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Soejima M, Koda Y. Detection of c.375A>G, c.385A>T, c.571C>T, and sedel2 of FUT2 via Real-Time PCR in a Single Tube. Diagnostics (Basel) 2023; 13:2022. [PMID: 37370917 DOI: 10.3390/diagnostics13122022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
α(1,2)fucosyltransferase (Se enzyme) encoded by FUT2 is involved in the secretor status of ABH(O) blood group antigens. The sedel2 allele is one of the non-functional FUT2 (se) alleles in which 9.3 kb, containing the entire coding region of FUT2, is deleted by Alu-mediated nonhomologous recombination. In addition to this allele, three SNPs of FUT2, c.375A>G, c.385A>T, and c.571C>T, appear to be prevalent in certain Oceanian populations such as Polynesians. Recently, we developed an endpoint genotyping assay to determine sedel2 zygosity, using a FAM-labeled probe for detection of the sedel2 allele and a VIC-labeled probe for the detection of FUT2. In this study, instead of the VIC probe, a HEX-labeled probe covering both c.375A>G and c.385A>T and a Cy5-labeled probe covering c.571C>T were added to the sedel2 allele assay mixture to allow for the simultaneous detection of these four variations via endpoint genotyping for sedel2 zygosity and fluorescence melting curve analysis for c.375A>G, c.385A>T, and c.571C>T genotyping. The results obtained from 24 Samoan subjects using this method were identical to those obtained using previous methods. Therefore, it appears that the present method can accurately determine these four variations simultaneously.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
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2
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Jajosky RP, Wu SC, Zheng L, Jajosky AN, Jajosky PG, Josephson CD, Hollenhorst MA, Sackstein R, Cummings RD, Arthur CM, Stowell SR. ABO blood group antigens and differential glycan expression: Perspective on the evolution of common human enzyme deficiencies. iScience 2023; 26:105798. [PMID: 36691627 PMCID: PMC9860303 DOI: 10.1016/j.isci.2022.105798] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enzymes catalyze biochemical reactions and play critical roles in human health and disease. Enzyme variants and deficiencies can lead to variable expression of glycans, which can affect physiology, influence predilection for disease, and/or directly contribute to disease pathogenesis. Although certain well-characterized enzyme deficiencies result in overt disease, some of the most common enzyme deficiencies in humans form the basis of blood groups. These carbohydrate blood groups impact fundamental areas of clinical medicine, including the risk of infection and severity of infectious disease, bleeding risk, transfusion medicine, and tissue/organ transplantation. In this review, we examine the enzymes responsible for carbohydrate-based blood group antigen biosynthesis and their expression within the human population. We also consider the evolutionary selective pressures, e.g. malaria, that may account for the variation in carbohydrate structures and the implications of this biology for human disease.
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Affiliation(s)
- Ryan Philip Jajosky
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
- Biconcavity Inc, Lilburn, GA, USA
| | - Shang-Chuen Wu
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Leon Zheng
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Audrey N. Jajosky
- University of Rochester Medical Center, Department of Pathology and Laboratory Medicine, West Henrietta, NY, USA
| | | | - Cassandra D. Josephson
- Cancer and Blood Disorders Institute and Blood Bank/Transfusion Medicine Division, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
- Departments of Oncology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marie A. Hollenhorst
- Department of Pathology and Department of Medicine, Stanford University, Stanford, CA, USA
| | - Robert Sackstein
- Translational Glycobiology Institute, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Richard D. Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Connie M. Arthur
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Sean R. Stowell
- Joint Program in Transfusion Medicine, Brigham and Women’s Hospital, Harvard Medical School, 630E New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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3
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Saikia K, Saharia N, Singh CS, Borah PP, Namsa ND. Association of histo-blood group antigens and predisposition to gastrointestinal diseases. J Med Virol 2022; 94:5149-5162. [PMID: 35882942 DOI: 10.1002/jmv.28028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/26/2022] [Accepted: 07/23/2022] [Indexed: 12/15/2022]
Abstract
Infectious gastroenteritis is a common illness afflicting people worldwide. The two most common etiological agents of viral gastroenteritis, rotavirus and norovirus are known to recognize histo-blood group antigens (HBGAs) as attachment receptors. ABO, Lewis, and secretor HBGAs are distributed abundantly on mucosal epithelia, red blood cell membranes, and also secreted in biological fluids, such as saliva, intestinal content, milk, and blood. HBGAs are fucosylated glycans that have been implicated in the attachment of some enteric pathogens such as bacteria, parasites, and viruses. Single nucleotide polymorphisms in the genes encoding ABO (H), fucosyltransferase gene FUT2 (Secretor/Se), FUT3 (Lewis/Le) have been associated with changes in enzyme expression and HBGAs production. The highly polymorphic HBGAs among different populations and races influence genotype-specific susceptibility or resistance to enteric pathogens and its epidemiology, and vaccination seroconversion. Therefore, there is an urgent need to conduct population-based investigations to understand predisposition to enteric infections and gastrointestinal diseases. This review focuses on the relationship between HBGAs and predisposition to common human gastrointestinal illnesses caused by viral, bacterial, and parasitic agents.
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Affiliation(s)
- Kasturi Saikia
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Assam, India
| | - Niruprabha Saharia
- Department of Paediatrics, Tezpur Medical College and Hospital, Bihaguri, Tezpur, Assam, India
| | - Chongtham S Singh
- Department of Paediatrics, Regional Institute of Medical Sciences, Imphal, India
| | - Partha P Borah
- Department of Paediatrics and Neonatology, Pratiksha Hospital, Guwahati, Assam, India
| | - Nima D Namsa
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, Assam, India.,Centre for Multi-disciplinary Research, Tezpur University, Napaam, Assam, India
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4
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Urine Microscopy Score and Neutrophil Lymphocyte Ratio at Presentation are Good Biomarkers of Acute Kidney Injury in Patients with Upper Urinary Tract Infection when Assessed in Correlation with Virulence Factors of Escherichia coli and Blood Group Secretor Status. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acute kidney injury (AKI) is a leading cause of morbidity in urinary tract infection (UTI). We aimed to identify simple biomarkers and bacterial virulence factors associated with AKI in a setting of upper UTI due to uropathogenic Escherichia coli (UPEC). We designed a cross-sectional study to analyse biomarkers of AKI in upper UTI patients. A total of 2758 patients presenting to a tertiary care center with symptoms of upper UTI were assessed for the presence of diabetes mellitus, AKI, blood group non-secretors, urine microscopy and hemogram. 300 patients with UPEC in bacterial culture were studied for bacterial virulence factors by phenotypic and genotypic methods and the patients were followed up for a minimum period of two weeks. Patients with diabetes mellitus, non-secretors, Urine microscopy (UM) score > 2 and higher (> 3.9) neutrophil-lymphocyte ratio (NLR) at initial presentation, were found to be significantly associated with AKI at presentation and predicted AKI at 7th and 14th day follow up. They were also significantly associated with need and increased duration of hospitalization. There was no association of virulence factors of UPEC with diabetes mellitus, AKI or need for hospitalization. However, virulence factors had a significant association (p<0.001)with non-secretors. UM score and NLR are simple tools to identify AKI at presentation and predict AKI during follow-up and the need for hospitalization. Patients with diabetes mellitus and non-secretors are also at higher risk of AKI. Non-secretors are significantly associated with both phenotypic and genotypic expression of virulence factors of UPEC.
