Faculty Bibliography

To better characterize murine intestinal microbiota, a large number (187) of Gram-positive staining, rod- and coccoid-shaped facultative and strictly anaerobic bacteria were isolated from small and large intestinal contents from mice. Based on 16S rRNA gene sequencing, a total 115 isolates formed three phylogenetically distinct clusters located within the family Erysipelotrichaceae. Group 1, as represented by strain NYU-BL-A3T, was most closely related to Allobaculum stercoricanis, with 16S rRNA gene similarity values of 87.7%. A second group, represented by NYU-BL-A4T, was most closely related to Faecalibaculum rodentium, with 86.6% 16S rRNA gene similarity. A third group had a nearly identical 16S rRNA gene sequence (99.9%) compared to the recently described Faecalibaculum rodentium, also recovered from a laboratory mouse; however, this strain had a few differences in biochemical characteristics, which are detailed in an emended description. The predominant (>10%) cellular fatty acids of strains NYU-BL-A3T were C16:0, and C18:0 and for NYU-BL-A4T were C10:0, C16:0, C18:0 and C18:1 omega9c. The two groups could also be distinguished by multiple biochemical reactions, with the group represented by NYU-BL-A4T being considerably more active. Based on phylogenetic, biochemical and chemotaxonomic criteria, two novel genera are proposed. Ileibacterium valens gen. nov., sp. nov. with NYU-BL-A3T (ATCC TSD-63 = DSM 103668) as the type strain and Dubosiella newyorkensis gen. nov., sp. nov. with NYU-BL-A4T (ATCC TSD-64 = DSM 103457) as the type strain.

BACKGROUND: H. pylori colonizes the human stomach of approximately 50% of the world's population, and increases the risk of several gastric diseases. The goal of this study is to compare the gastric microbiota in pediatric patients with and without H. pylori colonization. METHODS: We studied 51 children that underwent gastric endoscopy due to dyspeptic symptoms (18 H. pylori-positive and 33 negative). Gastric biopsies were obtained for Rapid Urease Test, culture, histology and DNA extraction. H. pylori was quantified by qPCR and the gastric microbiome studied by V4-16S rRNA gene high-throughput sequencing. RESULTS: Bacterial richness and diversity of H. pylori-positive specimens were lower than those of negative and both groups were clearly separated according to beta diversity. Taxonomic analysis confirmed that H. pylori-positive subjects had a higher relative abundance of Helicobacter genus (66.3%) than H. pylori-negative subjects (0.45%). Four phyla (Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria) accounted for >97% of all reads in both groups. Within Proteobacteria, gamma- and beta-proteobacteria were the most abundant for H. pylori-negative patients, whilst epsilon-proteobacteria was for H. pylori positive. H. pylori-positive patients were associated with low Body Mass Index (BMI). In the group of underweight patients (BMI<18.5) there were 46.1% of H. pylori-positive patients compared with 24% in the non-underweight group (p=0.049). Patients with active superficial gastritis in H. pylori-positive patients had the lowest alpha diversity (p=0.035). CONCLUSIONS: We characterized the gastric microbiota for the first time in children with and without H. pylori and observed that when H. pylori is present, it tends to dominate the microbial community. In the H. pylori-negative patients, there was more relative abundance of Gamaproteobacteria, Betaproteobacteria, Bacteroidia and Clostridia classes and a higher bacterial richness and diversity.

Helicobacter pylori (H. pylori) is a gastric human pathogen associated with acute and chronic gastritis, 70% of all gastric ulcers, 85% of all duodenal ulcers, and both forms of stomach cancer, mucosal-associated lymphoid tissue (MALT) lymphoma and adenocarcinoma. Recently, attention has focused on possible relationship between presence of certain virulence factor and H. pylori-associated diseases. Some contradictory data between this bacterium and related disorders has been observed since not all the colonized individuals develop to severe disease. The reported diseases plausibility related to H. pylori specific virulence factors became an interesting story about this organism. Although a number of putative virulence factors have been identified including cytotoxin-associated gene a (cagA) and vacA, there are conflicting data about their actual participation as specific risk factor for H. pylori-related diseases. Duodenal ulcer promoting gene a (dupA) is a virulence factor of H. pylori that is highly associated with duodenal ulcer development and reduced risk of gastric cancer. The prevalence of dupA in H. pylori strains isolated from western countries is relatively higher than in H. pylori strains from Asian countries. Current confusing epidemiological reports will continue unless future sophisticated and molecular studies provide data on functional and complete dupA cluster in H. pylori infected individuals. This paper elucidates available knowledge concerning role of dupA in virulence of H. pylori after a decade of its discovery.

