Last data update: May 16, 2025. (Total: 49299 publications since 2009)
Records 1-18 (of 18 Records) |
Query Trace: Bashir R[original query] |
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Health facility capacity and health-care worker knowledge, attitudes, and practices of hepatitis B vaccine birth-dose and maternal tetanus-diphtheria vaccine administration in Nigeria: A baseline assessment
Uba BV , Mohammed Y , Nwokoro UU , Fadahunsi R , Adewole A , Ugbenyo G , Simple E , Wisdom MO , Waziri NE , Michael CA , Okeke LA , Kanu F , Ikwe H , Sandhu HS , Asekun A , Tohme RA , Freeland C , Minta A , Bashir SS , Isa A , Vasumu JJ , Bahuli AU , Ugwu GO , Obi EI , Ismail BA , Okposen BB , Bolu OO , Shuaib F . Ann Afr Med 2024 BACKGROUND: Hepatitis B virus (HBV) and neonatal tetanus infections remain endemic in Nigeria despite the availability of safe, effective vaccines. We aimed to determine health facilities' capacity for hepatitis B vaccine birth dose (HepB-BD) and maternal tetanus-diphtheria (Td) vaccination and to assess knowledge, attitudes, and practices of HepB-BD and maternal Td vaccine administration among health facility staff in Nigeria. MATERIALS AND METHODS: This was a cross-sectional study assessing public primary and secondary health facilities in Adamawa and Enugu States. A multistage sampling approach was used to select 40 facilities and 79 health-care workers (HCWs) from each state. A structured facility assessment tool and standardized questionnaire evaluated facility characteristics and HCW knowledge, attitudes, and practices related to HepB-BD and maternal Td vaccination. Frequencies and proportions were reported as descriptive statistics. RESULTS: The survey of 80 facilities revealed that 73.8% implemented HepB-BD and maternal Td vaccination policies. HepB-BD was administered within 24 h of birth at 61.3% of facilities and at all times at 57.5%. However, administration seldom occurred in labor and delivery (35%) or maternity wards (16.3%). Nearly half of the facilities (46.3%) had HCWs believing there were contraindications to HepB-BD vaccination. Among 158 HCWs, 26.5% believed tetanus could be transmitted through unprotected sex, prevented by vaccination at birth (46.1%), or by avoiding sharing food and utensils. 65% of HCWs knew HBV infection had the worst outcome for newborns. CONCLUSIONS: The limited implementation of national policies on HepB-BD and maternal Td vaccination, coupled with knowledge gaps among HCWs, pose significant challenges to timely vaccination, necessitating interventions to address these gaps. |
Evaluation of interventions to improve timely hepatitis B birth dose vaccination among infants and maternal tetanus vaccination among pregnant women in Nigeria
Kanu FA , Freeland C , Nwokoro UU , Mohammed Y , Ikwe H , Uba B , Sandhu H , An Q , Asekun A , Akataobi C , Adewole A , Fadahunsi R , Wisdom M , Akudo OL , Ugbenyo G , Simple E , Waziri N , Vasumu JJ , Bahuli AU , Bashir SS , Isa A , Ugwu G , Obi EI , Binta H , Bassey BO , Shuaib F , Bolu O , Tohme RA . Vaccine 2024 42 (24) 126222 BACKGROUND: Nigeria has the largest number of children infected with hepatitis B virus (HBV) globally and has not yet achieved maternal and neonatal tetanus elimination. In Nigeria, maternal tetanus diphtheria (Td) vaccination is part of antenatal care and hepatitis B birth dose (HepB-BD) vaccination for newborns has been offered since 2004. We implemented interventions targeting healthcare workers (HCWs), community volunteers, and pregnant women attending antenatal care with the goal of improving timely (within 24 hours) HepB-BD vaccination among newborns and Td vaccination coverage among pregnant women. METHODS: We selected 80 public health facilities in Adamawa and Enugu states, with half intervention facilities and half control. Interventions included HCW and community volunteer trainings, engagement of pregnant women, and supportive supervision at facilities. Timely HepB-BD coverage and at least two doses of Td (Td2+) coverage were assessed at baseline before project implementation (January-June 2021) and at endline, one year after implementation (January-June 2022). We held focus group discussions at intervention facilities to discuss intervention strengths, challenges, and improvement opportunities. RESULTS: Compared to baseline, endline median