Combined functional genomic and metabolomic approaches identify new genes required for growth in human urine by multidrug-resistant Escherichia coli ST131

Author:

Phan Minh-Duy123ORCID,Schirra Horst Joachim456ORCID,Nhu Nguyen Thi Khanh123ORCID,Peters Kate M.123,Sarkar Sohinee2,Allsopp Luke P.2ORCID,Achard Maud E. S.2,Kappler Ulrike23ORCID,Schembri Mark A.123ORCID

Affiliation:

1. Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia

2. School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia

3. Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia

4. School of Environment and Science, Griffith University, Nathan, Queensland, Australia

5. Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia

6. Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia

Abstract

ABSTRACT Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, with ~400 million cases across the globe each year. Uropathogenic Escherichia coli (UPEC) is the major cause of UTI and increasingly associated with antibiotic resistance. This scenario has been worsened by the emergence and spread of pandemic UPEC sequence type 131 (ST131), a multidrug-resistant clone associated with extraordinarily high rates of infection. Here, we employed transposon-directed insertion site sequencing in combination with metabolomic profiling to identify genes and biochemical pathways required for growth and survival of the UPEC ST131 reference strain EC958 in human urine (HU). We identified 24 genes required for growth in HU, which mapped to diverse pathways involving small peptide, amino acid and nucleotide metabolism, the stringent response pathway, and lipopolysaccharide biosynthesis. We also discovered a role for UPEC resistance to fluoride during growth in HU, most likely associated with fluoridation of drinking water. Complementary nuclear magnetic resonance (NMR)-based metabolomics identified changes in a range of HU metabolites following UPEC growth, the most pronounced being L-lactate, which was utilized as a carbon source via the L-lactate dehydrogenase LldD. Using a mouse UTI model with mixed competitive infection experiments, we demonstrated a role for nucleotide metabolism and the stringent response in UPEC colonization of the mouse bladder. Together, our application of two omics technologies combined with different infection-relevant settings has uncovered new factors required for UPEC growth in HU, thus enhancing our understanding of this pivotal step in the UPEC infection pathway. IMPORTANCE Uropathogenic Escherichia coli (UPEC) cause ~80% of all urinary tract infections (UTIs), with increasing rates of antibiotic resistance presenting an urgent threat to effective treatment. To cause infection, UPEC must grow efficiently in human urine (HU), necessitating a need to understand mechanisms that promote its adaptation and survival in this nutrient-limited environment. Here, we used a combination of functional genomic and metabolomic techniques and identified roles for the metabolism of small peptides, amino acids, nucleotides, and L-lactate, as well as the stringent response pathway, lipopolysaccharide biosynthesis, and fluoride resistance, for UPEC growth in HU. We further demonstrated that pathways involving nucleotide metabolism and the stringent response are required for UPEC colonization of the mouse bladder. The UPEC genes and metabolic pathways identified in this study represent targets for the development of innovative therapeutics to prevent UPEC growth during human UTI, an urgent need given the rapidly rising rates of global antibiotic resistance.

Funder

DHAC | National Health and Medical Research Council

Publisher

American Society for Microbiology

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