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In the HTML version of this Letter, the affiliations for authors Andrew S. Azman, Dhirendra Kumar and Thandavarayan Ramamurthy were inverted (the PDF and print versions of the Letter were correct); the affiliations have been corrected online.
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Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1. Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V. cholerae serogroups O1 and O139 biotype El Tor2-4. We show that the isolates from Yemen that were collected during the two epidemiological waves of the epidemic1-the first between 28 September 2016 and 23 April 2017 (25,839 suspected cases) and the second beginning on 24 April 2017 (more than 1 million suspected cases)-are V. cholerae serotype Ogawa isolates from a single sublineage of the seventh pandemic V. cholerae O1 El Tor (7PET) lineage. Using genomic approaches, we link the epidemic in Yemen to global radiations of pandemic V. cholerae and show that this sublineage originated from South Asia and that it caused outbreaks in East Africa before appearing in Yemen. Furthermore, we show that the isolates from Yemen are susceptible to several antibiotics that are commonly used to treat cholera and to polymyxin B, resistance to which is used as a marker of the El Tor biotype.
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Cólera/epidemiología , Cólera/microbiología , Genoma Bacteriano/genética , Genómica , Vibrio cholerae/genética , Vibrio cholerae/aislamiento & purificación , Humanos , Filogenia , Vibrio cholerae/clasificación , Yemen/epidemiologíaRESUMEN
In 2018, a hepatitis A virus outbreak was identified among internally displaced persons in Syria. Sequence analysis based on the viral protein 1/2A junction revealed that the causative virus belonged to genotype IB. A high displacement rate, deteriorated sanitary and health conditions, and poor water quality likely contributed to this outbreak.
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Virus de la Hepatitis A/aislamiento & purificación , Hepatitis A/epidemiología , Refugiados , Adolescente , Adulto , Niño , Brotes de Enfermedades , Femenino , Genotipo , Hepatitis A/etiología , Virus de la Hepatitis A/genética , Humanos , Masculino , Persona de Mediana Edad , Siria/epidemiología , Abastecimiento de Agua , Adulto JovenRESUMEN
Ceftriaxone-resistant Salmonella enterica serotype Typhi (Typhi), the bacterium that causes typhoid fever, is a growing public health threat. Extensively drug-resistant (XDR) Typhi is resistant to ceftriaxone and other antibiotics used for treatment, including ampicillin, chloramphenicol, ciprofloxacin, and trimethoprim-sulfamethoxazole (1). In March 2018, CDC began enhanced surveillance for ceftriaxone-resistant Typhi in response to an ongoing outbreak of XDR typhoid fever in Pakistan. CDC had previously reported the first five cases of XDR Typhi in the United States among patients who had spent time in Pakistan (2). These illnesses represented the first cases of ceftriaxone-resistant Typhi documented in the United States (3). This report provides an update on U.S. cases of XDR typhoid fever linked to Pakistan and describes a new, unrelated cluster of ceftriaxone-resistant Typhi infections linked to Iraq. Travelers to areas with endemic Typhi should receive typhoid vaccination before traveling and adhere to safe food and water precautions (4). Treatment of patients with typhoid fever should be guided by antimicrobial susceptibility testing whenever possible (5), and clinicians should consider travel history when selecting empiric therapy.
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Ceftriaxona/farmacología , Brotes de Enfermedades , Farmacorresistencia Microbiana , Salmonella typhi/efectos de los fármacos , Enfermedad Relacionada con los Viajes , Fiebre Tifoidea/epidemiología , Fiebre Tifoidea/microbiología , Adolescente , Adulto , Anciano , Ceftriaxona/uso terapéutico , Niño , Preescolar , Femenino , Humanos , Lactante , Irak/epidemiología , Masculino , Persona de Mediana Edad , Pakistán/epidemiología , Fiebre Tifoidea/tratamiento farmacológico , Estados Unidos/epidemiología , Adulto JovenRESUMEN
BACKGROUND: Cholera remains a persistent health problem in sub-Saharan Africa and worldwide. Cholera can be controlled through appropriate water and sanitation, or by oral cholera vaccination, which provides transient (â¼3 years) protection, although vaccine supplies remain scarce. We aimed to map cholera burden in sub-Saharan Africa and assess how geographical targeting could lead to more efficient interventions. METHODS: We combined information on cholera incidence in sub-Saharan Africa (excluding Djibouti and Eritrea) from 2010 to 2016 from datasets from WHO, Médecins Sans Frontières, ProMED, ReliefWeb, ministries of health, and the scientific literature. We divided the study region into 20 kmâ×â20 km grid cells and modelled annual cholera incidence in each grid cell assuming a Poisson process adjusted for covariates and spatially correlated random effects. We combined these findings with data on population distribution to estimate the number of people living in areas of high cholera incidence (>1 case per 1000 people per year). We further estimated the reduction in cholera incidence that could be achieved by targeting cholera prevention and control interventions at areas of high cholera incidence. FINDINGS: We included 279 datasets covering 2283 locations in our analyses. In sub-Saharan Africa (excluding Djibouti and Eritrea), a mean of 141â918 cholera cases (95% credible interval [CrI] 141â538-146â505) were reported per year. 4·0% (95% CrI 1·7-16·8) of districts, home to 87·2 million people (95% CrI 60·3 million to 118·9 million), have high cholera incidence. By focusing on the highest incidence districts first, effective targeted interventions could eliminate 50% of the region's cholera by covering 35·3 million people (95% CrI 26·3 million to 62·0 million), which is less than 4% of the total population. INTERPRETATION: Although cholera occurs throughout sub-Saharan Africa, its highest incidence is concentrated in a small proportion of the continent. Prioritising high-risk areas could substantially increase the efficiency of cholera control programmes. FUNDING: The Bill & Melinda Gates Foundation.