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Heindel D, Chen S, Aziz PV, Chung JY, Marth JD, Mahal LK. Glycomic Analysis Reveals a Conserved Response to Bacterial Sepsis Induced by Different Bacterial Pathogens. ACS Infect Dis 2022; 8:1075-1085. [PMID: 35486714 PMCID: PMC9112329 DOI: 10.1021/acsinfecdis.2c00082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 12/15/2022]
Abstract
Sepsis is an extreme inflammatory response to infection that occurs in the bloodstream and causes damage throughout the body. Glycosylation is known to play a role in immunity and inflammation, but the role of glycans in sepsis is not well-defined. Herein, we profiled the serum glycomes of experimental mouse sepsis models to identify changes induced by 4 different clinical bacterial pathogens (Gram-positive: Streptococcus pneumoniae and Staphylococcus aureus, Gram-negative: Escherichia coli and Salmonella Typhimurium) using our lectin microarray technology. We observed global shifts in the blood sera glycome that were conserved across all four species, regardless of whether they were Gram positive or negative. Bisecting GlcNAc was decreased upon sepsis and a strong increase in core 1/3 O-glycans was observed. Lectin blot analysis revealed a high molecular weight protein induced in sepsis by all four bacteria as the major cause of the core 1/3 O-glycan shift. Analysis of this band by mass spectrometry identified interalpha-trypsin inhibitor heavy chains (ITIHs) and fibronectin, both of which are associated with human sepsis. Shifts in the glycosylation of these proteins were observed. Overall, our work points toward a common mechanism for bacterially induced sepsis, marked by conserved changes in the glycome.
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Affiliation(s)
- Daniel
W. Heindel
- Biomedical
Research Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Shuhui Chen
- Biomedical
Research Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Peter V. Aziz
- SBP
Medical Discovery Institute, La Jolla, California 92037, United States
| | - Jonathan Y. Chung
- Biomedical
Research Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Jamey D. Marth
- SBP
Medical Discovery Institute, La Jolla, California 92037, United States
| | - Lara K. Mahal
- Biomedical
Research Institute, Department of Chemistry, New York University, New York, New York 10003, United States
- Department
of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
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6
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Soejima M, Koda Y. Simultaneous genotyping of three major Se enzyme inactivating SNPs of FUT2 based on a triplex probe-based fluorescence melting-curve analysis. Clin Chim Acta 2022; 530:50-54. [PMID: 35271838 DOI: 10.1016/j.cca.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/04/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND The ABO(H) secretor status is controlled by FUT2-encoded α(1,2)fucosyltransferase (Se enzyme) activity. Three SNPs of FUT2, 302C>T (rs200157007), 385A>T (rs1047781), and 428G>A (rs601338), cause three major variants of nonsecretor (se) or weak-secretor (Sew) alleles. Evidence has been accumulating that suggests the secretor status is associated with various conditions including infectious diseases but a robust multiplex method for assaying relatively large-scale samples to determine the genotype of these three SNPs simultaneously has not been developed yet. METHODS By combined usage of two Eprobes and a dual-labeled fluorescence probe, we developed a real-time PCR, followed by triplex probe-based fluorescent melting-curve analysis (FMCA) for genotyping of 302C>T, 385A>T, and 428G>A of FUT2 in a single tube. RESULTS Three genotypes of each of three variants of FUT2 were accurately determined by the triplex probe-based FMCA. We then validated this method using genomic DNA samples of 47 Bangladeshis, and the results obtained by using this method were fully concordant with those by previous Sanger sequencing. CONCLUSIONS Since the present single triplex probe-based FMCA is robust, fast, and cost-effective, we are able to effectively estimate the secretor status of subjects on a large scale in many populations around the world.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume 830-0011, Japan.
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7
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Vinjamuri A, Davis JCC, Totten SM, Wu LD, Klein LD, Martin M, Quinn EA, Scelza B, Breakey A, Gurven M, Jasienska G, Kaplan H, Valeggia C, Hinde K, Smilowitz JT, Bernstein RM, Zivkovic AM, Barratt MJ, Gordon JI, Underwood MA, Mills DA, German JB, Lebrilla CB. Human Milk Oligosaccharide Compositions Illustrate Global Variations in Early Nutrition. J Nutr 2022; 152:1239-1253. [PMID: 35179194 PMCID: PMC9071347 DOI: 10.1093/jn/nxac027] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/26/2022] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human milk oligosaccharides (HMOs) are an abundant class of compounds found in human milk and have been linked to the development of the infant, and specifically the brain, immune system, and gut microbiome. OBJECTIVES Advanced analytical methods were used to obtain relative quantitation of many structures in approximately 2000 samples from over 1000 mothers in urban, semirural, and rural sites across geographically diverse countries. METHODS LC-MS-based analytical methods were used to profile the compounds with broad structural coverage and quantitative information. The profiles revealed their structural heterogeneity and their potential biological roles. Comparisons of HMO compositions were made between mothers of different age groups, lactation periods, infant sexes, and residing geographical locations. RESULTS A common behavior found among all sites was a decrease in HMO abundances during lactation until approximately postnatal month 6, where they remained relatively constant. The greatest variations in structural abundances were associated with the presence of α(1,2)-fucosylated species. Genomic analyses of the mothers were not performed; instead, milk was phenotyped according to the abundances of α(1,2)-fucosylated structures. Mothers from the South American sites tended to have higher proportions of phenotypic secretors [mothers with relatively high concentrations of α(1,2)-fucosylated structures] in their populations compared to the rest of the globe, with Bolivia at ∼100% secretors, Peru at ∼97%, Brazil at ∼90%, and Argentina at ∼85%. Conversely, the cohort sampled in Africa manifested the lowest proportion of secretors (South Africa ∼ 63%, the Gambia ∼ 64%, and Malawi ∼ 75%). Furthermore, we compared total abundances of HMOs in secretors compared with nonsecretors and found that nonsecretors have lower abundances of HMOs compared to secretors, regardless of geographical location. We also observed compositional differences of the 50+ most abundant HMOs between milk types and geographical locations. CONCLUSIONS This study represents the largest structural HMO study to date and reveals the general behavior of HMOs during lactation among different populations.
