Faculty Bibliography

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.

Helicobacter pylori is a late-in-life human pathogen with potential early-life benefits. Although H. pylori is disappearing from the human population, little is known about the influence of H. pylori on the host's microbiota and immunity. Studying the interactions of H. pylori with murine hosts over 6 months, we found stable colonization accompanied by gastric histologic and antibody responses. Analysis of gastric and pulmonary tissues revealed increased expression of multiple immune response genes, conserved across mice and over time in the stomach and more transiently in the lungs. Moreover, H. pylori infection led to significantly different population structures in both the gastric and intestinal microbiota. These studies indicate that H. pylori influences the microbiota and host immune responses not only locally in the stomach, but distantly as well, affecting important target organs.

The epidemiology of Helicobacter pylori (H. pylori) infection is related to human poverty with marked differences between developing and developed countries. Socioeconomic factors and living standards are the main determinants of the age-dependent acquisition rate of H. pylori, and consequently its prevalence. The aim of this study was to assess the risk and sero-prevalence of H. pylori colonization among Orang Asli in Peninsula Malaysia. This cross-sectional study was conducted on Orang Asli subjects in seven isolated settlements spanning across all three major tribes (Negrito, Proto Malay and Senoi) in Malaysia. Socio-demographic characteristics of the subjects were obtained through interview. Subjects were tested for H. pylori colonization based on CagA and whole cell (WC) antigen serological assays. A total of 275 subjects participated in this study. Among these subjects, 115 (44.7%) were H. pylori sero-positive with highest sero-prevalence among Negrito (65.7%). Among subjects who were H. pylori sero-positive, CagA sero positivity was also significantly higher among Negrito. The highest proportion of respondents reported to be H. pylori sero-positive was from age group 30 years old and below (57.9%), males (56.2%), Negrito (48.6%) and live in bamboo house (92.3%). The highest proportion of respondents reported to be CagA sero-positive was from age group 30 years old and below (41.4%), males (35.6%) and Negrito (48.6%). The results of this study demonstrate that H. pylori colonization can be related to age, gender, tribes and house materials and CagA sero-positive stain closely associated with age, gender and tribes.

BACKGROUND: Accumulating evidence shows that Helicobacter pylori protects against some metabolic and immunological diseases in which the development of these diseases coincide with temporal or permanent dysbiosis. The aim of this study was to assess the effect of H. pylori eradication on the human gut microbiome. METHODS: As part of the currently on-going ESSAY (Eradication Study in Stable Adults/Youths) study, we collected stool samples from 17 H. pylori-positive young adult (18-30 years-old) volunteers. The same cohort was followed up 6, 12 and 18 months-post H. pylori eradication. The impact of H. pylori on the human gut microbiome pre- and post-eradication was investigated using high throughput 16S rRNA gene (V3-V4 region) sequencing using the Illumina Miseq followed by data analysis using Qiime pipeline. RESULTS: We compared the composition and diversity of bacterial communities in the fecal microbiome of the H. pylori-positive volunteers, before and after H. pylori eradication therapy. The 16S rRNA gene was sequenced at an average of 150,000-170,000 reads/sample. The microbial diversity were similar pre- and post-H. pylori eradication with no significant differences in richness and evenness of bacterial species. Despite that the general profile of the gut microbiome was similar pre- and post-eradication, some changes in the bacterial communities at the phylum and genus levels were notable, particularly the decrease in relative abundance of Bacterioidetes and corresponding increase in Firmicutes after H. pylori eradication. The significant increase of short-chain fatty acids (SCFA)-producing bacteria genera could also be associated with increased risk of metabolic disorders. CONCLUSIONS: Our preliminary stool metagenomics study shows that eradication of H. pylori caused perturbation of the gut microbiome and may indirectly affect the health of human. Clinicians should be aware of the effect of broad spectrum antibiotics used in H. pylori eradication regimen and be cautious in the clinical management of H. pylori infection, particularly in immunocompromised patients.

We studied skin microbiota present in three skin sites (forearm, axilla, scalp) in men from six ethnic groups living in New York City. METHODS: Samples were obtained at baseline and after four days following use of neutral soap and stopping regular hygiene products, including shampoos and deodorants. DNA was extracted using the MoBio Power Lyzer kit and 16S rRNA gene sequences determined on the IIlumina MiSeq platform, using QIIME for analysis. RESULTS: Our analysis confirmed skin swabbing as a useful method for sampling different areas of the skin because DNA concentrations and number of sequences obtained across subject libraries were similar. We confirmed that skin location was the main factor determining the composition of bacterial communities. Alpha diversity, expressed as number of species observed, was greater in arm than on scalp or axilla in all studied groups. We observed an unexpected increase in alpha-diversity on arm, with similar tendency on scalp, in the South Asian group after subjects stopped using their regular shampoos and deodorants. Significant differences at phylum and genus levels were observed between subjects of the different ethnic origins at all skin sites. CONCLUSIONS: We conclude that ethnicity and particular soap and shampoo practices are secondary factors compared to the ecological zone of the human body in determining cutaneous microbiota composition.

