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Ballard SA, Sherry NL, Howden BP. Public health implementation of pathogen genomics: the role for accreditation and application of ISO standards. Microb Genom 2023; 9:mgen001097. [PMID: 37590046 PMCID: PMC10483410 DOI: 10.1099/mgen.0.001097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/04/2023] [Indexed: 08/18/2023] Open
Abstract
Pathogen genomics has transitioned rapidly from the research setting into a powerful tool now routinely used in public health microbiology, for surveillance, outbreak investigations and disease control. As these investigations can have significant public health, treatment and legal impacts, we must ensure the accuracy of these results through validation of testing processes. For laboratories working in this space, it is important to approach this work with a quality and accreditation framework in mind, working towards implementation of quality systems and test validation that meet international regulatory standards. Here we outline the key international standards and processes that lead toward accreditation for pathogen genomics.
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Affiliation(s)
- Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St Melbourne, 3000, Australia
| | - Norelle L. Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St Melbourne, 3000, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, Austin Hospital, 145 Studley Rd., Heidelberg, Victoria 3084, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St Melbourne, 3000, Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Infectious Diseases, Austin Hospital, 145 Studley Rd., Heidelberg, Victoria 3084, Australia
- Centre for Pathogen Genomics, The University of Melbourne, Melbourne, Australia
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Taylor-Brown A, Afrad MH, Khan AI, Lassalle F, Islam MT, Tanvir NA, Thomson NR, Qadri F. Genomic epidemiology of Vibrio cholerae during a mass vaccination campaign of displaced communities in Bangladesh. Nat Commun 2023; 14:3773. [PMID: 37355673 PMCID: PMC10290697 DOI: 10.1038/s41467-023-39415-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
Ongoing diarrheal disease surveillance throughout Bangladesh over the last decade has revealed seasonal localised cholera outbreaks in Cox's Bazar, where both Bangladeshi Nationals and Forcibly Displaced Myanmar Nationals (FDMNs) reside in densely populated settlements. FDMNs were recently targeted for the largest cholera vaccination campaign in decades. We aimed to infer the epidemic risk of circulating Vibrio cholerae strains by determining if isolates linked to the ongoing global cholera pandemic ("7PET" lineage) were responsible for outbreaks in Cox's Bazar. We found two sublineages of 7PET in this setting during the study period; one with global distribution, and a second lineage restricted to Asia and the Middle East. These subclades were associated with different disease patterns that could be partially explained by genomic differences. Here we show that as the pandemic V. cholerae lineage circulates in this vulnerable population, without a vaccine intervention, the risk of an epidemic was very high.
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Affiliation(s)
- Alyce Taylor-Brown
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Mokibul Hassan Afrad
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Ashraful Islam Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Florent Lassalle
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Md Taufiqul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- School of Medical Science, Griffith University, Gold Coast, QLD, Australia
| | - Nabid Anjum Tanvir
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nicholas R Thomson
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.
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Redae GA, Mengestu TK, Abdalla FM, Slim SN, Simon VT, Ali AO, Saguti GE, Habtu MM, Tegegne SG, Msambazi MJ, Zabulon Y. Towards cholera elimination in Zanzibar: analysis of evidences on what have worked. Pan Afr Med J 2023; 45:6. [PMID: 37538360 PMCID: PMC10395108 DOI: 10.11604/pamj.supp.2023.45.1.39828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/12/2023] [Indexed: 08/05/2023] Open
Abstract
Cholera, an enteric disease caused by Vibrio cholera claims thousands of lives yearly. The disease is a disease of inequality that affect populations which have poor access to safe water and sanitation facilities. Zanzibar, an archipelago in the Indian ocean which is part of the United Republic of Tanzania has been affected by recurrent cholera outbreak for the past decades. A multi-sectoral and multi-year three pillar approach namely Enabling Environment, Prevention and Response, for the elimination of cholera were initiated by the stewardship of the government, engagement of the community and technical and financial support of partners. The approach has enabled Zanzibar to interrupt the recurrent cholera outbreak for the past five years. The analysis of evidences have proven that creating an enabling environment through multi-sectoral involvement, mobilizing communities, intensifying surveillance complemented by the traditional disease prevention and control interventions has resulted to interruption of cholera transmission in the country.