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Affiliation(s)
- Anita Vinjamuri
- Department of Chemistry, University of California, Davis, CA, USA,Foods for Health Institute, University of California, Davis, CA, USA
| | - Jasmine C C Davis
- Department of Chemistry, University of California, Davis, CA, USA,Foods for Health Institute, University of California, Davis, CA, USA
| | - Sarah M Totten
- Department of Chemistry, University of California, Davis, CA, USA,Foods for Health Institute, University of California, Davis, CA, USA
| | - Lauren D Wu
- Department of Chemistry, University of California, Davis, CA, USA,Foods for Health Institute, University of California, Davis, CA, USA
| | - Laura D Klein
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Melanie Martin
- Department of Anthropology, University of Washington, Seattle, WA, USA
| | - E A Quinn
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO, USA
| | - Brooke Scelza
- Department of Anthropology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Michael Gurven
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Grazyna Jasienska
- Department of Environmental Health, Faculty of Health Sciences, Jagiellonian University Medical College, Krakow, Poland
| | | | | | - Katie Hinde
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ,
USA
| | - Jennifer T Smilowitz
- Foods for Health Institute, University of California, Davis, CA, USA,Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Robin M Bernstein
- Department of Anthropology, University of Colorado, Boulder, CO, USA,Institute of Behavioral Science, University of Colorado, Boulder, CO, USA
| | - Angela M Zivkovic
- Foods for Health Institute, University of California, Davis, CA, USA,Department of Nutrition, University of California, Davis, CA, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis MO,
USA,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, MO, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis MO,
USA,Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, MO, USA
| | - Mark A Underwood
- Foods for Health Institute, University of California, Davis, CA, USA,Department of Pediatrics, University of California, Davis, CA, USA
| | - David A Mills
- Foods for Health Institute, University of California, Davis, CA, USA,Department of Food Science and Technology, University of California, Davis, CA, USA
| | - J Bruce German
- Foods for Health Institute, University of California, Davis, CA, USA,Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, USA,Foods for Health Institute, University of California, Davis, CA, USA
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Binia A, Siegwald L, Sultana S, Shevlyakova M, Lefebvre G, Foata F, Combremont S, Charpagne A, Vidal K, Sprenger N, Rahman M, Palleja A, Eklund AC, Nielsen HB, Brüssow H, Sarker SA, Sakwinska O. The Influence of FUT2 and FUT3 Polymorphisms and Nasopharyngeal Microbiome on Respiratory Infections in Breastfed Bangladeshi Infants from the Microbiota and Health Study. mSphere 2021; 6:e0068621. [PMID: 34756056 PMCID: PMC8579893 DOI: 10.1128/msphere.00686-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Acute respiratory infections (ARIs) are one of the most common causes of morbidity and mortality in young children. The aim of our study was to examine whether variation in maternal FUT2 (α1,2-fucosyltransferase 2) and FUT3 (α1,3/4-fucosyltransferase 3) genes, which shape fucosylated human milk oligosaccharides (HMOs) in breast milk, are associated with the occurrence of ARIs in breastfed infants as well as the influence of the nasopharyngeal microbiome on ARI risk. Occurrences of ARIs were prospectively recorded in a cohort of 240 breastfed Bangladeshi infants from birth to 2 years. Secretor and Lewis status was established by sequencing of FUT2/3 genes. The nasopharyngeal microbiome was characterized by shotgun metagenomics, complemented by specific detection of respiratory pathogens; 88.6% of mothers and 91% of infants were identified as secretors. Maternal secretor status was associated with reduced ARI incidence among these infants in the period from birth to 6 months (incidence rate ratio [IRR], 0.66; 95% confidence interval [CI], 0.47 to 0.94; P = 0.020), but not at later time periods. The nasopharyngeal microbiome, despite precise characterization to the species level, was not predictive of subsequent ARIs. The observed risk reduction of ARIs among infants of secretor mothers during the predominant breastfeeding period is consistent with the hypothesis that fucosylated oligosaccharides in human milk contribute to protection against respiratory infections. However, we found no evidence that modulation of the nasopharyngeal microbiome influenced ARI risk. IMPORTANCE The observed risk reduction of acute respiratory infections (ARIs) among infants of secretor mothers during the predominant breastfeeding period is consistent with the hypothesis that fucosylated oligosaccharides in human milk contribute to protection against respiratory infections. Respiratory pathogens were only weak modulators of risk, and the nasopharyngeal microbiome did not influence ARI risk, suggesting that the associated protective effects of human milk oligosaccharides (HMOs) are not conveyed via changes in the nasopharyngeal microbiome. Our observations add to the evidence for a role of fucosylated HMOs in protection against respiratory infections in exclusively or predominantly breastfed infants in low-resource settings. There is no indication that the nasopharyngeal microbiome substantially modulates the risk of subsequent mild ARIs. Larger studies are needed to provide mechanistic insights on links between secretor status, HMOs, and risk of respiratory infections.
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Affiliation(s)
| | | | - Shamima Sultana
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | | | | | | | | | | | | | - Mahbubar Rahman
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | | | | | | | - Shafiqul Alam Sarker
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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9
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Porter CK, Talaat KR, Isidean SD, Kardinaal A, Chakraborty S, Gutiérrez RL, Sack DA, Bourgeois AL. The Controlled Human Infection Model for Enterotoxigenic Escherichia coli. Curr Top Microbiol Immunol 2021. [PMID: 34669040 DOI: 10.1007/82_2021_242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The controlled human infection model (CHIM) for enterotoxigenic Escherichia coli (ETEC) has been instrumental in defining ETEC as a causative agent of acute watery diarrhea, providing insights into disease pathogenesis and resistance to illness, and enabling preliminary efficacy evaluations for numerous products including vaccines, immunoprophylactics, and drugs. Over a dozen strains have been evaluated to date, with a spectrum of clinical signs and symptoms that appear to replicate the clinical illness seen with naturally occurring ETEC. Recent advancements in the ETEC CHIM have enhanced the characterization of clinical, immunological, and microbiological outcomes. It is anticipated that omics-based technologies applied to ETEC CHIMs will continue to broaden our understanding of host-pathogen interactions and facilitate the development of primary and secondary prevention strategies.
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Affiliation(s)
- Chad K Porter
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, 20910, USA.
| | - Kawsar R Talaat
- Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Sandra D Isidean
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation, Bethesda, MD, 20817, USA
| | - Alwine Kardinaal
- NIZO Food Research, Ede, P.O. Box 20, 6710 BA EDE, Kernhemseweg 2, 6718 ZB EDE, The Netherlands
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Ramiro L Gutiérrez
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, 20910, USA
| | - David A Sack
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - A Louis Bourgeois
- PATH|Center for Vaccine Innovation and Access, 455 Massachusetts Avenue NW, Suite 1000, Washington, DC, 20001, USA
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10
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Predisposition of Blood group Non-secretors to Urinary tract infection with Escherichia coli Anti-microbial Resistance and Acute Kidney Injury. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.31] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Urinary tract infection (UTI) causes significant renal damage and disease severity is compounded by antimicrobial resistance (AMR) and other comorbidities in the patient. Blood group antigens secreted in body fluids (secretor status) are known to play a role in bacterial adhesion and we studied its influence on AMR in UTI. A total of 2758 patients with UTI were studied with urine culture, qualitative and semiquantitative urine microscopy, serum creatinine and secretor status in saliva samples by adsorption-inhibition method. Of these, AMR from 300 patients with E. coli infection were assessed as per CLSI 2019 guidelines and extended-spectrum beta-lactamase (ESBL) genes (bla TEM, bla CTX-M, bla SHV) and NDM1 genes were studied using TaqMan probes in Real-time polymerase chain reaction. Patients with UTI were followed up for two weeks. Female patients had higher predilection (57%) for E. coli infection while patients with diabetes or non-secretors had none. In our study, ESBL producers were seen in 62% of the E. coli isolates and fosfomycin had 100% susceptibility. Non-secretors were significantly associated with acute kidney injury (AKI), AMR and ESBL genes. Multidrug-resistance (MDR) was noted in 127/160 (79.4%) ESBL and 17/18 (94%) NDM1 gene encoding strains. Quantitative urine microscopy scoring predicted AKI both at presentation and at end of follow up. ESBL producers were common in our study population and non-secretors had a significant association with AMR genes. Urine microscopy scoring system may be a useful tool to predict AKI in patients with UTI.
