Numbers of L. (L.) deliense larvae were determined in adjacent habitats over a 16 month period. Both R. argentiventer and R. tiomanicus were highly efficient hosts for L. (L.) deliense. R. argentiventer was host to significantly greater numbers of chiggers per rat than was R. tiomanicus. The 2 habitats were similar in numbers of chiggers collected. No consistent correlation was apparent between numbers of chiggers and any single weather factor, but the chigger population seemed to be adversely affected by a 2 month period during which total evaporation greatly exceeded total rainfall. Direct fluorescent antibody examination of tissues from unfed L. (L.) deliense showed that 2 of 420 larvae (0.5%) contained organisms morphologically resembling R. tsutsugamushi. Considering the vector load and numbers of chiggers being returned to the ground by a given host, a rate of 0.5% appeared adequate to account for the prevalence rate of R. tsutsugamushi observed in the 2 host species.
Recurrent urinary tract infections (rUTIs) are extremely common, with ~ 25% of all women experiencing a recurrence within 1 year of their original infection. Escherichia coli ST131 is a globally dominant multidrug resistant clone associated with high rates of rUTI. Here, we show the dynamics of an ST131 population over a 5-year period from one elderly woman with rUTI since the 1970s. Using whole genome sequencing, we identify an indigenous clonal lineage (P1A) linked to rUTI and persistence in the fecal flora, providing compelling evidence of an intestinal reservoir of rUTI. We also show that the P1A lineage possesses substantial plasmid diversity, resulting in the coexistence of antibiotic resistant and sensitive intestinal isolates despite frequent treatment. Our longitudinal study provides a unique comprehensive genomic analysis of a clonal lineage within a single individual and suggests a population-wide resistance mechanism enabling rapid adaptation to fluctuating antibiotic exposure.
Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to characterise a hospital outbreak of blaIMP-4 carbapenemase-producing E. hormaechei. Using Illumina sequencing, we determined that all outbreak strains were sequence type 90 (ST90) and near-identical. Comparison to publicly available data linked all outbreak isolates to a 2013 isolate from the same ward, suggesting an environmental source in the hospital. Using Pacific Biosciences sequencing, we resolved the complete context of the blaIMP-4 gene on a large IncHI2 plasmid carried by all IMP-4-producing strains across different hospitals. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing. Finally, Oxford Nanopore sequencing rapidly resolved the true relationship of subsequent isolates to the initial outbreak. Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak.