Evolution of fluoroquinolone-resistant Escherichia coli in the gut after ciprofloxacin treatment

BackgroundThree healthy volunteers carried similar quinolone-resistant E. coli (QREC) (pulsed field gel electrophoresis profiles) in their gut before and after 14 days ciprofloxacin treatment. Given the intensity of the selective pressure and the mutagenic properties of quinolones, we determined whether these strains had evolved at the phenotypic and/or genomic levels.Material and methodsCommensal QREC from before day-0 (D0), and a month after 14 days of ciprofloxacin (D42) were compared in 3 volunteers. Growth experiments were performed; acetate levels, mutation frequencies, quinolone MICs and antibiotic tolerance were measured at D0 and D42. Genomes were sequenced and single nucleotide polymorphisms (SNPs) between D0 and D42 were analyzed using DiscoSNP and breseq methods. Cytoplasmic proteins were extracted, HPLC performed and proteins identified using X!tandem software; abundances were measured by mass spectrometry using the Spectral Counting (SC) and eXtraction Ion Chromatograms (XIC) integration methods.ResultsNo difference was found in MICs, growth characteristics, acetate concentrations, mutation frequencies, tolerance profiles, phylogroups, O-and H-types, fimH alleles and sequence types between D0 and D42. No SNP variation was evidenced between D0 and D42 isolates for 2/3 subjects; 2 SNP variations were evidenced in one. At the protein level, very few significant protein abundance differences were identified between D0 and D42.ConclusionNo fitness, tolerance, metabolic or genomic evolution of commensal QREC was observed overtime, despite massive exposure to ciprofloxacin in the gut. The three strains behaved as if they had been unaffected by ciprofloxacin, suggesting that gut may act as a sanctuary where bacteria would be protected from the effect of antibiotics and survive without any detrimental effect of stress.     

Intestinal microbiota in health and disease: Role of bifidobacteria in gut homeostasis

The pool of microbes inhabiting our body is known as “microbiota” and their collective genomes as “microbiome”. The colon is the most densely populated organ in the human body, although other parts, such as the skin, vaginal mucosa, or respiratory tract, also harbour specific microbiota. This microbial community regulates some important metabolic and physiological functions of the host, and drives the maturation of the immune system in early life, contributing to its homeostasis during life. Alterations of the intestinal microbiota can occur by changes in composition (dysbiosis), function, or microbiota-host interactions and they can be directly correlated with several diseases. The only disease in which a clear causal role of a dysbiotic microbiota has been demonstrated is the case of Clostridium difficile infections. Nonetheless, alterations in composition and function of the microbiota have been associated with several gastrointestinal diseases (inflammatory bowel disease, colorectal cancer, or irritable bowel syndrome), as well as extra-intestinal pathologies, such as those affecting the liver, or the respiratory tract (e.g., allergy, bronchial asthma, and cystic fibrosis), among others. Species of Bifidobacterium genus are the normal inhabitants of a healthy human gut and alterations in number and composition of their populations is one of the most frequent features present in these diseases. The use of probiotics, including bifidobacteria strains, in preventive medicine to maintain a healthy intestinal function is well documented. Probiotics are also proposed as therapeutic agents for gastrointestinal disorders and other pathologies. The World Gastroenterology Organization recently published potential clinical applications for several probiotic formulations, in which species of lactobacilli are predominant. This review is focused on probiotic preparations containing Bifidobacterium strains, alone or in combination with other bacteria, which have been tested in human clinical studies. In spite of extensive literature on and research into this topic, the degree of scientific evidence of the effectiveness of probiotics is still insufficient in most cases. More effort need to be made to design and conduct accurate human studies demonstrating the efficacy of probiotics in the prevention, alleviation, or treatment of different pathologies.     

