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Danielle G. Lemay - One of the best experts on this subject based on the ideXlab platform.
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fecal metatranscriptomics of macaques with idiopathic Chronic Diarrhea reveals altered mucin degradation and fucose utilization
Microbiome, 2019Co-Authors: Samuel T. Westreich, Amir Ardeshir, Zeynep Alkan, Mary E. Kable, Danielle G. Lemay, Ian F KorfAbstract:Idiopathic Chronic Diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by Chronic inflammation of the colon and repeated bouts of Diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease. Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes. The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.
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Fecal metatranscriptomics of macaques with idiopathic Chronic Diarrhea reveals altered mucin degradation and fucose utilization
BMC, 2019Co-Authors: Samuel T. Westreich, Amir Ardeshir, Zeynep Alkan, Mary E. Kable, Ian Korf, Danielle G. LemayAbstract:Abstract Background Idiopathic Chronic Diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by Chronic inflammation of the colon and repeated bouts of Diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease. Results Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes. Conclusions The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites
Amir Ardeshir - One of the best experts on this subject based on the ideXlab platform.
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idiopathic Chronic Diarrhea in rhesus macaques is not associated with enteric viral infections
bioRxiv, 2021Co-Authors: Eric Delwart, M J Tisza, E Altan, Xutao Deng, J D Hartiganoconnor, Amir ArdeshirAbstract:While recent changes in treatment have reduced the lethality of idiopathic Chronic Diarrhea (ICD), this condition remains one of the most common causes of rhesus macaque deaths in non-human primate research centers. We compared the eukaryotic viromes in fecal swabs from 52 animals with ICD and 41 healthy animals. Viral metagenomics targeting virus-like particles was used to identify viruses shed by each animal. Five viruses belonging to the Picornaviridae, one to the Caliciviridae, one to the Parvoviridae, and one to the Adenoviridae families were identified. The fraction of reads matching each viral species was then used to estimate and compare viral loads in ICD cases versus healthy controls. None of the eukaryotic viruses detected in fecal swabs were strongly associated with ICD. Other potential causes of ICD are discussed.
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enteric viruses nucleic acids distribution along the digestive tract of rhesus macaques with idiopathic Chronic Diarrhea
bioRxiv, 2021Co-Authors: Eric Delwart, E Altan, Xutao Deng, Amir Ardeshir, D Merriam, J D HartiganoconnorAbstract:Idiopathic Chronic Diarrhea (ICD) is a common clinical condition in captive rhesus macaques, claiming 33% of medical culls (i.e. deaths unrelated to research). Using viral metagenomics we characterized the eukaryotic virome in digestive tract tissues collected at necropsy from nine animals with ICD. We show the presence of multiple viruses in the Parvoviridae and Picornaviridae family. We then compared the distribution of viral reads in the stomach, duodenum, jejunum, ileum, and the proximal, transverse, and distal colons. Tissues and mucosal scraping from the same locations showed closely related results while different gut tissues from the same animal varied widely. Picornavirus reads were generally more abundant in the lower digestive tract, particularly in the descending (distal) colon. Parvoviruses were more abundant in the upper reach particularly in the stomach. In situ hydridization (ISH) of fixed tissues showed punctuated staining for both these RNA and DNA viruses in the distal colon. Parvovirus ISH staining was also detected in the stomach/duodenum/jejunum in distinct oval-shaped structures. Therefore, the location of enteric viral nucleic acid differed widely between different viral families and along the length of the digestive tract.
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fecal metatranscriptomics of macaques with idiopathic Chronic Diarrhea reveals altered mucin degradation and fucose utilization
Microbiome, 2019Co-Authors: Samuel T. Westreich, Amir Ardeshir, Zeynep Alkan, Mary E. Kable, Danielle G. Lemay, Ian F KorfAbstract:Idiopathic Chronic Diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by Chronic inflammation of the colon and repeated bouts of Diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease. Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes. The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.
