Crohn's Disease Mortality and Ambient Air Pollution in New York City.

BACKGROUND: The worldwide increase in Crohn's disease (CD) has accelerated alongside rising urbanization and accompanying decline in air quality. Air pollution affects epithelial cell function, modulates immune responses, and changes the gut microbiome composition. In epidemiologic studies, ambient air pollution has a demonstrated relationship with incident CD and hospitalizations. However, no data exist on the association of CD-related death and air pollution. METHODS: We conducted an ecologic study comparing the number of CD-related deaths of individuals residing in given zip codes, with the level of air pollution from nitric oxide, nitrogen dioxide, sulfur dioxide (SO2), and fine particulate matter. Air pollution was measured by the New York Community Air Survey. We conducted Pearson correlations and a Poisson regression with robust standard errors. Each pollution component was modeled separately. RESULTS: There was a higher risk of CD-related death in zip codes with higher levels of SO2 (incidence rate ratio [IRR], 1.16; 95% confidence interval [CI], 1.06-1.27). Zip codes with higher percentage of Black or Latinx residents were associated with lower CD-related death rates in the SO2 model (IRR, 0.58; 95% CI, 0.35-0.98; and IRR, 0.13; 95% CI, 0.05-0.30, respectively). There was no significant association of either population density or area-based income with the CD-related death rate. CONCLUSIONS: In New York City from 1993 to 2010, CD-related death rates were higher among individuals from neighborhoods with higher levels of SO2 but were not associated with levels of nitric oxide, nitrogen dioxide, and fine particulate matter. These findings raise an important and timely public health issue regarding exposure of CD patients to environmental SO2, warranting further exploration.

Ecologic study comparing the number of Crohn's disease related deaths of individuals residing in given zip codes within New York City, with levels of air pollution from nitric oxide, nitrogen dioxide, sulfur dioxide, and fine particulate matter.

Effects of Milkfat on the Gut Microbiome of Patients After Bariatric Surgery, a Pilot Study.

BACKGROUND: The efficacy of bariatric surgery may be in part attributed to altered metabolism via new gut microbiome. Milkfat may promote the growth of microbes that are beneficial in long-term weight loss. Understanding the specific gut microbiome changes after surgery and their relationship to milkfat consumption may yield important strategies for managing obesity after bariatric procedures. METHODS: In this pilot study, stool samples were collected from nine patients before and at the time of surgery, and at 1, 3, and 6 months post-surgery. At each time-point, dairy consumption was determined from dietary surveys. 16 s rRNA gene sequencing was performed followed by alpha diversity analysis. Comparisons of relative abundances of microbial taxa and analyses of fatty acids changes were performed. RESULTS: Bariatric surgery led to enrichment of (i) Roseburia, associated with weight loss and (ii) Christensenellaceae, inversely related to body mass index. High milk-fat consumption correlated with enrichment of Blautia, inversely associated with visceral fat accumulation. Faecalibacterium, possibly associated with obesity, increased in patients with low milk-fat consumption. Butter was associated with decreased alpha diversity in all subjects (p-value = 0.038) and the frequency of its use was associated with decreased alpha diversity in patients (correlation = - 0.68, p-value = 0.042). Low-milk-fat consumers showed higher concentration of saturated fatty acids. CONCLUSIONS: Our results suggest that incorporating dairy products in post-bariatric-surgery dietary plans may help cultivate a gut microbiome that is effective in regulating fat storage as well as digesting beneficial metabolites. These observations will be helpful for the management of obesity in general population as well.

Characterization of gut microbiome and metabolome in Helicobacter pylori patients in an underprivileged community in the United States.

