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Chibuye M, Mende DR, Spijker R, Simuyandi M, Luchen CC, Bosomprah S, Chilengi R, Schultsz C, Harris VC. Systematic review of associations between gut microbiome composition and stunting in under-five children. NPJ Biofilms Microbiomes 2024; 10:46. [PMID: 38782939 PMCID: PMC11116508 DOI: 10.1038/s41522-024-00517-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Childhood stunting is associated with impaired cognitive development and increased risk of infections, morbidity, and mortality. The composition of the enteric microbiota may contribute to the pathogenesis of stunting. We systematically reviewed and synthesized data from studies using high-throughput genomic sequencing methods to characterize the gut microbiome in stunted versus non-stunted children under 5 years in LMICs. We included 14 studies from Asia, Africa, and South America. Most studies did not report any significant differences in the alpha diversity, while a significantly higher beta diversity was observed in stunted children in four out of seven studies that reported beta diversity. At the phylum level, inconsistent associations with stunting were observed for Bacillota, Pseudomonadota, and Bacteroidota phyla. No single genus was associated with stunted children across all 14 studies, and some associations were incongruent by specific genera. Nonetheless, stunting was associated with an abundance of pathobionts that could drive inflammation, such as Escherichia/Shigella and Campylobacter, and a reduction of butyrate producers, including Faecalibacterium, Megasphera, Blautia, and increased Ruminoccoccus. An abundance of taxa thought to originate in the oropharynx was also reported in duodenal and fecal samples of stunted children, while metabolic pathways, including purine and pyrimidine biosynthesis, vitamin B biosynthesis, and carbohydrate and amino acid degradation pathways, predicted linear growth. Current studies show that stunted children can have distinct microbial patterns compared to non-stunted children, which could contribute to the pathogenesis of stunting.
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Affiliation(s)
- Mwelwa Chibuye
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Daniel R Mende
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Rene Spijker
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Michelo Simuyandi
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Chaluma C Luchen
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Samuel Bosomprah
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Department of Biostatistics, School of Public Health, University of Ghana, Legon, Accra, Ghana
| | - Roma Chilengi
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- The Zambia National Public Health Institute (ZNPHI), Lusaka, Zambia
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Vanessa C Harris
- Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Institute of Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
- Division of Infectious Diseases, Department of Internal Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
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Tikhomirova A, McNabb ER, Petterlin L, Bellamy GL, Lin KH, Santoso CA, Daye ES, Alhaddad FM, Lee KP, Roujeinikova A. Campylobacter jejuni virulence factors: update on emerging issues and trends. J Biomed Sci 2024; 31:45. [PMID: 38693534 PMCID: PMC11064354 DOI: 10.1186/s12929-024-01033-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024] Open
Abstract
Campylobacter jejuni is a very common cause of gastroenteritis, and is frequently transmitted to humans through contaminated food products or water. Importantly, C. jejuni infections have a range of short- and long-term sequelae such as irritable bowel syndrome and Guillain Barre syndrome. C. jejuni triggers disease by employing a range of molecular strategies which enable it to colonise the gut, invade the epithelium, persist intracellularly and avoid detection by the host immune response. The objective of this review is to explore and summarise recent advances in the understanding of the C. jejuni molecular factors involved in colonisation, invasion of cells, collective quorum sensing-mediated behaviours and persistence. Understanding the mechanisms that underpin the pathogenicity of C. jejuni will enable future development of effective preventative approaches and vaccines against this pathogen.
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Affiliation(s)
- Alexandra Tikhomirova
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Emmylee R McNabb
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Luca Petterlin
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Georgia L Bellamy
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Kyaw H Lin
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Christopher A Santoso
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Ella S Daye
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Fatimah M Alhaddad
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Kah Peng Lee
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Anna Roujeinikova
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia.
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3
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Schiaffino F, Parker CT, Paredes Olortegui M, Pascoe B, Manzanares Villanueva K, Garcia Bardales PF, Mourkas E, Huynh S, Peñataro Yori P, Romaina Cachique L, Gray HK, Salvatierra G, Silva Delgado H, Sheppard SK, Cooper KK, Kosek MN. Genomic resistant determinants of multidrug-resistant Campylobacter spp. isolates in Peru. J Glob Antimicrob Resist 2024; 36:309-318. [PMID: 38272215 PMCID: PMC11092888 DOI: 10.1016/j.jgar.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/14/2023] [Accepted: 01/06/2024] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVES Antimicrobial resistant (AMR) Campylobacter is a global health threat; however, there is limited information on genomic determinants of resistance in low- and middle-income countries. We evaluated genomic determinants of AMR using a collection of whole genome sequenced Campylobacter jejuni and C. coli isolates from Iquitos, Peru. METHODS Campylobacter isolates from two paediatric cohort studies enriched with isolates that demonstrated resistance to ciprofloxacin and azithromycin were sequenced and mined for AMR determinants. RESULTS The gyrA mutation leading to the Thr86Ile amino acid change was the only gyrA mutation associated with fluoroquinolone resistance identified. The A2075G mutation in 23S rRNA was present, but three other 23S rRNA mutations previously associated with macrolide resistance were not identified. A resistant-enhancing variant of the cmeABC efflux pump genotype (RE-cmeABC) was identified in 36.1% (35/97) of C. jejuni genomes and 17.9% (12/67) of C. coli genomes. Mutations identified in the CmeR-binding site, an inverted repeat sequence in the cmeABC promoter region that increases expression of the operon, were identified in 24/97 C. jejuni and 14/67 C. coli genomes. The presence of these variants, in addition to RE-cmeABC, was noted in 18 of the 24 C. jejuni and 9 of the 14 C. coli genomes. CONCLUSIONS Both RE-cmeABC and mutations in the CmeR-binding site were strongly associated with the MDR phenotype in C. jejuni and C. coli. This is the first report of RE-cmeABC in Peru and suggests it is a major driver of resistance to the principal therapies used to treat human campylobacteriosis in this setting.
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Affiliation(s)
- Francesca Schiaffino
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia; Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - Craig T Parker
- Agricultural Research Service, U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, California
| | | | - Ben Pascoe
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom; Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | | | | | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Steven Huynh
- Agricultural Research Service, U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, California
| | - Pablo Peñataro Yori
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia; Asociacion Benefica Prisma, Iquitos, Peru
| | | | - Hannah K Gray
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Guillermo Salvatierra
- School of Veterinary Medicine, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | | | - Samuel K Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona; The BIO5 Institute, University of Arizona, Tucson, Arizona.
| | - Margaret N Kosek
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia; Asociacion Benefica Prisma, Iquitos, Peru.
