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Shahzad M, Arshad M, Ahmad HA, Iddrissu I, Bailey EH, Dru N, Khan S, Khan H, Andrews SC. Nutritional status reshapes gut microbiota composition in adolescent Afghan refugees in Peshawar, Pakistan. Nutr Res 2025; 138:55-67. [PMID: 40311534 DOI: 10.1016/j.nutres.2025.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 04/03/2025] [Accepted: 04/03/2025] [Indexed: 05/03/2025]
Abstract
Although the human gut microbiome, and its role in health and disease, have been extensively studied in different populations, a comprehensive assessment of gut microbiome composition has not been performed in vulnerable refugee populations. In this study, we hypothesized that overall nutritional status, as indicated by serum micronutrients concentrations, is an important driver of variations in gut microbiome composition. Therefore, gut-microbiome diversity and associated demographic, health and nutritional factors were assessed in adolescent Afghan refugees (n=206). Blood and faecal samples were collected and analysed for nutrition status markers and 16S rRNA gene amplicon-based community profiling, respectively. Bioinformatics and statistical analysis were performed using SPSS, QIIME and R. Overall, 56 distinct phyla, 117 families and 252 genera were identified in the faecal samples. Bacterial diversity (alpha and beta diversity) and the Firmicutes:Bacteroidetes (F/B) ratio were significantly higher in the 15 to 19 year old age group (cf. the 10-14 age group) but were lower in the underweight and vitamin D deficient groups. Furthermore, LEfSe analysis identified significant differences in the relative abundance of bacterial genera based on age, BMI and micronutrient (vitamins and minerals) status. These results were further scrutinised by correlation analysis which confirmed that age, BMI and micronutrient status show significant correlations with F/B ratio and the relative abundance of specific bacterial taxa. Collectively, our study provides the first indication of how the gut-microbiota profile of adolescent Afghan refugees is associated with a range of nutrition-status factors. These findings can thus provide a basis for translational microbiota research aimed at improving the health of such understudied and vulnerable populations.
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Affiliation(s)
- Muhammad Shahzad
- Faculty of Dentistry, Zarqa University, Zarqa, Jordan; Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Muhammad Arshad
- Center for Genomics and Systems Biology, New York University, Abu Dhabi, United Arab Emirates
| | - Habab Ali Ahmad
- Department of Biological and Health Sciences, Pak-Austria Fachhochschule Institute of Applied Science and Technology (PAF-IAST), Haripur, Pakistan
| | - Ishawu Iddrissu
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Reading, United Kingdom
| | - Elizabeth H Bailey
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Nizar Dru
- Center for Genomics and Systems Biology, New York University, Abu Dhabi, United Arab Emirates
| | - Shabir Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Haris Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Simon C Andrews
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Reading, United Kingdom.
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Hermsen ED, Amos J, Townsend A, Becker T, Hargreaves S. Antimicrobial resistance among refugees and asylum seekers: a global systematic review and meta-analysis. THE LANCET. INFECTIOUS DISEASES 2025; 25:e34-e43. [PMID: 39527961 DOI: 10.1016/s1473-3099(24)00578-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/08/2024] [Accepted: 08/27/2024] [Indexed: 11/16/2024]
Abstract
Refugees and asylum seekers might have an increased risk of antimicrobial resistance (AMR) carriage or infection due to several factors, with conflict and war known to accelerate the spread of AMR. However, data are scarce on prevalence and risk factors for AMR among refugees and asylum seekers and how they are affected globally; in addition, how their risk compares to that of the host-country population is unclear. We aimed to explore and assess global AMR data among refugees and asylum seekers. Ovid (MEDLINE and Embase) and PubMed were searched for peer-reviewed primary research articles from Jan 1, 2015, to Oct 23, 2023, and articles were included if they reported carriage or infection with laboratory-confirmed drug-resistant organisms in refugees or asylum seekers from any country. Of 884 articles identified, 41 reported prevalence of AMR among 16 970 refugees and asylum seekers and were included in the study. The most common phenotypes reported were multidrug-resistant Gram-negative bacteria (n=26; prevalence ranged from 4·2% to 60·8%), methicillin-resistant Staphylococcus aureus (n=24; 0·92% to 73%), and extended-spectrum β-lactamase-producing Gram-negative bacteria (n=20; 1·6% to 61·1%). Refugees and asylum seekers had a higher likelihood of carriage or infection with any AMR than the host-country population (n=7849 vs n=81 283, respectively; odds ratio 2·88, 95% CI 2·61-3·18; I2=94%). Refugees and asylum seekers are at an increased risk of AMR carriage and infection, with our data suggesting that refugees and asylum seekers might be exposed to conditions that support the emergence of drug resistance (including living in overcrowded camps and facing barriers to health and vaccine systems). Hence, more global and regional data on AMR are needed through strengthened surveillance programmes and health-care facilities, especially in low-income and middle-income countries. Increased efforts are needed to drive improvements in infection prevention and control (including vaccination), antimicrobial stewardship, treatment strategies tailored to groups at high risk, accessiblity to quality health care in these populations at risk globally, and address risk factors such as poor living and transit conditions.