BACKGROUND: Helicobacter pylori (H. pylori), a bacterium that infects approximately half of the world's population, is associated with various gastrointestinal diseases, including peptic ulcers, non-ulcer dyspepsia, gastric adenocarcinoma, and gastric lymphoma. As the burden of antibiotic resistance increases, the need for new adjunct therapies designed to facilitate H. pylori eradication and reduce negative distal outcomes associated with infection has become more pressing. Characterization of the interactions between H. pylori, the fecal microbiome, and fecal fatty acid metabolism, as well as the mechanisms underlying these interactions, may offer new therapeutic approaches. AIM: To characterize the gut microbiome and metabolome in H. pylori patients in a socioeconomically challenged and underprivileged inner-city community. METHODS: Stool samples from 19 H. pylori patients and 16 control subjects were analyzed. 16S rRNA gene sequencing was performed on normalized pooled amplicons using the Illumina MiSeq System using a MiSeq reagent kit v2. Alpha and beta diversity analyses were performed in QIIME 2. Non-targeted fatty acid analysis of the samples was carried out using gas chromatography-mass spectrometry, which measures the total content of 30 fatty acids in stool after conversion into their corresponding fatty acid methyl esters. Multi-dimensional scaling (MDS) was performed on Bray-Curtis distance matrices created from both the metabolomics and microbiome datasets and a Procrustes test was performed on the metabolomics and microbiome MDS coordinates. RESULTS: Fecal microbiome analysis showed that alpha diversity was lowest in H. pylori patients over 40 years of age compared to control subjects of similar age group. Beta diversity analysis of the samples revealed significant differences in microbial community structure between H. pylori patients and control subjects across all ages. Thirty-eight and six taxa had lower and higher relative abundance in H. pylori patients, respectively. Taxa that were enriched in H. pylori patients included Atopobium, Gemellaceae, Micrococcaceae, Gemellales and Rothia (R. mucilaginosa). Notably, relative abundance of the phylum Verrucomicrobia was decreased in H. pylori patients compared to control subjects. Procrustes analysis showed a significant relationship between the microbiome and metabolome datasets. Stool samples from H. pylori patients showed increases in several fatty acids including the polyunsaturated fatty acids (PUFAs) 22:4n6, 22:5n3, 20:3n6 and 22:2n6, while decreases were noted in other fatty acids including the PUFA 18:3n6. The pattern of changes in fatty acid concentration correlated to the Bacteroidetes:Firmicutes ratio determined by 16S rRNA gene analysis. CONCLUSION: This exploratory study demonstrates H. pylori-associated changes to the fecal microbiome and fecal fatty acid metabolism. Such changes may have implications for improving eradication rates and minimizing associated negative distal outcomes.

Designing strategies for eradication of Helicobacter pylori based on prevalence patterns of infection and antibiotic resistance in a low-income, medically underserved community in the United States.

BACKGROUND: Regional variation in Helicobacter pylori resistance patterns is a significant contributing factor for the ineffectiveness of traditional treatments. To improve treatment outcomes, we sought to create an individualized, susceptibility-driven therapeutic approach among our patient population, which is one of the poorest in the nation. It is medically underserved, minority-predominant and has high incidence of H pylori infection. METHODS: We compiled various factors involved in the antibiotic resistance of H pylori from literature. We then created a predictive model to customize therapies based on analyzed data from 2,014 H pylori patients with respect to several of these factors. The predictions of the model were further tested with analysis of patient stool samples. RESULTS: A clear pattern of H pylori prevalence and antibiotic resistance was observed in our patients. We observed that majority of H pylori patients were women (62%) and over the age of 40 years (80%). 30% and 36% of the H pylori patients were African American and Hispanic, respectively. A median household income of less than $54,000, past H pylori infection, previous use of certain antibiotics for any infection decreased the chance of eradication. Results of the stool testing were consistent with model predictions (90% accuracy). CONCLUSION: This model demonstrates the predictive accuracy of H pylori infection and antibiotic resistance based on patient attributes and previous treatment history. It will be useful to formulate customized treatments with predicted outcomes to minimize failures. Our community attributes may contribute toward broad applicability of model for other similar communities.

Fecal microbiota transplantation: Uses, questions, and ethics.

