carla
Brisse, Sylvain
Holt, Kathryn E
Wyres, Kelly L
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2022
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The Klebsiella pneumoniae species complex (KpSC) is a set of seven Klebsiella taxa that are found in a variety of niches and are an important cause of opportunistic health care-associated infections in humans. Because of increasing rates of multi-drug resistance within the KpSC, there is a growing interest in better understanding the biology and metabolism of these organisms to inform novel control strategies. We collated 37 sequenced KpSC isolates isolated from a variety of niches, representing all seven taxa. We generated strain-specific genome-scale metabolic models (GEMs) for all 37 isolates and simulated growth phenotypes on 511 distinct carbon, nitrogen, sulfur, and phosphorus substrates. Models were curated and their accuracy was assessed using matched phenotypic growth data for 94 substrates (median accuracy of 96%). We explored species-specific growth capabilities and examined the impact of all possible single gene deletions using growth simulations in 145 core carbon substrates. These analyses revealed multiple strain-specific differences, within and between species, and highlight the importance of selecting a diverse range of strains when exploring KpSC metabolism. This diverse set of highly accurate GEMs could be used to inform novel drug design, enhance genomic analyses, and identify novel virulence and resistance determinants. We envisage that these 37 curated strain-specific GEMs, covering all seven taxa of the KpSC, provide a valuable resource to the Klebsiella research community.

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Genome Research

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32

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5

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© 2022 Hawkey et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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Science & Technology

Life Sciences & Biomedicine

Biochemistry & Molecular Biology

Biotechnology & Applied Microbiology

Genetics & Heredity

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Hawkey, J; Vezina, B; Monk, JM; Judd, LM; Harshegyi, T; Lopez-Fernandez, S; Rodrigues, C; Brisse, S; Holt, KE; Wyres, KL, A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality, Genome Research, 2022, 32 (5), pp. 1004-1014

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