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Affiliation(s)
| | | | | | | | - Sally Hargreaves
- The Migrant Health Research Group, Institute for Infection and Immunity, St George's Hospital, University of London, London, UK
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Alahdal H, Almuneef G, Alkhulaifi MM, Aldibasi O, Aljouie A, Alharbi O, Almohawes ZN, Basingab F, Rejili M. Gut microbiota composition in patients with Crohn's disease in Saudi Arabia. PLoS One 2024; 19:e0299749. [PMID: 38656971 PMCID: PMC11042705 DOI: 10.1371/journal.pone.0299749] [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: 09/07/2023] [Accepted: 02/14/2024] [Indexed: 04/26/2024] Open
Abstract
Crohn's disease (CD) entails intricate interactions with gut microbiome diversity, richness, and composition. The relationship between CD and gut microbiome is not clearly understood and has not been previously characterized in Saudi Arabia. We performed statistical analysis about various factors influencing CD activity and microbiota dysbiosis, including diagnosis, treatment, and its impact on their quality of life as well as high-throughput metagenomic V3-V4 16S rRNA encoding gene hypervariable region of a total of eighty patients with CD, both in its active and inactive state with healthy controls. The results were correlated with the demographic and lifestyle information, which the participants provided via a questionnaire. α-diversity measures indicated lower bacterial diversity and richness in the active and inactive CD groups compared to the control group. Greater dysbiosis was observed in the active CD patients compared to the inactive form of the disease, showed by a reduction in microbial diversity. Specific pathogenic bacteria such as Filifactor, Peptoniphilus, and Sellimonas were identified as characteristic of CD groups. In contrast, anti-inflammatory bacteria like Defluviitalea, Papillibacter, and Petroclostridium were associated with the control group. Among the various factors influencing disease activity and microbiota dysbiosis, smoking emerged as the most significant, with reduced α-diversity and richness for the smokers in all groups, and proinflammatory Fusobacteria was more present (p<0.05). Opposite to the control group, microbial diversity and richness were lower in CD participants of older age compared to younger ones, and male CD participants showed less diversity compared to women participants from the same groups. Our results describe the first report on the relationship between microbiota and Crohn's disease progress in Saudi Arabia, which may provide a theoretical basis for the application of therapeutic methods to regulate gut microbes in CD.
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Affiliation(s)
- Hadil Alahdal
- Department of Biology, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ghaida Almuneef
- Department of Biology, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Manal Muhammed Alkhulaifi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Omar Aldibasi
- Biostatistics Section, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman Aljouie
- Artificial Intelligence and Bioinformatics Department, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- Department of Health Informatics, College of Public Health and Health Informatics, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Othman Alharbi
- Department of Medicine, College of Medicine, King Khalid University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Zakiah Naser Almohawes
- Department of Biology, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Immunology Unit, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mokhtar Rejili
- Department of Life Sciences, College of Sciences, Al Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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Topluoglu S, Taylan-Ozkan A, Alp E. Impact of wars and natural disasters on emerging and re-emerging infectious diseases. Front Public Health 2023; 11:1215929. [PMID: 37727613 PMCID: PMC10505936 DOI: 10.3389/fpubh.2023.1215929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/17/2023] [Indexed: 09/21/2023] Open
Abstract
Emerging Infectious Diseases (EIDs) and Re-Emerging Infectious Diseases (REIDs) constitute significant health problems and are becoming of major importance. Up to 75% of EIDs and REIDs have zoonotic origin. Several factors such as the destruction of natural habitats leading humans and animals to live in close proximity, ecological changes due to natural disasters, population migration resulting from war or conflict, interruption or decrease in disease prevention programs, and insufficient vector control applications and sanitation are involved in disease emergence and distribution. War and natural disasters have a great impact on the emergence/re-emergence of diseases in the population. According to a World Bank estimation, two billion people are living in poverty and fragility situations. Wars destroy health systems and infrastructure, curtail existing disease control programs, and cause population movement leading to an increase in exposure to health risks and favor the emergence of infectious diseases. A total of 432 catastrophic cases associated with natural disasters were recorded globally in 2021. Natural disasters increase the risk of EID and REID outbreaks by damaging infrastructure and leading to displacement of populations. A Generic National Action Plan covering risk assessment, mechanism for action, determination of roles and responsibilities of each sector, the establishment of a coordination mechanism, etc. should be developed.
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Affiliation(s)
- Seher Topluoglu
- Provincial Health Directorate of Ankara, Republic of Türkiye Ministry of Health, Ankara, Türkiye
| | - Aysegul Taylan-Ozkan
- Department of Medical Microbiology, Medical Faculty, TOBB University of Economics and Technology, Ankara, Türkiye
| | - Emine Alp
- Department of Clinical Microbiology and Infectious Diseases, Medical Faculty, Ankara Yildirim Beyazit University, Ankara, Türkiye
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Yusuff SI, Tajudeen YA, Oladunjoye IO, Oladipo HJ, Bolarinwa OV, Popoola OT, Ahmed AF, Olana MD. The need to increase antimicrobial resistance surveillance among forcibly displaced persons (FDPs). Trop Dis Travel Med Vaccines 2023; 9:12. [PMID: 37653439 PMCID: PMC10472691 DOI: 10.1186/s40794-023-00198-6] [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: 09/27/2022] [Accepted: 06/19/2023] [Indexed: 09/02/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to human health as 4.95 million deaths were associated with bacterial AMR in 2019 and is projected to reach 10 million by 2050. To mitigate AMR, surveillance is an essential tool for determining the burden of AMR and providing the necessary information for its control. However, the global AMR surveillance is inadequate and particularly limited among forcibly displaced persons (FDPs) despite having higher risks of harboring these pathogens. Predisposing factors among this group include poor living conditions, limited access to treatment and diagnostic tests, and inadequate trained health professionals in refugee camps. Strengthening AMR surveillance among FDPs would address the identified gaps and facilitate formulation and implementation of evidence-based policies on AMR control and prevention response. This article provides information on the growing population of FDPs, factors contributing to the AMR burden and AMR surveillance gaps in FDPs and highlighted recommendations for control.