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Cólera/epidemiología , Cólera/prevención & control , Vacunación/métodos , África del Sur del Sahara/epidemiología , Demografía , Humanos , Incidencia , Cadenas de Markov , Vacunación Masiva , Densidad de Población , SaneamientoRESUMEN
Combining the official cholera line list data and outbreak investigation reports from the ministries of health in Uganda and South Sudan with molecular analysis of Vibrio cholerae strains revealed the interrelatedness of the epidemics in both countries in 2014. These results highlight the need for collaboration to control cross-border outbreaks.
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Cólera/epidemiología , Cólera/prevención & control , Epidemias , Cooperación Internacional , Humanos , Sudán del Sur/epidemiología , Factores de Tiempo , Uganda/epidemiologíaRESUMEN
October 2018 would be two years since the world came to know of the first case of cholera in war-torn Yemen. Soon after, the outbreak developed at an unprecedented scale and turned into one of the worst historical cholera events in terms of cases reported. By the end of September 2018, more than one million suspected cases had been reported across the country in all but one governorate, where approximately 60% of these cases remained concentrated in roughly half of the 330 districts in the country.
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Cólera/epidemiología , Brotes de Enfermedades , Conflictos Armados , Cólera/prevención & control , Vacunas contra el Cólera/administración & dosificación , Humanos , Programas de Inmunización/organización & administración , Aceptación de la Atención de Salud , Vigilancia en Salud Pública , Saneamiento/normas , Organización Mundial de la Salud , Yemen/epidemiologíaAsunto(s)
COVID-19/epidemiología , Pandemias , COVID-19/diagnóstico , COVID-19/prevención & control , COVID-19/transmisión , Prueba de COVID-19 , Control de Enfermedades Transmisibles , Humanos , Región Mediterránea/epidemiología , Vigilancia de la Población , SARS-CoV-2 , Organización Mundial de la SaludRESUMEN
Following mass population displacements in South Sudan, preventive cholera vaccination campaigns were conducted in displaced persons camps before a 2014 cholera outbreak. We compare cholera transmission in vaccinated and unvaccinated areas and show vaccination likely halted transmission within vaccinated areas, illustrating the potential for oral cholera vaccine to stop cholera transmission in vulnerable populations.
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Vacunas contra el Cólera/inmunología , Cólera/epidemiología , Cólera/prevención & control , Vibrio cholerae/inmunología , Administración Oral , Adolescente , Adulto , Anciano , Niño , Preescolar , Vacunas contra el Cólera/administración & dosificación , Femenino , Humanos , Lactante , Recién Nacido , Masculino , Persona de Mediana Edad , Evaluación de Resultado en la Atención de Salud , Vigilancia de la Población , Sudán del Sur/epidemiología , Vacunación , Adulto JovenAsunto(s)
Infecciones por Coronavirus/terapia , Política de Salud , Liderazgo , Pandemias , Neumonía Viral/terapia , Betacoronavirus , COVID-19 , Infecciones por Coronavirus/prevención & control , Infecciones por Coronavirus/transmisión , Salud Global , Humanos , Pandemias/prevención & control , Neumonía Viral/prevención & control , Neumonía Viral/transmisión , Política , SARS-CoV-2RESUMEN
The aim of this study is to assess WHO/Eastern Mediterranean region (WHO/EMR) countries capacities, operations and outbreak response capabilities. Cross-sectional study was conducted targeting 22 WHO/EMR countries from May to June 2021. The survey covers 8 domains related to 15 milstones and key performance indicators (KPIs) for RRT. Responses were received from 14 countries. RRTs are adequately organised in 9 countries (64.3%). The mean retention rate of RRT members was 85.5% ± 22.6. Eight countries (57.1%) reported having standard operating procedures, but only three countries (21.4%) reported an established mechanism of operational fund allocation. In the last 6 months, 10,462 (81.9%) alerts were verified during the first 24 h. Outbreak response was completed by the submission of final RRT response reports in 75% of analysed outbreaks. Risk Communication and Community Engagement (RCCE) activities were part of the interventional response in 59.5% of recent outbreaks. Four countries (28.6%) reported an adequate system to assess RRTs operations. The baseline data highlights four areas to focus on: developing and maintaining the multidisciplinary nature of RRTs through training, adequate financing and timely release of funds, capacity and system building for implementing interventions, for instance, RCCE, and establishing national monitoring and evaluation systems for outbreak response.
