Evolutionary selection of biofilm-mediated extended phenotypes in Yersinia pestis in response to a fluctuating environment

Abstract

Yersinia pestis is transmitted from fleas to rodents when the bacterium develops an extensive biofilm in the foregut of a flea, starving it into a feeding frenzy, or, alternatively, during a brief period directly after feeding on a bacteremic host. These two transmission modes are in a trade-off regulated by the amount of biofilm produced by the bacterium. Here by investigating 446 global isolated Y. pestis genomes, including 78 newly sequenced isolates sampled over 40 years from a plague focus in China, we provide evidence for strong selection pressures on the RNA polymerase ω-subunit encoding gene rpoZ. We demonstrate that rpoZ variants have an increased rate of biofilm production in vitro, and that they evolve in the ecosystem during colder and drier periods. Our results support the notion that the bacterium is constantly adapting-through extended phenotype changes in the fleas-in response to climate-driven changes in the niche. w | www.nature.com/naturecommunications 1 1234567890():,; † Two small clusters (at CO92 position 2,577,933 and 2,606,316) were excluded as they were the result of copy-number variations in tandem repeat loci * K, the number of variations within a cluster # N, region size of the cluster NATURE COMMUNICATIONS | https://doi.

Development and evaluation of loop-mediated isothermal amplification for detection of Yersinia pestis in plague biological samples

“…This technique would not be able to detect Y . pestis strains with a deletion of all or part of the caf1 gene or a loss of the entire pFra/pMT1 plasmid [ 7 , 31 ] but these modifications are rare for Y . pestis .…”

“…Although LAMP caf1 assay is highly promising, the technique presents some limitation and some challenges. This technique would not be able to detect Y. pestis strains with a deletion of all or part of the caf1 gene or a loss of the entire pFra/pMT1 plasmid [7,31] but these modifications are rare for Y. pestis. Our LAMP assay uses SYBR Green I to visually confirm amplification of DNA.…”

New Genotype of Yersinia pestis Found in Live Rodents in Yunnan Province, China

“…The indel loci and the 300-bp sequences flanking the indels were extracted and compared with the nucleotide sequences in the NCBI database 4 to obtain the alleles. The annotation information was obtained according to the position of the alleles (Cui et al, 2020). All the assemblies were used in Prokka (Seemann, 2014) for gene annotation, and the annotation results (gff3 files) were used in Roary (Page et al, 2015) to identify the pan-genome and generate a matrix of the presence/absence of the genes in each sample as described previously (Yang et al, 2019).…”

The first step in the success or failure of emerging pathogens

“…Today, despite a high degree of genetic similarity, marked differences in pathology (mortality) appear among strains isolated from different species of rodents ( 4 ). In part this can be due to host physiology, yet factors like sociality, population density, and dynamics can play an important role in transmission and hence will have selective effects on the agent’s phenotype and greater pathology ( 5 ).…”