From microbial gene essentiality to novel antimicrobial drug targets.
BACKGROUND
Bacterial respiratory tract infections, mainly caused by Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are among the leading causes of global mortality and morbidity. Increased resistance of these pathogens to existing antibiotics necessitates the search for novel targets to develop potent antimicrobials.


RESULTS
Here, we report a proof of concept study for the reliable identification of potential drug targets in these human respiratory pathogens by combining high-density transposon mutagenesis, high-throughput sequencing, and integrative genomics. Approximately 20% of all genes in these three species were essential for growth and viability, including 128 essential and conserved genes, part of 47 metabolic pathways. By comparing these essential genes to the human genome, and a database of genes from commensal human gut microbiota, we identified and excluded potential drug targets in respiratory tract pathogens that will have off-target effects in the host, or disrupt the natural host microbiota. We propose 249 potential drug targets, 67 of which are targets for 75 FDA-approved antimicrobials and 35 other researched small molecule inhibitors. Two out of four selected novel targets were experimentally validated, proofing the concept.


CONCLUSIONS
Here we have pioneered an attempt in systematically combining the power of high-density transposon mutagenesis, high-throughput sequencing, and integrative genomics to discover potential drug targets at genome-scale. By circumventing the time-consuming and expensive laboratory screens traditionally used to select potential drug targets, our approach provides an attractive alternative that could accelerate the much needed discovery of novel antimicrobials.
Fredrick M
FM
Mobegi
Radboud Institute for Molecular Life Sciences, Laboratory of Paediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands. Sacha.vanHijum@radboudumc.nl.
Sacha A F T
SA
van Hijum
Peter
P
Burghout
Hester J
HJ
Bootsma
Stefan P W
SP
de Vries
Christa E
CE
van der Gaast-de Jongh
Elles
E
Simonetti
Jeroen D
JD
Langereis
Peter W M
PW
Hermans
Marien I
MI
de Jonge
Aldert
A
Zomer
D000890:Anti-Infective Agents / Q000494:pharmacology*; D001419:Bacteria / Q000187:drug effects / Q000235:genetics*; D002460:Cell Line; D017124:Conserved Sequence / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D041981:Gastrointestinal Tract / Q000276:immunology; D020043:Genes, Essential; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008826:Microbial Sensitivity Tests; D064307:Microbiota; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D016366:Open Reading Frames / Q000235:genetics; D015203:Reproducibility of Results; D013347:Subcellular Fractions / Q000378:metabolism
D000890:Anti-Infective Agents; D004251:DNA Transposable Elements