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Affiliation(s)
- Sodiq Inaolaji Yusuff
- Department of Medicine, Faculty of Clinical Sciences, Obafemi Awolowo University, Ibadan-Ife Rd, Ife, 220101, Osun State, Nigeria
| | - Yusuf Amuda Tajudeen
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin, P.M.B. 1515, Ilorin, 240003, Nigeria
- Department of Epidemiology and Medical Statistics, Faculty of Public Health, College of Medicine, University of Ibadan, P.M.B 5017 G.P.O, Ibadan, Oyo State, Nigeria
| | - Iyiola Olatunji Oladunjoye
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin, P.M.B. 1515, Ilorin, 240003, Nigeria
| | - Habeebullah Jayeola Oladipo
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin, P.M.B. 1515, Ilorin, 240003, Nigeria
- Faculty of Pharmaceutical Sciences, University of Ilorin, P.M.B. 1515, Ilorin, 240003, Nigeria
| | | | - Olalekan Tolulope Popoola
- Department of Public Health, Health Sciences Centre, University College, Dublin, 4 Stillorgan Rd, Belfield, Dublin 4, Ireland
| | - Abdulhakeem Funsho Ahmed
- Faculty of Health Sciences, Department of Public Health, Al-Hikmah University, Ilorin, 240281, Kwara State, Nigeria
- Institute of Basic and Applied Science, Department of Science Laboratory Technology, Kwara State Polytechnic, P.M.B 1375, Ilorin, Kwara State, Nigeria
| | - Matifan Dereje Olana
- Department of Medical Laboratory Sciences, Collage of Medicine and Health Sciences, Ambo University, Ambo, Ethiopia.
- Department of Microbiology, Immunology and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box 9086, Addis Ababa, Ethiopia.
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Rahimitabar P, Kraemer A, Bozorgmehr K, Ebrahimi F, Takian A. Health condition of Afghan refugees residing in Iran in comparison to Germany: a systematic review of empirical studies. Int J Equity Health 2023; 22:16. [PMID: 36681845 PMCID: PMC9862781 DOI: 10.1186/s12939-023-01832-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The re-emerging dominance of the Taliban in Afghanistan in 2021 caused a new wave of Afghan refugees heading Iran and neighboring countries. Iran in the Middle East and Germany in Europe are two major host countries to the largest populations of Afghan refugees. In both countries, several studies have been done to assess the health condition of refugees. OBJECTIVES To systematically review the existing literature to identify similarities and differences of health conditions of Afghan refugees living in the two countries, and to synthesize evidence on the health status and health care access of these populations. METHODS Related electronic databases and grey literature of Iran and Germany on the health of Afghan refugees were scanned and searched up for the period 2000-2020. Key terms were formed by combining "Afghan refugees or immigrants or populations or asylum seekers", "Physical or mental health", "Healthcare service or access or use", "Iran or Germany". Empirical studies were considered if they contained samples of Afghan refugees with particular outcomes for Afghans. Results were categorized for both countries in the three main areas of physical health, mental health, and access/use of healthcare services. RESULTS Nine hundred twenty-two documents were extracted, of which 75 full-texts were finally reviewed. 60 documents belonged to the health condition of Afghan refugees residing in Iran including 43 in physical health, 6 in mental health, 8 in healthcare access and use, and 3 in multiple aspects of health, and 15 belonged to Germany including 7 in physical health, 4 in mental health, 2 in healthcare access and use, and 2 in multiple aspects of health. A less explicit evaluation of the overall health condition of Afghan refugees was observable, particularly for Germany. While matches on the study subject exist for both countries, in comparison to Germany, we extracted more quantitative and qualitative health studies on Afghan refugees of the mentioned areas from Iran. German health studies were rare, less qualitative, and more on the health condition of diverse refugee groups in general. CONCLUSIONS Wide gaps and unanswered questions related to mental health and overall health status of the Afghan refugee population are observable, especially in Germany. Our systematic review identified the gap in evidence, which we would recommend to bridge using a wider lens to comprehensively assess the overall condition of refugees considering associations between health and socio-economic and cultural determinants instead of a one-dimensional approach. Further, within health studies on refugee populations, we recommend stratification of results by the country of origin to capture the within-group diversity among refugees with different countries of origin.