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11
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Thiagarajan S, Stephen S, Kanagamuthu S, Ambroise S, Viswanathan P, Chinnakali P, Ganesh RN. Predisposition of Blood group Non-secretors to Urinary tract infection with Escherichia coli Anti-microbial Resistance and Acute Kidney Injury. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: https://doi.org/10.22207/jpam.15.4.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Urinary tract infection (UTI) causes significant renal damage and disease severity is compounded by antimicrobial resistance (AMR) and other comorbidities in the patient. Blood group antigens secreted in body fluids (secretor status) are known to play a role in bacterial adhesion and we studied its influence on AMR in UTI. A total of 2758 patients with UTI were studied with urine culture, qualitative and semiquantitative urine microscopy, serum creatinine and secretor status in saliva samples by adsorption-inhibition method. Of these, AMR from 300 patients with E. coli infection were assessed as per CLSI 2019 guidelines and extended-spectrum beta-lactamase (ESBL) genes (bla TEM, bla CTX-M, bla SHV) and NDM1 genes were studied using TaqMan probes in Real-time polymerase chain reaction. Patients with UTI were followed up for two weeks. Female patients had higher predilection (57%) for E. coli infection while patients with diabetes or non-secretors had none. In our study, ESBL producers were seen in 62% of the E. coli isolates and fosfomycin had 100% susceptibility. Non-secretors were significantly associated with acute kidney injury (AKI), AMR and ESBL genes. Multidrug-resistance (MDR) was noted in 127/160 (79.4%) ESBL and 17/18 (94%) NDM1 gene encoding strains. Quantitative urine microscopy scoring predicted AKI both at presentation and at end of follow up. ESBL producers were common in our study population and non-secretors had a significant association with AMR genes. Urine microscopy scoring system may be a useful tool to predict AKI in patients with UTI.
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12
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Hill DR, Chow JM, Buck RH. Multifunctional Benefits of Prevalent HMOs: Implications for Infant Health. Nutrients 2021; 13:3364. [PMID: 34684364 PMCID: PMC8539508 DOI: 10.3390/nu13103364] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022] Open
Abstract
Breastfeeding is the best source of nutrition during infancy and is associated with a broad range of health benefits. However, there remains a significant and persistent need for innovations in infant formula that will allow infants to access a wider spectrum of benefits available to breastfed infants. The addition of human milk oligosaccharides (HMOs) to infant formulas represents the most significant innovation in infant nutrition in recent years. Although not a direct source of calories in milk, HMOs serve as potent prebiotics, versatile anti-infective agents, and key support for neurocognitive development. Continuing improvements in food science will facilitate production of a wide range of HMO structures in the years to come. In this review, we evaluate the relationship between HMO structure and functional benefits. We propose that infant formula fortification strategies should aim to recapitulate a broad range of benefits to support digestive health, immunity, and cognitive development associated with HMOs in breastmilk. We conclude that acetylated, fucosylated, and sialylated HMOs likely confer important health benefits through multiple complementary mechanisms of action.
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Affiliation(s)
| | | | - Rachael H. Buck
- Abbott Nutrition, 3300 Stelzer Road, Columbus, OH 43219, USA; (D.R.H.); (J.M.C.)
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13
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Soejima M, Koda Y. Rapid detection of phenotypes Bombay se del and nonsecretor rs200157007 SNP (302C > T) by real-time PCR-based methods. Sci Rep 2021; 11:14996. [PMID: 34294843 PMCID: PMC8298435 DOI: 10.1038/s41598-021-94659-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 11/12/2022] Open
Abstract
The sedel allele is one of the nonsecretor alleles (se) of FUT2 generated by an Alu-mediated recombination event and was first found in Indian Bombay phenotype individuals who have anti-H, anti-A, and anti-B antibodies in their serum. As well as anti-A, and anti-B antibodies, anti-H is clinically significant because it causes sever hemolytic transfusion reactions. Like sedel, se302 having a missense single nucleotide polymorphism (SNP), 302C > T, is characteristic of South Asians with a frequency of 10-30%. We developed a real-time PCR melting curve analysis for detection of sedel using a 127-bp amplicon encompassing the breakpoint junction. In addition, by performing duplex PCR by amplifying a 65-bp amplicon of the FUT2 coding region at the same time, we could determine the zygosity of sedel in a single tube. We also developed an Eprobe-mediated PCR assay (Eprobe-PCR) for detection of 302C > T of FUT2. These methods were validated by analyzing 58 Tamils and 54 Sinhalese in Sri Lanka. Both the duplex PCR melting curve analysis for determination of sedel zygosity and the Eprobe-PCR assay for detection of 302C > T exactly determined three genotypes. In addition, the results of the present methods were in complete agreement with those obtained by previously established methods. The two present methods were reliable and seem to be advantageous for large-scale association studies of FUT2 polymorphisms in South Asian populations.
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Affiliation(s)
- Mikiko Soejima
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine, Kurume University School of Medicine, Kurume, 830-0011, Japan.
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14
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Khalil I, Walker R, Porter CK, Muhib F, Chilengi R, Cravioto A, Guerrant R, Svennerholm AM, Qadri F, Baqar S, Kosek M, Kang G, Lanata C, Armah G, Wierzba T, Hasso-Agopsowicz M, Giersing B, Louis Bourgeois A. Enterotoxigenic Escherichia coli (ETEC) vaccines: Priority activities to enable product development, licensure, and global access. Vaccine 2021; 39:4266-4277. [PMID: 33965254 PMCID: PMC8273896 DOI: 10.1016/j.vaccine.2021.04.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 02/08/2023]
Abstract
Diarrhoeal disease attributable to enterotoxigenic Escherichia coli (ETEC) causes substantial morbidity and mortality predominantly in paediatric populations in low- and middle-income countries. In addition to acute illness, there is an increasing appreciation of the long-term consequences of enteric infections, including ETEC, on childhood growth and development. Provision of potable water and sanitation and appropriate clinical care for acute illness are critical to reduce the ETEC burden. However, these interventions are not always practical and may not achieve equitable and sustainable coverage. Vaccination may be the most cost-effective and equitable means of primary prevention; however, additional data are needed to accelerate the investment and guide the decision-making process for ETEC vaccines. First, to understand and quantify the ETEC disease burden, additional data are needed on the association between ETEC infection and physical and cognitive stunting as well as delayed educational attainment. Furthermore, the role of inappropriate or inadequate antibiotic treatment of ETEC-attributable diarrhoea may contribute to the development of antimicrobial resistance (AMR) and needs further elucidation. An ETEC vaccine that mitigates acute diarrhoeal illness and minimizes the longer-term disease manifestations could have significant public health impact and be a cost-effective countermeasure. Herein we review the ETEC vaccine pipeline, led by candidates compatible with the general parameters of the Preferred Product Characteristics (PPC) recently developed by the World Health Organization. Additionally, we have developed an ETEC Vaccine Development Strategy to provide a framework to underpin priority activities for researchers, funders and vaccine manufacturers, with the goal of addressing globally unmet data needs in the areas of research, product development, and policy, as well as commercialization and delivery. The strategy also aims to guide prioritization and co-ordination of the priority activities needed to minimize the timeline to licensure and use of ETEC vaccines, especially in in low- and middle-income countries, where they are most urgently needed.
