Robust Salmonella metabolism limits possibilities for new antimicrobials

New antibiotics are urgently needed to control infectious diseases. Metabolic enzymes could represent attractive targets for such antibiotics, but in vivo target validation is largely lacking. Here we have obtained in vivo information about over 700 Salmonella enterica enzymes from network analysis of mutant phenotypes, genome comparisons and Salmonella proteomes from infected mice. Over 400 of these enzymes are non-essential for Salmonella virulence, reflecting extensive metabolic redundancies and access to surprisingly diverse host nutrients. The essential enzymes identified were almost exclusively associated with a small subgroup of pathways, enabling us to perform a nearly exhaustive screen. Sixty-four enzymes identified as essential in Salmonella are conserved in other important human pathogens, but almost all belong to metabolic pathways that are inhibited by current antibiotics or that have previously been considered for antimicrobial development. Our comprehensive in vivo analysis thus suggests a shortage of new metabolic targets for broad-spectrum antibiotics, and draws attention to some previously known but unexploited targets.

[1]  R. Curtiss,et al.  Immunology and Immunopathology of the Intestines: Recombinant Avirulent Salmonella Vaccine Strains with Stable Maintenance and High Level Expression of Cloned Genes in Vivo , 1989 .

[2]  F. Heffron,et al.  Salmonella typhimurium loci involved in survival within macrophages , 1994, Infection and immunity.

[3]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[4]  B Wieland,et al.  Identification of novel essential Escherichia coli genes conserved among pathogenic bacteria. , 2001, Journal of molecular microbiology and biotechnology.

[5]  R. Wilson,et al.  Complete genome sequence of Salmonella enterica serovar Typhimurium LT2 , 2001, Nature.

[6]  R J Heath,et al.  Lipid biosynthesis as a target for antibacterial agents. , 2001, Progress in lipid research.

[7]  Kim Rutherford,et al.  Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 , 2001, Nature.

[8]  R. L. Santos,et al.  Animal models of Salmonella infections: enteritis versus typhoid fever. , 2001, Microbes and infection.

[9]  J. Shendure,et al.  Selection analyses of insertional mutants using subgenic-resolution arrays , 2001, Nature Biotechnology.

[10]  Dirk Bumann,et al.  Optimization of GFP levels for analyzing Salmonella gene expression during an infection , 2002, FEBS letters.

[11]  D. Bumann.  Examination of Salmonella gene expression in an infected mammalian host using the green fluorescent protein and two‐colour flow cytometry , 2002, Molecular microbiology.

[12]  Mark D'Souza,et al.  From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways , 2002, Journal of bacteriology.

[13]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[14]  D. Hughes.  Microbial genetics: Exploiting genomics, genetics and chemistry to combat antibiotic resistance , 2003, Nature Reviews Genetics.

[15]  Guy Plunkett,et al.  Comparative Genomics of Salmonellaenterica Serovar Typhi Strains Ty2 and CT18 , 2003, Journal of bacteriology.

[16]  Arthur Thompson,et al.  Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica , 2002, Molecular microbiology.

[17]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[18]  Rekha R Meyer,et al.  Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid , 2004, Nature Genetics.

[19]  C. J. Thomson,et al.  Antibacterial research and development in the 21(st) Century--an industry perspective of the challenges. , 2004, Current opinion in microbiology.

[20]  B. Palsson,et al.  Genome-scale models of microbial cells: evaluating the consequences of constraints , 2004, Nature Reviews Microbiology.

[21]  T. Fuchs,et al.  Large‐scale identification of essential Salmonella genes by trapping lethal insertions , 2004, Molecular microbiology.

[22]  L. Florea,et al.  Differences in Gene Content between Salmonella enterica Serovar Enteritidis Isolates and Comparison to Closely Related Serovars Gallinarum and Dublin , 2005, Journal of bacteriology.

[23]  Hinrich W. H. Göhlmann,et al.  A Diarylquinoline Drug Active on the ATP Synthase of Mycobacterium tuberculosis , 2005, Science.

[24]  Roger Finch,et al.  Lack of development of new antimicrobial drugs: a potential serious threat to public health. , 2005, The Lancet. Infectious diseases.

[25]  U. Sauer,et al.  Metabolic functions of duplicate genes in Saccharomyces cerevisiae. , 2005, Genome research.

[26]  J. Hodgson,et al.  Novel target sites in bacteria for overcoming antibiotic resistance. , 2005, Advanced drug delivery reviews.

[27]  L. Pickering,et al.  A millennium update on pediatric diarrheal illness in the developing world. , 2005, Seminars in pediatric infectious diseases.

[28]  Peter D. Karp,et al.  EcoCyc: a comprehensive database resource for Escherichia coli , 2004, Nucleic Acids Res..

[29]  J. Gorvel,et al.  Identification of Salmonella functions critical for bacterial cell division within eukaryotic cells , 2005, Molecular microbiology.

[30]  R. Bahl,et al.  Typhoid and paratyphoid fever , 2005, The Lancet.

[31]  S. Hapfelmeier,et al.  A mouse model for S. typhimurium-induced enterocolitis. , 2005, Trends in microbiology.

[32]  R. Guimerà,et al.  Functional cartography of complex metabolic networks , 2005, Nature.

[33]  Claudia Rollenhagen,et al.  Salmonella enterica Highly Expressed Genes Are Disease Specific , 2006, Infection and Immunity.