[Show abstract][Hide abstract] ABSTRACT: Vibrio cholerae is endemic in South Asia and Africa where outbreaks of cholera occur widely and are particularly associated with poverty and poor sanitation. Knowledge of the genetic diversity of toxigenic V. cholerae isolates, particularly in Africa, remains scarce. The constraints in improving this understanding is not only the lack of regular cholera disease surveillance, but also the lack of laboratory capabilities in endemic countries to preserve, store and ship isolates in a timely manner. We evaluated the use of simplified sample preservation methods for molecular characterization using multi-locus variable-number tandem-repeat analysis (MLVA) for differentiation of Vibrio cholerae genotypes.
[Show abstract][Hide abstract] ABSTRACT: Globally, diarrheal diseases are the second leading cause of death among children under 5 years old. Few case-control studies on the etiology of diarrhea have been conducted in China.
Preview · Article · Dec 2015 · Clinical Microbiology and Infection
[Show abstract][Hide abstract] ABSTRACT: To examine rates of Shigella infections in household contacts of pediatric shigellosis patients, we followed contacts and controls prospectively for 1 week after the index patient obtained care. Household contacts of patients were 44 times more likely to develop a Shigella infection than were control contacts (odds ratio 44.7, 95% CI 5.5-361.6); 29 (94%) household contacts of shigellosis patients were infected with the same species and serotype as the index patient's. Pulsed-field gel electrophoresis showed that 14 (88%) of 16 with infected contacts had strains that were indistinguishable from or closely related to the index patient's strain. Latrine area fly counts were higher in patient households compared with control households, and 2 patient household water samples were positive for Shigella. We show high susceptibility of household contacts of shigellosis patients to Shigella infections and found environmental risk factors to be targeted in future interventions.
Full-text · Article · Nov 2015 · Emerging infectious diseases
[Show abstract][Hide abstract] ABSTRACT: Infectious diarrhea leads to significant mortality in children, with 40 % of these deaths occurring in Africa. Classic human astroviruses are a well-established etiology of diarrhea. In recent years, seven novel astroviruses have been discovered (MLB1, MLB2, MLB3, VA1/HMO-C, VA2/HMO-B, VA3/HMO-A, VA4); however, there have been few studies on their prevalence or potential association with diarrhea.
To investigate the prevalence and diversity of these classic and recently described astroviruses in a pediatric population, a case-control study was performed. Nine hundred and forty nine stools were previously collected from cases of moderate-to-severe diarrhea and matched controls of patients less than 5 years of age in Kenya and The Gambia. RT-PCR screening was performed using pan-astrovirus primers.
Astroviruses were present in 9.9 % of all stool samples. MLB3 was the most common astrovirus with a prevalence of 2.6 %. Two subtypes of MLB3 were detected that varied based on location in Africa. In this case-control study, Astrovirus MLB1 was associated with diarrhea in Kenya, whereas Astrovirus MLB3 was associated with the control state in The Gambia. Classic human astrovirus was not associated with diarrhea in this study. Unexpectedly, astroviruses with high similarity to Canine Astrovirus and Avian Nephritis Virus 1 and 2 were also found in one case of diarrhea and two control stools respectively.
Astroviruses including novel MLB- and VA-clade members are commonly found in pediatric stools in Kenya and The Gambia. The most recently discovered astrovirus, MLB3, was the most prevalent and was found more commonly in control stools in The Gambia, while astrovirus MLB1 was associated with diarrhea in Kenya. Furthermore, a distinct subtype of MLB3 was noted, as well as 3 unanticipated avian or canine astroviruses in the human stool samples. As a result of a broadly reactive PCR screen for astroviruses, new insight was gained regarding the epidemiology of astroviruses in Africa, where a large proportion of diarrheal morbidity and mortality occur.