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Affiliation(s)
| | | | | | | | - Roma Chilengi
- Centre for Infectious Disease Research in Zambia, Zambia
| | | | | | | | | | - Shahida Baqar
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, USA
| | | | | | | | - George Armah
- Noguchi Memorial Institute for Medical Research, Ghana
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15
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van Lier YF, Davids M, Haverkate NJE, de Groot PF, Donker ML, Meijer E, Heubel-Moenen FCJI, Nur E, Zeerleder SS, Nieuwdorp M, Blom B, Hazenberg MD. Donor fecal microbiota transplantation ameliorates intestinal graft-versus-host disease in allogeneic hematopoietic cell transplant recipients. Sci Transl Med 2021; 12:12/556/eaaz8926. [PMID: 32801142 DOI: 10.1126/scitranslmed.aaz8926] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/28/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022]
Abstract
Disruption of the intestinal microbiota occurs frequently in allogeneic hematopoietic cell transplantation (allo-HCT) recipients and predisposes them to development of graft-versus-host disease (GvHD). In a prospective, single-center, single-arm study, we investigated the effect of donor fecal microbiota transplantation (FMT) on symptoms of steroid-refractory or steroid-dependent, acute or late-onset acute intestinal GvHD in 15 individuals who had undergone allo-HCT. Study participants received a fecal suspension from an unrelated healthy donor via nasoduodenal infusion. Donor FMT was well tolerated, and infection-related adverse events did not seem to be related to the FMT procedure. In 10 of 15 study participants, a complete clinical response was observed within 1 month after FMT, without additional interventions to alleviate GvHD symptoms. This response was accompanied by an increase in gut microbial α-diversity, a partial engraftment of donor bacterial species, and increased abundance of butyrate-producing bacteria, including Clostridiales and Blautia species. In 6 of the 10 responding donor FMT recipients, immunosuppressant drug therapy was successfully tapered. Durable remission of steroid-refractory or steroid-dependent GvHD after donor FMT was associated with improved survival at 24 weeks after donor FMT. This study highlights the potential of donor FMT as a treatment for steroid-refractory or steroid-dependent GvHD, but larger clinical trials are needed to confirm the safety and efficacy of this procedure.
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Affiliation(s)
- Yannouck F van Lier
- Department of Hematology, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands.,Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity (AII), Cancer Center Amsterdam, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Mark Davids
- Department of Vascular Medicine, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Nienke J E Haverkate
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity (AII), Cancer Center Amsterdam, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Pieter F de Groot
- Department of Vascular Medicine, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Marjolein L Donker
- Department of Hematology, Amsterdam UMC, location VUMC, 1081 HV Amsterdam, Netherlands
| | - Ellen Meijer
- Department of Hematology, Amsterdam UMC, location VUMC, 1081 HV Amsterdam, Netherlands
| | | | - Erfan Nur
- Department of Hematology, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Sacha S Zeerleder
- Department of Hematology, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands.,Department of Immunopathology, Sanquin Research, 1066 CX Amsterdam, Netherlands.,Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland.,Department for BioMedical Research, University of Bern, 3010 Bern, Switzerland
| | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands.,Diabetes Center, Department of Internal Medicine, Amsterdam UMC, location VUMC, 1081 HV Amsterdam, Netherlands.,Institute for Cardiovascular Research (ICaR), Amsterdam UMC, location VUMC, 1081 HV Amsterdam, Netherlands.,Wallenberg Laboratory, University of Gothenburg, SE-413 45 Goteborg, Sweden
| | - Bianca Blom
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity (AII), Cancer Center Amsterdam, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Mette D Hazenberg
- Department of Hematology, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands. .,Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity (AII), Cancer Center Amsterdam, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands.,Department of Hematopoiesis, Sanquin Research, 1066 CX Amsterdam, Netherlands
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16
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Evaluating the Robustness of Biomarkers of Dairy Food Intake in a Free-Living Population Using Single- and Multi-Marker Approaches. Metabolites 2021; 11:metabo11060395. [PMID: 34204298 PMCID: PMC8235731 DOI: 10.3390/metabo11060395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/08/2021] [Accepted: 06/12/2021] [Indexed: 12/23/2022] Open
Abstract
Studies examining associations between self-reported dairy intake and health are inconclusive, but biomarkers hold promise for elucidating such relationships by offering objective measures of dietary intake. Previous human intervention studies identified several biomarkers for dairy foods in blood and urine using non-targeted metabolomics. We evaluated the robustness of these biomarkers in a free-living cohort in the Netherlands using both single- and multi-marker approaches. Plasma and urine from 246 participants (54 ± 13 years) who completed a food frequency questionnaire were analyzed using liquid and gas chromatography-mass spectrometry. The targeted metabolite panel included 37 previously-identified candidate biomarkers of milk, cheese, and/or yoghurt consumption. Associations between biomarkers and energy-adjusted dairy food intakes were assessed by a ‘single-marker’ generalized linear model, and stepwise regression was used to select the best ‘multi-marker’ panel. Multi-marker models that also accounted for common covariates better captured the subtle differences for milk (urinary galactose, galactitol; sex, body mass index, age) and cheese (plasma pentadecanoic acid, isoleucine, glutamic acid) over single-marker models. No significant associations were observed for yogurt. Further examination of other facets of validity of these biomarkers may improve estimates of dairy food intake in conjunction with self-reported methods, and help reach a clearer consensus on their health impacts.
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17
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Abd El Ghany M, Barquist L, Clare S, Brandt C, Mayho M, Joffre´ E, Sjöling Å, Turner AK, Klena JD, Kingsley RA, Hill-Cawthorne GA, Dougan G, Pickard D. Functional analysis of colonization factor antigen I positive enterotoxigenic Escherichia coli identifies genes implicated in survival in water and host colonization. Microb Genom 2021; 7:000554. [PMID: 34110281 PMCID: PMC8461466 DOI: 10.1099/mgen.0.000554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) expressing the colonization pili CFA/I are common causes of diarrhoeal infections in humans. Here, we use a combination of transposon mutagenesis and transcriptomic analysis to identify genes and pathways that contribute to ETEC persistence in water environments and colonization of a mammalian host. ETEC persisting in water exhibit a distinct RNA expression profile from those growing in richer media. Multiple pathways were identified that contribute to water survival, including lipopolysaccharide biosynthesis and stress response regulons. The analysis also indicated that ETEC growing in vivo in mice encounter a bottleneck driving down the diversity of colonizing ETEC populations.
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Affiliation(s)
- Moataz Abd El Ghany
- The Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
- The Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Simon Clare
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Cordelia Brandt
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Mayho
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Enrique Joffre´
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - A. Keith Turner
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - John D. Klena
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Robert A. Kingsley
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Gordon Dougan
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Derek Pickard
- The Wellcome Trust Sanger Institute (WTSI), the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
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18
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From lab bench to formulated ingredient: Characterization, production, and commercialization of human milk oligosaccharides. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104052] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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19
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Bode L, Raman AS, Murch SH, Rollins NC, Gordon JI. Understanding the mother-breastmilk-infant "triad". Science 2020; 367:1070-1072. [PMID: 32139527 DOI: 10.1126/science.aaw6147] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation, Mother-Milk-Infant Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA.
| | - Arjun S Raman
- The Edison Family Center for Genome Sciences and Systems Biology, and the Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Simon H Murch
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Nigel C Rollins
- Departments of Maternal, Newborn, Child, and Adolescent Health and Ageing, World Health Organization, Geneva, Switzerland
| | - Jeffrey I Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, and the Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO, USA.