vaccination coverage increased for timely HepB-BD from 2.6% to 61.8% and for Td2+ from 20.4% to 26.9% in intervention facilities (p < 0.05). In comparison, at endline in control facilities median vaccination coverage for timely HepB-BD was 7.9% (p < 0.0001) and Td2+ coverage was 22.2% (p = 0.14). Focus group discussions revealed that HCWs felt empowered to administer vaccination due to increased knowledge on hepatitis B and tetanus, pregnant women had increased knowledge that led to improved health seeking behaviors including Td vaccination, and transportation support was needed to reach those in far communities. CONCLUSION: Targeted interventions significantly increased timely HepB-BD and Td vaccination rates in intervention facilities. Continued support of these successful interventions could help Nigeria reach hepatitis B and maternal and neonatal tetanus elimination goals. |
Historical reconstruction of inaccessibility status in Local Government Areas (LGAs) of Borno and Yobe States, Nigeria, 2010-2020
Forbi JC , Musa MS , Salawu M , Idris JM , Ba'aba AI , Higgins J , Musa AI , Bashir B , Shettima A , Njeakor N , Uzoma I , Mshelia H , Nganda GW , Mohammed KI , Bomoi IM , Chiroma U , Kovacs SD , Biya O , Waziri NE , Aina M , Adamu US , Shuaib F , Bolu O , Franka R , Wiesen E . Pan Afr Med J 2023 45 7 INTRODUCTION: ultimately detected in 2016, wild poliovirus (WPV) transmission continued undetected after 2011 in Northeast Nigeria Borno and Yobe States in security-compromised areas, inaccessible due to armed insurgency. Varying inaccessibility prevented children aged <5 years in these areas from polio vaccination interventions and surveillance, while massive population displacements occurred. We examined progress in access over time to provide data supporting a very low probability of undetected WPV circulation within remaining trapped populations after 2016. METHODS: to assess the extent of inaccessibility in security-compromised areas, we obtained empirical historical data in 2020 on a quarterly and annual basis from relevant polio eradication staff for the period 2010-2020. The extent of access to areas for immunization by recall was compared to geospatial data from vaccinator tracking. Population estimates over time in security-compromised areas were extracted from satellite imagery. We compared the historical access data from staff with tracking and population esimates. RESULTS: access varied during 2010-2020, with inaccessibility peaking during 2014-2016. We observed concurrent patterns between historical recalled data on inaccessibility and contemporaneous satellite imagery on population displacements, which increased confidence in the quality of recalled data. CONCLUSION: staff-recalled access was consistent with vaccinator tracking and satellite imagery of population displacments. Despite variability in inaccessibility over time, innovative immunization initiatives were implemented as access allowed and surveillance initiatives were initiated to search for poliovirus transmission. Along with escape and liberation of residents by the military in some geographic areas, these initiatives resulted in a massive reduction in the size of the unvaccinated population remaining resident. |
Barriers and facilitators to hepatitis B birth dose vaccination: Perspectives from healthcare providers and pregnant women accessing antenatal care in Nigeria
Freeland C , Kanu F , Mohammed Y , Nwokoro UU , Sandhu H , Ikwe H , Uba B , Asekun A , Akataobi C , Adewole A , Fadahunsi R , Wisdom M , Akudo OL , Ugbenyo G , Simple E , Waziri N , Vasumu JJ , Bahuli AU , Bashir SS , Isa A , Ugwu GO , Obi EI , Binta H , Bassey BO , Shuaib F , Bolu O , Tohme RA . PLOS Glob Public Health 2023 3 (6) e0001332 Nigeria is estimated to have the largest number of children worldwide, living with chronic hepatitis B virus (HBV) infection, the leading cause of liver cancer. Up to 90% of children infected at birth develop chronic HBV infection. A birth dose of the hepatitis B vaccine (HepB-BD) followed by at least two additional vaccine doses is recommended for prevention. This study assessed barriers and facilitators of HepB-BD administration and uptake, using structured interviews with healthcare providers and pregnant women in Adamawa and Enugu States, Nigeria. The Consolidated Framework for Implementation Sciences