[Show abstract][Hide abstract] ABSTRACT: Potential contributions of the host-associated gut microbiota to human physiology continue to receive extensive research interest. While various lines of evidence support a role of the microbiota in maintaining human health, perturbations in normal microbiota composition have been correlated with various dietary changes and disease states,1 particularly diarrhoea.2 We have long known that close interactions between microbiota and the host’s immune system occur in the distal small intestine and that microbes are highly metabolically active in the proximal large intestine. Recent global efforts have accumulated a wealth of data on the diversity of human gut-associated microbiota. These studies confirmed that even in healthy individuals a large degree of intraindividual as well as interindividual variation in microbiota composition and although to a lesser degree, microbial activities occur. However, what represents ‘normal’ gut microbiota is still not fully understood, which is largely due to the observed variation within and among individuals. While recent work based on phylogenetic analysis of both the small subunit (16S) of ribosomal RNA as well as metagenomic datasets suggests the existence of … [Full text of this article]
[Show abstract][Hide abstract] ABSTRACT: Pathogens in the gastrointestinal tract exist within a vast population of microbes. We examined associations between pathogens and composition of gut microbiota as they relate to Shigella spp./enteroinvasive Escherichia coli infection. We analyzed 3,035 stool specimens (1,735 nondiarrheal and 1,300 moderate-to-severe diarrheal) from the Global Enteric Multicenter Study for 9 enteropathogens. Diarrheal specimens had a higher number of enteropathogens (diarrheal mean 1.4, nondiarrheal mean 0.95; p<0.0001). Rotavirus showed a negative association with Shigella spp. in cases of diarrhea (odds ratio 0.31, 95% CI 0.17-0.55) and had a large combined effect on moderate-to-severe diarrhea (odds ratio 29, 95% CI 3.8-220). In 4 Lactobacillus taxa identified by 16S rRNA gene sequencing, the association between pathogen and disease was decreased, which is consistent with the possibility that Lactobacillus spp. are protective against Shigella spp.-induced diarrhea. Bacterial diversity of gut microbiota was associated with diarrhea status, not high levels of the Shigella spp. ipaH gene.
Full-text · Article · Feb 2015 · Emerging infectious diseases
[Show abstract][Hide abstract] ABSTRACT: Diarrhea causes substantial morbidity and mortality in children in low-income countries. Although numerous pathogens cause diarrhea, the etiology of many episodes remains unknown. Serratia marcescens is incriminated in hospital-associated infections, and HIV/AIDS associated diarrhea. We have recently found that Serratia spp. may be found more commonly in the stools of patients with diarrhea than in asymptomatic control children. We therefore investigated the possible enteric pathogenicity of S. marcescens in vitro employing a polarized human colonic epithelial cell (T84) monolayer. Infected monolayers were assayed for bacterial invasion, transepithelial electrical resistance (TEER), cytotoxicity, interleukin-8 (IL-8) release and morphological changes by scanning electron microscopy. We observed significantly greater epithelial cell invasion by S. marcescens compared to Escherichia coli strain HS (p = 0.0038 respectively). Cell invasion was accompanied by reduction in TEER and secretion of IL-8. Lactate dehydrogenase (LDH) extracellular concentration rapidly increased within a few hours of exposure of the monolayer to S. marcescens. Scanning electron microscopy of S. marcescens-infected monolayers demonstrated destruction of microvilli and vacuolization. Our results suggest that S. marcescens interacts with intestinal epithelial cells in culture and induces dramatic alterations similar to those produced by known enteric pathogens.
[Show abstract][Hide abstract] ABSTRACT: The Global Enteric Multicenter Study (GEMS) is a prospective collaborative study to determine the pathogen specific, diarrhea associated attributable disease burden of diarrhea in Africa and Asia in children less than 5 years of age. Using samples from children that participated in this case-control study and were seen at in the GEMS clinics in The Gambia and Kenya, we conducted a host gene candidate study that examined the association of the host DNA single nucleotide polymorphisms (SNPs) and specific bacterial enteropathogens causing diarrhea.
Cases of diarrhea were matched with healthy controls from the same area. Stool was collected and examined comprehensively for the presence of enteropathogens and host DNA polymorphisms. We studied de-identified fecal DNA for the presence of SNPs (N=144) in 26 genes that code for host proteins involved in pathogen attachment, inflammation, innate and acquired immune responses to enteropathogens. We analyzed the distribution of host genotypes and compared cases vs. controls according to enteropathogens identified. Comparisons were made using SNPSTATs software following an additive model. A mixed logistic regression model was used to adjust for potential confounding factors including site, age, weight for height and weight for age scores.
Microbiological and genotype data were available in 1,164 subjects. Diarrhea was associated with 6 SNPs located in SELPLG, CD55, LPLUNC, IL12 B, and CORO1C. In The Gambia, diarrhea due to Shigella was associated with a SNP in SELPLG, diarrhea from enterotoxigenic E. coli was associated with SNPs in DAF (CD55), LPLUNC, SELPLG, diarrhea from enteroaggregative E. coli was associated with SNPs in CORO1C. In Kenya, diarrhea from enteroaggregative E.coli was associated with SNPs in IL12B and CORO1C
Distinct SNPs were associated with pathogen specific diarrhea in children under 5 years of age living in two African countries.