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Affiliation(s)
- Parisa Rahimitabar
- grid.7491.b0000 0001 0944 9128FlüGe Research Project (Refugee Health), School of Public Health, Bielefeld University, P.O. Box 100131, 33501 Bielefeld, Germany
| | - Alexander Kraemer
- grid.7491.b0000 0001 0944 9128FlüGe Research Project, School of Public Health, Bielefeld University, Bielefeld, Germany
| | - Kayvan Bozorgmehr
- grid.7491.b0000 0001 0944 9128Department of Population Medicine and Health Services Research, School of Public Health, Bielefeld University, P.O. Box 100131, 33501 Bielefeld, Germany ,grid.5253.10000 0001 0328 4908Section for Health Equity Studies & Migration, University Hospital Heidelberg, Heidelberg, Germany
| | - Fatemeh Ebrahimi
- grid.7491.b0000 0001 0944 9128School of Public Health, Bielefeld University, P.O. Box 100131, 33501 Bielefeld, Germany
| | - Amirhossein Takian
- grid.411705.60000 0001 0166 0922Department of Global Health and Public Policy, School of Public Health, Tehran University of Medical Sciences (TUMS), P.O. Box 1417613151, Tehran, Iran ,grid.411705.60000 0001 0166 0922Department of Health Management, Policy & Economics, School of Public Health, TUMS, Tehran, Iran ,grid.411705.60000 0001 0166 0922Heath Equity Research Center (HERC), TUMS, Tehran, Iran
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Osman M, Cummings KJ, El Omari K, Kassem II. Catch-22: War, Refugees, COVID-19, and the Scourge of Antimicrobial Resistance. Front Med (Lausanne) 2022; 9:921921. [PMID: 35814789 PMCID: PMC9263824 DOI: 10.3389/fmed.2022.921921] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/27/2022] [Indexed: 12/03/2022] Open
Abstract
Wars have hidden repercussions beyond the immediate losses of life, well-being, and prosperity. Those that flee wars and seek refuge in safer locations are not immune to the tragic impacts. Of particular concern is the susceptibility of the refugee populations to infectious diseases and antimicrobial-resistant pathogens. This poses a detrimental risk to these disenfranchised populations, who often have limited access to medical care, sanitation, and nutritious and safe food. Furthermore, antimicrobial-resistant pathogens in refugees can be both transmitted to and acquired from their hosting communities. The latter is particularly problematic when the host countries suffer from serious challenges such as limited resources, pollution, and widespread antimicrobial resistance (AMR). Here, we discuss AMR in refugees of the ongoing Syrian war, a conflict that resulted in the largest population displacement in recent history. We argue that Syrian refugees and their hosting communities are at an elevated risk of complicated and life-threatening AMR infections. We also call on the international community to address this grievous problem that threatens the disenfranchised refugee populations and can spill over across geographic borders to affect multiple countries.
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Affiliation(s)
- Marwan Osman
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY, United States
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
- *Correspondence: Marwan Osman
| | - Kevin J. Cummings
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Khaled El Omari
- Quality Control Center Laboratories at the Chamber of Commerce, Industry & Agriculture of Tripoli & North Lebanon, Tripoli, Lebanon
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Issmat I. Kassem
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA, United States
- Issmat I. Kassem
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Chuang JY. Stressor-Specific Microbiota Intervention. Front Nutr 2022; 9:870665. [PMID: 35520283 PMCID: PMC9063858 DOI: 10.3389/fnut.2022.870665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
To date, mental disorders are diagnosed and treated by the subjective judgment of psychiatrists based on diagnostic criteria and treatment guidelines, respectively. Mental disorders are heterogeneous illnesses with a substantial treatment-refractory rate. Thus, there is a great need for novel treatment approaches. This article proposes a treatment approach centered on the concept of the gut–brain axis. There is mounting evidence indicating an association between stressors, microbiota, microglia, and mental disorders. Stressors might facilitate dysbiosis, inflammation, and the occurrence of mental disorders. This novel treatment approach is based on the idea that stressor types instead of the heterogeneous psychiatric diagnosis might be closer to the neurobiological underpinnings of mental disorders. First of all, patients with treatment-resistant mental disorders will be asked to describe their major stressors. Then, clinicians will calculate the total threat score and the total deprivation score. Subsequently, treatment tailored to the major stressor type will be administered to restore a healthy gut microbiome. Presumably, treatment will be aimed at increasing microbiota diversity in those who mainly have deprivation stressors and boosting Actinobacteria in those who have mainly threat stressors. Large-scale clinical trials are warranted to test this hypothetical approach.
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Affiliation(s)
- Jie-Yu Chuang
- Department of Psychiatry, Cardinal Tien Hospital, New Taipei City, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
- *Correspondence: Jie-Yu Chuang
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Osman M, Rafei R, Ismail MB, Omari SA, Mallat H, Dabboussi F, Cazer C, Karah N, Abbara A, Hamze M. Antimicrobial resistance in the protracted Syrian conflict: halting a war in the war. Future Microbiol 2021; 16:825-845. [PMID: 34223789 DOI: 10.2217/fmb-2021-0040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The Syrian conflict has damaged key infrastructure and indirectly affected almost all parts of the Middle East and Europe, with no end in sight. Exhausting conditions created by the Syrian crisis and related massive displacement promote the emergence of numerous public health problems that fuel antimicrobial resistance (AMR) development. Here, we explore the current situation of the Syrian displaced population, and AMR inside Syria and among refugees in host countries. We then suggest a roadmap of selected key interventions and strategies to address the threat of AMR in the context of the Syrian crisis. These recommendations are intended to urge health policy-makers in governments and international health organizations to optimize and push for implementing an effective policy taking into consideration the current obstacles.