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Mendoza AP, Muñoz-Maceda A, Ghersi BM, De La Puente M, Zariquiey C, Cavero N, Murillo Y, Sebastian M, Ibañez Y, Parker PG, Perez A, Uhart M, Robinson J, Olson SH, Rosenbaum MH. Diversity and prevalence of zoonotic infections at the animal-human interface of primate trafficking in Peru. PLoS One 2024; 19:e0287893. [PMID: 38324542 PMCID: PMC10849265 DOI: 10.1371/journal.pone.0287893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/01/2023] [Indexed: 02/09/2024] Open
Abstract
Wildlife trafficking creates favorable scenarios for intra- and inter-specific interactions that can lead to parasite spread and disease emergence. Among the fauna affected by this activity, primates are relevant due to their potential to acquire and share zoonoses - infections caused by parasites that can spread between humans and other animals. Though it is known that most primate parasites can affect multiple hosts and that many are zoonotic, comparative studies across different contexts for animal-human interactions are scarce. We conducted a multi-parasite screening targeting the detection of zoonotic infections in wild-caught monkeys in nine Peruvian cities across three contexts: captivity (zoos and rescue centers, n = 187); pet (households, n = 69); and trade (trafficked or recently confiscated, n = 132). We detected 32 parasite taxa including mycobacteria, simian foamyvirus, bacteria, helminths, and protozoa. Monkeys in the trade context had the highest prevalence of hemoparasites (including Plasmodium malariae/brasilianum, Trypanosoma cruzi, and microfilaria) and enteric helminths and protozoa were less common in pet monkeys. However, parasite communities showed overall low variation between the three contexts. Parasite richness (PR) was best explained by host genus and the city where the animal was sampled. Squirrel (genus Saimiri) and wooly (genus Lagothrix) monkeys had the highest PR, which was ~2.2 times the PR found in tufted capuchins (genus Sapajus) and tamarins (genus Saguinus/Leontocebus) in a multivariable model adjusted for context, sex, and age. Our findings illustrate that the threats of wildlife trafficking to One Health encompass exposure to multiple zoonotic parasites well-known to cause disease in humans, monkeys, and other species. We demonstrate these threats continue beyond the markets where wildlife is initially sold; monkeys trafficked for the pet market remain a reservoir for and contribute to the translocation of zoonotic parasites to households and other captive facilities where contact with humans is frequent. Our results have practical applications for the healthcare of rescued monkeys and call for urgent action against wildlife trafficking and ownership of monkeys as pets.
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Affiliation(s)
- A. Patricia Mendoza
- Wildlife Conservation Society - Peru Program, Lima, Peru
- Department of Biology, University of Missouri - Saint Louis, St Louis, Missouri, United States of America
- Asociación Neotropical Primate Conservation – Perú, Moyobamba, San Martín, Perú
| | - Ana Muñoz-Maceda
- School of Anthropology and Conservation, Durrell Institute of Conservation and Ecology, University of Kent, Canterbury, Kent, United Kingdom
| | - Bruno M. Ghersi
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
| | | | | | - Nancy Cavero
- Wildlife Conservation Society - Peru Program, Lima, Peru
| | - Yovana Murillo
- Wildlife Conservation Society - Peru Program, Lima, Peru
| | | | - Yohani Ibañez
- Wildlife Conservation Society - Peru Program, Lima, Peru
| | - Patricia G. Parker
- Department of Biology, University of Missouri - Saint Louis, St Louis, Missouri, United States of America
| | - Alberto Perez
- Servicio Nacional de Sanidad y Calidad Agroalimentaria, Buenos Aires, Argentina
| | - Marcela Uhart
- One Health Institute, University of California - Davis, Davis, California, United States of America
| | - Janine Robinson
- School of Anthropology and Conservation, Durrell Institute of Conservation and Ecology, University of Kent, Canterbury, Kent, United Kingdom
| | - Sarah H. Olson
- Wildlife Conservation Society - Health Program, Bronx, New York, United States of America
| | - Marieke H. Rosenbaum
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
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5
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Bhatt AP, Arnold JW, Awoniyi M, Sun S, Santiago VF, Quintela PH, Walsh K, Ngobeni R, Hansen B, Gulati A, Carroll IM, Azcarate-Peril MA, Fodor AA, Swann J, Bartelt LA. Giardia Antagonizes Beneficial Functions of Indigenous and Therapeutic Intestinal Bacteria during Malnutrition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.575921. [PMID: 38328247 PMCID: PMC10849499 DOI: 10.1101/2024.01.22.575921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Undernutrition in children commonly disrupts the structure and function of the small intestinal microbial community, leading to enteropathies, compromised metabolic health, and impaired growth and development. The mechanisms by which diet and microbes mediate the balance between commensal and pathogenic intestinal flora remain elusive. In a murine model of undernutrition, we investigated the direct interactions Giardia lamblia, a prevalent small intestinal pathogen, on indigenous microbiota and specifically on Lactobacillus strains known for their mucosal and growth homeostatic properties. Our research reveals that Giardia colonization shifts the balance of lactic acid bacteria, causing a relative decrease in Lactobacillus spp . and an increase in Bifidobacterium spp . This alteration corresponds with a decrease in multiple indicators of mucosal and nutritional homeostasis. Additionally, protein-deficient conditions coupled with Giardia infection exacerbate the rise of primary bile acids and susceptibility to bile acid-induced intestinal barrier damage. In epithelial cell monolayers, Lactobacillus spp . mitigated bile acid-induced permeability, showing strain-dependent protective effects. In vivo, L. plantarum, either alone or within a Lactobacillus spp consortium, facilitated growth in protein-deficient mice, an effect attenuated by Giardia , despite not inhibiting Lactobacillus colonization. These results highlight Giardia's potential role as a disruptor of probiotic functional activity, underscoring the imperative for further research into the complex interactions between parasites and bacteria under conditions of nutritional deficiency.
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6
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Rhoades NS, Cinco IR, Hendrickson SM, Prongay K, Haertel AJ, Flores GE, Slifka MK, Messaoudi I. Infant diarrheal disease in rhesus macaques impedes microbiome maturation and is linked to uncultured Campylobacter species. Commun Biol 2024; 7:37. [PMID: 38182754 PMCID: PMC10770169 DOI: 10.1038/s42003-023-05695-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
Diarrheal diseases remain one of the leading causes of death for children under 5 globally, disproportionately impacting those living in low- and middle-income countries (LMIC). Campylobacter spp., a zoonotic pathogen, is one of the leading causes of food-borne infection in humans. Yet to be cultured Campylobacter spp. contribute to the total burden in diarrheal disease in children living in LMIC thus hampering interventions. We performed microbiome profiling and metagenomic genome assembly on samples collected from over 100 infant rhesus macaques longitudinally and during cases of clinical diarrhea within the first year of life. Acute diarrhea was associated with long-lasting taxonomic and functional shifts of the infant gut microbiome indicative of microbiome immaturity. We constructed 36 Campylobacter metagenomic assembled genomes (MAGs), many of which fell within 4 yet to be cultured species. Finally, we compared the uncultured Campylobacter MAGs assembled from infant macaques with publicly available human metagenomes to show that these uncultured species are also found in human fecal samples from LMIC. These data highlight the importance of unculturable Campylobacter spp. as an important target for reducing disease burden in LMIC children.
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Affiliation(s)
- Nicholas S Rhoades
- Department of Molecular biology and Biochemistry, University of California Irvine, Irvine, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Isaac R Cinco
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Sara M Hendrickson
- Division of Neuroscience, Oregon National Primate Research Center, Portland, OR, USA
| | - Kamm Prongay
- Division of Animal Resources and Research Support, Oregon National Primate Research Center, Oregon Health and Science University West Campus, Portland, OR, USA
| | - Andrew J Haertel
- Division of Animal Resources and Research Support, Oregon National Primate Research Center, Oregon Health and Science University West Campus, Portland, OR, USA
| | - Gilberto E Flores
- Department of Biology, California State University, Northridge, Northridge, CA, USA
| | - Mark K Slifka
- Division of Neuroscience, Oregon National Primate Research Center, Portland, OR, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA.