Since many years ago, several studies reported the endosymbiosis between bacteria species and free living amoebas. However, the mechanisms involved in the bacteria penetration and release from the amoeba are not clear. The free living amoebas especially Acanthamoeba castellanii are considered important bacteria predators, for that reason they have a significant role in the control of microbial populations in particular environments. However, some bacteria are capable to avoid the digestion from the amoeba and take advantage of this intimate relationship. A. castellanii is an ubiquitous organism present in aquatic and soil environments. Particularly in humid environments they are found sharing with different bacteria species, including those pathogen for humans transmitted by animals. The interaction between the bacteria and the amoebas may result in a close endosymbiotic relationship that allows the bacteria to survive inside the vacuoles of the protozoa for days or months. The purpose of this review is to describe the relevant aspects of the interaction between A. castellanii and different bacteria species, mostly those with relevance in public health and related with zoonosis.

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.

Aims: To compare the taxonomical distribution of the gastric microbiota in pediatric patients with and without H. pylori (Hp) colonization. Methods: We studied 51 children [32 males/19 females, mean age 11.1 years, range 1-17) that underwent gastric endoscopy due to dyspeptic symptoms. Gastric biopsies were obtained for RUT, DNA extraction and culture (only for the positive RUT). Total bacteria and Hp were enumerated by qPCR and V4 16S rRNA high-throughput sequencing (Illumina) was performed. Results: A total of 16 children were Hp positive and 35 were negative. We found a good correlation between RUT and qPCR results to determine Hp status. Hp positive and negative specimens were similar in alpha and beta diversity, regardless of subject clinical condition, gender and age. Taxonomic analysis of the gastric microbiota at species level confirmed that Hp positive subjects had a higher relative abundance of Hp sequences (mean 50%) than Hp negative subjects (mean 0.1%). By LEfSe analysis, the samples from Hp positive were dominated by Proteobacteria phyla. In contrast Hp negative were dominated by Firmicutes and Bacteroidetes phyla. Proteobacteria was present in Hp positive and negative biopsies but with different families represented. For Hp negative gamma-and beta-Proteobacteria were the most abundant. For Hp positive as expected was epsilon-proteobacteria. Four phyla (Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria) accounted for >97% of all reads. Conclusions. In the gastric microbiota, Hp is an important component of the community. However, the rest of the gastric microbiota is nearly identical in children independently of the Hp status

OBJECTIVE: Helicobacter pylori colonisation rates in childhood have declined in Western populations, but it is unknown whether this trend is similar in children of non-Western ethnic backgrounds, born in a Western country. We aimed to identify H. pylori status in children, and determine mother-to-child transmission and risk factors for colonisation. DESIGN: Antibodies against H. pylori and cytotoxin-associated gene A (CagA) were measured in children participating in a population-based prospective cohort study in Rotterdam, the Netherlands. Information on demographics and characteristics was collected using questionnaires. RESULTS: We analysed the serum of 4467 children (mean age 6.2 years+/-0.4 SD) and compared the results with the H. pylori status of their mothers (available for 3185 children). Overall, 438 (10%) children were H. pylori-positive, of whom 142 (32%) were CagA-positive. Independent risk factors for colonisation were: maternal H. pylori positivity (OR 2.12; 95% CI 1.62 to 2.77), non-Dutch ethnicity (OR 2.05; 95% CI 1.54 to 2.73), female gender (OR 1.47; 95% CI 1.20 to 1.80) and lower maternal education level (OR 1.38; 95% CI 1.06 to 1.79). Comparing mothers and children, we found an intergenerational decrease of 76% and 77% for Hp(+)CagA(-) and Hp(+)CagA(+)-strains, respectively, consistent across all nine ethnic groups studied. Male gender, higher maternal educational level and no older siblings, were independently associated with absence of H. pylori. CONCLUSIONS: Although the highest H. pylori and CagA prevalence was found in children of non-Dutch ethnicities, the decreased colonisation rates were uniform across all ethnic groups, implying the importance of environmental factors in H. pylori transmission in modern cities, independent of ethnicity.