Research (CFIR) guided data collection and analysis. We interviewed 87 key informants (40 healthcare providers and 47 pregnant women) and created a codebook for data analysis. Codes were developed by reviewing the literature and reading a subsample of queries line-by-line. The overarching themes identified as barriers among healthcare providers were: the lack of hepatitis B knowledge, limited availability of HepB-BD to vaccination days only, misconceptions about HepB-BD vaccination, challenges in health facility staffing capacity, costs associated with vaccine transportation, and concerns related to vaccine wastage. Facilitators of timely HepB-BD vaccination included: vaccine availability, storage, and hospital births occurring during immunization days. Overarching themes identified as barriers among pregnant women were lack of hepatitis B knowledge, limited understanding of HepB-BD importance, and limited access to vaccines for births occurring outside of a health facility. Facilitators were high vaccine acceptance and willingness for their infants to receive HepB-BD if recommended by providers. Findings indicate the need for enhanced HepB-BD vaccination training for HCWs, educating pregnant women on HBV and the importance of timely HepB-BD, updating policies to enable HepB-BD administration within 24 hours of birth, expanding HepB-BD availability in public and private hospital maternity wards for all facility births, and outreach activities to reach home births. |
An outbreak of Burkholderia cepacia bloodstream infections in a tertiary-care facility in northern India detected by a healthcare-associated infection surveillance network
Fomda B , Velayudhan A , Siromany VA , Bashir G , Nazir S , Ali A , Katoch O , Karoung A , Gunjiyal J , Wani N , Roy I , VanderEnde D , Gupta N , Sharma A , Malpiedi P , Walia K , Mathur P . Infect Control Hosp Epidemiol 2022 44 (3) 1-7 OBJECTIVE: The burden of healthcare-associated infections (HAIs) is higher in low- and middle-income countries, but HAIs are often missed because surveillance is not conducted. Here, we describe the identification of and response to a cluster of Burkholderia cepacia complex (BCC) bloodstream infections (BSIs) associated with high mortality in a surgical ICU (SICU) that joined an HAI surveillance network. SETTING: A 780-bed, tertiary-level, public teaching hospital in northern India. METHODS: After detecting a cluster of BCC in the SICU, cases were identified by reviewing laboratory registers and automated identification and susceptibility testing outputs. Sociodemographic details, clinical records, and potential exposure histories were collected, and a self-appraisal of infection prevention and control (IPC) practices using assessment tools from the World Health Organization and the US Centers for Disease Control and Prevention was conducted. Training and feedback were provided to hospital staff. Environmental samples were collected from high-touch surfaces, intravenous medications, saline, and mouthwash. RESULTS: Between October 2017 and October 2018, 183 BCC BSI cases were identified. Case records were available for 121 case patients. Of these 121 cases, 91 (75%) were male, the median age was 35 years, and 57 (47%) died. IPC scores were low in the areas of technical guidelines, human resources, and monitoring and evaluation. Of the 30 environmental samples, 4 grew BCC. A single source of the outbreak was not identified. CONCLUSIONS: Implementing standardized HAI surveillance in a low-resource setting detected an ongoing Burkholderia cepacia outbreak. The outbreak investigation and use of a multimodal approach reduced incident cases and informed changes in IPC practices. |
Infiltrating Kaposi sarcoma presenting as acute kidney injury: An unexpected consequence of deliberate hepatitis C positive organ transplantation
Story M , Sanders ML , Bashir A , Longo J , Abel S , Dollard S , Grodstein E , Thomas C , Katz D . Transpl Infect Dis 2020 23 (2) e13481 Kaposi sarcoma (KS) following kidney transplantation can result from recipient reactivation of latent human herpesvirus 8 (HHV-8) infection or activation of donor acquired HHV-8 infection. Post-transplant KS typically manifests with cutaneous pathology, but rare cases of renal allograft involvement have been reported. We describe two cases of donor derived HHV-8 infection in two hepatitis C (HCV) viremia negative transplant recipients who each received a kidney from a donor with HCV viremia. One recipient did not develop KS while the other presented with acute kidney injury due to extensive KS infiltration of the renal parenchyma and metastatic disease. This report reviews the literature for cases of KS involving the renal allograft and highlights an unexpected consequence of deliberate HCV positive organ transplantation. |