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Jones HJ, Bourke CD, Swann JR, Robertson RC. Malnourished Microbes: Host-Microbiome Interactions in Child Undernutrition. Annu Rev Nutr 2023; 43:327-353. [PMID: 37207356 DOI: 10.1146/annurev-nutr-061121-091234] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Childhood undernutrition is a major global health burden that is only partially resolved by nutritional interventions. Both chronic and acute forms of child undernutrition are characterized by derangements in multiple biological systems including metabolism, immunity, and endocrine systems. A growing body of evidence supports a role of the gut microbiome in mediating these pathways influencing early life growth. Observational studies report alterations in the gut microbiome of undernourished children, while preclinical studies suggest that this can trigger intestinal enteropathy, alter host metabolism, and disrupt immune-mediated resistance against enteropathogens, each of which contribute to poor early life growth. Here, we compile evidence from preclinical and clinical studies and describe the emerging pathophysiological pathways by which the early life gut microbiome influences host metabolism, immunity, intestinal function, endocrine regulation, and other pathways contributing to child undernutrition. We discuss emerging microbiome-directed therapies and consider future research directions to identify and target microbiome-sensitive pathways in child undernutrition.
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Affiliation(s)
- Helen J Jones
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
| | - Claire D Bourke
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
| | - Jonathan R Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ruairi C Robertson
- Centre for Genomics & Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom;
- Microenvironment and Immunity Unit, INSERM U1224, Institut Pasteur, Université Paris Cité, Paris, France
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Deblais L, Ojeda A, Brhane M, Mummed B, Hassen KA, Ahmedo BU, Weldesenbet YD, Amin JK, Ahmed IA, Usmane IA, Yusuf EA, Seran AJ, Abrahim FI, Game HT, Mummed BA, Usmail MM, Umer KA, Dawid MM, Gebreyes W, French N, Hassen JY, Roba KT, Mohammed A, Yimer G, Saleem C, Chen D, Singh N, Manary MJ, McKune SL, Havelaar AH, Rajashekara G. Prevalence and Load of the Campylobacter Genus in Infants and Associated Household Contacts in Rural Eastern Ethiopia: a Longitudinal Study from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project. Appl Environ Microbiol 2023; 89:e0042423. [PMID: 37310259 PMCID: PMC10370295 DOI: 10.1128/aem.00424-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/22/2023] [Indexed: 06/14/2023] Open
Abstract
In our previous cross-sectional study, multiple species of Campylobacter were detected (88%) in stool samples from children (12 to 14 months of age) in rural eastern Ethiopia. This study assessed the temporal fecal carriage of Campylobacter in infants and identified putative reservoirs associated with these infections in infants from the same region. The prevalence and load of Campylobacter were determined using genus-specific real-time PCR. Stool samples from 106 infants (n = 1,073) were collected monthly from birth until 376 days of age (DOA). Human stool samples (mothers and siblings), livestock feces (cattle, chickens, goats, and sheep), and environmental samples (soil and drinking water) from the 106 households were collected twice per household (n = 1,644). Campylobacter was most prevalent in livestock feces (goats, 99%; sheep, 98%; cattle, 99%; chickens, 93%), followed by human stool samples (siblings, 91%; mothers, 83%; infants, 64%) and environmental samples (soil, 58%; drinking water, 43%). The prevalence of Campylobacter in infant stool samples significantly increased with age, from 30% at 27 DOA to 89% at 360 DOA (1% increase/day in the odds of being colonized) (P < 0.001). The Campylobacter load increased linearly (P < 0.001) with age from 2.95 logs at 25 DOA to 4.13 logs at 360 DOA. Within a household, the Campylobacter load in infant stool samples was positively correlated with the load in mother stool samples (r2 = 0.18) and soil collected inside the house (r2 = 0.36), which were in turn both correlated with Campylobacter loads in chicken and cattle feces (0.60 < r2 < 0.63) (P < 0.01). In conclusion, a high proportion of infants are infected with Campylobacter in eastern Ethiopia, and contact with the mother and contaminated soil may be associated with early infections. IMPORTANCE A high Campylobacter prevalence during early childhood has been associated with environmental enteric dysfunction (EED) and stunting, especially in low-resource settings. Our previous study demonstrated that Campylobacter was frequently found (88%) in children from eastern Ethiopia; however, little is known about potential Campylobacter reservoirs and transmission pathways leading to infection of infants by Campylobacter during early growth. In the longitudinal study presented here, Campylobacter was frequently detected in infants within the 106 surveyed households from eastern Ethiopia, and the prevalence was age dependent. Furthermore, preliminary analyses highlighted the potential role of the mother, soil, and livestock in the transmission of Campylobacter to the infant. Further work will explore the species and genetic composition of Campylobacter in infants and putative reservoirs using PCR and whole-genome and metagenomic sequencing. The findings from these studies can lead to the development of interventions to minimize the risk of transmission of Campylobacter to infants and, potentially, EED and stunting.
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Affiliation(s)
| | - Amanda Ojeda
- University of Florida, Gainesville, Florida, USA
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- Massey University, Palmerston North, New Zealand
| | | | | | | | - Getnet Yimer
- Global One Health Initiative, The Ohio State University, Addis Ababa, Ethiopia
| | - Cyrus Saleem
- University of Florida, Gainesville, Florida, USA
| | - Dehao Chen
- University of Florida, Gainesville, Florida, USA
| | - Nitya Singh
- University of Florida, Gainesville, Florida, USA
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9
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Kabir F, Iqbal J, Jamil Z, Iqbal NT, Mallawaarachchi I, Aziz F, Kalam A, Muneer S, Hotwani A, Ahmed S, Umrani F, Syed S, Sadiq K, Ma JZ, Moore SR, Ali A. Impact of enteropathogens on faltering growth in a resource-limited setting. Front Nutr 2023; 9:1081833. [PMID: 36704796 PMCID: PMC9871909 DOI: 10.3389/fnut.2022.1081833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/08/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction Environmental enteropathy is an important contributor to childhood malnutrition in the developing world. Chronic exposure to fecal pathogens leads to alteration in intestinal structure and function, resulting in impaired gut immune function, malabsorption, and growth faltering leading to environmental enteropathy. Methods A community-based intervention study was carried out on children till 24 months of age in Matiari district, Pakistan. Blood and fecal specimens were collected from the enrolled children aged 3-6 and 9 months. A real-time PCR-based TaqMan array card (TAC) was used to detect enteropathogens. Results Giardia, Campylobacter spp., enteroaggregative Escherichia coli (EAEC), Enteropathogenic Escherichia coli (EPEC), Enterotoxigenic Escherichia coli (ETEC), and Cryptosporidium spp. were the most prevailing enteropathogens in terms of overall positivity at both time points. Detection of protozoa at enrollment and 9 months was negatively correlated with rate of change in height-for-age Z (ΔHAZ) scores during the first and second years of life. A positive association was found between Giardia, fecal lipocalin (LCN), and alpha 1-Acid Glycoprotein (AGP), while Campylobacter spp. showed positive associations with neopterin (NEO) and myeloperoxidase (MPO). Conclusion Protozoal colonization is associated with a decline in linear growth velocity during the first 2 years of life in children living in Environmental enteric dysfunction (EED) endemic settings. Mechanistic studies exploring the role of cumulative microbial colonization, their adaptations to undernutrition, and their influence on gut homeostasis are required to understand symptomatic enteropathogen-induced growth faltering.