Fecal microbiota transplantation (FMT) has rapidly grown in notoriety and popularity worldwide as a treatment for both recurrent and refractory C. difficile infection (CDI), as well as for a myriad of other indications, with varying levels of evidence to justify its use. At present, FMT use in the U.S. has not received marketing approval from the U.S. Food and Drug Administration (FDA), but is permitted under "enforcement discretion" for CDI not responding to standard therapy. Meanwhile, the rising interest in the gut microbiome throughout mainstream media has paved the way for "do-it-yourself" (DIY) adaptations of the procedure. This access and unregulated use, often outside any clinical supervision, has quickly outpaced the medical community's research and regulatory efforts. While some studies have been able to demonstrate the success of FMT in treating conditions other than CDI-studies on ulcerative colitis have been particularly promising-little is still known about the treatmen's mechanism of action or long-term side effects. Likewise, screening of donor stool is in its early stages in terms of protocol standardization. In this paper, we explore the regulatory and ethical concerns that arise from the need to balance access to a nascent but promising innovative treatment with the need for research into its efficacy, risk profile, and long-term impact.

Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile.

OBJECTIVES: The gut microbiome is believed to play a role in the susceptibility to and treatment of Clostridium difficile infections (CDIs). It is, however, unknown whether the gut microbiome is also affected by asymptomatic C difficile colonization. Our study aimed to evaluate the fecal microbiome of children based on C difficile colonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease (IBD). METHODS: Subjects with IBD and non-IBD controls were prospectively enrolled from pediatric clinics for a biobanking project (n = 113). A fecal sample was collected from each subject for research purposes only and was evaluated for asymptomatic toxigenic C difficile colonization. Fecal microbiome composition was determined by 16S rRNA sequencing. RESULTS: We found reduced bacterial diversity and altered microbiome composition in subjects with C difficile colonization, concurrent antibiotic use, and/or concomitant IBD (all P < 0.05). Accounting for antibiotic use and IBD status, children colonized with C difficile had significant enrichment in taxa from the genera Ruminococcus, Eggerthella, and Clostridium. Children without C difficile had increased relative abundances of Faecalibacterium and Rikenellaceae. Imputed metagenomic functions of those colonized were enriched for genes in oxidative phosphorylation and beta-lactam resistance, whereas in the subjects without C difficile, several functions in translation and metabolism were over-represented. CONCLUSIONS: In children, C difficile colonization, or factors that predispose to colonization such as antibiotic use and IBD status were associated with decreased gut bacterial diversity and altered microbiome composition. Averting such microbiome alterations may be a method to prevent or treat CDI.

Malnutrition prevalence and nutrition barriers in children under 5 years: a mixed methods study in Madagascar.

BACKGROUND: Limited data exist on malnutrition prevalence in Madagascar. We aimed to assess the point prevalence of childhood malnutrition in the Anivorano region, and to explore mothers' perceptions of barriers to proper nutrition. METHODS: In a mixed methods study we measured height and weight for 313 children, aged 6 months to 5 years during summer 2011 using a recumbent measuring board and calibrated scale, and simultaneously conducted semi-structured interviews with 60 mothers of malnourished (n=19) and healthy (n=41) children. Multivitamins and high-energy supplemental food were provided to malnourished children. Mothers were trained how to prepare high-energy supplemental food. RESULTS: Prevalence of wasting defined by low weight-for-height was 10.3% (31/301); stunting or low height-for-age was 36.2% (109/301). The majority of families interviewed cultivated their own rice and other crops. Major themes regarding barriers to proper nutrition included inadequate purchasing power and access issues, low health literacy and misconceptions regarding proper nutrition and malnutrition, and insufficient variety of crops produced. CONCLUSIONS: Malnutrition rates are alarming. Health and nutritional education to improve health literacy and address misconceptions, and improvement in social services, are warranted. A multilateral approach with involvement of health and social service agencies and non-governmental organizations to plan effective preventative strategies, along with broader national and transnational strategies are instrumental to address the fundamental causes of lack of access to proper nutrition.

The infant microbiome development: mom matters.

The infant microbiome plays an essential role in human health and its assembly is determined by maternal-offspring exchanges of microbiota. This process is affected by several practices, including Cesarean section (C-section), perinatal antibiotics, and formula feeding, that have been linked to increased risks of metabolic and immune diseases. Here we review recent knowledge about the impacts on infant microbiome assembly, discuss preventive and restorative strategies to ameliorate the effects of these impacts, and highlight where research is needed to advance this field and improve the health of future generations.

Perceptions of malaria and acceptance of rapid diagnostic tests and related treatment practises among community members and health care providers in Greater Garissa, North Eastern Province, Kenya.