Contrasting trends of smoking cessation status: Insights from the stages of change theory using repeat data from the Global Adult Tobacco Survey, Thailand (2009 and 2011) and Turkey (2008 and 2012)
Mbulo L , Murty KS , Husain MJ , Bashir R , Blutcher-Nelson G , Benjakul S , Kengganpanich M , Erguder T , Keskinkilic B , Polat S , Sinha N , Palipudi K , Ahluwalia IB . Prev Chronic Dis 2017 14 E42 OBJECTIVE: The World Health Organization recommends that smokers be offered help to quit. A better understanding of smokers' interest in and commitment to quitting could guide tobacco control efforts. We assessed temporal differences in stages of change toward quitting among smokers in Thailand and Turkey. METHODS: Two waves (independent samples) of data from the Global Adult Tobacco Survey, a national household survey of adults aged 15 years or older, were assessed for Thailand (2009 and 2011) and Turkey (2008 and 2012). Current smokers were categorized into 3 stages of change based on their cessation status: precontemplation, contemplation, and preparation. Relative change in the proportion of smokers in each stage between waves 1 and 2 was computed for each country. RESULTS: Between waves, overall current tobacco smoking did not change in Thailand (23.7% to 24.0%) but declined in Turkey (31.2% to 27.1%; P < .001). Between 2009 and 2011, precontemplation increased among smokers in Thailand (76.1% to 85.4%; P < .001), whereas contemplation (17.6% to 12.0%; P < .001) and preparation (6.3% to 2.6%; P < .001) declined. Between 2008 and 2012, there were declines in precontemplation among smokers in Turkey (72.2% to 64.6%; P < .001), whereas there were increases in contemplation (21.2% to 26.9%; P = .008) and no significant change in preparation (6.5% to 8.5%; P = .097). CONCLUSION: Nearly two-thirds of smokers in Turkey and more than two-thirds in Thailand were in the precontemplation stage during the last survey wave assessed. The proportion of smokers in the preparation stage increased in Turkey but declined in Thailand. Identifying stages of cessation helps guide population-based targeted interventions to support smokers at varying stages of change toward quitting. |
Transmission of Middle East Respiratory Syndrome Coronavirus Infections in Healthcare Settings, Abu Dhabi.
Hunter JC , Nguyen D , Aden B , Al Bandar Z , Al Dhaheri W , Abu Elkheir K , Khudair A , Al Mulla M , El Saleh F , Imambaccus H , Al Kaabi N , Sheikh FA , Sasse J , Turner A , Abdel Wareth L , Weber S , Al Ameri A , Abu Amer W , Alami NN , Bunga S , Haynes LM , Hall AJ , Kallen AJ , Kuhar D , Pham H , Pringle K , Tong S , Whitaker BL , Gerber SI , Al Hosani FI . Emerg Infect Dis 2016 22 (4) 647-56 ![]() Middle East respiratory syndrome coronavirus (MERS-CoV) infections sharply increased in the Arabian Peninsula during spring 2014. In Abu Dhabi, United Arab Emirates, these infections occurred primarily among healthcare workers and patients. To identify and describe epidemiologic and clinical characteristics of persons with healthcare-associated infection, we reviewed laboratory-confirmed MERS-CoV cases reported to the Health Authority of Abu Dhabi during January 1, 2013-May 9, 2014. Of 65 case-patients identified with MERS-CoV infection, 27 (42%) had healthcare-associated cases. Epidemiologic and genetic sequencing findings suggest that 3 healthcare clusters of MERS-CoV infection occurred, including 1 that resulted in 20 infected persons in 1 hospital. MERS-CoV in healthcare settings spread predominantly before MERS-CoV infection was diagnosed, underscoring the importance of increasing awareness and infection control measures at first points of entry to healthcare facilities. |
Secondhand smoke exposure at home among one billion children in 21 countries: findings from the Global Adult Tobacco Survey (GATS)