[Show abstract][Hide abstract] ABSTRACT: Background: The Global Enteric Multicenter Study (GEMS) is a prospective case control study to determine pathogen specific diarrheal disease burden among children <5 years of age in Africa and Asia. Using samples from children in The Gambia and Kenya, we conducted a gene candidate study that examined the association of the host DNA single nucleotide polymorphisms (SNPs) and specific viral enteropathogens rotavirus and norovirus causing diarrhea.
Methods: Stool specimens from moderate to severe diarrhea cases and their age, sex and area matched controls were examined for the presence of enteropathogens and host DNA SNPs (N=144) in 26 genes that code for host proteins involved in pathogen attachment, inflammation, innate and acquired immune responses to enteropathogens. We analyzed the distribution of SNPs and compared cases vs. controls according to enteropathogens identified. Comparisons were made using SNPSTATs software following the dominant model. Logistic regression model was used to adjust for potential confounders including site and age.
Results: Microbiological and genotype data were available in 1,164 subjects. In The Gambia, diarrhea due to norovirus was associated with SNP in C3orf23 (69% vs. 36%, OR=4.0, CI=1.1.5-13.7, P=0.03), SNPs in IL12B (67% vs. 32%, OR=4.2, CI=1.19-15, P=0.025) and a SNP in MBL (29% vs. 58%, OR=0.3, CI=0.08-0.9, P=0.045) and diarrhea from rotavirus was associated with SNPs in CD180 (88% vs. 49%, OR=8, CI=1.66-35, P=0.003). In Kenya, diarrhea from norovirus was associated with a SNP in C3orf23 (71% vs. 23%, OR=8, CI=1.4-42, P=0.013), and SNPs in LPLUNC (50% vs.15%, OR=6, CI=1.5-21, P=0.012) and diarrhea from rotavirus was associated with LPLUNC (61% vs. 40%, OR=2.5, CI=1.2-5.3, P=0.011).
Conclusion: Distinct SNPs were associated with pathogen specific viral diarrhea in children under 5 years of age living in two African countries.
[Show abstract][Hide abstract] ABSTRACT: Little is known about the population of eukaryotic viruses in the human gut ("virome") or the potential role it may play in disease. We used a metagenomic approach to define and compare the eukaryotic viromes in pediatric diarrhea cohorts from two locations (Melbourne and Northern Territory, Australia). We detected viruses known to cause diarrhea, non-pathogenic enteric viruses, viruses not associated with an enteric reservoir, viruses of plants, and novel viruses. Viromes from Northern Territory children contained more viral families per sample than viromes from Melbourne, which could be attributed largely to an increased number of sequences from the families Adenoviridae and Picornaviridae (genus enterovirus). qRT-PCR/PCR confirmed the increased prevalence of adenoviruses and enteroviruses. Testing of additional diarrhea cohorts by qRT-PCR/PCR demonstrated statistically different prevalences in different geographic sites. These findings raise the question of whether the virome plays a role in enteric diseases and conditions that vary with geography.
[Show abstract][Hide abstract] ABSTRACT: Background
Diarrheal diseases continue to contribute significantly to morbidity and mortality in infants and young children in developing countries. There is an urgent need to better understand the contributions of novel, potentially uncultured, diarrheal pathogens to severe diarrheal disease, as well as distortions in normal gut microbiota composition that might facilitate severe disease.
We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. Our study includes 992 children from four low-income countries in West and East Africa, and Southeast Asia. Known pathogens, as well as bacteria currently not considered as important diarrhea-causing pathogens, are positively associated with MSD, and these include Escherichia/Shigella, and Granulicatella species, and Streptococcus mitis/pneumoniae groups. In both cases and controls, there tend to be distinct negative correlations between facultative anaerobic lineages and obligate anaerobic lineages. Overall genus-level microbiota composition exhibit a shift in controls from low to high levels of Prevotella and in MSD cases from high to low levels of Escherichia/Shigella in younger versus older children; however, there was significant variation among many genera by both site and age.
Our findings expand the current understanding of microbiota-associated diarrhea pathogenicity in young children from developing countries. Our findings are necessarily based on correlative analyses and must be further validated through epidemiological and molecular techniques.
