Drying-wetting cycle enhances stress resistance of Escherichia coli O157:H7 in a model soil.

Outbreaks of Escherichia coli (E. coli) O157:H7 in farms are often triggered by heavy rains and flooding. Most cells die with the decreasing of soil moisture, while few cells enter a dormant state and then resuscitate after rewetting. The resistance of dormant cells to stress has been extensively studied, whereas the molecular mechanisms of the cross-resistance development of the resuscitated cells are poorly known. We performed a comparative proteomic analysis on O157:H7 before and after undergoing soil dry-wet alternation. A differential expression of 820 proteins was identified in resuscitated cells compared to exponential-phase cells, as determined by proteomics analysis. The GO and KEGG pathway enrichment analyses revealed that up-regulated proteins were associated with oxidative phosphorylation, glycolysis/gluconeogenesis, the citrate cycle (TCA cycle), aminoacyl-tRNA biosynthesis, ribosome activity, and transmembrane transporters, indicating increased energy production and protein synthesis in resuscitated O157:H7. Moreover, proteins related to acid, osmotic, heat, oxidative, antibiotic stress and horizontal gene transfer efficiency were up-regulated, suggesting a potential improvement in stress resistance. Subsequent validation experiments demonstrated that the survival rates of the resuscitated cells were 476.54 and 7786.34 times higher than the exponential-phase cells, with pH levels of 1.5 and 2.5, respectively. Similarly, resuscitated cells showed higher survival rates under osmotic stress, with 7.5%, 15%, and 30% NaCl resulting in survival rates that were 460.58, 1974.55, and 3475.31 times higher. Resuscitated cells also exhibited increased resistance to heat stress, with survival rates 69.64 and 139.72 times higher at 55 °C and 90 °C, respectively. Furthermore, the horizontal gene transfer (HGT) efficiency of resuscitated cells was significantly higher (153.12-fold) compared to exponential phase cells. This study provides new insights into bacteria behavior under changing soil moisture and this may explain O157:H7 outbreaks following rainfall and flooding, as the dry-wet cycle promotes stress cross-resistance development.

Neglected Drivers of Antibiotic Resistance: Survival of Extended-Spectrum ß-Lactamase-Producing Pathogenic Escherichia coli from Livestock Waste through Dormancy and Release of Transformable Extracellular Antibiotic Resistance Genes under Heat Treatment.

Extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae has caused a global pandemic with high prevalence in livestock and poultry, which could disseminate into the environment and humans. To curb this risk, heat-based harmless treatment of livestock waste was carried out. However, some risks of the bacterial persistence have not been thoroughly assessed. This study demonstrated that antibiotic-resistant bacteria (ARB) could survive at 55 °C through dormancy, and simultaneously transformable extracellular antibiotic resistance genes (eARGs) would be released. The ESBL-producing pathogenic Escherichia coli CM1 from chicken manure could enter a dormant state at 55 °C and reactivate at 37 °C. Dormant CM1 had stronger ß-lactam resistance, which was associated with high expression of ß-lactamase genes and low expression of outer membrane porin genes. Resuscitated CM1 maintained its virulence expression and multidrug resistance and even had stronger cephalosporin resistance, which might be due to the ultra-low expression of the porin genes. Besides, heat at 55 °C promoted the release of eARGs, some of which possessed a certain nuclease stability and heat persistence, and even maintained their transformability to an Acinetobacter baylyi strain. Therefore, dormant multidrug-resistant pathogens from livestock waste will still pose a direct health risk to humans, while the resuscitation of dormant ARB and the transformation of released eARGs will jointly promote the proliferation of ARGs and the spread of antibiotic resistance.

Crop rotation stage has a greater effect than fertilisation on soil microbiome assembly and enzymatic stoichiometry.

Agronomic practises, such as fertilisation and crop rotation, affect soil microbial communities and functions. However, limited information is available regarding the relative importance of fertilisation and crop rotation stages in determining the soil microbiome and assembly processes. In addition, insights into the connections between the soil microbiome and enzymatic stoichiometry are scarce. In this study, soil samples were collected from a wheat-rice rotation system that received mineral and organic fertiliser inputs for 6 years to investigate soil microbiome assembly, and the relationship between the soil microbiome and enzymatic stoichiometry. Our results revealed that the crop rotation stage strongly affected the soil microbial community structure, assembly, and enzymatic functions compared to that of the fertilisation regime. Enzymatic stoichiometry results and vector analysis implied that mineral and organic fertilisation could alleviate the microbial N limitation. However, no-manure fertilisation led to microbial P limitation during the wheat stage. The decreases in soil pH mainly drove microbial P limitation due to the acidification induced by the mineral fertilisers. Microbial N/P limitation correlated more strongly with the bacterial assembly than with fungal assembly. Moreover, co-occurrence network analysis showed that ecological relationships between microbial taxa and enzymes were more complex during the wheat stage than that during the rice stage. Microbial nodes linked to acid phosphomonoesterase correlated significantly with the soil pH. Our study highlights the distinct responses of the soil microbiome to fertilisation in different crop-rotation stages, and provides novel insights into connections between microbial assembly and enzymatic stoichiometry.