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Affiliation(s)
- Furqan Kabir
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Zehra Jamil
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Najeeha Talat Iqbal
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
| | - Indika Mallawaarachchi
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Fatima Aziz
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Adil Kalam
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sahrish Muneer
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Fayaz Umrani
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sana Syed
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, Charlottesville, VA, United States
| | - Kamran Sadiq
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Jennie Z. Ma
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - Sean R. Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, Charlottesville, VA, United States,*Correspondence: Sean R. Moore,
| | - Asad Ali
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan,Asad Ali,
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10
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Parker CT, Schiaffino F, Huynh S, Paredes Olortegui M, Peñataro Yori P, Garcia Bardales PF, Pinedo Vasquez T, Curico Huansi GE, Manzanares Villanueva K, Shapiama Lopez WV, Cooper KK, Kosek MN. Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species. PLoS Negl Trop Dis 2022; 16:e0010815. [PMID: 36194603 PMCID: PMC9565744 DOI: 10.1371/journal.pntd.0010815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/14/2022] [Accepted: 09/13/2022] [Indexed: 12/11/2022] Open
Abstract
Campylobacter spp. are a major cause of bacterial diarrhea worldwide and are associated with high rates of mortality and linear growth faltering in children living in low- to middle-income countries (LMICs). Campylobacter jejuni and Campylobacter coli are most often the causative agents of enteric disease among children in LMICs. However, previous work on a collection of stool samples from children under 2 years of age, living in a low resource community in Peru with either acute diarrheal disease or asymptomatic, were found to be qPCR positive for Campylobacter species but qPCR negative for C. jejuni and C. coli. The goal of this study was to determine if whole-genome shotgun metagenomic sequencing (WSMS) could identify the Campylobacter species within these samples. The Campylobacter species identified in these stool samples included C. jejuni, C. coli, C. upsaliensis, C. concisus, and the potential new species of Campylobacter, "Candidatus Campylobacter infans". Moreover, WSMS results demonstrate that over 65% of the samples represented co-infections with multiple Campylobacter species present in a single stool sample, a novel finding in human populations. Analysis of shotgun metagenomic data obtained from fecal samples of children living in a low resource tropical community of Peru revealed multiple Campylobacter species. Co-infections with more than one Campylobacter species within the same sample was a common finding. A potential new species of Campylobacter was also detected within these samples.
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Affiliation(s)
- Craig T. Parker
- Agricultural Research Service, U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, California, United States of America
| | - Francesca Schiaffino
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia, United States of America
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Steven Huynh
- Agricultural Research Service, U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, California, United States of America
| | | | - Pablo Peñataro Yori
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia, United States of America
- Asociacion Benefica Prisma, Iquitos, Peru
| | | | | | | | | | | | - Kerry K. Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
- * E-mail: (KKC); (MNK)
| | - Margaret N. Kosek
- Division of Infectious Diseases, University of Virginia, Charlottesville, Virginia, United States of America
- Asociacion Benefica Prisma, Iquitos, Peru
- * E-mail: (KKC); (MNK)
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11
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Russotto Y, Micali C, Pellicanò GF, Nunnari G, Venanzi Rullo E. HIV and Mediterranean Zoonoses: A Review of the Literature. Infect Dis Rep 2022; 14:694-709. [PMID: 36136825 PMCID: PMC9498920 DOI: 10.3390/idr14050075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/21/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
A zoonosis is an infectious disease that has jumped from a non-human animal to humans. Some zoonoses are very common in the Mediterranean area and endemic in specific regions, so they represent an important problem for public health. Human Immunodeficiency Virus (HIV) is a virus that has originated as a zoonosis and is now diffused globally, with the most significant numbers of infected people among the infectious diseases. Since the introduction of antiretroviral therapy (ART), the history for people living with HIV (PLWH) has changed drastically, and many diseases are now no different in epidemiology and prognosis as they are in not-HIV-infected people. Still, the underlying inflammatory state that is correlated with HIV and other alterations related to the infection itself can be a risk factor when infected with other bacteria, parasites or viruses. We reviewed the literature for infection by the most common Mediterranean zoonoses, such as Campylobacter, Salmonella, Brucella, Rickettsia, Borrelia, Listeria and Echinococcus, and a possible correlation with HIV. We included Monkeypox, since the outbreak of cases is becoming a concern lately. We found that HIV may be related with alterations of the microbiome, as for campylobacteriosis, and that there are some zoonoses with a significant prevalence in PLWH, as for salmonellosis.
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Affiliation(s)
- Ylenia Russotto
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Cristina Micali
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
- Correspondence: ; Tel.: +39-09-0221-2032
| | - Giovanni Francesco Pellicanò
- Department of Human Pathology of the Adult and the Developmental Age “G. Barresi”, University of Messina, 98124 Messina, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
| | - Emmanuele Venanzi Rullo
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Messina, 98124 Messina, Italy
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12
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Rouhani S, Peñataro Yori P, Paredes Olortegui M, Lima AA, Ahmed T, Mduma ER, George A, Samie A, Svensen E, Lima I, Mondal D, Mason CJ, Kalam A, Guerrant RL, Lang D, Zaidi A, Kang G, Houpt E, Kosek MN. The Epidemiology of Sapovirus in the Etiology, Risk Factors, and Interactions of Enteric Infection and Malnutrition and the Consequences for Child Health and Development (MAL-ED) Study: Evidence of Protection Following Natural Infection. Clin Infect Dis 2022; 75:1334-1341. [PMID: 36094137 PMCID: PMC9555839 DOI: 10.1093/cid/ciac165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Sapovirus is one of the principal agents of acute viral enteritis in children. Because it has not been routinely included in diagnostic evaluations, the epidemiology and natural history remain poorly described. METHODS A birth cohort of 1715 children from 8 countries contributed surveillance samples (n = 35 620) and diarrheal specimens (n = 6868) from 0 to 24 months of age. Sapovirus was detected by quantitative polymerase chain reaction concurrently to other enteropathogens using multiarray cards. Logistic regression was used to identify risk factors, and longitudinal models were employed to estimate incidence rates and evaluate evidence of protective immunity. RESULTS Sapovirus was detected in 24.7% (n = 1665) of diarrheal stools and 12.8% (n = 4429) of monthly surveillance samples. More than 90% of children were infected and 60% experienced sapovirus diarrhea in the first 2 years of life. Breastfeeding and higher socioeconomic status were associated with reduced incidence of infection and illness. Specimens with sapovirus detected had an increased odds of coinfection with rotavirus (odds ratio [OR], 1.6 [95% confidence interval {CI}, 1.3-2.0]), astrovirus (OR, 1.5 [95% CI, 1.3-1.7]), adenovirus (OR, 1.3 [95% CI, 1.1-1.5]), and Shigella (OR, 1.4 [95% CI, 1.3-1.6]). Prior infection with sapovirus conferred a risk reduction of 22% for subsequent infection (hazard ratio [HR], 0.78 [95% CI, .74-.85]) and 24% for subsequent diarrhea (95% CI, 11.0%-35.0%; HR, 0.76). CONCLUSIONS Sapovirus is a common cause of early childhood diarrhea. Further research on coinfections is warranted. Evidence of acquired immunity was observed even in the absence of genotype-specific analysis for this pathogen of known genetic diversity.