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Equipo Hospitalario de Respuesta Rápida , Humanos , Estudios Transversales , Brotes de Enfermedades/prevención & control , Encuestas y Cuestionarios , Región Mediterránea/epidemiologíaRESUMEN
The Eastern Mediterranean Region (EMR) faces ongoing challenges in its public health system due to limited resources, logistical issues, and political disruptions. The COVID-19 pandemic accelerated the need for stronger laboratory capacities to handle the increased demand for testing. In a phased response, EMR countries utilized the National Influenza Centers to rapidly establish and scale molecular testing for SARS-CoV-2, the causative agent of COVID-19. The expansion of capacity included strong collaborations between public health bodies and private and academic sectors to decentralize and expand testing to the subnational level. To ensure that the quality of testing was not impacted by rapid expansion, national and subnational laboratories were enrolled in external quality assurance programs for the duration of the response. Implementation of genomic surveillance was prioritized for variant tracking, leading to the establishment of regional sequencing reference laboratories and the distribution of MinION sequencing platforms to complex emergency countries who previously had limited experience with pathogen sequencing. Challenges included a lack of technical expertise, including in implementing novel diagnostic assays and sequencing, a lack of bioinformatics expertise in the region, and significant logistical and procurement challenges. The collaborative approach, coordinated through the WHO Eastern Mediterranean Regional Office, enabled all 22 countries to achieve SARS-CoV-2 diagnostic capabilities, highlighting the pivotal role of laboratories in global health security.
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COVID-19 , Humanos , COVID-19/epidemiología , SARS-CoV-2 , Laboratorios , Pandemias , Región Mediterránea/epidemiologíaRESUMEN
The COVID-19 transmission in the Eastern Mediterranean Region (EMR) was influenced by various factors such as conflict, demographics, travel and social restrictions, migrant workers, weak health systems, and mass gatherings. The countries that responded well to COVID-19 had high-level political commitment, multisectoral coordination, and existing infrastructures that could quickly mobilize. However, some EMR countries faced challenges due to political instability and fragile health systems, which hindered their response strategies. The pandemic highlighted the region's weak health systems and preparedness, fragmented surveillance systems, and lack of trust in information sharing. COVID-19 exposed the disruption of access and delivery of essential health services as a major health system fragility. In 2020, the World Health Organization (WHO) conducted a global pulse survey, which demonstrated that the EMR experienced the highest disruption in health services compared to other WHO regions. However, thanks to prioritization by the WHO and its member states, significant improvement was observed in 2021 during the second round of the WHO's National Pulse Survey. The pandemic underscored the importance of political leadership, community engagement, and trust and emphasized that investing in health security benefits everyone. Increasing vaccine coverage, building regional capacities, strengthening health systems, and working toward universal health coverage and health security are all priorities in the EMR. Emergency public health plays a key role in preparing for and responding to pandemics and biological threats. Integrating public health into primary care and investing in public health workforce capacity building is essential to reshaping public health and health emergency preparedness.
