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Bashir IM, Al-Waleedi AA, Al-Shaibani SM, Rajamanar M, Al-Akbari S, Al-Harazi A, Salim Aliwah L, Ahmed Salem N, Al-Ademi D, Barakat A, Sarkis N, Abubakar A, Senga M, Musani A, Abdel Moneim ARI, Mahmoud N. Strengthening laboratories in response to outbreaks in humanitarian emergencies and conflict settings: Results, challenges and lessons from expanding PCR diagnostic capacities for COVID-19 testing in Yemen. PLoS One 2024; 19:e0298603. [PMID: 38394178 PMCID: PMC10889613 DOI: 10.1371/journal.pone.0298603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND When the COVID-19 pandemic was declared, Yemen, a country facing years of conflict had only one laboratory with PCR testing capacity. In this article, we describe the outcome of the implementation of molecular based diagnostics platform in Yemen and highlight the key milestones the country went through to increase access to testing for its populations residing in a geographically vast and politically divided country. METHODS A retrospective assessment of COVID-19 laboratory response activities was done detailing the needs assessment process, timelines, geographical coverage, and outcomes of the activities. Laboratory data was analyzed to construct the geographical locations of COVID-19 testing laboratories and the numbers of tests performed in each facility to highlight the demands of testing for travelers. Finally, we discuss the impact these activities had in enabling the movement of people across international borders for economic gains and in delivery of critical humanitarian aid. OUTCOME PCR testing capacities in Yemen significantly improved, from one laboratory in Sanaa in April 2020 to 18 facilities across the country by June 2022. In addition, the number of functional Real-Time PCR thermocyclers increased from one to 32, the PCR tests output per day improved from 192 to 6144 tests per day. Results from analysis of laboratory data showed there were four peaks of COVID-19 in Yemen as October 2022. The majority of laboratory tests were performed for travelers than for medical or public health reasons. Demand for laboratory testing in Yemen was generally low and waned over time as the perceived risk of COVID-19 declined, in parallel with rollout of the COVID-19 vaccines. DISCUSSION/CONCLUSION The successful expansion of laboratory testing capacity was instrumental in the control and management of COVID-19 cases and critical in the implementation of public response strategies, including restrictions on gathering. Laboratory testing also facilitated the movement of humanitarian agencies and delivery of aid and enabled hundreds of thousands of Yemeni nationals to travel internationally. By virtue of these outcomes, the impact of laboratory strengthening activities was thus felt in the health sector and beyond.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Amal Barakat
- World Health Organization, East Mediterranean Regional Office, Cairo, Egypt
| | | | - Abdinasir Abubakar
- World Health Organization, East Mediterranean Regional Office, Cairo, Egypt
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Lassalle F, Al-Shalali S, Al-Hakimi M, Njamkepo E, Bashir IM, Dorman MJ, Rauzier J, Blackwell GA, Taylor-Brown A, Beale MA, Cazares A, Al-Somainy AA, Al-Mahbashi A, Almoayed K, Aldawla M, Al-Harazi A, Quilici ML, Weill FX, Dhabaan G, Thomson NR. Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen. Nat Microbiol 2023; 8:1787-1798. [PMID: 37770747 PMCID: PMC10539172 DOI: 10.1038/s41564-023-01472-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Since 2016, Yemen has been experiencing the largest cholera outbreak in modern history. Multidrug resistance (MDR) emerged among Vibrio cholerae isolates from cholera patients in 2018. Here, to characterize circulating genotypes, we analysed 260 isolates sampled in Yemen between 2018 and 2019. Eighty-four percent of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sub-lineage T13, whereas 16% were non-toxigenic, from divergent non-7PET lineages. Treatment of severe cholera with macrolides between 2016 and 2019 coincided with the emergence and dominance of T13 subclones carrying an incompatibility type C (IncC) plasmid harbouring an MDR pseudo-compound transposon. MDR plasmid detection also in endemic non-7PET V. cholerae lineages suggested genetic exchange with 7PET epidemic strains. Stable co-occurrence of the IncC plasmid with the SXT family of integrative and conjugative element in the 7PET background has major implications for cholera control, highlighting the importance of genomic epidemiological surveillance to limit MDR spread.
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Affiliation(s)
- Florent Lassalle
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
| | | | | | - Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | | | - Matthew J Dorman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- Churchill College, Cambridge, UK
| | - Jean Rauzier
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | - Grace A Blackwell
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- EMBL-EBI, Hinxton, UK
| | - Alyce Taylor-Brown
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Mathew A Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Adrián Cazares
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Khaled Almoayed
- National Centre of Public Health Laboratories, Sana'a, Yemen
| | - Mohammed Aldawla
- Ministry of Public Health, Infection Control Unit, Sana'a, Yemen
| | | | - Marie-Laure Quilici
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Paris, France
| | - Ghulam Dhabaan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
- London School of Hygiene and Tropical Medicine, London, UK.