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Affiliation(s)
| | | | | | | | | | - Ali Omar Ali
- World Health Organization Country Office, Dar es Salaam, Tanzania
| | | | | | | | | | - Yoti Zabulon
- World Health Organization Country Office, Dar es Salaam, Tanzania
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Huo X, Yu H, Xing B, Zuo X, Zhang N. Review of High Entropy Alloys Electrocatalysts for Hydrogen Evolution, Oxygen Evolution, and Oxygen Reduction Reaction. CHEM REC 2022; 22:e202200175. [PMID: 36108141 DOI: 10.1002/tcr.202200175] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/13/2022] [Indexed: 12/14/2022]
Abstract
Recently, high-entropy alloys (HEAs) have been extensively investigated due to their unique structural design, superior stability, excellent functional feature and superior mechanical performance. However, most of the reported HEAs focus on studying the compositional design and microstructure and mechanical properties of materials. There are relatively few studies on electrochemical performance and theoretical studies of HEAs. In addition, the potential applications of HEAs as energy storage materials for electrocatalysts have attracted widely attention in the development and application aspects of electrocatalysis. It can be attributed to their high conductivity, excellent structural stability and superior electrocatalytic activities with small overpotential and abundant active sites, which is comparable to the commercial noble metal catalysts. In this review, firstly, we briefly discuss the concept and structure characteristics of high entropy alloys. Then, the research progress of high-entropy alloys as electrocatalysis are also summarized, including hydrogen evolution reaction (HER), oxygen evolution reaction (OER) and oxygen reduction reaction (ORR), respectively. Finally, the future development trend of HEAs is also prospected for energy conversion fields.
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Affiliation(s)
- Xiaoran Huo
- School of Materials Science and Engineering, Shenyang University of Technology, Shenyang, 110870, P. R. China
| | - Huishu Yu
- School of Materials Science and Engineering, Shenyang University of Technology, Shenyang, 110870, P. R. China
| | - Bowei Xing
- School of Materials Science and Engineering, Shenyang University of Technology, Shenyang, 110870, P. R. China
| | - Xiaojiao Zuo
- School of Materials Science and Engineering, Shenyang University of Technology, Shenyang, 110870, P. R. China
| | - Nannan Zhang
- School of Materials Science and Engineering, Shenyang University of Technology, Shenyang, 110870, P. R. China
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Usmani M, Brumfield KD, Magers BM, Huq A, Barciela R, Nguyen TH, Colwell RR, Jutla A. Predictive Intelligence for Cholera in Ukraine? GEOHEALTH 2022; 6:e2022GH000681. [PMID: 36185317 PMCID: PMC9514009 DOI: 10.1029/2022gh000681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/02/2022] [Accepted: 08/06/2022] [Indexed: 06/16/2023]
Abstract
Cholera, an ancient waterborne diarrheal disease, remains a threat to public health, especially when climate/weather processes, microbiological parameters, and sociological determinants intersect with population vulnerabilities of loss of access to safe drinking water and sanitation infrastructure. The ongoing war in Ukraine has either damaged or severely crippled civil infrastructure, following which the human population is at risk of health disasters. This editorial highlights a perspective on using predictive intelligence to combat potential (and perhaps impending) cholera outbreaks in various regions of Ukraine. Reliable and judicious use of existing earth observations inspired mathematical algorithms integrating heuristic understanding of microbiological, sociological, and weather parameters have the potential to save or reduce the disease burden.