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Affiliation(s)
- Marwan Osman
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine & Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Rayane Rafei
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Mohamad Bachar Ismail
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Faculty of Sciences, Lebanese University, Tripoli, Lebanon
| | - Sarah Al Omari
- Department of Epidemiology & Population Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Hassan Mallat
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Casey Cazer
- Department of Population Medicine & Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Nabil Karah
- Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Aula Abbara
- Department of Infection, Imperial College, London, UK
| | - Monzer Hamze
- Laboratoire Microbiologie, Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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10
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Louka C, Ravensbergen SJ, Ott A, Zhou X, García-Cobos S, Friedrich AW, Pournaras S, Rosema S, Rossen JW, Stienstra Y, Bathoorn E. Predominance of CTX-M-15-producing ST131 strains among ESBL-producing Escherichia coli isolated from asylum seekers in the Netherlands. J Antimicrob Chemother 2021; 76:70-76. [PMID: 33009805 PMCID: PMC7729386 DOI: 10.1093/jac/dkaa395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/19/2020] [Indexed: 11/13/2022] Open
Abstract
Objectives Numerous studies show increased prevalence of MDR bacteria amongst asylum seekers, but data on the molecular profiles of such strains are limited. We aimed to evaluate the molecular profiles of ESBL-producing Escherichia coli (ESBL-E. coli) strains isolated from asylum seekers and investigate their phylogenetic relatedness. Methods WGS data of ESBL-E. coli isolates from asylum seekers, retrieved from 1 January to 31 December 2016, were analysed to assess MLST STs, fim types, phylogroups and resistance genes. Fifty-two ESBL-E. coli isolates from the Dutch–German border region were used for genome comparison purposes as a control group. Results Among 112 ESBL-E. coli isolates from asylum seekers, originating mostly from Syria (n = 40) and Iraq (n = 15), the majority belonged to ST131 (21.4%) and ST10 (17.0%). The predominant gene for β-lactam resistance was blaCTX-M-15 (67.9%), followed by the often co-detected blaTEM-1B (39.3%). No mcr or carbapenemase genes were detected. The majority of the strains belonged to phylogroups B2 (38.4%) and A (32.1%), carrying fimH27 (25%) and fimH30 (19.6%). A core genome MLST minimum spanning tree did not reveal clusters containing strains from the asylum seekers and the control group. Five clusters were formed within the asylum seeker group, by strains isolated from people originating from different countries. Conclusions The most frequently isolated clones in this study were isolated on a regular basis within the Dutch population before the increase in the asylum seeker population. No mcr- or carbapenemase-producing clones were detected among the asylum seeker population. Minor clustering was observed amongst the asylum seeker strains.
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Affiliation(s)
- Christina Louka
- University of Groningen, University Medical Center Groningen, Department of Internal Medicine/Infectious Diseases, Groningen, The Netherlands.,ESCMID Study Group for Infections in Travellers and Migrants, Basel, Switzerland
| | - Sofanne J Ravensbergen
- University of Groningen, University Medical Center Groningen, Department of Internal Medicine/Infectious Diseases, Groningen, The Netherlands.,ESCMID Study Group for Infections in Travellers and Migrants, Basel, Switzerland
| | - Alewijn Ott
- Department of Medical Microbiology and Infection Prevention, Certe, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Xuewei Zhou
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Silvia García-Cobos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Alexander W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Spyros Pournaras
- Department of Medical Microbiology, 'ATTIKON' University Hospital of Athens, Athens, Greece
| | - Sigrid Rosema
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - John W Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - Ymkje Stienstra
- University of Groningen, University Medical Center Groningen, Department of Internal Medicine/Infectious Diseases, Groningen, The Netherlands.,ESCMID Study Group for Infections in Travellers and Migrants, Basel, Switzerland
| | - Erik Bathoorn
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
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11
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Zhang Q, Zhang Z, Zhou S, Jin M, Lu T, Cui L, Qian H. Macleaya cordata extract, an antibiotic alternative, does not contribute to antibiotic resistance gene dissemination. JOURNAL OF HAZARDOUS MATERIALS 2021; 412:125272. [PMID: 33550129 DOI: 10.1016/j.jhazmat.2021.125272] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/14/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
The abuse of antibiotics and their associated health risks are receiving global attention. The use of antibiotic additives in fodder has been banned in the European Union since 2006 and in China since 2020. Antibiotic alternatives are being developed, but their risks to the soil ecosystem remain poorly understood. Here, we compared the effects of the antibiotic oxytetracycline (OTC10, 10 mg/kg) with those of a Macleaya cordata extract (MCE, 10 and 100 mg/kg), the major antibiotic substitute. All tested concentrations of MCE and OTC10 exerted slight effects on the soil microbiome, but OTC10 and MCE100 could interfere with the structures and functions of the gut microbiome and might thus affect the soil ecological functions of Enchytraeus crypticus. Furthermore, OTC10 exposure inevitably increased the antibiotic resistance gene (ARG) abundance by 213%, whereas MCE did not induce ARG dissemination, which explains why MCE is considered to be associated with a low ecological risk. Our research provides the first demonstration of the risks posed by antibiotic alternatives to soil animals from the perspective of environmental toxicology and explores the potential development of antibiotic alternatives associated with a low ecological risk from a new perspective.
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Affiliation(s)
- Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Shuyidan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Mingkang Jin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China.
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12
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Ho J, Yeoh YK, Barua N, Chen Z, Lui G, Wong SH, Yang X, Chan MCW, Chan PKS, Hawkey PM, Ip M. Systematic review of human gut resistome studies revealed variable definitions and approaches. Gut Microbes 2020; 12:1700755. [PMID: 31942825 PMCID: PMC7524153 DOI: 10.1080/19490976.2019.1700755] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.