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20
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Colston JM, Francois R, Pisanic N, Peñataro Yori P, McCormick BJJ, Olortegui MP, Gazi MA, Svensen E, Ahmed MMM, Mduma E, Liu J, Houpt ER, Klapheke R, Schwarz JW, Atmar RL, Black RE, Kosek MN. Effects of Child and Maternal Histo-Blood Group Antigen Status on Symptomatic and Asymptomatic Enteric Infections in Early Childhood. J Infect Dis 2020; 220:151-162. [PMID: 30768135 PMCID: PMC6548901 DOI: 10.1093/infdis/jiz072] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/13/2019] [Indexed: 01/01/2023] Open
Abstract
Background Histo-blood group antigens (HBGAs) such as fucosyltransferase (FUT)2 and 3 may act as innate host factors that differentially influence susceptibility of individuals and their offspring to pediatric enteric infections. Methods In 3 community-based birth cohorts, FUT2 and FUT3 statuses were ascertained for mother-child dyads. Quantitative polymerase chain reaction panels tested 3663 diarrheal and 18 148 asymptomatic stool samples for 29 enteropathogens. Cumulative diarrhea and infection incidence were compared by child (n = 520) and mothers’ (n = 519) HBGA status and hazard ratios (HRs) derived for all-cause diarrhea and specific enteropathogens. Results Children of secretor (FUT2 positive) mothers had a 38% increased adjusted risk of all-cause diarrhea (HR = 1.38; 95% confidence interval (CI), 1.15–1.66) and significantly reduced time to first diarrheal episode. Child FUT2 and FUT3 positivity reduced the risk for all-cause diarrhea by 29% (HR = 0.81; 95% CI, 0.71–0.93) and 27% (HR = 0.83; 95% CI, 0.74–0.92), respectively. Strong associations between HBGAs and pathogen-specific infection and diarrhea were observed, particularly for noroviruses, rotaviruses, enterotoxigenic Escherichia coli, and Campylobacter jejuni/coli. Conclusions Histo-blood group antigens affect incidence of all-cause diarrhea and enteric infections at magnitudes comparable to many common disease control interventions. Studies measuring impacts of interventions on childhood enteric disease should account for both child and mothers’ HBGA status.
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Affiliation(s)
- Josh M Colston
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ruthly Francois
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, Maryland
| | - Nora Pisanic
- Department of Environmental Health and Engineering, Johns Hopkins School of Public Health, Baltimore, Maryland
| | - Pablo Peñataro Yori
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | | | | | - Md Amran Gazi
- International Centre for Diarrhoeal Disease Research, Bangladesh
| | | | | | - Esto Mduma
- Haydom Global Health Institute, Haydom, Tanzania
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | | | | | | | - Robert E Black
- Department of International Health, Johns Hopkins School of Public Health, Baltimore, Maryland
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
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21
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Paganini D, Uyoga MA, Kortman GAM, Boekhorst J, Schneeberger S, Karanja S, Hennet T, Zimmermann MB. Maternal Human Milk Oligosaccharide Profile Modulates the Impact of an Intervention with Iron and Galacto-Oligosaccharides in Kenyan Infants. Nutrients 2019; 11:nu11112596. [PMID: 31671757 PMCID: PMC6893608 DOI: 10.3390/nu11112596] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
There is little data on human milk oligosaccharide (HMO) composition in Sub-Saharan Africa. Iron fortificants adversely affect the infant gut microbiota, while co-provision of prebiotic galacto-oligosaccharides (GOS) mitigates most of the adverse effects. Whether variations in maternal HMO profile can influence the infant response to iron and/or GOS fortificants is unknown. The aim of this study was to determine HMO profiles and the secretor/non-secretor phenotype of lactating Kenyan mothers and investigate their effects on the maternal and infant gut microbiota, and on the infant response to a fortification intervention with 5 mg iron (2.5 mg as sodium iron ethylenediaminetetraacetate and 2.5 mg as ferrous fumarate) and 7.5 g GOS. We studied mother–infant pairs (n = 80) participating in a 4-month intervention trial in which the infants (aged 6.5–9.5 months) received daily a micronutrient powder without iron, with iron or with iron and GOS. We assessed: (1) maternal secretor status and HMO composition; (2) effects of secretor status on the maternal and infant gut microbiota in a cross-sectional analysis at baseline of the intervention trial; and (3) interactions between secretor status and intervention groups during the intervention trial on the infant gut microbiota, gut inflammation, iron status, growth and infectious morbidity. Secretor prevalence was 72% and HMOs differed between secretors and non-secretors and over time of lactation. Secretor status did not predict the baseline composition of the maternal and infant gut microbiota. There was a secretor-status-by-intervention-group interaction on Bifidobacterium (p = 0.021), Z-scores for length-for-age (p = 0.022) and weight-for-age (p = 0.018), and soluble transferrin receptor (p = 0.041). In the no iron group, longitudinal prevalence of diarrhea was higher among infants of non-secretors (23.8%) than of secretors (10.4%) (p = 0.001). In conclusion, HMO profile may modulate the infant gut microbiota response to fortificant iron; compared to infants of secretor mothers, infants of non-secretor mothers may be more vulnerable to the adverse effect of iron but also benefit more from the co-provision of GOS.
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Affiliation(s)
- Daniela Paganini
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland.
| | - Mary A Uyoga
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland.
- Department of Medical Epidemiology, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, 00200 Nairobi, Kenya.
| | | | - Jos Boekhorst
- NIZO Food Research BV, 6718 ZB Ede, The Netherlands.
| | - Sacha Schneeberger
- Department of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, 8057 Zurich, Switzerland.
| | - Simon Karanja
- Department of Medical Epidemiology, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, 00200 Nairobi, Kenya.
| | - Thierry Hennet
- Department of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, 8057 Zurich, Switzerland.
| | - Michael B Zimmermann
- Laboratory of Human Nutrition, Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland.
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22
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Mottram L, Chakraborty S, Cox E, Fleckenstein J. How genomics can be used to understand host susceptibility to enteric infection, aiding in the development of vaccines and immunotherapeutic interventions. Vaccine 2019; 37:4805-4810. [PMID: 30709726 PMCID: PMC6663652 DOI: 10.1016/j.vaccine.2019.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/26/2018] [Accepted: 01/10/2019] [Indexed: 12/27/2022]
Abstract
Thanks to the modern sequencing era, the extent to which infectious disease imposes selective pressures on the worldwide human population is being revealed. This is aiding our understanding of the underlying immunological and host mechanistic defenses against these pathogens, as well as potentially assisting in the development of vaccines and therapeutics to control them. As a consequence, the workshop "How genomics can be used to understand host susceptibility to enteric infection, aiding in the development of vaccines and immunotherapeutic interventions" at the VASE 2018 meeting, aimed to discuss how genomics and related tools could be used to assist Shigella and ETEC vaccine development. The workshop featured four short presentations which highlighted how genomic applications can be used to assist in the identification of genetic patterns related to the virulence of disease, or host genetic factors that could contribute to immunity or successful vaccine responses. Following the presentations, there was an open debate with workshop attendees to discuss the best ways to utilise such genomic studies, to improve or accelerate the process of both Shigella and ETEC vaccine development. The workshop concluded by making specific recommendations on how genomic research methods could be strengthened and harmonised within the ETEC and Shigella research communities.
