Klebsiella pneumoniae
is a ubiquitous human pathogen, and its clinical treatment faces two major challenges: multidrug resistance and the pathogenesis of hypervirulent
K. pneumoniae
. The discovery and study of conditionally essential (CE) genes that can function as potential antimicrobial targets has always been a research concern due to their restriction in the development of novel antibiotics. However, the lack of essential functional genomic data has hampered the study of the mechanisms of essential genes related to antimicrobial susceptibility. In this study, we developed a pooled CE genes mobile clustered regularly interspaced short palindromic repeat (CRISPR) interference screening method (Mobile-CRISPRi-seq) for
K. pneumoniae
to identify genes that play critical roles in antimicrobial fitness
in vitro
and host immunity
in vivo
. Targeting 870 predicted CE genes in
K. pneumoniae
, Mobile-CRISPRi-seq uncovered the depletion of tetrahydrofolate synthesis pathway genes
folB
and
folP
under trimethoprim pressure. Our screening also identified genes
waaE
and
fldA
related to polymyxin and β-lactam susceptibility by applying a screening strategy based on Mobile-CRISPRi-seq and comparative genomics. Furthermore, using a mouse infection model and Mobile-CRISPRi-seq, multiple virulence genes were identified, and among these genes,
pal
,
yciS,
and
ribB
were demonstrated to contribute to the pathogenesis of
K. pneumoniae
. This study provides a simple, rapid, and effective platform for screening potential antimicrobial targets and virulence genes in
K. pneumoniae
, and this broadly applicable system can be expanded for high-throughput functional gene study in multiple pathogenic bacteria, especially in gram-negative bacteria.
IMPORTANCE
The discovery and investigation of conditionally essential (CE) genes that can function as potential antimicrobial targets has always been a research concern because of the restriction of antimicrobial targets in the development of novel antibiotics. In this study, we developed a pooled CE gene-wide mobile clustered regularly interspaced short palindromic repeat (CRISPR) interference sequencing (Mobile-CRISPRi-seq) strategy in
Klebsiella pneumoniae
to identify genes that play critical roles in the fitness of antimicrobials
in vitro
and host immunity
in vivo
. The data suggest a robust tool to screen for loss-of-function phenotypes in a pooled gene knockdown library in
K. pneumoniae
, and Mobile-CRISPRi-seq may be expanded to multiple bacteria for screening and identification of genes with crucial roles in the fitness of antimicrobials and hosts.