[Show abstract][Hide abstract] ABSTRACT: We describe the identification of a novel picornavirus recovered from the fecal specimen of a child in The Gambia, provisionally named rosavirus 2. Comparison of the rosavirus 2 complete genome demonstrated 71.9% nucleotide identity to its closest relative rosavirus M-7, an unclassified picornavirus identified from rodent fecal material. A unique RNA structure was predicted in the 3' UTR of rosavirus 2 that was conserved with rosavirus M-7 and cadiciviruses. We detected rosavirus 2 in four pediatric fecal specimens (0.55% prevalence) in a Gambian diarrheal case-control cohort, but we did not detect it in a panel of 634 pediatric diarrheal stool specimens from the USA. There was no statistical evidence that rosavirus 2 was associated with diarrheal cases. This study broadens our understanding of unknown viruses present in children in developing country settings.
[Show abstract][Hide abstract] ABSTRACT: Although the prothrombin G20210A mutation has been implicated as a risk factor for venous thrombosis, its role in arterial ischemic stroke is unclear, particularly among young adults. To address this issue, we examined the association between prothrombin G20210A and ischemic stroke in a white case-control population and additionally performed a meta-analysis.
From the population-based Genetics of Early Onset Stroke (GEOS) study, we identified 397 individuals of European ancestry aged 15 to 49 years with first-ever ischemic stroke and 426 matched controls. Logistic regression was used to calculate odds ratios (ORs) in the entire population and for subgroups stratified by sex, age, oral contraceptive use, migraine, and smoking status. A meta-analysis of 17 case-control studies (n=2305 cases <55 years) was also performed with and without GEOS data.
Within GEOS, the association of the prothrombin G20210A mutation with ischemic stroke did not achieve statistical significance (OR=2.5; 95% confidence interval [CI]=0.9-6.5; P=0.07). However, among adults aged 15 to 42 years (younger than median age), cases were significantly more likely than controls to have the mutation (OR=5.9; 95% CI=1.2-28.1; P=0.03), whereas adults aged 42 to 49 years were not (OR=1.4; 95% CI=0.4-5.1; P=0.94). In our meta-analysis, the mutation was associated with significantly increased stroke risk in adults ≤55 years (OR=1.4; 95% CI=1.1-1.9; P=0.02), with significance increasing with addition of the GEOS results (OR=1.5; 95% CI=1.1-2.0; P=0.005).
The prothrombin G20210A mutation is associated with ischemic stroke in young adults and may have an even stronger association among those with earlier onset strokes. Our finding of a stronger association in the younger young adult population requires replication.
[Show abstract][Hide abstract] ABSTRACT: Cholera Cholera is still a major public health problem. The underlying bacterial pathogen Vibrio cholerae Vibrio cholerae (V. cholerae) is evolving and some of its mutations have set the stage for outbreaks outbreaks . After V. cholerae acquired the mobile elements VSP I & II, the El Tor pandemic began and spread across the tropics. The replacement of the O1 serotype encoding genes with the O139 encoding genes triggered an outbreak that swept across the Indian subcontinent. The sxt element generated a third selective sweep and most recently a fourth sweep was associated with the exchange of the El Tor ctx allele for a classical ctx allele in the El Tor background. In Kenya, variants of this fourth selective sweep have differentiated and become endemic residing in and emerging from environmental reservoirs. On a local level, studies in Bangladesh have revealed that outbreaks may arise from a nonrandom subset of the genetic lineages in the environment and as the population of the pathogen expands, many novel mutations may be found increasing the amount of genetic variation genetic variation , a phenomenon known as a founder flush. In Haiti, after the initial invasion and expansion of V. cholerae in 2010, a second outbreak occurred in the winter of 2011-2012 driven by natural selection of specific mutations.
No preview · Article · Jan 2014 · Current topics in microbiology and immunology
[Show abstract][Hide abstract] ABSTRACT: Cholera remains a major public health problem. To compare the relative contribution of strains from the environment with strains isolated from patients during outbreaks, we performed multilocus variable tandem repeat analyses on samples collected during the 2010 and 2011 outbreak seasons in 2 geographically distinct areas of Bangladesh. A total of 222 environmental and clinical isolates of V. cholerae O1 were systematically collected from Chhatak and Mathbaria. In Chhatak, 75 of 79 isolates were from the same clonal complex, in which extensive differentiation was found in a temporally consistent pattern of successive mutations at single loci. A total of 59 isolates were collected from 6 persons; most isolates from 1 person differed by sequential single-locus mutations. In Mathbaria, 60 of 84 isolates represented 2 separate clonal complexes. The small number of genetic lineages in isolates from patients, compared with those from the environment, is consistent with accelerated transmission of some strains among humans during an outbreak.
Full-text · Article · Jan 2014 · Emerging Infectious Diseases