Mbulo L , Palipudi KM , Andes L , Morton J , Bashir R , Fouad H , Ramanandraibe N , Caixeta R , Dias RC , Wijnhoven TM , Kashiwabara M , Sinha DN , Tursan d'Espaignet E . Tob Control 2016 25 e95-e100 OBJECTIVE: Children are vulnerable to secondhand smoke (SHS) exposure because of limited control over their indoor environment. Homes remain the major place where children may be exposed to SHS. Our study examines the magnitude, patterns and determinants of SHS exposure in the home among children in 21 countries (19 low-income and middle-income countries and 2 high-income countries). METHODS: Global Adult Tobacco Survey (GATS) data, a household survey of people 15 years of age or older. Data collected during 2009-2013 were analysed to estimate the proportion of children exposed to SHS in the home. GATS estimates and 2012 United Nations population projections for 2015 were also used to estimate the number of children exposed to SHS in the home. RESULTS: The proportion of children younger than 15 years of age exposed to SHS in the home ranged from 4.5% (Panama) to 79.0% (Indonesia). Of the approximately one billion children younger than 15 years of age living in the 21 countries under study, an estimated 507.74 million were exposed to SHS in the home. China, India, Bangladesh, Indonesia and the Philippines accounted for almost 84.6% of the children exposed to SHS. The prevalence of SHS exposure was higher in countries with higher adult smoking rates and was also higher in rural areas than in urban areas, in most countries. CONCLUSIONS: A large number of children were exposed to SHS in the home. Encouraging of voluntary smoke-free rules in homes and cessation in adults has the potential to reduce SHS exposure among children and prevent SHS-related diseases and deaths. |
Design of a study to determine the impact of insecticide resistance on malaria vector control: a multi-country investigation
Kleinschmidt I , Mnzava AP , Kafy HT , Mbogo C , Bashir AI , Bigoga J , Adechoubou A , Raghavendra K , Knox TB , Malik EM , Nkuni ZJ , Bayoh N , Ochomo E , Fondjo E , Kouambeng C , Awono-Ambene HP , Etang J , Akogbeto M , Bhatt R , Swain DK , Kinyari T , Njagi K , Muthami L , Subramaniam K , Bradley J , West P , Massougbodji A , Okê-Sopoh M , Hounto A , Elmardi K , Valecha N , Kamau L , Mathenge E , Donnelly MJ . Malar J 2015 14 282 BACKGROUND: Progress in reducing the malaria disease burden through the substantial scale up of insecticide-based vector control in recent years could be reversed by the widespread emergence of insecticide resistance. The impact of insecticide resistance on the protective effectiveness of insecticide-treated nets (ITN) and indoor residual spraying (IRS) is not known. A multi-country study was undertaken in Sudan, Kenya, India, Cameroon and Benin to quantify the potential loss of epidemiological effectiveness of ITNs and IRS due to decreased susceptibility of malaria vectors to insecticides. The design of the study is described in this paper. METHODS: Malaria disease incidence rates by active case detection in cohorts of children, and indicators of insecticide resistance in local vectors were monitored in each of approximately 300 separate locations (clusters) with high coverage of malaria vector control over multiple malaria seasons. Phenotypic and genotypic resistance was assessed annually. In two countries, Sudan and India, clusters were randomly assigned to receive universal coverage of ITNs only, or universal coverage of ITNs combined with high coverage of IRS. Association between malaria incidence and insecticide resistance, and protective effectiveness of vector control methods and insecticide resistance were estimated, respectively. RESULTS: Cohorts have been set up in all five countries, and phenotypic resistance data have been collected in all clusters. In Sudan, Kenya, Cameroon and Benin data collection is due to be completed in 2015. In India data collection will be completed in 2016. DISCUSSION: The paper discusses challenges faced in the design and execution of the study, the analysis plan, the strengths and weaknesses, and the possible alternatives to the chosen study design. |
Strengthening the influenza vaccine virus selection and development process: Report of the 3rd WHO Informal Consultation for Improving Influenza Vaccine Virus Selection held at WHO headquarters, Geneva, Switzerland, 1-3 April 2014.