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Fecal metatranscriptomics of macaques with idiopathic Chronic Diarrhea reveals altered mucin degradation and fucose utilization
BMC, 2019Co-Authors: Samuel T. Westreich, Amir Ardeshir, Zeynep Alkan, Mary E. Kable, Ian Korf, Danielle G. LemayAbstract:Abstract Background Idiopathic Chronic Diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by Chronic inflammation of the colon and repeated bouts of Diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease. Results Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes. Conclusions The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites
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case control comparison of enteric viromes in captive rhesus macaques with acute or idiopathic Chronic Diarrhea
Journal of Virology, 2017Co-Authors: Beatrix Kapusinszky, Amir Ardeshir, Xutao Deng, Usha S Mulvaney, Eric DelwartAbstract:Diarrhea is the major cause of non-research-associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic Chronic Diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, one form of human inflammatory bowel disease. To test for viral etiologies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute Diarrhea, and 29 animals with ICD. The overall fractions of eukaryotic viral reads were 0.063% for the healthy group, 0.131% for the acute-Diarrhea group, and 0.297% for the Chronic-Diarrhea group. Eukaryotic viruses belonging to 6 viral families, as well as numerous circular Rep-encoding single-stranded DNA (CRESS DNA) viral genomes, were identified. The most commonly detected sequences were from picornaviruses, making up 59 to 88% of all viral reads, followed by 9 to 17% for CRESS DNA virus sequences. The remaining 5 virus families, Adenoviridae, Astroviridae, Anelloviridae, Picobirnaviridae, and Parvoviridae, collectively made up 1 to 3% of the viral reads, except for parvoviruses, which made up 23% of the viral reads in the healthy group. Detected members of the families Picornaviridae and Parvoviridae were highly diverse, consisting of multiple genera, species, and genotypes. Coinfections with members of up to six viral families were detected. Complete and partial viral genomes were assembled and used to measure the number of matching short sequence reads in feces from the 92 animals in the two clinical and the healthy control groups. Several enterovirus genotypes and CRESS DNA genomes were associated with ICD relative to healthy animals. Conversely, higher read numbers from different parvoviruses were associated with healthy animals. Our study reveals a high level of enteric coinfections with diverse viruses in a captive rhesus macaque colony and identifies several viruses positively or negatively associated with ICD.
Scott Friedman - One of the best experts on this subject based on the ideXlab platform.
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aga technical review malnutrition and cachexia Chronic Diarrhea and hepatobiliary disease in patients with human immunodeficiency virus infection
Gastroenterology, 1996Co-Authors: Mel C Wilcox, Linda Rabeneck, Scott FriedmanAbstract:Abstract Disorders of the gastrointestinal tract and hepatobiliary system are among the most common complications associated with human immunodeficiency virus (HIV) infection. These disorders not only result in major morbidity but mortality as well. With increasing use of prophylaxis against Pneumocystis carinii pneumonia, the incidence of opportunistic gastrointestinal disorders has increased. 1–3 Significant progress has been made in the last decade in characterizing the spectrum of pathogens involving the gastrointestinal and hepatobiliary systems, determining the pathophysiological mechanisms of these diverse processes, and defining management options. Despite these encouraging advancements, many questions remain unanswered. The purpose of this review is to evaluate and synthesize the published clinical research pertaining to three important HIV-related complications: malnutrition and cachexia, Chronic Diarrhea, and hepatobiliary disease. A separate review addresses disorders of the esophagus. 4 Attention here is focused on etiology and pathogenesis, clinical features, diagnostic strategies, and efficacy of current treatment options. Recommendations for managing patients with these complications are provided based on the weight of the clinical evidence. GASTROENTEROLOGY 1996;111:1724-1752
Mel C Wilcox - One of the best experts on this subject based on the ideXlab platform.