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Affiliation(s)
- Saba Rouhani
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA.,Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Pablo Peñataro Yori
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | - Aldo A Lima
- Federal University of Ceará, Fortaleza, Brazil
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | | | | | | | - Ila Lima
- Federal University of Ceará, Fortaleza, Brazil
| | - Dinesh Mondal
- Nutrition Infection Interaction Research Group, Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Carl J Mason
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Richard L Guerrant
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Dennis Lang
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USAand
| | - Anita Zaidi
- Enteric and Diarrheal Diseases Programme, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | | | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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13
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Cannon JL, Seabolt MH, Xu R, Montmayeur A, Suh SH, Diez-Valcarce M, Bucardo F, Becker-Dreps S, Vinjé J. Gut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua. Viruses 2022; 14:v14071395. [PMID: 35891376 PMCID: PMC9323674 DOI: 10.3390/v14071395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Noroviruses are associated with one fifth of diarrheal illnesses globally and are not yet preventable with vaccines. Little is known about the effects of norovirus infection on infant gut microbiome health, which has a demonstrated role in protecting hosts from pathogens and a possible role in oral vaccine performance. In this study, we characterized infant gut microbiome changes occurring with norovirus-associated acute gastroenteritis (AGE) and the extent of recovery. Metagenomic sequencing was performed on the stools of five infants participating in a longitudinal birth cohort study conducted in León, Nicaragua. Taxonomic and functional diversities of gut microbiomes were profiled at time points before, during, and after norovirus infection. Initially, the gut microbiomes resembled those of breastfeeding infants, rich in probiotic species. When disturbed by AGE, Gammaproteobacteria dominated, particularly Pseudomonas species. Alpha diversity increased but the genes involved in carbohydrate metabolism and glycan biosynthesis decreased. After the symptoms subsided, the gut microbiomes rebounded with their taxonomic and functional communities resembling those of the pre-infection microbiomes. In this study, during disruptive norovirus-associated AGE, the gut microbiome was temporarily altered, returning to a pre-infection composition a median of 58 days later. Our study provides new insights for developing probiotic treatments and furthering our understanding of the role that episodes of AGE have in shaping the infant gut microbiome, their long-term outcomes, and implications for oral vaccine effectiveness.
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Affiliation(s)
- Jennifer L. Cannon
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
- CDC Foundation, Atlanta, GA 30329, USA
- Correspondence: ; Tel.: +1-404-639-2396
| | - Matthew H. Seabolt
- Office of Advanced Molecular Detection, National Center for Emerging & Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA;
- Leidos Inc., Reston, VA 20190, USA
| | - Ruijie Xu
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
| | - Anna Montmayeur
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
| | - Soo Hwan Suh
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
- Ministry of Food and Drug Safety, Cheonju-Si 28159, Korea
| | - Marta Diez-Valcarce
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
| | - Filemón Bucardo
- Center for Infectious Diseases Research, National Autonomous University of Nicaragua—León (UNAN-León), León 21000, Nicaragua;
| | - Sylvia Becker-Dreps
- Department of Family Medicine and Epidemiology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Jan Vinjé
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (R.X.); (A.M.); (S.H.S.); (M.D.-V.); (J.V.)
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14
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Dynamic of the human gut microbiome under infectious diarrhea. Curr Opin Microbiol 2022; 66:79-85. [PMID: 35121284 DOI: 10.1016/j.mib.2022.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 11/20/2022]
Abstract
Despite the widespread implementation of sanitation, immunization and appropriate treatment, infectious diarrheal diseases still inflict a great health burden to children living in low resource settings. Conventional microbiology research in diarrhea have focused on the pathogen's biology and pathogenesis, but initial enteric infections could trigger subsequent perturbations in the gut microbiome, leading to short-term or long-term health effects. Conversely, such pre-existing perturbations could render children more vulnerable to enteropathogen colonization and diarrhea. Recent advances in DNA sequencing and bioinformatic analyses have been integrated in well-designed clinical and epidemiological studies, which allow us to track how the gut microbiome changes from disease onset to recovery. Here, we aim to summarize the current understanding on the diarrheal gut microbiome, stratified into different disease stages. Furthermore, we discuss how such perturbations could have impacts beyond an acute diarrhea episode, specifically on the child's nutritional status and the facilitation of antimicrobial resistance.
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15
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Colston JM, Taniuchi M, Ahmed T, Ferdousi T, Kabir F, Mduma E, Nshama R, Iqbal NT, Haque R, Ahmed T, Ali Bhutta Z, Kosek MN, Platts-Mills JA. Intestinal Colonization With Bifidobacterium longum Subspecies Is Associated With Length at Birth, Exclusive Breastfeeding, and Decreased Risk of Enteric Virus Infections, but Not With Histo-Blood Group Antigens, Oral Vaccine Response or Later Growth in Three Birth Cohorts. Front Pediatr 2022; 10:804798. [PMID: 35252058 PMCID: PMC8888871 DOI: 10.3389/fped.2022.804798] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/13/2022] [Indexed: 11/30/2022] Open
Abstract
Bifidobacterium longum subspecies detected in infant stool have been associated with numerous subsequent health outcomes and are potential early markers of deviation from healthy developmental trajectories. This analysis derived indicators of carriage and early colonization with B. infantis and B. longum and quantified their associations with a panel of early-life exposures and outcomes. In a sub-study nested within a multi-site birth cohort, extant stool samples from infants in Bangladesh, Pakistan and Tanzania were tested for presence and quantity of two Bifidobacterium longum subspecies. The results were matched to indicators of nutritional status, enteropathogen infection, histo-blood group antigens, vaccine response and feeding status and regression models were fitted to test for associations while adjusting for covariates. B. infantis was associated with lower quantity of and decreased odds of colonization with B. longum, and vice versa. Length at birth was associated with a 0.36 increase in log10 B. infantis and a 0.28 decrease in B. longum quantity at 1 month of age. B. infantis colonization was associated with fewer viral infections and small reductions in the risk of rotavirus and sapovirus infections, but not reduced overall diarrheal disease risk. No associations with vaccine responses, HBGAs or later nutritional status were identified. Suboptimal intrauterine growth and a shorter duration of exclusive breastfeeding may predispose infants to early intestinal colonization with the B. longum subspecies at the expense of B. infantis, thus denying them potential benefits of reduced enteric virus episodes.
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Affiliation(s)
- Josh M Colston
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
| | - Tahmina Ahmed
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
| | - Tania Ferdousi
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Estomih Mduma
- Haydom Global Health Research Centre, Haydom, Tanzania
| | | | - Najeeha Talat Iqbal
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Zulfiqar Ali Bhutta
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States.,Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
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16
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Huus KE, Hoang TT, Creus-Cuadros A, Cirstea M, Vogt SL, Knuff-Janzen K, Sansonetti PJ, Vonaesch P, Finlay BB. Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition. Nat Commun 2021; 12:6860. [PMID: 34824233 PMCID: PMC8617199 DOI: 10.1038/s41467-021-27191-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 11/08/2021] [Indexed: 12/18/2022] Open
Abstract
Child undernutrition is a global health issue associated with a high burden of infectious disease. Undernourished children display an overabundance of intestinal pathogens and pathobionts, and these bacteria induce enteric dysfunction in undernourished mice; however, the cause of their overgrowth remains poorly defined. Here, we show that disease-inducing human isolates of Enterobacteriaceae and Bacteroidales spp. are capable of multi-species symbiotic cross-feeding, resulting in synergistic growth of a mixed community in vitro. Growth synergy occurs uniquely under malnourished conditions limited in protein and iron: in this context, Bacteroidales spp. liberate diet- and mucin-derived sugars and Enterobacteriaceae spp. enhance the bioavailability of iron. Analysis of human microbiota datasets reveals that Bacteroidaceae and Enterobacteriaceae are strongly correlated in undernourished children, but not in adequately nourished children, consistent with a diet-dependent growth synergy in the human gut. Together these data suggest that dietary cross-feeding fuels the overgrowth of pathobionts in undernutrition.