Ampofo WK , Azziz-Baumgartner E , Bashir U , Cox NJ , Fasce R , Giovanni M , Grohmann G , Huang S , Katz J , Mironenko A , Mokhtari-Azad T , Sasono PM , Rahman M , Sawanpanyalert P , Siqueira M , Waddell AL , Waiboci L , Wood J , Zhang W , Ziegler T . Vaccine 2015 33 (36) 4368-82 ![]() ![]() Despite long-recognized challenges and constraints associated with their updating and manufacture, influenza vaccines remain at the heart of public health preparedness and response efforts against both seasonal and potentially pandemic influenza viruses. Globally coordinated virological and epidemiological surveillance is the foundation of the influenza vaccine virus selection and development process. Although national influenza surveillance and reporting capabilities are being strengthened and expanded, sustaining and building upon recent gains has become a major challenge. Strengthening the vaccine virus selection process additionally requires the continuation of initiatives to improve the timeliness and representativeness of influenza viruses shared by countries for detailed analysis by the WHO Global Influenza Surveillance and Response System (GISRS). Efforts are also continuing at the national, regional, and global levels to better understand the dynamics of influenza transmission in both temperate and tropical regions. Improved understanding of the degree of influenza seasonality in tropical countries of the world should allow for the strengthening of national vaccination policies and use of the most appropriate available vaccines. There remain a number of limitations and difficulties associated with the use of HAI assays for the antigenic characterization and selection of influenza vaccine viruses by WHOCCs. Current approaches to improving the situation include the more-optimal use of HAI and other assays; improved understanding of the data produced by neutralization assays; and increased standardization of serological testing methods. A number of new technologies and associated tools have the potential to revolutionize influenza surveillance and response activities. These include the increasingly routine use of whole genome next-generation sequencing and other high-throughput approaches. Such approaches could not only become key elements in outbreak investigations but could drive a new surveillance paradigm. However, despite the advances made, significant challenges will need to be addressed before next-generation technologies become routine, particularly in low-resource settings. Emerging approaches and techniques such as synthetic genomics, systems genetics, systems biology and mathematical modelling are capable of generating potentially huge volumes of highly complex and diverse datasets. Harnessing the currently theoretical benefits of such bioinformatics ("big data") concepts for the influenza vaccine virus selection and development process will depend upon further advances in data generation, integration, analysis and dissemination. Over the last decade, growing awareness of influenza as an important global public health issue has been coupled to ever-increasing demands from the global community for more-equitable access to effective and affordable influenza vaccines. The current influenza vaccine landscape continues to be dominated by egg-based inactivated and live attenuated vaccines, with a small number of cell-based and recombinant vaccines. Successfully completing each step in the annual influenza vaccine manufacturing cycle will continue to rely upon timely and regular communication between the WHO GISRS, manufacturers and regulatory authorities. While the pipeline of influenza vaccines appears to be moving towards a variety of niche products in the near term, it is apparent that the ultimate aim remains the development of effective "universal" influenza vaccines that offer longer-lasting immunity against a broad range of influenza A subtypes. |
Middle East respiratory syndrome coronavirus not detected in children hospitalized with acute respiratory illness in Amman, Jordan, March 2010 to September 2012
Khuri-Bulos N , Payne DC , Lu X , Erdman D , Wang L , Faouri S , Shehabi A , Johnson M , Becker MM , Denison MR , Williams JV , Halasa NB . Clin Microbiol Infect 2014 20 (7) 678-82 Hospitalized children < 2 years of age in Amman, Jordan, admitted for fever and/or respiratory symptoms, were tested for Middle East respiratory syndrome coronavirus (MERS-CoV): MERS-CoV by real-time RT-PCR (rRT-PCR). This was a prospective year-round viral surveillance study in children <2 years of age admitted with acute respiratory symptoms and/or fever from March 2010 to September 2012 and enrolled from a government-run hospital, Al-Bashir in Amman, Jordan. Clinical and demographic data, including antibiotic use, were collected. Combined nasal/throat swabs were collected, aliquoted, and frozen at -80 degrees C. Specimen aliquots were shipped to Vanderbilt University and the Centers for Disease Control and Prevention (CDC), and tested by rRT-PCR for MERS-CoV. Of the 2433 subjects enrolled from 16 March 2010 to 10 September 2012, 2427 subjects had viral testing and clinical data. Of 1898 specimens prospectively tested for other viruses between 16 March 2010 and 18 March 2012, 474 samples did not have other common respiratory viruses detected. These samples were tested at CDC for MERS-CoV and all were negative by rRT-PCR for MERS-CoV. Of the remaining 531 samples, collected from 19 March 2012 to 10 September 2012 and tested at Vanderbilt, none were positive for MERS-CoV. Our negative findings from a large sample of young Jordanian children hospitalized with fever and/or respiratory symptoms suggest that MERS-CoV was not widely circulating in Amman, Jordan, during the 30-month period of prospective, active surveillance occurring before and after the first documented MERS-CoV outbreak in the Middle East region. |
Actionable diagnosis of neuroleptospirosis by next-generation sequencing.