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Affiliation(s)
- Jeffery Ho
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yun Kit Yeoh
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nilakshi Barua
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Grace Lui
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,Department of Medicine & Therapeutics, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H Wong
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,Department of Medicine & Therapeutics, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Martin CW Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul KS Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peter M Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,CONTACT Margaret Ip Department of Microbiology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
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13
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Moltzau Anderson J, Lipinski S, Sommer F, Pan WH, Boulard O, Rehman A, Falk-Paulsen M, Stengel ST, Aden K, Häsler R, Bharti R, Künzel S, Baines JF, Chamaillard M, Rosenstiel P. NOD2 Influences Trajectories of Intestinal Microbiota Recovery After Antibiotic Perturbation. Cell Mol Gastroenterol Hepatol 2020; 10:365-389. [PMID: 32289499 PMCID: PMC7327897 DOI: 10.1016/j.jcmgh.2020.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Loss-of-function variants in nucleotide-binding oligomerization domain-containing protein 2 (NOD2) impair the recognition of the bacterial cell wall component muramyl-dipeptide and are associated with an increased risk for developing Crohn's disease. Likewise, exposure to antibiotics increases the individual risk for developing inflammatory bowel disease. Here, we studied the long-term impact of NOD2 on the ability of the gut bacterial and fungal microbiota to recover after antibiotic treatment. METHODS Two cohorts of 20-week-old and 52-week-old wild-type (WT) C57BL/6J and NOD2 knockout (Nod2-KO) mice were treated with broad-spectrum antibiotics and fecal samples were collected to investigate temporal dynamics of the intestinal microbiota (bacteria and fungi) using 16S ribosomal RNA and internal transcribed spacer 1 sequencing. In addition, 2 sets of germ-free WT mice were colonized with either WT or Nod2-KO after antibiotic donor microbiota and the severity of intestinal inflammation was monitored in the colonized mice. RESULTS Antibiotic exposure caused long-term shifts in the bacterial and fungal community composition. Genetic ablation of NOD2 was associated with delayed body weight gain after antibiotic treatment and an impaired recovery of the bacterial gut microbiota. Transfer of the postantibiotic fecal microbiota of Nod2-KO mice induced an intestinal inflammatory response in the colons of germ-free recipient mice compared with respective microbiota from WT controls based on histopathology and gene expression analyses. CONCLUSIONS Our data show that the bacterial sensor NOD2 contributes to intestinal microbial community composition after antibiotic treatment and may add to the explanation of how defects in the NOD2 signaling pathway are involved in the etiology of Crohn's disease.
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Affiliation(s)
| | | | - Felix Sommer
- Institute of Clinical Molecular Biology, Kiel, Germany
| | - Wei-Hung Pan
- Institute of Clinical Molecular Biology, Kiel, Germany
| | - Olivier Boulard
- University of Lille, Centre national de la recherche scientifique, Inserm, Centre Hospitalier Universitaire de Lille Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Lille, France
| | | | | | | | - Konrad Aden
- Institute of Clinical Molecular Biology, Kiel, Germany,First Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Kiel, Germany
| | - Richa Bharti
- Institute of Clinical Molecular Biology, Kiel, Germany
| | - Sven Künzel
- Evolutionary Genomics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - John F. Baines
- Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany,Evolutionary Genomics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Mathias Chamaillard
- University of Lille, Centre national de la recherche scientifique, Inserm, Centre Hospitalier Universitaire de Lille Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel, Germany,Correspondence Address correspondence to: Philip Rosenstiel, MD, Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Rosalind-Franklin-Str. 12, Kiel D-24105, Germany. fax: (49) 4315971842.
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14
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Abd El Ghany M, Fouz N, Hill-Cawthorne GA. Human Movement and Transmission of Antimicrobial-Resistant Bacteria. THE HANDBOOK OF ENVIRONMENTAL CHEMISTRY 2020:311-344. [DOI: 10.1007/698_2020_560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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15
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Alaryan T, Hasan TA, Eshelli M, Alzeer S. The Misuse of Prescribed Drugs During the Syrian Crisis: a Cross-sectional Study. Int J Ment Health Addict 2019. [DOI: 10.1007/s11469-019-00180-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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16
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Trumble BC, Finch CE. THE EXPOSOME IN HUMAN EVOLUTION: FROM DUST TO DIESEL. THE QUARTERLY REVIEW OF BIOLOGY 2019; 94:333-394. [PMID: 32269391 PMCID: PMC7141577 DOI: 10.1086/706768] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Global exposures to air pollution and cigarette smoke are novel in human evolutionary history and are associated with about 16 million premature deaths per year. We investigate the history of the human exposome for relationships between novel environmental toxins and genetic changes during human evolution in six phases. Phase I: With increased walking on savannas, early human ancestors inhaled crustal dust, fecal aerosols, and spores; carrion scavenging introduced new infectious pathogens. Phase II: Domestic fire exposed early Homo to novel toxins from smoke and cooking. Phases III and IV: Neolithic to preindustrial Homo sapiens incurred infectious pathogens from domestic animals and dense communities with limited sanitation. Phase V: Industrialization introduced novel toxins from fossil fuels, industrial chemicals, and tobacco at the same time infectious pathogens were diminishing. Thereby, pathogen-driven causes of mortality were replaced by chronic diseases driven by sterile inflammogens, exogenous and endogenous. Phase VI: Considers future health during global warming with increased air pollution and infections. We hypothesize that adaptation to some ancient toxins persists in genetic variations associated with inflammation and longevity.