BACKGROUND: Conventional diagnosis of malaria has relied upon either clinical diagnosis or microscopic examination of peripheral blood smears. These methods, if not carried out exactly, easily result in the over- or under-diagnosis of malaria. The reliability and accuracy of malaria RDTs, even in extremely challenging health care settings, have made them a staple in malaria control programmes. Using the setting of a pilot introduction of malaria RDTs in Greater Garissa, North Eastern Province, Kenya, this study aims to identify and understand perceptions regarding malaria diagnosis, with a particular focus on RDTs, and treatment among community members and health care workers (HCWs). METHODS: The study was conducted in five districts of Garissa County. Focus group discussions (FGD) were performed with community members that were recruited from health facilities (HFs) supported by the MENTOR Initiative. In-depth interviews (IDIs) and FGDs with HCWs were also carried out. Interview transcripts were then coded and analysed for major themes. Two researchers reviewed all codes, first separately and then together, discussed the specific categories, and finally characterized, described, and agreed upon major important themes. RESULTS: Thirty-four FGDs were carried out with a range of two to eight participants (median of four). Of 157 community members, 103 (65.6%) were women. The majority of participants were illiterate and the highest level of education was secondary school. Some 76% of participants were of Somali ethnicity. Whilst community members and HCWs demonstrated knowledge of aspects of malaria transmission, prevention, diagnosis, and treatment, gaps and misconceptions were identified. Poor adherence to negative RDT results, unfamiliarity and distrust of RDTs, and an inconsistent RDT supply were the main challenges to become apparent in FGDs and IDIs. CONCLUSION: Gaps in knowledge or incorrect beliefs exist in Greater Garissa and have the potential to act as barriers to complete and correct malaria case management. Addressing these knowledge gaps requires comprehensive education campaigns and a reliable and constant RDT supply. The results of this study highlight education and supply chain as key factors to be addressed in order to make large scale roll out of RDTs as successful and effective as possible.

Community perception, misconception, and discord regarding prevention and treatment of infection with human immunodeficiency virus in Addis Ababa, Ethiopia.

Approximately one million persons infected with human immunodeficiency virus (HIV) live in Ethiopia. Socio-cultural factors influence prevention and treatment adherence. We applied a qualitative descriptive approach to evaluate community perception, knowledge, and the role of spiritual factors in regard to HIV. We conducted 14 focus groups with sampling of HIV+ and HIV- participants (n = 52) by using open-ended questions. We coded and analyzed data for major themes. There are misconceptions, including transmission via casual contact, and pervasive beliefs of holy water as a cure. Many HIV-participants believe treatment is ineffective or incompatible with holy water. Most HIV+ participants believe treatment and holy water can be taken together, but experienced either pressure to stop treatment or stigma when taking medications. Participants emphasized the role of spiritual leaders in directing and shaping community perspectives on HIV. Ongoing community education via local initiatives, nation-wide structural and environmental strategies, and efforts tailored toward Ethiopian society to reconcile treatment with faith are crucial.

Lack of patient risk counselling and a broader provider training affect malaria control in remote Somalia Kenya border: Qualitative assessment.

Effectiveness of providing health education solely via mass media and the providers' targeted training in malaria control needs further exploration. During pre-epidemic season, we conducted a qualitative study of 40 providers and community leaders using focus groups, comprehensive semi-structured interviews and consultation observations. Interviews were transcribed, coded and analysed for major themes. Community leaders believe that they can acquire malaria from contaminated water, animal products, air or garbage. Consequently, they under-utilise bed nets and other protective measures due to perceived continued exposure to other potential malaria sources. Practitioners do not provide individualised health counselling and risk assessment to patients during sick visits, leading to a range of misconceptions about malaria based on limited knowledge from rumours and mass media, and a strong belief in the curative power of traditional medicine. Providers overdiagnose malaria clinically and underutilise available tests due to time constraints, and the lack of training and resources to correctly diagnose other illnesses. Subsequently, misdiagnoses lead them to question the efficacy of recommended treatments. Promoting counselling during clinical encounters to address patient misconception and change risky behaviour is warranted. Wider-ranging ongoing training could enable providers to properly diagnose and manage differential diagnoses to manage malaria better.