Wilson MR , Naccache SN , Samayoa E , Biagtan M , Bashir H , Yu G , Salamat SM , Somasekar S , Federman S , Miller S , Sokolic R , Garabedian E , Candotti F , Buckley RH , Reed KD , Meyer TL , Seroogy CM , Galloway R , Henderson SL , Gern JE , DeRisi JL , Chiu CY . N Engl J Med 2014 370 (25) 2408-17 ![]() A 14-year-old boy with severe combined immunodeficiency presented three times to a medical facility over a period of 4 months with fever and headache that progressed to hydrocephalus and status epilepticus necessitating a medically induced coma. Diagnostic workup including brain biopsy was unrevealing. Unbiased next-generation sequencing of the cerebrospinal fluid identified 475 of 3,063,784 sequence reads (0.016%) corresponding to leptospira infection. Clinical assays for leptospirosis were negative. Targeted antimicrobial agents were administered, and the patient was discharged home 32 days later with a status close to his premorbid condition. Polymerase-chain-reaction (PCR) and serologic testing at the Centers for Disease Control and Prevention (CDC) subsequently confirmed evidence of Leptospira santarosai infection. |
Assessment of blood lead levels among children aged ≤ 5 years - Zamfara State, Nigeria, June-July 2012
Bashir M , Umar-Tsafe N , Getso K , Kaita IM , Nasidi A , Sani-Gwarzo N , Nguku P , Davis L , Brown MJ . MMWR Morb Mortal Wkly Rep 2014 63 (15) 325-7 Since 2010, Nigerian state and federal governments and the international community have been responding to an outbreak of lead poisoning caused by the processing of lead-containing gold ore in Zamfara State, Nigeria, that resulted in the deaths of approximately 400 children aged ≤5 years. Widespread education, surveys of high-risk villages, testing of blood lead levels (BLLs), medical treatment, and environmental cleanup all have been implemented. To evaluate the success of these remediation efforts in reducing the prevalence of lead poisoning and dangerous work practices, a population-based assessment of children's BLLs and ore processing techniques was conducted during June-July 2012. The assessment found few children in need of medical treatment, significantly lower BLLs, and substantially less exposure of children to dangerous work practices. Public health strategies designed to identify and treat children with lead poisoning, clean up existing environmental hazards, and prevent children from being exposed to dangerous ore processing techniques can produce a sustained reduction in BLLs. |
Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti
Katz LS , Petkau A , Beaulaurier J , Tyler S , Antonova ES , Turnsek MA , Guo Y , Wang S , Paxinos EE , Orata F , Gladney LM , Stroika S , Folster JP , Rowe L , Freeman MM , Knox N , Frace M , Boncy J , Graham M , Hammer BK , Boucher Y , Bashir A , Hanage WP , Van Domselaar G , Tarr CL . mBio 2013 4 (4) ![]() ![]() Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of Vibrio cholerae O1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and >7,500 deaths in the first two years of the epidemic. We applied whole-genome sequencing to a temporal series of V. cholerae isolates from Haiti to gain insight into the mode and tempo of evolution in this isolated population of V. cholerae O1. Phylogenetic and Bayesian analyses supported the hypothesis that all isolates in the sample set diverged from a common ancestor within a time frame that is consistent with epidemiological observations. A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates. Nine nearly closed genomes assembled from continuous-long-read data showed evidence of genome rearrangements and supported the observation of no gene acquisition among isolates. Thus, intrinsic mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT). Consistent with this, the 12 Haiti isolates tested by laboratory HGT assays were severely impaired for transformation, although unlike previously characterized noncompetent V. cholerae isolates, each expressed hapR and possessed a functional quorum-sensing system. Continued monitoring of V. cholerae in Haiti will illuminate the processes influencing the origin and fate of genome variants, which will facilitate interpretation of genetic variation in future epidemics. IMPORTANCE Vibrio cholerae is the cause of substantial morbidity and mortality worldwide, with over three million cases of disease each year. An understanding of the mode and rate of evolutionary change is critical for proper interpretation of genome sequence data and attribution of outbreak sources. The Haiti epidemic provides an unprecedented opportunity to study an isolated, single-source outbreak of Vibrio cholerae O1 over an established time frame. By using multiple approaches to assay genetic variation, we found no evidence that the Haiti strain has acquired any genes by horizontal gene transfer, an observation that led us to discover that it is also poorly transformable. We have found no evidence that environmental strains have played a role in the evolution of the outbreak strain. |
Molecular epidemiology of influenza A(H1N1)pdm09 viruses from Pakistan in 2009-2010.
