Molecular and Evolutionary Bases of Within-Patient Genotypic and Phenotypic Diversity in Escherichia coli Extraintestinal Infections

Although polymicrobial infections, caused by combinations of viruses, bacteria, fungi and parasites, are being recognised with increasing frequency, little is known about the occurrence of within-species diversity in bacterial infections and the molecular and evolutionary bases of this diversity. We used multiple approaches to study the genomic and phenotypic diversity among 226 Escherichia coli isolates from deep and closed visceral infections occurring in 19 patients. We observed genomic variability among isolates from the same site within 11 patients. This diversity was of two types, as patients were infected either by several distinct E. coli clones (4 patients) or by members of a single clone that exhibit micro-heterogeneity (11 patients); both types of diversity were present in 4 patients. A surprisingly wide continuum of antibiotic resistance, outer membrane permeability, growth rate, stress resistance, red dry and rough morphotype characteristics and virulence properties were present within the isolates of single clones in 8 of the 11 patients showing genomic micro-heterogeneity. Many of the observed phenotypic differences within clones affected the trade-off between self-preservation and nutritional competence (SPANC). We showed in 3 patients that this phenotypic variability was associated with distinct levels of RpoS in co-existing isolates. Genome mutational analysis and global proteomic comparisons in isolates from a patient revealed a star-like relationship of changes amongst clonally diverging isolates. A mathematical model demonstrated that multiple genotypes with distinct RpoS levels can co-exist as a result of the SPANC trade-off. In the cases involving infection by a single clone, we present several lines of evidence to suggest diversification during the infectious process rather than an infection by multiple isolates exhibiting a micro-heterogeneity. Our results suggest that bacteria are subject to trade-offs during an infectious process and that the observed diversity resembled results obtained in experimental evolution studies. Whatever the mechanisms leading to diversity, our results have strong medical implications in terms of the need for more extensive isolate testing before deciding on antibiotic therapies

Physicochemical composition and fermentation kinetics of a novel Palm Sap-based Kefir Beverage from the fermentation of Borassus aethiopum Mart. fresh sap with kefir grains and ferments

International audiencePalm sap collected (sugary juice) from palm trees is very widespread in the intertropical regions of Asia, America and Africa. This study aimed to evaluate the use of kefir grains and ferments as starters for the fermentation of fresh palm sap (PS) from Borassus aethiopum Mart. to produce new kefir-like beverages (KLBs). The batch fermentation was performed statically at room temperature (22 °C) during 48 h. Physicochemical analysis were performed using standard and HPLC methods. The KLBs (kefir-like beverages) from PS showed low ethanol and glycerol contents ranging from 0.84 ± 0.14 to 17.30 ± 2.06 g/L (0.07 to 1.38% v/v) and 0 to 0.67 g/L respectively. The pH value decreased significantly during 24 h of fermentation and ranging from 3.98 to 4.40 at the end of fermentation. The organic acids (lactate, acetate, propionate, citrate, succinate and pyruvate) were detected in KLBs from PS. There was an increase in the content of lactate, acetate, propionate and succinate during fermentation process, except citrate content. Lactate and acetate content reached maximum values ranging between 5.18 and 9.31 g/L, 0.94 and 1.69 g/L respectively. Sucrose concentration decreased significantly and reached a value ranging from 0 to 0.84 g/L, except in KLBs fermented using milk ferments (9.45 g/L). The study showed that water and milk kefir grains as well as kefir ferments were well adapted to ferment Borassus aethiopum Mart. fresh sap for KLBs production. Palm sap could be an ideal alternative base substrate to produce non-dairy probiotic fermented beverage with low ethanol and sugar contents