Infectious etiopathogenesis of Crohn’s disease

Important advances during the last decade have been made in understanding the complex etiopathogenesis of Crohn’s disease(CD).While many gaps in our knowledge still exist,it has been suggested that the etiology of CD is multifactorial including genetic,environmental and infectious factors.The most widely accepted theory states that CD is caused by an aggressive immune response to infectious agents in genetically predisposed individuals.The rise of genome-wide association studies allowed the identification of loci and genetic variants in several components of host innate and adaptive immune responses to microorganisms in the gut,highlighting an implication of intestinal microbiota in CD etiology.Moreover,numerous independent studies reported a dysbiosis,i.e.,a modification of intestinal microbiota composition,with an imbalance between the abundance of beneficial and harmful bacteria.Although microorganisms including viruses,yeasts,fungi and bacteria have been postulated as potential CD pathogens,based on epidemiological,clinicopathological,genetic and experimental evidence,their precise role in this disease is not clearly defined.This review summarizes the current knowledge of the infectious agents associated with an increased risk of developing CD.Therapeutic approaches to modulate the intestinal dysbiosis and to target the putative CD-associated pathogens,as well as their potential mechanisms of action are also discussed.     

Gut Microbiota Functional Dysbiosis Relates to Individual Diet in Subclinical Carotid Atherosclerosis

Gut Microbiota (GM) dysbiosis associates with Atherosclerotic Cardiovascular Diseases (ACVD), but whether this also holds true in subjects without clinically manifest ACVD represents a challenge of personalized prevention. We connected exposure to diet (self-reported by food diaries) and markers of Subclinical Carotid Atherosclerosis (SCA) with individual taxonomic and functional GM profiles (from fecal metagenomic DNA) of 345 subjects without previous clinically manifest ACVD. Subjects without SCA reported consuming higher amounts of cereals, starchy vegetables, milky products, yoghurts and bakery products versus those with SCA (who reported to consume more mechanically separated meats). The variety of dietary sources significantly overlapped with the separations in GM composition between subjects without SCA and those with SCA (RV coefficient between nutrients quantities and microbial relative abundances at genus level = 0.65, p-value = 0.047). Additionally, specific bacterial species (Faecalibacterium prausnitzii in the absence of SCA and Escherichia coli in the presence of SCA) are directly related to over-representation of metagenomic pathways linked to different dietary sources (sulfur oxidation and starch degradation in absence of SCA, and metabolism of amino acids, syntheses of palmitate, choline, carnitines and Trimethylamine n-oxide in presence of SCA). These findings might contribute to hypothesize future strategies of personalized dietary intervention for primary CVD prevention setting.     

新生儿呼吸窘迫综合征肠道菌谱分析

目的 分析新生儿呼吸窘迫综合征(NRDS)患儿肠道菌群结构变化的特征,为临床应用益生菌进行NRDS辅助治疗提供理论基础。方法 选择2020年1—5月因NRDS在济南市中心医院新生儿科住院治疗的早产儿15例为NRDS组。同时选择在本科排除NRDS诊断的早产儿15例作为对照组。收集研究对象的临床资料、血浆标本和粪便标本,提取粪便 DNA,进行高通量16S rRNA基因测序,并进行生物信息学分析,比较两组间肠道菌群的差异。结果 1)与对照组相比,NRDS组肠道菌群在种、属、科、目、纲、门各水平细菌分类OTU数均较少;2)β多样性分析说明 NRDS组和对照组新生儿肠道菌群结构存在明显差异;3)“科”水平上,肠杆菌科在NRDS组富集(Z＝2.78,P=0.009);“门”水平上,厚壁菌门在对照组中富集(Z＝2.18,P=0.021)、变形菌门在NRDS组富集(Z＝2.02,P=0.014)。结论 NRDS患儿存在肠道菌群生态失衡,并且菌群物种的丰富度及多样性降低;NRDS患儿与正常早产儿肠道菌群结构分布存在明显差异。     

Development of gut immunoglobulin A production in piglet in response to innate and environmental factors

The current review focuses on pre- and post-natal development of intestinal immunoglobulin A (IgA) production in pig. IgA production is influenced by intrinsic genetic factors in the foetus as well as extrinsic environmental factors during the post-natal period. At birth, piglets are exposed to new antigens through maternal colostrums/milk as well as exogenous microbiota. This exposure to new antigens is critical for the proper development of the gut mucosal immune system and is characterized mainly by the establishment of IgA response. A second critical period for neonatal intestinal immune system development occurs at weaning time when the gut environment is exposed to new dietary antigens. Neonate needs to establish oral tolerance and in the absence of protective milk need to fight potential new pathogens.