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Affiliation(s)
- K. E. Huus
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - T. T. Hoang
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - A. Creus-Cuadros
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - M. Cirstea
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - S. L. Vogt
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - K. Knuff-Janzen
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - P. J. Sansonetti
- grid.428999.70000 0001 2353 6535Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France ,grid.429007.80000 0004 0627 2381Present Address: Center for Microbes, Development and Health, Institut Pasteur de Shanghai, Shanghai, China
| | - P. Vonaesch
- grid.428999.70000 0001 2353 6535Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France ,grid.416786.a0000 0004 0587 0574Present Address: Human and Animal Health Unit, Swiss Tropical and Public Health Institute & University of Basel, Basel, Switzerland
| | - B. B. Finlay
- grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada ,grid.440050.50000 0004 0408 2525Canadian Institute for Advanced Research, Toronto, Ontario Canada
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17
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Age and Giardia intestinalis Infection Impact Canine Gut Microbiota. Microorganisms 2021; 9:microorganisms9091862. [PMID: 34576757 PMCID: PMC8469385 DOI: 10.3390/microorganisms9091862] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/16/2022] Open
Abstract
Giardia intestinalis is a flagellated protozoan responsible for giardiosis (also called giardiasis in humans), the most prevalent and widespread parasitic infection in humans and mammals worldwide. The intestinal microbiota is highly diverse and any alteration in its composition may impact on the health of the host. While studies on the mouse model of giardiosis described the role of the gut microbiota in host susceptibility to infection by the parasite, little is known about the gut microbiota during natural infections in dogs and particularly in puppies. In this study, we monitored naturally G. intestinalis-infected puppies for 3 months and quantified cyst excretion every 2 weeks. All puppies remained subclinically infected during the sampling period as confirmed by fecal examination. In parallel, we performed 16S Illumina sequencing of fecal samples from the different time points to assess the impact of G. intestinalis infection on gut microbiota development of the puppies, as well as gut health markers of immunity such as fecal IgA and calprotectin. Sequencing results revealed that the canine fecal microbiota of Giardia-infected puppies becomes more complex and less diverse with increasing age. In addition, significant differences in the structure of the microbiota were observed between puppies with high and low Giardia cyst excretion. Chronic subclinical G. intestinalis infection appears to be associated with some detrimental structural changes in the gut microbiota. G. intestinalis-associated dysbiosis is characterized by an enrichment of facultative anaerobic, mucus-degrading, pro-inflammatory species and opportunistic pathogens, as well as a reduction of Lactobacillus johnsonii at specific time points. Calprotectin levels increased with age, suggesting the establishment of chronic low-grade inflammation in puppies. Further work is needed to demonstrate whether these alterations in the canine gut microbiota could lead to a dysbiosis-related disease, such as irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD).
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18
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Patuzzi I, Orsini M, Cibin V, Petrin S, Mastrorilli E, Tiengo A, Gobbo F, Catania S, Barco L, Ricci A, Losasso C. The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time. Microorganisms 2021; 9:221. [PMID: 33499060 PMCID: PMC7911313 DOI: 10.3390/microorganisms9020221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/27/2022] Open
Abstract
Campylobacter is the most frequent foodborne zoonotic bacteria worldwide, with chicken meat being overwhelmingly the most important reservoir for human infections. Control measures implemented at the farm level (i.e., biosecurity or vaccination), which have been successfully applied to limit other pathogens, such as Salmonella, have not been effective in reducing Campylobacter occurrence. Thus, new approaches are needed to fully understand the ecological interactions of Campylobacter with host animals to effectively comprehend its epidemiology. The objective of this study was to analyse longitudinally the gut microbiota composition of Campylobacter-infected and non-infected farms to identify any difference that could potentially be indicative of gut colonization by Campylobacter spp. Differences in the colonization rate and timing were observed at the farms that became positive for Campylobacter jejuni over the investigated time points, even though in positive tests, the occurrence of Campylobacter jejuni gut colonization was not observed before the second week of the life of the birds. Significant differences were observed in the abundances of specific bacterial taxa between the microbiota of individuals belonging to farms that became Campylobacter positive during the study and those who remained negative with particular reference to Bacteroidales and Clostridiales, respectively. Moreover, Campylobacter colonization dramatically influenced the microbiota richness, although to a different extent depending on the infection timing. Finally, a key role of Faecalibacterium and Lactobacillus genera on the Campylobacter microbial network was observed. Understanding the ecology of the Campylobacter interaction with host microbiota during infection could support novel approaches for broiler microbial barrier restoration. Therefore, evidence obtained through this study can be used to identify options to reduce the incidence of infection at a primary production level based on the targeted influence of the intestinal microbiota, thus helping develop new control strategies in order to mitigate the risk of human exposure to Campylobacter by chicken meat consumption.
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Affiliation(s)
- Ilaria Patuzzi
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Massimiliano Orsini
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Veronica Cibin
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Sara Petrin
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Eleonora Mastrorilli
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
| | - Alessia Tiengo
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Federica Gobbo
- Avian Pathology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (F.G.); (S.C.)
| | - Salvatore Catania
- Avian Pathology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (F.G.); (S.C.)
| | - Lisa Barco
- Experimental Microbiology Department, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy;
| | - Antonia Ricci
- National Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (V.C.); (A.T.); (A.R.)
| | - Carmen Losasso
- Microbial Ecology and Genomics Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università 10, 35120 Legnaro, Italy; (I.P.); (M.O.); (S.P.); (E.M.)
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19
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Rhoades NS, Hendrickson SM, Prongay K, Haertel A, Gill L, Edwards RA, Garzel L, Slifka MK, Messaoudi I. Growth faltering regardless of chronic diarrhea is associated with mucosal immune dysfunction and microbial dysbiosis in the gut lumen. Mucosal Immunol 2021; 14:1113-1126. [PMID: 34158595 PMCID: PMC8379072 DOI: 10.1038/s41385-021-00418-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 02/04/2023]
Abstract
Despite the impact of childhood diarrhea on morbidity and mortality, our understanding of its sequelae has been significantly hampered by the lack of studies that examine samples across the entire intestinal tract. Infant rhesus macaques are naturally susceptible to human enteric pathogens and recapitulate the hallmarks of diarrheal disease such as intestinal inflammation and growth faltering. Here, we examined intestinal biopsies, lamina propria leukocytes, luminal contents, and fecal samples from healthy infants and those experiencing growth faltering with distant acute or chronic active diarrhea. We show that growth faltering in the presence or absence of active diarrhea is associated with a heightened systemic and mucosal pro-inflammatory state centered in the colon. Moreover, polyclonal stimulation of colonic lamina propria leukocytes resulted in a dampened cytokine response, indicative of immune exhaustion. We also detected a functional and taxonomic shift in the luminal microbiome across multiple gut sites including the migration of Streptococcus and Prevotella species between the small and large intestine, suggesting a decompartmentalization of gut microbial communities. Our studies provide valuable insight into the outcomes of diarrheal diseases and growth faltering not attainable in humans and lays the groundwork to test interventions in a controlled and reproducible setting.
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Affiliation(s)
- Nicholas S. Rhoades
- grid.266093.80000 0001 0668 7243Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA USA
| | - Sara M. Hendrickson
- grid.410436.40000 0004 0619 6542Division of Neuroscience, Oregon National Primate Research Center, Portland, OR USA
| | - Kamm Prongay
- grid.5288.70000 0000 9758 5690Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University West Campus, Portland, OR USA
| | - Andrew Haertel
- grid.5288.70000 0000 9758 5690Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University West Campus, Portland, OR USA
| | - Leanne Gill
- grid.27860.3b0000 0004 1936 9684California National Primate Research Center, Davis, Davis, CA USA
| | - Robert A. Edwards
- grid.266093.80000 0001 0668 7243Department of Pathology and Laboratory Medicine, University of California, Irvine, CA USA
| | - Laura Garzel
- grid.27860.3b0000 0004 1936 9684California National Primate Research Center, Davis, Davis, CA USA
| | - Mark K. Slifka
- grid.410436.40000 0004 0619 6542Division of Neuroscience, Oregon National Primate Research Center, Portland, OR USA
| | - Ilhem Messaoudi
- grid.266093.80000 0001 0668 7243Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA USA
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20
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Natural Infection with Giardia Is Associated with Altered Community Structure of the Human and Canine Gut Microbiome. mSphere 2020; 5:5/4/e00670-20. [PMID: 32759335 PMCID: PMC7407069 DOI: 10.1128/msphere.00670-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
While enteric parasitic infections are among the most important infections in lower- and middle-income countries, their impact on gut microbiota is poorly understood. We reasoned that clinical symptoms associated with these infections may be influenced by alterations of the microbiome that occur during infection. To explore this notion, we took a two-pronged approach. First, we studied a cohort of dogs naturally infected with various enteric parasites and found a strong association between parasite infection and altered gut microbiota composition. Giardia, one of the most prevalent parasite infections globally, had a particularly large impact on the microbiome. Second, we took a database-driven strategy to integrate microbiome data with clinical data from large human field studies and found that Giardia infection is also associated with marked alteration of the gut microbiome of children, suggesting a possible explanation for why Giardia has been reported to be associated with protection from moderate to severe diarrhea. Enteric parasitic infections are among the most prevalent infections in lower- and middle-income countries (LMICs) and have a profound impact on global public health. While the microbiome is increasingly recognized as a key determinant of gut health and human development, the impact of naturally acquired parasite infections on microbial community structure in the gut, and the extent to which parasite-induced changes in the microbiome may contribute to gastrointestinal symptoms, is poorly understood. Enteric parasites are routinely identified in companion animals in the United States, presenting a unique opportunity to leverage this animal model to investigate the impact of naturally acquired parasite infections on the microbiome. Clinical, parasitological, and microbiome profiling of a cohort of 258 dogs revealed a significant correlation between parasite infection and composition of the bacterial community in the gut. Relative to other enteric parasites, Giardia was associated with a more pronounced perturbation of the microbiome. To compare our findings to large-scale epidemiological studies of enteric diseases in humans, a database mining approach was employed to integrate clinical and microbiome data. Substantial and consistent alterations to microbiome structure were observed in Giardia-infected children. Importantly, infection was associated with a reduction in the relative abundance of potential pathobionts, including Gammaproteobacteria, and an increase in Prevotella—a profile often associated with gut health. Taken together, these data show that widespread Giardia infection in young animals and humans is associated with significant remodeling of the gut microbiome and provide a possible explanation for the high prevalence of asymptomatic Giardia infections observed across host species. IMPORTANCE While enteric parasitic infections are among the most important infections in lower- and middle-income countries, their impact on gut microbiota is poorly understood. We reasoned that clinical symptoms associated with these infections may be influenced by alterations of the microbiome that occur during infection. To explore this notion, we took a two-pronged approach. First, we studied a cohort of dogs naturally infected with various enteric parasites and found a strong association between parasite infection and altered gut microbiota composition. Giardia, one of the most prevalent parasite infections globally, had a particularly large impact on the microbiome. Second, we took a database-driven strategy to integrate microbiome data with clinical data from large human field studies and found that Giardia infection is also associated with marked alteration of the gut microbiome of children, suggesting a possible explanation for why Giardia has been reported to be associated with protection from moderate to severe diarrhea.
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21
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Huus KE, Rodriguez-Pozo A, Kapel N, Nestoret A, Habib A, Dede M, Manges A, Collard JM, Sansonetti PJ, Vonaesch P, Finlay BB. Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study. MICROBIOME 2020; 8:113. [PMID: 32718353 PMCID: PMC7385872 DOI: 10.1186/s40168-020-00890-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/05/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Child undernutrition is a global health issue that is associated with poor sanitation and an altered intestinal microbiota. Immunoglobulin (Ig) A mediates host-microbial homeostasis in the intestine, and acutely undernourished children have been shown to have altered IgA recognition of the fecal microbiota. We sought to determine whether chronic undernutrition (stunting) or intestinal inflammation were associated with antibody recognition of the microbiota using two geographically distinct populations from the Afribiota project. Fecal bacteria from 200 children between 2 and 5 years old in Antananarivo, Madagascar, and Bangui, Central African Republic (CAR), were sorted into IgA-positive (IgA+) and IgA-negative (IgA-) populations by flow cytometry and subsequently characterized by 16S rRNA gene sequencing to determine IgA-bacterial targeting. We additionally measured IgG+ fecal bacteria by flow cytometry in a subset of 75 children. RESULTS Stunted children (height-for-age z-score ≤ -2) had a greater proportion of IgA+ bacteria in the fecal microbiota compared to non-stunted controls. This trend was consistent in both countries, despite the higher overall IgA-targeting of the microbiota in Madagascar, but lost significance in each country individually. Two of the most highly IgA-recognized bacteria regardless of nutritional status were Campylobacter (in CAR) and Haemophilus (in both countries), both of which were previously shown to be more abundant in stunted children; however, there was no association between IgA-targeting of these bacteria and either stunting or inflammatory markers. IgG-bound intestinal bacteria were rare in both stunted and non-stunted children, similar to levels observed in healthy populations. CONCLUSIONS Undernourished children carry a high load of intestinal pathogens and pathobionts. Our data suggest that stunted children have a greater proportion of IgA-recognized fecal bacteria. We moreover identify two putative pathobionts, Haemophilus and Campylobacter, that are broadly targeted by intestinal IgA. This study furthers our understanding of host-microbiota interactions in undernutrition and identifies immune-recognized microbes for future study.
