Genome-wide screen of genetic determinants of Escherichia coli growth and persistence in lake water

Although enteric bacteria commonly reside within the animal intestine, the ability to persist extraintestinally is an important part of their overall lifestyle, and it might contribute to transmission between hosts. Genetic factors are known to affect growth and survival of enteric bacteria outside the host, but even for the best-studied Escherichia coli model only few such factors have been established. In this work, we used a genome-wide library of barcoded transposon insertions to systematically identify functional clusters of genes that are crucial for E. coli growth and persistence in lake water. Our results revealed that inactivation of pathways involved in the maintenance of outer membrane integrity, nucleotide biosynthesis and chemotaxis has negative impact on E. coli fitness in this extraintestinal environment. In contrast, inactivation of another group of genes apparently benefited E. coli growth in filtered lake water. This group included rpoS, which encodes the general stress response sigma factor sigma-S, genes encoding several other global transcriptional regulators and RNA chaperones, as well as several poorly annotated genes. Based on this co-enrichment, we identified these gene products as novel positive regulators of RpoS activity. We further observed that, despite their enhanced growth, E. coli mutants with inactive RpoS had reduced viability, and they were not enriched in presence of the autochthonic microbiota, highlighting the dualism of the general stress response pathway for E. coli growth outside the host.