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Al-Waleedi AA, Naiene JD, Thabet AAK, Dandarawe A, Salem H, Mohammed N, Al Noban M, Bin-Azoon NS, Shawqi A, Rajamanar M, Al-Jariri R, Al Hyubaishi M, Khanbari L, Thabit N, Obaid B, Baaees M, Assaf D, Senga M, Bashir IM, Mahmoud N, Cosico R, Smith P, Musani A. The first 2 months of the SARS-CoV-2 epidemic in Yemen: Analysis of the surveillance data. PLoS One 2020; 15:e0241260. [PMID: 33119720 PMCID: PMC7595428 DOI: 10.1371/journal.pone.0241260] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/12/2020] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Yemen was one of the last countries in the world to declare the first case of the pandemic, on 10 April 2020. Fear and concerns of catastrophic outcomes of the epidemic in Yemen were immediately raised, as the country is facing a complex humanitarian crisis. The purpose of this report is to describe the epidemiological situation in Yemen during the first 2 months of the SARS-CoV-2 epidemic. METHODS We analyzed the epidemiological data from 18 February to 05 June 2020, including the 2 months before the confirmation of the first case. We included in our analysis the data from 10 out of 23 governorates of Yemen, located in southern and eastern part of the country. RESULTS A total of 469 laboratory confirmed, 552 probable and 55 suspected cases with onset of symptoms between 18 February and 5 June 2020 were reported through the surveillance system. The median age among confirmed cases was 46 years (range: 1-90 years), and 75% of the confirmed cases were male. A total of 111 deaths were reported among those with confirmed infection. The mean age among those who died was 53 years (range: 14-88 years), with 63% of deaths (n = 70) occurring in individuals under the age 60 years. A total of 268 individuals with confirmed SARS-CoV-2 infection were hospitalized (57%), among whom there were 95 in-hospital deaths. CONCLUSIONS The surveillance strategy implemented in the first 2 months of the SARS CoV 2 in the southern and eastern governorates of Yemen, captured mainly severe cases. The mild and moderate cases were not self-reported to the health facilities and surveillance system due to limited resources, stigma, and other barriers. The mortality appeared to be higher in individuals aged under 60 years, and most fatalities occurred in individuals who were in critical condition when they reached the health facilities. It is unclear whether the presence of other acute comorbidities contributed to the high death rate among SARS-CoV-2 cases. The findings only include the southern and eastern part of the country, which is home to 31% of the total population of Yemen, as the data from the northern part of the country was inaccessible for analysis. This makes our results not generalizable to the rest of the country.
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Affiliation(s)
| | | | | | | | - Hanan Salem
- Ministry of Public Health and Population, Aden, Yemen
| | | | | | | | - Ammar Shawqi
- Ministry of Public Health and Population, Aden, Yemen
| | | | | | | | | | | | | | | | | | | | | | | | - Roy Cosico
- World Health Organization, Sana’a, Yemen
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Bashir IM, Nyakoe N, van der Sande M. Targeting remaining pockets of malaria transmission in Kenya to hasten progress towards national elimination goals: an assessment of prevalence and risk factors in children from the Lake endemic region. Malar J 2019; 18:233. [PMID: 31299976 PMCID: PMC6624951 DOI: 10.1186/s12936-019-2876-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With an overall decline of malaria incidence, elimination of malaria is gradually becoming the next target for many of countries affected by the disease. In Kenya the national malaria control strategy is aiming to reach pre-elimination for most parts of the country. However, considerable heterogeneity in prevalence of the disease within the country and especially the remaining high prevalent region of the Lake endemic region is likely to slow progress towards this target. To achieve a sustained control and an eventual elimination, a clear understanding of drivers of ongoing malaria transmission in remaining hotspots is needed. METHODS Data from the 2015 Malaria Indicator Survey (MIS) were analysed for prevalence of malaria parasitaemia in children (6 months to 14 years) of different countries within the highly endemic Lake region. Univariate and multivariate logistic regression analysis were preformed to explore associations between selected risk factors and being parasitaemic. A predictive model was built for the association between malaria and the risk factors with the aim of identifying heterogeneities of the disease at the lower administrative levels. RESULTS Overall, 604/2253 (27%, 95% CI 21.8-32.2) children were parasitaemic. The highest prevalence was observed in Busia County (37%) and lowest in Bungoma County (18%). Multivariate logistic regression analysis showed that the 10-14 years age group (OR = 3.0, 95% CI 2.3-4.1), households in the poorest socio-economic class (OR = 2.1, 95% CI 1.3-3.3), farming (OR = 1.4, 95% CI 1.2-2.5) and residence in Busia (OR = 4.6, 95% CI 2.1-8.2), Kakamega (OR = 2.6, 95% CI 1.3-5.4), and Migori counties (OR = 4.6 95% CI 2.1-10.3) were associated with higher risk of parasitaemia. Having slept under a long-lasting insecticide-treated bed net (LLIN) was associated with a lower risk (OR = 0.7, 95% CI 0.6-0.9). No association were found between malaria infection and the gender of the child, the household head, and the education status of the household head. DISCUSSION AND CONCLUSION Detailed analysis of malaria prevalence data in a hotspot area can identify new threats and avail opportunities for directing intervention. In the Lake endemic region of Kenya, interventions should be focused more on counties with the highest prevalence, and should target older children as well as children from the lower socio-economic strata. Precisely targeting interventions in remaining hotspots and high-risk populations will likely make impact and accelerate progress towards pre-elimination targets.
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Affiliation(s)
- Ismail Mahat Bashir
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Nancy Nyakoe
- Walter Reed Project, Kenya Medical Research Institute, Kisumu, Kenya
| | - Marianne van der Sande
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium.,Julius Global Health Center, Julius Center for Health Sciences and Primary Care, Utrecht University, Utrecht, The Netherlands
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