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COVID-19 , Humanos , COVID-19/epidemiología , Salud Pública , Organización Mundial de la Salud , Región Mediterránea/epidemiologíaRESUMEN
In 2020-2021, all countries of the WHO Eastern Mediterranean Region [EMR] introduced COVID-19 vaccine with inequalities in coverage across countries. As for 2023, we reviewed subsequent progress in deployment, coverage, acceptance, and integration. As of 31 December 2023, coverage in EMR reached 51% for primary series and 19 % for the first booster, higher in high income countries (77 % and 44 %, respectively) than in upper middle-income countries (49 % and 20 %), Advance Market Commitment [AMC] non-Gavi eligible countries (47 % and 15 %) and AMC Gavi eligible countries (49 % and 16 %). Thirteen countries measured coverage among healthcare workers (76 % and 43 %, respectively) and 15 among elderly (69 % and 38 %, respectively). Three rounds of the regional Knowledge, Attitudes, and Practices [KAP] survey on COVID-19 vaccine acceptance in 2021-2022 indicated that acceptance increased from 20 % in June-July 2021 to 62 % in October-November 2021, and 77 % in June-July 2022. Those unvaccinated but intending to be vaccinated decreased from 60 % to 23 % and 11 %, respectively. Unvaccinated without intention to be vaccinated decreased from 15 % to 10 % and 11 %, respectively. Twenty out of 22 countries in the region had completely or partially integrated COVID-19 vaccination into the Expanded Programme on Immunization [EPI] and Primary Health Care [PHC]. Overall, challenges to reach high-risk groups persisted as the population was less concerned about Omicron variant of the SARS-CoV-2 virus. Countries should build on the trust, momentum, and lesson-learned generated from COVID-19 vaccination to get the highest risk groups vaccinated and switch from a time bound and project type approach to a sustainable and long-term approach for COVID-19 vaccine delivery that would be integrated into the routine EPI and PHC.
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Vacunas contra la COVID-19 , COVID-19 , Organización Mundial de la Salud , Humanos , Vacunas contra la COVID-19/administración & dosificación , Vacunas contra la COVID-19/inmunología , COVID-19/prevención & control , COVID-19/epidemiología , Región Mediterránea , SARS-CoV-2/inmunología , Cobertura de Vacunación/estadística & datos numéricos , Personal de Salud/estadística & datos numéricos , Vacunación/estadística & datos numéricos , Programas de Inmunización/estadística & datos numéricos , Conocimientos, Actitudes y Práctica en SaludRESUMEN
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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Prueba de COVID-19 , COVID-19 , Humanos , Yemen/epidemiología , COVID-19/diagnóstico , COVID-19/epidemiología , Vacunas contra la COVID-19 , Laboratorios , Urgencias Médicas , Pandemias , Estudios Retrospectivos , Brotes de Enfermedades/prevención & control , Reacción en Cadena de la PolimerasaRESUMEN
Cholera is a life-threatening gastrointestinal infection caused by a toxigenic bacterium, Vibrio cholerae. After a lull of almost 30 years, a first case of cholera was detected in Lebanon in October 2022. The outbreak lasted three months, with 8007 suspected cases (671 laboratory-confirmed) and 23 deaths. In this study, we use phenotypic methods and microbial genomics to study 34 clinical and environmental Vibrio cholerae isolates collected throughout this outbreak. All isolates are identified as V. cholerae O1, serotype Ogawa strains from wave 3 of the seventh pandemic El Tor (7PET) lineage. Phylogenomic analysis unexpectedly reveals the presence of two different strains of the seventh pandemic El Tor (7PET) lineage. The dominant strain has a narrow antibiotic resistance profile and is phylogenetically related to South Asian V. cholerae isolates and derived African isolates from the AFR15 sublineage. The second strain is geographically restricted and extensively drug-resistant. It belongs to the AFR13 sublineage and clusters with V. cholerae isolates collected in Yemen. In conclusion, the 2022-2023 Lebanese cholera outbreak is caused by the simultaneous introduction of two different 7PET strains. Genomic surveillance with cross-border collaboration is therefore crucial for the identification of new introductions and routes of circulation of cholera, improving our understanding of cholera epidemiology.
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Cólera , Brotes de Enfermedades , Filogenia , Líbano/epidemiología , Humanos , Cólera/epidemiología , Cólera/microbiología , Genoma Bacteriano/genética , Genómica/métodos , Vibrio cholerae/genética , Vibrio cholerae/aislamiento & purificación , Vibrio cholerae/clasificación , Masculino , Antibacterianos/farmacología , Femenino , Vibrio cholerae O1/genética , Vibrio cholerae O1/aislamiento & purificación , Vibrio cholerae O1/clasificación , Adolescente , Adulto , Adulto Joven , Persona de Mediana Edad , Niño , Epidemiología MolecularRESUMEN
Countries in the WHO Eastern Mediterranean Region (EMR) are currently experiencing a resurgence of cholera. As of 31 December 2022, 8 of the 22 Member States in the region - Afghanistan, Islamic Republic of Iran, Iraq, Lebanon, Pakistan, Somalia, Syria, and Yemen - were grappling with outbreaks of cholera and acute watery diarrhoea (AWD). More than 1 000 000 suspected AWD/cholera cases, more than 7500 laboratory-confirmed cases, and 375 cholera-associated deaths were reported across the region in 2022.