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Affiliation(s)
- Benjamin C Trumble
- School of Human Evolution & Social Change and Center for Evolution and Medicine, Arizona State University Tempe, Arizona 85287 USA
| | - Caleb E Finch
- Leonard Davis School of Gerontology and Dornsife College, University of Southern California Los Angeles, California 90089-0191 USA
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17
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Zhu D, Xiang Q, Yang XR, Ke X, O'Connor P, Zhu YG. Trophic Transfer of Antibiotic Resistance Genes in a Soil Detritus Food Chain. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:7770-7781. [PMID: 31244079 DOI: 10.1021/acs.est.9b00214] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The presence and spread of antibiotic resistance genes (ARGs) are causing substantial global public concern; however, the dispersal of ARGs in the food chain is poorly understood. Here, we experimented with a soil collembolan ( Folsomia candida)-predatory mite ( Hypoaspis aculeifer) model food chain to study trophic transfer of ARGs in a manure-contaminated soil ecosystem. Our results showed that manure amendment of soil could significantly increase ARGs in the soil collembolan microbiome. With the ARGs in the prey collembolan microbiome increasing, an increase in ARGs in the predatory mite microbiome was also observed, especially for three high abundant ARGs ( blaSHV, fosX and aph6ia). Three unique ARGs were transferred into the microbiome of the predatory mite from manure amended soil via the prey collembolan ( aac(6' )-lb(akaaacA4), yidY_mdtL and tolC). Manure amendment altered the composition and structure and reduced the diversity of the microbiomes of the prey collembolan and the predatory mite. We further reveal that bacterial communities and mobile genetic elements were two important drivers for the trophic transfer of ARGs, not just for ARGs distribution in the samples. These findings suggest that the importance of food chain transmission of ARGs for the dispersal of resistance genes in soil ecosystems may be underestimated.
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Affiliation(s)
- Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , 1799 Jimei Road , Xiamen 361021 , China
- University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Qian Xiang
- University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , 1799 Jimei Road , Xiamen 361021 , China
| | - Xin Ke
- Institute of Plant Physiology and Ecology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences , Shanghai 200032 , China
| | - Patrick O'Connor
- Centre for Global Food and Resources, University of Adelaide , Adelaide 5005 , Australia
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , 1799 Jimei Road , Xiamen 361021 , China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
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18
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Dhakan DB, Maji A, Sharma AK, Saxena R, Pulikkan J, Grace T, Gomez A, Scaria J, Amato KR, Sharma VK. The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. Gigascience 2019; 8:giz004. [PMID: 30698687 PMCID: PMC6394208 DOI: 10.1093/gigascience/giz004] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 11/02/2018] [Accepted: 01/10/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health; however, the Indian gut microbiome has not been well explored. We analyzed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole-genome shotgun metagenomic sequencing, and metabolomic profiling of fecal and serum samples. RESULTS The gene catalogue established in this study emphasizes the uniqueness of the Indian gut microbiome in comparison to other populations. The gut microbiome of the cohort from North-Central India, which was primarily consuming a plant-based diet, was found to be associated with Prevotella and also showed an enrichment of branched chain amino acid (BCAA) and lipopolysaccharide biosynthesis pathways. In contrast, the gut microbiome of the cohort from Southern India, which was consuming an omnivorous diet, showed associations with Bacteroides, Ruminococcus, and Faecalibacterium and had an enrichment of short chain fatty acid biosynthesis pathway and BCAA transporters. This corroborated well with the metabolomics results, which showed higher concentration of BCAAs in the serum metabolome of the North-Central cohort and an association with Prevotella. In contrast, the concentration of BCAAs was found to be higher in the fecal metabolome of the Southern-India cohort and showed a positive correlation with the higher abundance of BCAA transporters. CONCLUSIONS The study reveals the unique composition of the Indian gut microbiome, establishes the Indian gut microbial gene catalogue, and compares it with the gut microbiome of other populations. The functional associations revealed using metagenomic and metabolomic approaches provide novel insights on the gut-microbe-metabolic axis, which will be useful for future epidemiological and translational researches.