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Affiliation(s)
- Moiz Usmani
- GeoHealth and Hydrology LaboratoryDepartment of Environmental Engineering SciencesUniversity of FloridaGainesvilleFLUSA
| | - Kyle D. Brumfield
- Maryland Pathogen Research InstituteUniversity of MarylandCollege ParkMDUSA
- University of Maryland Institute for Advanced Computer StudiesUniversity of MarylandCollege ParkMDUSA
| | - Bailey M. Magers
- GeoHealth and Hydrology LaboratoryDepartment of Environmental Engineering SciencesUniversity of FloridaGainesvilleFLUSA
| | - Anwar Huq
- Maryland Pathogen Research InstituteUniversity of MarylandCollege ParkMDUSA
- University of Maryland Institute for Advanced Computer StudiesUniversity of MarylandCollege ParkMDUSA
| | | | - Thanh H. Nguyen
- Department of Civil and Environmental EngineeringUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Rita R. Colwell
- Maryland Pathogen Research InstituteUniversity of MarylandCollege ParkMDUSA
- University of Maryland Institute for Advanced Computer StudiesUniversity of MarylandCollege ParkMDUSA
| | - Antarpreet Jutla
- GeoHealth and Hydrology LaboratoryDepartment of Environmental Engineering SciencesUniversity of FloridaGainesvilleFLUSA
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Benamrouche N, Belkader C, Njamkepo E, Zemam SS, Sadat S, Saighi K, Boutabba DT, Mechouet F, Benhadj-Slimani R, Zmit FZ, Rauzier J, Kias F, Zouagui S, Ruckly C, Yousfi M, Zertal A, Chouikrat R, Quilici ML, Weill FX. Outbreak of Imported Seventh Pandemic Vibrio cholerae O1 El Tor, Algeria, 2018. Emerg Infect Dis 2022; 28:1241-1245. [PMID: 35608654 PMCID: PMC9155889 DOI: 10.3201/eid2806.212451] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
After a lull of >20 years, Algeria experienced a cholera outbreak in 2018 that included 291 suspected cases. We found that outbreak isolates were Vibrio cholerae O1 serotype Ogawa from seventh pandemic El Tor sublineage AFR14, which corresponds to a new introduction of cholera into Africa from South Asia.
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Rouard C, Njamkepo E, Quilici ML, Weill FX. Contribution of microbial genomics to cholera epidemiology. C R Biol 2022; 345:37-56. [DOI: 10.5802/crbiol.77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/28/2022] [Indexed: 11/24/2022]
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Usmani M, Brumfield KD, Jamal Y, Huq A, Colwell RR, Jutla A. A Review of the Environmental Trigger and Transmission Components for Prediction of Cholera. Trop Med Infect Dis 2021; 6:tropicalmed6030147. [PMID: 34449728 PMCID: PMC8396309 DOI: 10.3390/tropicalmed6030147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 11/16/2022] Open
Abstract
Climate variables influence the occurrence, growth, and distribution of Vibrio cholerae in the aquatic environment. Together with socio-economic factors, these variables affect the incidence and intensity of cholera outbreaks. The current pandemic of cholera began in the 1960s, and millions of cholera cases are reported each year globally. Hence, cholera remains a significant health challenge, notably where human vulnerability intersects with changes in hydrological and environmental processes. Cholera outbreaks may be epidemic or endemic, the mode of which is governed by trigger and transmission components that control the outbreak and spread of the disease, respectively. Traditional cholera risk assessment models, namely compartmental susceptible-exposed-infected-recovered (SEIR) type models, have been used to determine the predictive spread of cholera through the fecal–oral route in human populations. However, these models often fail to capture modes of infection via indirect routes, such as pathogen movement in the environment and heterogeneities relevant to disease transmission. Conversely, other models that rely solely on variability of selected environmental factors (i.e., examine only triggers) have accomplished real-time outbreak prediction but fail to capture the transmission of cholera within impacted populations. Since the mode of cholera outbreaks can transition from epidemic to endemic, a comprehensive transmission model is needed to achieve timely and reliable prediction with respect to quantitative environmental risk. Here, we discuss progression of the trigger module associated with both epidemic and endemic cholera, in the context of the autochthonous aquatic nature of the causative agent of cholera, V. cholerae, as well as disease prediction.