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Affiliation(s)
- Lynda Mottram
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Eric Cox
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - James Fleckenstein
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States; Medicine Service, Veterans Affairs Medical Center, St. Louis, MO, United States
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23
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Suwandi A, Galeev A, Riedel R, Sharma S, Seeger K, Sterzenbach T, García Pastor L, Boyle EC, Gal-Mor O, Hensel M, Casadesús J, Baines JF, Grassl GA. Std fimbriae-fucose interaction increases Salmonella-induced intestinal inflammation and prolongs colonization. PLoS Pathog 2019; 15:e1007915. [PMID: 31329635 PMCID: PMC6675130 DOI: 10.1371/journal.ppat.1007915] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/01/2019] [Accepted: 06/13/2019] [Indexed: 12/14/2022] Open
Abstract
Expression of ABO and Lewis histo-blood group antigens by the gastrointestinal epithelium is governed by an α-1,2-fucosyltransferase enzyme encoded by the Fut2 gene. Alterations in mucin glycosylation have been associated with susceptibility to various bacterial and viral infections. Salmonella enterica serovar Typhimurium is a food-borne pathogen and a major cause of gastroenteritis. In order to determine the role of Fut2-dependent glycans in Salmonella-triggered intestinal inflammation, Fut2+/+ and Fut2-/- mice were orally infected with S. Typhimurium and bacterial colonization and intestinal inflammation were analyzed. Bacterial load in the intestine of Fut2-/- mice was significantly lower compared to Fut2+/+ mice. Analysis of histopathological changes revealed significantly lower levels of intestinal inflammation in Fut2-/- mice compared to Fut2+/+ mice and measurement of lipocalin-2 level in feces corroborated histopathological findings. Salmonella express fimbriae that assist in adherence of bacteria to host cells thereby facilitating their invasion. The std fimbrial operon of S. Typhimurium encodes the π-class Std fimbriae which bind terminal α(1,2)-fucose residues. An isogenic mutant of S. Typhimurium lacking Std fimbriae colonized Fut2+/+ and Fut2-/- mice to similar levels and resulted in similar intestinal inflammation. In vitro adhesion assays revealed that bacteria possessing Std fimbriae adhered significantly more to fucosylated cell lines or primary epithelial cells in comparison to cells lacking α(1,2)-fucose. Overall, these results indicate that Salmonella-triggered intestinal inflammation and colonization are dependent on Std-fucose interaction.
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Affiliation(s)
- Abdulhadi Suwandi
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany
| | - Alibek Galeev
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany
| | - René Riedel
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, Plön, Germany and Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Samriti Sharma
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany
| | - Katrin Seeger
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany
| | - Torsten Sterzenbach
- Division of Microbiology and CellNanOs–Center for Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Lucía García Pastor
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Erin C. Boyle
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
- Department of Cardiothoracic, Transplantation, and Vascular Surgery, Hannover Medical School, Hannover, Germany
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michael Hensel
- Division of Microbiology and CellNanOs–Center for Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - John F. Baines
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, Plön, Germany and Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Guntram A. Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany
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24
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Parker EPK, Whitfield H, Baskar C, Giri S, John J, Grassly NC, Kang G, Praharaj I. FUT2 Secretor Status Is Not Associated With Oral Poliovirus Vaccine Immunogenicity in South Indian Infants. J Infect Dis 2019; 219:578-581. [PMID: 30239830 PMCID: PMC6350944 DOI: 10.1093/infdis/jiy553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/17/2018] [Indexed: 01/29/2023] Open
Abstract
FUT2 determines whether histo-blood group antigens are secreted at mucosal surfaces. Secretor status influences susceptibility to enteric viruses, potentially including oral poliovirus vaccine (OPV). We performed a nested case-control study to determine the association between FUT2 genotype (single-nucleotide polymorphisms G428A, C302T, and A385T) and seroconversion among Indian infants who received a single dose of monovalent type 3 OPV. Secretor prevalence was 75% (89 of 118) in infants who seroconverted and 80% (97 of 122) in infants who did not seroconvert (odds ratio, 0.79; 95% confidence interval, .43-1.45). Our findings suggest that FUT2 genotype is not a key determinant of variation in OPV immunogenicity.
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Affiliation(s)
- Edward P K Parker
- Department of Infectious Disease Epidemiology, St Mary’s Campus, Imperial College London, United Kingdom
| | - Helena Whitfield
- Department of Infectious Disease Epidemiology, St Mary’s Campus, Imperial College London, United Kingdom
| | - Chudarkodi Baskar
- Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Sidhartha Giri
- Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Jacob John
- Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Nicholas C Grassly
- Department of Infectious Disease Epidemiology, St Mary’s Campus, Imperial College London, United Kingdom
| | - Gagandeep Kang
- Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Ira Praharaj
- Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
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25
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Glyco-engineered cell line and computational docking studies reveals enterotoxigenic Escherichia coli CFA/I fimbriae bind to Lewis a glycans. Sci Rep 2018; 8:11250. [PMID: 30050155 PMCID: PMC6062558 DOI: 10.1038/s41598-018-29258-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022] Open
Abstract
We have previously reported clinical data to suggest that colonization factor I (CFA/I) fimbriae of enterotoxigenic Escherichia coli (ETEC) can bind to Lewis a (Lea), a glycan epitope ubiquitous in the small intestinal mucosa of young children (<2 years of age), and individuals with a genetic mutation of FUT2. To further elucidate the physiological binding properties of this interaction, we engineered Chinese Hamster Ovary (CHO-K1) cells to express Lea or Leb determinants on both N- and O-glycans. We used our glyco-engineered CHO-K1 cell lines to demonstrate that CfaB, the major subunit of ETEC CFA/I fimbriae, as well as four related ETEC fimbriae, bind more to our CHO-K1 cell-line expressing Lea, compared to cells carrying Leb or the CHO-K1 wild-type glycan phenotype. Furthermore, using in-silico docking analysis, we predict up to three amino acids (Glu25, Asn27, Thr29) found in the immunoglobulin (Ig)-like groove region of CfaB of CFA/I and related fimbriae, could be important for the preferential and higher affinity binding of CFA/I fimbriae to the potentially structurally flexible Lea glycan. These findings may lead to a better molecular understanding of ETEC pathogenesis, aiding in the development of vaccines and/or anti-infection therapeutics.
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26
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Palus M, Sohrabi Y, Broman KW, Strnad H, Šíma M, Růžek D, Volkova V, Slapničková M, Vojtíšková J, Mrázková L, Salát J, Lipoldová M. A novel locus on mouse chromosome 7 that influences survival after infection with tick-borne encephalitis virus. BMC Neurosci 2018; 19:39. [PMID: 29976152 PMCID: PMC6034256 DOI: 10.1186/s12868-018-0438-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023] Open
Abstract
Background
Tick-borne encephalitis (TBE) is the main tick-borne viral infection in Eurasia. Its manifestations range from inapparent infections and fevers with complete recovery to debilitating or fatal encephalitis. The basis of this heterogeneity is largely unknown, but part of this variation is likely due to host genetic. We have previously found that BALB/c mice exhibit intermediate susceptibility to the infection of TBE virus (TBEV), STS mice are highly resistant, whereas the recombinant congenic strain CcS-11, carrying 12.5% of the STS genome on the background of the BALB/c genome is even more susceptible than BALB/c. Importantly, mouse orthologs of human TBE controlling genes Oas1b, Cd209, Tlr3, Ccr5, Ifnl3 and Il10, are in CcS-11 localized on segments derived from the strain BALB/c, so they are identical in BALB/c and CcS-11. As they cannot be responsible for the phenotypic difference of the two strains, we searched for the responsible STS-derived gene-locus. Of course the STS-derived genes in CcS-11 may operate through regulating or epigenetically modifying these non-polymorphic genes of BALB/c origin. Methods To determine the location of the STS genes responsible for susceptibility of CcS-11, we analyzed survival of TBEV-infected F2 hybrids between BALB/c and CcS-11. CcS-11 carries STS-derived segments on eight chromosomes. These were genotyped in the F2 hybrid mice and their linkage with survival was tested by binary trait interval mapping. We have sequenced genomes of BALB/c and STS using next generation sequencing and performed bioinformatics analysis of the chromosomal segment exhibiting linkage with TBEV survival. Results Linkage analysis revealed a novel suggestive survival-controlling locus on chromosome 7 linked to marker D7Nds5 (44.2 Mb). Analysis of this locus for polymorphisms between BALB/c and STS that change RNA stability and genes’ functions led to detection of 9 potential candidate genes: Cd33, Klk1b22, Siglece, Klk1b16, Fut2, Grwd1, Abcc6, Otog, and Mkrn3. One of them, Cd33, carried a nonsense mutation in the STS strain. Conclusions The robust genetic system of recombinant congenic strains of mice enabled detection of a novel suggestive locus on chromosome 7. This locus contains 9 candidate genes, which will be focus of future studies not only in mice but also in humans.
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Affiliation(s)
- Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005, České Budějovice, Czech Republic.,Department of Virology, Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic
| | - Yahya Sohrabi
- Department of Molecular and Cellular Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Karl W Broman
- Department of Biostatistics and Medical Informatics, 6770 Medical Sciences Center, 1300 University Avenue, Madison, WI, 53706-1532, USA
| | - Hynek Strnad
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Matyáš Šíma
- Department of Molecular and Cellular Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Daniel Růžek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005, České Budějovice, Czech Republic.,Department of Virology, Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic
| | - Valeriya Volkova
- Department of Molecular and Cellular Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Martina Slapničková
- Department of Molecular and Cellular Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Jarmila Vojtíšková
- Department of Molecular and Cellular Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Lucie Mrázková
- Department of Molecular and Cellular Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic.,Department of Natural Sciences, Faculty of Biomedical Engineering, Czech Technical University in Prague, Sítná 3105, 272 01, Kladno, Czech Republic
| | - Jiří Salát
- Department of Virology, Veterinary Research Institute, Hudcova 70, 62100, Brno, Czech Republic
| | - Marie Lipoldová
- Department of Molecular and Cellular Immunology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic. .,Department of Natural Sciences, Faculty of Biomedical Engineering, Czech Technical University in Prague, Sítná 3105, 272 01, Kladno, Czech Republic.
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27
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DeBoever C, Tanigawa Y, Lindholm ME, McInnes G, Lavertu A, Ingelsson E, Chang C, Ashley EA, Bustamante CD, Daly MJ, Rivas MA. Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study. Nat Commun 2018; 9:1612. [PMID: 29691392 PMCID: PMC5915386 DOI: 10.1038/s41467-018-03910-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/21/2018] [Indexed: 02/08/2023] Open
Abstract
Protein-truncating variants can have profound effects on gene function and are critical for clinical genome interpretation and generating therapeutic hypotheses, but their relevance to medical phenotypes has not been systematically assessed. Here, we characterize the effect of 18,228 protein-truncating variants across 135 phenotypes from the UK Biobank and find 27 associations between medical phenotypes and protein-truncating variants in genes outside the major histocompatibility complex. We perform phenome-wide analyses and directly measure the effect in homozygous carriers, commonly referred to as “human knockouts,” across medical phenotypes for genes implicated as being protective against disease or associated with at least one phenotype in our study. We find several genes with strong pleiotropic or non-additive effects. Our results illustrate the importance of protein-truncating variants in a variety of diseases. Protein-truncating variants (PTVs) are predicted to significantly affect a gene’s function and, thus, human traits. Here, DeBoever et al. systematically analyze PTVs in more than 300,000 individuals across 135 phenotypes and identify 27 associations between PTVs and medical conditions.
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Affiliation(s)
- Christopher DeBoever
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Yosuke Tanigawa
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | | | - Greg McInnes
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Adam Lavertu
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Erik Ingelsson
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chris Chang
- Grail, Inc., 1525 O'Brien Drive, Menlo Park, CA, 94025, USA
| | - Euan A Ashley
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Mark J Daly
- Analytical and Translational Genetics Unit, Boston, MA, 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
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28
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Ayechu-Muruzabal V, van Stigt AH, Mank M, Willemsen LEM, Stahl B, Garssen J, Van't Land B. Diversity of Human Milk Oligosaccharides and Effects on Early Life Immune Development. Front Pediatr 2018; 6:239. [PMID: 30250836 PMCID: PMC6140589 DOI: 10.3389/fped.2018.00239] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/07/2018] [Indexed: 12/12/2022] Open
Abstract
One of the well-known features of human milk, is the capacity to protect against the risk and impact of neonatal infections, as well as to influence the onset of allergic and metabolic disease manifestations. The major objective of this review is to provide a detailed overview regarding the role of human milk, more specifically the diversity in human milk oligosaccharides (HMOS), on early life immune development. Novel insights in immune modulatory effects of HMOS obtained by in vitro as well as in vivo studies, adds to the understanding on how early life nutrition may impact immune development. Extensive description and analysis of single HMOS contributing to the diversity within the composition provided during breastfeeding will be discussed with specific emphasis on immune development and the susceptibility to neonatal and childhood infections.
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Affiliation(s)
- Veronica Ayechu-Muruzabal
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Arthur H van Stigt
- Pediatric Immunology, Laboratory of Translational Immunology, The Wilhelmina Children's Hospital, University Medical Center, Utrecht, Netherlands
| | - Marko Mank
- Department of Immunology and Department of Human Milk Research & Analytical Science, Danone Nutricia Research, Utrecht, Netherlands
| | - Linette E M Willemsen
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Bernd Stahl
- Department of Immunology and Department of Human Milk Research & Analytical Science, Danone Nutricia Research, Utrecht, Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands.,Department of Immunology and Department of Human Milk Research & Analytical Science, Danone Nutricia Research, Utrecht, Netherlands
| | - Belinda Van't Land
- Pediatric Immunology, Laboratory of Translational Immunology, The Wilhelmina Children's Hospital, University Medical Center, Utrecht, Netherlands.,Department of Immunology and Department of Human Milk Research & Analytical Science, Danone Nutricia Research, Utrecht, Netherlands
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