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Affiliation(s)
- D B Dhakan
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Madhya Pradesh, 462066, India
| | - A Maji
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Madhya Pradesh, 462066, India
| | - A K Sharma
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Madhya Pradesh, 462066, India
| | - R Saxena
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Madhya Pradesh, 462066, India
| | - J Pulikkan
- Department of Genomic Science, Central University of Kerala, Periye Post, Kasargod, Kerala, 671316, India
| | - T Grace
- Department of Genomic Science, Central University of Kerala, Periye Post, Kasargod, Kerala, 671316, India
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, Kansas, KS 66506, USA
| | - A Gomez
- Microbiomics Laboratory, Department of Animal Science, University of Minnesota, 1988 Fitch Avenue, Minnesota, MN 55108, USA
| | - J Scaria
- Animal Disease Research & Diagnostic Laboratory, Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, South Dakota, SD 57007, USA
| | - K R Amato
- Department of Anthropology, Northwestern University, 1810 Hinman Avenue, Evanston, Illinois, IL 60208, USA
| | - V K Sharma
- Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Madhya Pradesh, 462066, India
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19
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Nuli R, Azhati J, Cai J, Kadeer A, Zhang B, Mohemaiti P. Metagenomics and Faecal Metabolomics Integrative Analysis towards the Impaired Glucose Regulation and Type 2 Diabetes in Uyghur-Related Omics. J Diabetes Res 2019; 2019:2893041. [PMID: 31828159 PMCID: PMC6885810 DOI: 10.1155/2019/2893041] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/02/2019] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE Gut microbiota and their metabolites play an important role in the development of type 2 diabetes mellitus (T2DM). This research was designed to study the relationship between gut microbiota and faecal metabolites of Uyghur newly onset T2DM and impaired glucose regulation (IGR) patients. MATERIALS AND METHODS A total of 60 different glycemic Uyghur subjects were enrolled and divided into T2DM, IGR, and normal glucose tolerance (NGT) groups. Metagenomics and LC-MS-based untargeted faecal metabolomics were employed. Correlations between bacterial composition and faecal metabolomics were evaluated. RESULTS We discovered that the composition and diversity of gut microbiota in newly onset T2DM and IGR were different from those in NGT. The α-diversity was higher in NGT than in T2DM and IGR; β-diversity analysis revealed apparent differences in the bacterial community structures between patients with T2DM, IGR, and NGT. LC-MS faecal metabolomics analysis discovered different metabolomics features in the three groups. Alchornoic acid, PE (14 : 0/20 : 3), PI, L-tyrosine, LysoPC (15 : 0), protorifamycin I, pimelic acid, epothilone A, 7-dehydro-desmosterol, L-lysine, LysoPC (14 : 1), and teasterone are the most significant differential enriched metabolites. Most of the differential enriched metabolites were involved in metabolic processes, including carbohydrate metabolism, starch and sucrose metabolism, phenylpropanoid biosynthesis, and biosynthesis of amino acids. Procrustes analysis and correlation analysis identified correlations between gut microbiota and faecal metabolites. Matricin was positively correlated with Bacteroides and negatively correlated with Actinobacteria; protorifamycin I was negatively correlated with Actinobacteria; epothilone A was negatively correlated with Actinobacteria and positively correlated with Firmicutes; PA was positively correlated with Bacteroides and negatively correlated with Firmicutes; and cristacarpin was positively correlated with Actinobacteria; however, this correlation relationship does not imply causality. CONCLUSIONS This study used joint metagenomics and metabolomics analyses to elucidate the relationship between gut microbiota and faecal metabolites in different glycemic groups, and the result suggested that metabolic disorders and gut microbiota dysbiosis occurred in Uyghur T2DM and IGR. The results provide a theoretical basis for studying the pathological mechanism for further research.
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Affiliation(s)
- Rebiya Nuli
- School of Public Health, Xinjiang Medical University, Urumqi 830011, China
- College of Basic Medical Science, Xinjiang Medical University, Urumqi 830011, China
| | - Jureti Azhati
- The People's Hospital of Xinjiang Uyghur Autonomous Region, Urumqi 830001, China
| | - Junxiu Cai
- The Fifth Affiliated Hospital of Xinjiang Medical University, Urumqi 830000, China
| | - Aizhatiguli Kadeer
- School of Public Health, Xinjiang Medical University, Urumqi 830011, China
| | - Bing Zhang
- College of Basic Medical Science, Xinjiang Medical University, Urumqi 830011, China
| | - Patamu Mohemaiti
- School of Public Health, Xinjiang Medical University, Urumqi 830011, China
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20
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Strategic Approach for Prioritising Local and Regional Sanitation Interventions for Reducing Global Antibiotic Resistance. WATER 2018. [DOI: 10.3390/w11010027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Globally increasing antibiotic resistance (AR) will only be reversed through a suite of multidisciplinary actions (One Health), including more prudent antibiotic use and improved sanitation on international scales. Relative to sanitation, advanced technologies exist that reduce AR in waste releases, but such technologies are expensive, and a strategic approach is needed to prioritize more affordable mitigation options, especially for Low- and Middle-Income Countries (LMICs). Such an approach is proposed here, which overlays the incremental cost of different sanitation options and their relative benefit in reducing AR, ultimately suggesting the “next-most-economic” options for different locations. When considering AR gene fate versus intervention costs, reducing open defecation (OD) and increasing decentralized secondary wastewater treatment, with condominial sewers, will probably have the greatest impact on reducing AR, for the least expense. However, the best option for a given country depends on the existing sewerage infrastructure. Using Southeast Asia as a case study and World Bank/WHO/UNICEF data, the approach suggests that Cambodia and East Timor should target reducing OD as a national priority. In contrast, increasing decentralized secondary treatment is well suited to Thailand, Vietnam and rural Malaysia. Our approach provides a science-informed starting point for decision-makers, for prioritising AR mitigation interventions; an approach that will evolve and refine as more data become available.
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21
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Abstract
Among migrants who arrived in the USA and Europe, communicable diseases such as dermatologic, gastrointestinal, and respiratory infections are frequent; non-communicable diseases including chronic diseases such as hypertension and diabetes, and vaccine-preventable diseases are also prevalent. Refugees are often not up to date on routine immunizations and screenings for chronic diseases and cancer. In addition, many immigrants have trauma-related mental health problems, which are often not addressed by the healthcare systems where they reside. Determining the healthcare needs of specific immigration groups should lead to the establishment of evidence-based guidelines for providing screening and healthcare services to immigrant populations, for the benefit of the individuals concerned, as well as the host countries.
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Affiliation(s)
- Talma Rosenthal
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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