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Affiliation(s)
- Moiz Usmani
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32603, USA; (M.U.); (Y.J.); (A.J.)
| | - Kyle D. Brumfield
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA; (K.D.B.); (A.H.)
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
| | - Yusuf Jamal
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32603, USA; (M.U.); (Y.J.); (A.J.)
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA; (K.D.B.); (A.H.)
| | - Rita R. Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA; (K.D.B.); (A.H.)
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
- Correspondence:
| | - Antarpreet Jutla
- Geohealth and Hydrology Laboratory, Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL 32603, USA; (M.U.); (Y.J.); (A.J.)
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Fennell TG, Blackwell GA, Thomson NR, Dorman MJ. gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae. Microb Genom 2021; 7:000594. [PMID: 34100695 PMCID: PMC8461464 DOI: 10.1099/mgen.0.000594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Members of the bacterial genus Vibrio utilize chitin both as a metabolic substrate and a signal to activate natural competence. Vibrio cholerae is a bacterial enteric pathogen, sub-lineages of which can cause pandemic cholera. However, the chitin metabolic pathway in V. cholerae has been dissected using only a limited number of laboratory strains of this species. Here, we survey the complement of key chitin metabolism genes amongst 195 diverse V. cholerae. We show that the gene encoding GbpA, known to be an important colonization and virulence factor in pandemic isolates, is not ubiquitous amongst V. cholerae. We also identify a putatively novel chitinase, and present experimental evidence in support of its functionality. Our data indicate that the chitin metabolic pathway within V. cholerae is more complex than previously thought, and emphasize the importance of considering genes and functions in the context of a species in its entirety, rather than simply relying on traditional reference strains.
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Affiliation(s)
- Thea G. Fennell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Churchill College, Storey’s Way, Cambridge, CB3 0DS, UK
- Present address: Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, UK
| | - Grace A. Blackwell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- London School of Hygiene and Tropical Medicine, Keppel St., Bloomsbury, London, WC1E 7HT, UK
| | - Matthew J. Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Churchill College, Storey’s Way, Cambridge, CB3 0DS, UK
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Assessment and Antibiotic Resistance Profiling in Vibrio Species Isolated from Wild Birds Captured in Danube Delta Biosphere Reserve, Romania. Antibiotics (Basel) 2021; 10:antibiotics10030333. [PMID: 33809945 PMCID: PMC8004222 DOI: 10.3390/antibiotics10030333] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial and multidrug-resistant bacteria are a major problem worldwide and, consequently, the surveillance of antibiotic-resistant bacteria and assessment of the dissemination routes are essential. We hypothesized that migratory birds, coming from various environments, would carry more numerous Vibrio strains than sedentary species, with increased risk to be passed to their contacts or environment in habitats they transit or nest in. Similarly, we presumed that strains from migratory birds will show multidrug resistance. A total of 170 oral and rectal swabs were collected from wild birds captured in different locations of the Danube Delta (Malic, Sfantu-Gheorghe, Letea Forest) and processed using standardized selective media. V. cholerae strains were confirmed by serology and molecular methods and, subsequently, their susceptibility was evaluated. The prevalence of Vibrio species by host species, habitat type, and location was interpreted. The isolated Vibrio species were identified as Vibrio cholerae 14.33%, V. fluvialis 13.33%, V. alginolyticus 12%, V. mimicus 17.33%, V. vulnificus 10.88%, with V. parahaemolyticus and V. metschnikovii (16%) also being prevalent. Of the 76 Vibrio spp. isolates, 18.42% were resistant towards at least three antimicrobials, and 81.57% demonstrated a multidrug resistance phenotype, including mainly penicillins, aminoglycosides, and macrolides. The results of the present study indicate higher numbers of Vibrio strains in migratory (74.66%) than in sedentary birds (25.33%), confirming our hypothesis. Furthermore, the increased pathogenicity of Vibrio spp. strains, isolated from wild migratory and sedentary birds, was confirmed by their increased multiple antibiotic resistance (MAR) index (0.09–0.81).
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