Genomic and transcriptomic analysis of NDM-1 Klebsiella pneumoniae in spaceflight reveal mechanisms underlying environmental adaptability

Abstract

The emergence and rapid spread of New Delhi Metallo-beta-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae strains has caused a great concern worldwide. To better understand the mechanisms underlying environmental adaptation of those highly drug-resistant K. pneumoniae strains, we took advantage of the China's Shenzhou 10 spacecraft mission to conduct comparative genomic and transcriptomic analysis of a NDM-1 K. pneumoniae strain (ATCC BAA-2146) being cultivated under different conditions. The samples were recovered from semisolid medium placed on the ground (D strain), in simulated space condition (M strain), or in Shenzhou 10 spacecraft (T strain) for analysis. Our data revealed multiple variations underlying pathogen adaptation into different environments in terms of changes in morphology, H2O2 tolerance and biofilm formation ability, genomic stability and regulation of metabolic pathways. Additionally, we found a few non-coding RNAs to be differentially regulated. The results are helpful for better understanding the adaptive mechanisms of drug-resistant bacterial pathogens.

Phosphorylation Events in the Multiple Gene Regulator of Group A Streptococcus Significantly Influence Global Gene Expression and Virulence

“…Population genomic analyses of the bacterial isolates recovered from epidemics have provided unprecedented insights into the evolution of the pathogens, genetic changes in the bacterial genome that contribute to altered virulence, and loci that are under strong selection during natural infection (14)(15)(16)(41)(42)(43)(44)(45)(46). Wholegenome sequencing analyses of ϳ800 strains of GAS serotype M59 from invasive epidemics revealed that the mga locus is under strong selection pressure, suggesting a critical role for the regulatory function of Mga in the pathogenesis of serotype M59 GAS (13,14,17).…”

Prevalence of Carbapenem-Resistant Klebsiella Pneumoniae (CRKP) and the Distribution of Class 1 Integron in Their Strains Isolated from a Hospital in Central China

“…1 It is widely recognized that Kp could cause multiple infections including liver abscess, urinary tract infection and surgical incision infection. Kp is also a potential nosocomial multidrug resistant bacterium.…”

Decreased biofilm formation ability of Acinetobacter baumannii after spaceflight on China's Shenzhou 11 spacecraft

“…Five genes associated with OmpA were downregulated; these normally play a key role in adhesion. Li et al () reported the same elongated cells in K. pneumoniae after spaceflight. Furthermore, Pyle et al () reported elongated Burkholderia cepacia cells and chains of cells after culture during spaceflight.…”

“…A few years later, 15 strains of microorganisms were harbored on the Shenzhou VIII spacecraft, and 2 years later, the Shenzhou X spacecraft, which carried nine different microorganisms, was launched. Phenotypic, genomic, and transcriptomic changes were detected in these microorganisms, including drug resistance mutations and metabolic adaptations to the space environment (Chang et al, ; Guo et al, ; Li et al, ; Su, Chang, & Liu, ; Su et al, ; Zhang, Fang, & Liu, ).…”