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aga technical review malnutrition and cachexia Chronic Diarrhea and hepatobiliary disease in patients with human immunodeficiency virus infection
Gastroenterology, 1996Co-Authors: Mel C Wilcox, Linda Rabeneck, Scott FriedmanAbstract:Abstract Disorders of the gastrointestinal tract and hepatobiliary system are among the most common complications associated with human immunodeficiency virus (HIV) infection. These disorders not only result in major morbidity but mortality as well. With increasing use of prophylaxis against Pneumocystis carinii pneumonia, the incidence of opportunistic gastrointestinal disorders has increased. 1–3 Significant progress has been made in the last decade in characterizing the spectrum of pathogens involving the gastrointestinal and hepatobiliary systems, determining the pathophysiological mechanisms of these diverse processes, and defining management options. Despite these encouraging advancements, many questions remain unanswered. The purpose of this review is to evaluate and synthesize the published clinical research pertaining to three important HIV-related complications: malnutrition and cachexia, Chronic Diarrhea, and hepatobiliary disease. A separate review addresses disorders of the esophagus. 4 Attention here is focused on etiology and pathogenesis, clinical features, diagnostic strategies, and efficacy of current treatment options. Recommendations for managing patients with these complications are provided based on the weight of the clinical evidence. GASTROENTEROLOGY 1996;111:1724-1752
Jean W. Pape - One of the best experts on this subject based on the ideXlab platform.
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Short Report: Presence of Enterocytozoon bieneusi Associated with Intestinal Coccidia in Patients with Chronic Diarrhea Visiting an HIV Center in Haiti
2014Co-Authors: Christian P. Raccurt, Bernadette Fouché, Patrice Agnamey, Jean Menotti, Taïeb Chouaki, Anne Totet, Jean W. PapeAbstract:Abstract. This study investigated the presence of Enterocytozoon bieneusi as a possible cause of Chronic Diarrhea in Haitian patients attending the GHESKIO AIDS clinic in Port-au-Prince, Haiti. Coccidian oocysts were found by polymerase chain reaction (PCR) in the stools of 58/74 patients with Chronic Diarrhea and included the following agents: 45 (60%) Cryptosporidium spp., 27 (34%) Cyclospora cayetanensis, and 11 (15%) Isospora belli. Four patients (5.5%) were co-infected with E. bieneusi and one (1.4%) had E. bieneusi alone. The PCR-restriction fragment length polymor-phism (RFLP) method made it possible to document the presence in human feces of E. bieneusi in Haiti. As in sub-Saharan Africa, the association of E. bieneusi with coccidian parasites found in Haitian patients with Diarrhea is probably caused by the high level of fecal contamination of soils and surface waters usually associated with countries with low hygienic standards. Chronic Diarrhea accompanied by weight loss is a common and often debilitating manifestation of the human immuno-deficiency virus (HIV) infection. Enterocytozoon bieneusi has been reported to be associated with Chronic Diarrhea and wasting in acquired immunodeficiency syndrome (AIDS) pa-tients in Europe, the United States, South America, and Af
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presence of enterocytozoon bieneusi associated with intestinal coccidia in patients with Chronic Diarrhea visiting an hiv center in haiti
American Journal of Tropical Medicine and Hygiene, 2008Co-Authors: Christian P. Raccurt, Bernadette Fouché, Patrice Agnamey, Jean Menotti, Taïeb Chouaki, Anne Totet, Jean W. PapeAbstract:This study investigated the presence of Enterocytozoon bieneusi as a possible cause of Chronic Diarrhea in Haitian patients attending the GHESKIO AIDS clinic in Port-au-Prince, Haiti. Coccidian oocysts were found by polymerase chain reaction (PCR) in the stools of 58/74 patients with Chronic Diarrhea and included the following agents: 45 (60%) Cryptosporidium spp., 27 (34%) Cyclospora cayetanensis, and 11 (15%) Isospora belli. Four patients (5.5%) were co-infected with E. bieneusi and one (1.4%) had E. bieneusi alone. The PCR-restriction fragment length polymorphism (RFLP) method made it possible to document the presence in human feces of E. bieneusi in Haiti. As in sub-Saharan Africa, the association of E. bieneusi with coccidian parasites found in Haitian patients with Diarrhea is probably caused by the high level of fecal contamination of soils and surface waters usually associated with countries with low hygienic standards.