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Affiliation(s)
- Kelsey E. Huus
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | | | - Nathalie Kapel
- Laboratoire de coprologie fonctionnelle, APHP.SU, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Alison Nestoret
- Laboratoire de coprologie fonctionnelle, APHP.SU, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Azimdine Habib
- Unité des Helminthiases, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Michel Dede
- Laboratoire d’Analyse médicale, Institut Pasteur de Bangui, Bangui, Central African Republic
| | - Amee Manges
- School of Population and Public Health, University of British Columbia, Vancouver, BC Canada
| | - Jean-Marc Collard
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Philippe J. Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
- Current address: Center for Microbes, Development and Health, Institut Pasteur de Shanghai, Shanghai, China
| | - Pascale Vonaesch
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
- Current address: Human and Animal Health Unit, Swiss Tropical and Public Health Institute & University of Basel, Basel, Switzerland
| | - B. Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC Canada
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22
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De R, Mukhopadhyay AK, Dutta S. Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter. Gut Pathog 2020; 12:32. [PMID: 32655699 PMCID: PMC7339541 DOI: 10.1186/s13099-020-00371-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Metagenomic analysis of the gut microbiome and resistome is instrumental for understanding the dynamics of diarrheal pathogenesis and antimicrobial resistance transmission (AMR). Metagenomic sequencing of 20 diarrheal fecal samples from Kolkata was conducted to understand the core and variable gut microbiota. Five of these samples were used for resistome analysis. The pilot study was conducted to determine a microbiota signature and the source of antimicrobial resistance genes (ARGs) in the diarrheal gut. RESULTS 16S rRNA amplicon sequencing was performed using Illumina MiSeq platform and analysed using the MGnify pipeline. The Genome Taxonomy Database (GTDB-Tk) was used for bacterial taxonomic identification. Diarrheal etiology was determined by culture method. Phylum Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were consistently present in 20 samples. Firmicutes was the most abundant phylum in 11 samples. The Bacteroidetes/Firmicutes ratio was less than 1 in 18 samples. 584 genera were observed. 18 of these were present in all the 20 samples. Proteobacteria was the dominant phylum in 6 samples associated with Vibrio cholerae infection. Conservation of operational taxonomic units (OTUs) among all the samples indicated the existence of a core microbiome. Asymptomatic carriage of pathogens like Vibrio cholerae and Helicobacter pylori was found. Signature of Candidate phyla or "microbial dark matter" occurred. Significant correlation of relative abundance of bacterial families of commensals and pathogens were found. Whole-genome sequencing (WGS) on Illumina MiSeq system and assembly of raw reads using metaSPAdes v3.9.1 was performed to study the resistome of 5 samples. ABRicate was used to assign ARG function. 491 resistance determinants were identified. In 80% of the samples tetracycline resistance was the most abundant resistance determinant. High abundance of ARGs against β-lactams, aminoglycosides, quinolones and macrolides was found. Eschericia sp. was the major contributor of ARGs. CONCLUSIONS This is the first comparative study of the gut microbiome associated with different diarrheal pathogens. It presents the first catalogue of different bacterial taxa representing the core and variable microbiome in acute diarrheal patients. The study helped to define a trend in the gut microbiota signature associated with diarrhea and revealed which ARGs are abundantly present and the metagenome-assembled genomes (MAGs) contributing to AMR.
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Affiliation(s)
- Rituparna De
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
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Core Genome Multilocus Sequence Typing for Food Animal Source Attribution of Human Campylobacter jejuni Infections. Pathogens 2020; 9:pathogens9070532. [PMID: 32630646 PMCID: PMC7400327 DOI: 10.3390/pathogens9070532] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 11/17/2022] Open
Abstract
Campylobacter jejuni is a major foodborne pathogen and common cause of bacterial enteritis worldwide. A total of 622 C. jejuni isolates recovered from food animals and retail meats in the United States through the National Antimicrobial Resistance Monitoring System between 2013 and 2017 were sequenced using an Illumina MiSeq. Sequences were combined with WGS data of 222 human isolates downloaded from NCBI and analyzed by core genome multilocus sequence typing (cgMLST) and traditional MLST. cgMLST allelic difference (AD) thresholds of 0, 5, 10, 25, 50, 100 and 200 identified 828, 734, 652, 543, 422, 298 and 197 cgMLST types among the 844 isolates, respectively, and traditional MLST identified 174 ST. The cgMLST scheme allowing an AD of 200 (cgMLST200) revealed strong correlation with MLST. cgMLST200 showed 40.5% retail chicken isolates, 56.5% swine, 77.4% dairy cattle and 78.9% beef cattle isolates shared cgMLST sequence type with human isolates. All ST-8 had the same cgMLST200 type (cgMLST200-12) and 74.3% of ST-8 and 75% cgMLST200-12 were confirmed as sheep abortion virulence clones by PorA analysis. Twenty-nine acquired resistance genes, including 21 alleles of blaOXA, tetO, aph(3′)-IIIa, ant(6)-Ia, aadE, aad9, aph(2′)-Ig, aph(2′)-Ih, sat4 plus mutations in gyrA, 23SrRNA and L22 were identified. Resistance genotypes were strongly linked with cgMLST200 type for certain groups including 12/12 cgMLST200-510 with the A103V substitution in L22 and 10/11 cgMLST200-608 with the T86I GyrA substitution associated with macrolide and quinolone resistance, respectively. In summary, the cgMLST200 threshold scheme combined with resistance genotype information could provide an excellent subtyping scheme for source attribution of human C. jejuni infections.
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Sanchez JJ, Alam MA, Stride CB, Haque MA, Das S, Mahfuz M, Roth DE, Sly PD, Long KZ, Ahmed T. Campylobacter infection and household factors are associated with childhood growth in urban Bangladesh: An analysis of the MAL-ED study. PLoS Negl Trop Dis 2020; 14:e0008328. [PMID: 32407313 PMCID: PMC7252635 DOI: 10.1371/journal.pntd.0008328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 05/27/2020] [Accepted: 04/27/2020] [Indexed: 01/24/2023] Open
Abstract
The dual burden of enteric infection and childhood malnutrition continues to be a global health concern and a leading cause of morbidity and death among children. Campylobacter infection, in particular, is highly prevalent in low- and middle-income countries, including Bangladesh. We examined longitudinal data to evaluate the trajectories of change in child growth, and to identify associations with Campylobacter infection and household factors. The study analyzed data from 265 children participating in the MAL-ED Study in Mirpur, Bangladesh. We applied latent growth curve modelling to evaluate the trajectories of change in children's height, as measured by length-for-age z-score (LAZ), from age 0-24 months. Asymptomatic and symptomatic Campylobacter infections were included as 3- and 6-month lagged time-varying covariates, while household risk factors were included as time-invariant covariates. Maternal height and birth order were positively associated with LAZ at birth. An inverse association was found between increasing age and LAZ. Campylobacter infection prevalence increased with age, with over 70% of children 18-24 months of age testing positive for infection. In the final model, Campylobacter infection in the preceding 3-month interval was negatively associated with LAZ at 12, 15, and 18 months of age; similarly, infection in the preceding 6-month interval was negatively associated with LAZ at 15, 18, and 21 months of age. Duration of antibiotic use and access to treated drinking water were negatively associated with Campylobacter infection, with the strength of the latter effect increasing with children's age. Campylobacter infection had a significant negative effect on child's growth and this effect was most powerful between 12 and 21 months. The treatment of drinking water and increased antibiotic use have a positive indirect effect on linear child growth trajectory, acting via their association with Campylobacter infection.
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Affiliation(s)
- J. Johanna Sanchez
- Children’s Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (JJS); (KZL)
| | - Md. Ashraful Alam
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Christopher B. Stride
- The Institute of Work Psychology, University of Sheffield, Sheffield, United Kingdom
| | - Md. Ahshanul Haque
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Subhasish Das
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Mustafa Mahfuz
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Daniel E. Roth
- Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Peter D. Sly
- Children’s Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Kurt Z. Long
- Children’s Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- * E-mail: (JJS); (KZL)
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh
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