Bashir Aamir U , Badar N , Mehmood MR , Nisar N , Suleman RM , Shaukat S , Sharif S , Kamran J , Zaidi SS , Kazi BM , Gubareva L , Xu X , Garten R , Klimov A . PLoS One 2012 7 (8) e41866 ![]() BACKGROUND: In early 2009, a novel influenza A(H1N1) virus that emerged in Mexico and United States rapidly disseminated worldwide. The spread of this virus caused considerable morbidity with over 18,000 recorded deaths. The new virus was found to be a reassortant containing gene segments from human, avian and swine influenza viruses. METHODS/RESULTS: The first case of human infection with A(H1N1)pdm09 in Pakistan was detected on 18(th) June 2009. Since then, 262 laboratory-confirmed cases have been detected during various outbreaks with 29 deaths (as of 31(st) August 2010). The peak of the epidemic was observed in December with over 51% of total respiratory cases positive for influenza. Representative isolates from Pakistan viruses were sequenced and analyzed antigenically. Sequence analysis of genes coding for surface glycoproteins HA and NA showed high degree of high levels of sequence identity with corresponding genes of regional viruses circulating South East Asia. All tested viruses were sensitive to Oseltamivir in the Neuraminidase Inhibition assays. CONCLUSIONS: Influenza A(H1N1)pdm09 viruses from Pakistan form a homogenous group of viruses. Their HA genes belong to clade 7 and show antigenic profile similar to the vaccine strain A/California/07/2009. These isolates do not show any amino acid changes indicative of high pathogenicity and virulence. It is imperative to continue monitoring of these viruses for identification of potential variants of high virulence or drug resistance. |
A hybrid approach for the automated finishing of bacterial genomes.
Bashir A , Klammer AA , Robins WP , Chin CS , Webster D , Paxinos E , Hsu D , Ashby M , Wang S , Peluso P , Sebra R , Sorenson J , Bullard J , Yen J , Valdovino M , Mollova E , Luong K , Lin S , Lamay B , Joshi A , Rowe L , Frace M , Tarr CL , Turnsek M , Davis BM , Kasarskis A , Mekalanos JJ , Waldor MK , Schadt EE . Nat Biotechnol 2012 30 (7) 701-707 ![]() Advances in DNA sequencing technology have improved our ability to characterize most genomic diversity. However, accurate resolution of large structural events is challenging because of the short read lengths of second-generation technologies. Third-generation sequencing technologies, which can yield longer multikilobase reads, have the potential to address limitations associated with genome assembly. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at >99.9% accuracy. Complex regions with clinically relevant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 cholera reference strain, we obtained 14 scaffolds of greater than 1 kb for the experimental data and 8 scaffolds of greater than 1 kb for the simulated data, which allowed us to correct several errors in contigs assembled from the short-read data alone. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly. |
Outbreak of fatal childhood lead poisoning related to artisanal gold mining in northwestern Nigeria, 2010
Dooyema CA , Neri A , Lo YC , Durant J , Dargan PI , Swarthout T , Biya O , Gidado SO , Haladu S , Sani-Gwarzo N , Nguku PM , Akpan H , Idris S , Bashir AM , Brown MJ . Environ Health Perspect 2011 120 (4) 601-7 BACKGROUND: In May 2010, a team of national and international organizations was assembled to investigate children's deaths due to lead poisoning in villages in northwestern Nigeria. OBJECTIVES: To determine the cause of the childhood lead poisoning outbreak, investigate risk factors for child mortality, and identify children aged <5 years in need of emergency chelation therapy for lead poisoning. METHODS: We administered a cross-sectional, door-to-door questionnaire in two affected villages, collected blood from children aged 2-59 months, and soil samples from family compounds. Descriptive and bivariate analyses were performed with survey, blood-lead, and environmental data. Multivariate logistic regression techniques were used to determine risk factors for childhood mortality. RESULTS: We surveyed 119 family compounds. One hundred eighteen of 463 (25%) children aged <5 years had died in the last year. We tested 59% (204/345) of children, aged <5 years, and all were lead poisoned (≥10 microg/dL); 97% (198/204) of children had blood-lead levels ≥45 microg/dL, the threshold for initiating chelation therapy. Gold ore was processed inside two-thirds of the family compounds surveyed. In multivariate modeling significant risk factors for death in the previous year from suspected lead poisoning included: the child's age, the mother performing ore-processing activities, community well as primary water source, and the soil-lead concentration in the compound. CONCLUSION: The high levels of environmental contamination, percentage of children aged <5 years with elevated blood-lead levels (97%, >45 microg/dL), and incidence of convulsions among children prior to death (82%) suggest that most of the recent childhood deaths in the two surveyed villages were caused by acute lead poisoning from gold ore-processing activities. Control measures included environmental remediation, chelation therapy, public health education, and control of mining activities. |
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