BACKGROUND: More than 50 years after the discovery of antibiotics, bacterial infections have decreased substantially; however, antibiotics also may have negative effects such as increasing susceptibility to pathogens. An intact microbiome is an important line of defense against pathogens. We sought to determine the effect of orally administered antibiotics both on susceptibility to pathogens and on impact to the microbiome. We studied Campylobacter jejuni, one of the most common causes of human diarrhea, and Acinetobacter baumannii, which causes wound infections. We examined the effects of antibiotic treatment on the susceptibility of mice to those pathogens as well as their influence on the mouse gut microbiome. RESULTS: In C57/BL6 mice models, we explored the effects of pathogen challenge, and antibiotic treatment on the intestinal microbiota. Mice were treated with either ciprofloxacin, penicillin, or water (control) for a 5-day period followed by a 5-day washout period prior to oral challenge with C. jejuni or A. baumannii to assess antibiotic effects on colonization susceptibility. Mice were successfully colonized with C. jejuni more than 118 days, but only transiently with A. baumannii. These challenges did not lead to any major effects on the composition of the gut microbiota. Although antibiotic pre-treatment did not modify pathogen colonization, it affected richness and community structure of the gut microbiome. However, the antibiotic dysbiosis was significantly reduced by pathogen challenge. CONCLUSIONS: We conclude that despite gut microbiota disturbance, susceptibility to gut colonization by these pathogens was unchanged. The major gut microbiome disturbance produced by antibiotic treatment may be reduced by colonization with specific microbial taxa.

Campylobacter jejuni and C. coli are zoonotic bacteria recognised as a major cause of human gastroenteritis and frequent cause of bacterial food-borne illness around the world. A great variety of food-producing animals, especially poultry are important reservoir involved in their spread to humans. Campylobacter gastroenteritis is generally a self-limiting disease avoiding antimicrobial prescription but, when antibiotic therapy is indicated, erythromycin and fluoroquinolone are the drugs of choice. However, Campylobacter has become increasingly resistant to fluoroquinolones with high isolation rates among human and animal strains. This review shows and discusses the data generated in Latin America in relation to fluoroquinolone resistance in Campylobacter highlighting that i) fluorquinolone resistant strains are reported with high frequencies in several countries; ii) the available data allows to confirm that human infection by fluoroquinolone-resistant Campylobacter are originated mainly from the food chain animals and environmental sources; iii) Campylobacter isolation, identification and antimicrobial susceptibility testing have been performed with different analytical methods making necessary the harmonisation and standardisation of diagnostic methods and iv) strengthening Campylobacter antimicrobial resistance surveillance programs and capacity building with the association between public health services and the academic world are necessary.

BACKGROUND AND AIM: Helicobacter pylori can survive long incubation periods under anaerobic conditions, and should be possible to isolate under anaerobic conditions. Our aim was to isolate H. pylori in anaerobic conditions, from gastric biopsies of H. pylori infected patients. METHODS: We enrolled 27 patients with bleeding (erosive) gastritis (mean age 36.3 years, 55.6% male) from Hanoi, Vietnam. H. pylori status was confirmed by qPCR. RESULTS: H. pylori were recovered under anaerobic and micro-aerobic conditions from gastric biopsies in 16 patients. Anaerobic conditions yielded significantly higher H. pylori recovery rates than micro-aerobic conditions (81.3% vs. 31.3%, P= 0.01). H. pylori isolates were characterized by PCR for specific virulence markers and the genotypes were similar to those previously described in this region of the world. CONCLUSIONS: H. pylori can be isolated under anaerobic conditions. These findings may provide new insight into the physiology of this human pathogen and help to identify the route of H. pylori transmission.

BACKGROUND: Highly virulent strains of the gastric pathogen Helicobacter pylori encode a type IV secretion system (T4SS) that delivers the effector protein CagA into gastric epithelial cells. Translocated CagA undergoes tyrosine phosphorylation by members of the oncogenic c-Src and c-Abl host kinases at EPIYA-sequence motifs A, B and D in East Asian-type strains. These phosphorylated EPIYA-motifs serve as recognition sites for various SH2-domains containing human proteins, mediating interactions of CagA with host signaling factors to manipulate signal transduction pathways. Recognition of phospho-CagA is mainly based on the use of commercial pan-phosphotyrosine antibodies that were originally designed to detect phosphotyrosines in mammalian proteins. Specific anti-phospho-EPIYA antibodies for each of the three sites in CagA are not forthcoming. RESULTS: This study was designed to systematically analyze the detection preferences of each phosphorylated East Asian CagA EPIYA-motif by pan-phosphotyrosine antibodies and to determine a minimal recognition sequence. We synthesized phospho- and non-phosphopeptides derived from each predominant EPIYA-site, and determined the recognition patterns by seven different pan-phosphotyrosine antibodies using Western blotting, and also investigated representative East Asian H. pylori isolates during infection. The results indicate that a total of only 9-11 amino acids containing the phosphorylated East Asian EPIYA-types are required and sufficient to detect the phosphopeptides with high specificity. However, the sequence recognition by the different antibodies was found to bear high variability. From the seven antibodies used, only four recognized all three phosphorylated EPIYA-motifs A, B and D similarly well. Two of the phosphotyrosine antibodies preferentially bound primarily to the phosphorylated motif A and D, while the seventh antibody failed to react with any of the phosphorylated EPIYA-motifs. Control experiments confirmed that none of the antibodies reacted with non-phospho-CagA peptides and in accordance were able to recognize phosphotyrosine proteins in human cells. CONCLUSIONS: The results of this study disclose the various binding preferences of commercial anti-phosphotyrosine antibodies for phospho-EPIYA-motifs, and are valuable in the application for further characterization of CagA phosphorylation events during infection with H. pylori and risk prediction for gastric disease development.

Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease.