Influenza hospitalization epidemiology from a severe acute respiratory infection surveillance system in Jordan, January 2008-February 2014.
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SUBMITTER: Al-Abdallat M
PROVIDER: S-EPMC4746565 | biostudies-other | 2016 Mar
REPOSITORIES: biostudies-other
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Project description:IntroductionInfluenza surveillance was conducted in Uganda from October 2008 to December 2014 to identify and understand the epidemiology of circulating influenza strains in out-patient clinic attendees with influenza-like illness and inform control strategies.MethodologySurveillance was conducted at five hospital-based sentinel sites. Nasopharyngeal and/or oropharyngeal samples, epidemiological and clinical data were collected from enrolled patients. Real-time reverse transcription polymerase chain reaction (RT-PCR) was performed to identify and subtype influenza strains. Data were double-entered into an Epi Info 3.5.3 database and exported to STATA 13.0 software for analysis.ResultsOf the 6,628 patient samples tested, influenza virus infection was detected in 10.4% (n = 687/6,628) of the specimens. Several trends were observed: influenza circulates throughout the year with two peaks; the major one from September to November and a minor one from March to June. The predominant strains of influenza varied over the years: Seasonal Influenza A(H3) virus was predominant from 2008 to 2009 and from 2012 to 2014; Influenza A(H1N1)pdm01 was dominant in 2010; and Influenza B virus was dominant in 2011. The peaks generally coincided with times of higher humidity, lower temperature, and higher rainfall.ConclusionInfluenza circulated throughout the year in Uganda with two major peaks of outbreaks with similar strains circulating elsewhere in the region. Data on the circulating strains of influenza and its patterns of occurrence provided critical insights to informing the design and timing of influenza vaccines for influenza prevention in tropical regions of sub-Saharan Africa.
| S-EPMC5068740 | biostudies-literature
Project description:BACKGROUND:The Binational Border Infectious Disease Surveillance program began surveillance for severe acute respiratory infections (SARI) on the US-Mexico border in 2009. Here, we describe patients in Southern Arizona. METHODS:Patients admitted to five acute care hospitals that met the SARI case definition (temperature ?37·8°C or reported fever or chills with history of cough, sore throat, or shortness of breath in a hospitalized person) were enrolled. Staff completed a standard form and collected a nasopharyngeal swab which was tested for selected respiratory viruses by reverse transcription polymerase chain reaction. RESULTS:From October 2010-September 2014, we enrolled 332 SARI patients. Fifty-two percent were male and 48% were white non-Hispanic. The median age was 63 years (47% ?65 years and 5·2% <5 years). During hospitalization, 51 of 230 (22%) patients required intubation, 120 of 297 (40%) were admitted to intensive care unit, and 28 of 278 (10%) died. Influenza vaccination was 56%. Of 309 cases tested, 49 (16%) were positive for influenza viruses, 25 (8·1%) for human metapneumovirus, 20 (6·5%) for parainfluenza viruses, 16 (5·2%) for coronavirus, 11 (3·6%) for respiratory syncytial virus, 10 (3·2%) for rhinovirus, 4 (1·3%) for rhinovirus/enterovirus, 3 (1·0%) for enteroviruses, and 3 (1·0%) for adenovirus. Among the 49 influenza-positive specimens, 76% were influenza A (19 H3N2, 17 H1N1pdm09, and 1 not subtyped), and 24% were influenza B. CONCLUSION:Influenza viruses were a frequent cause of SARI in hospitalized patients in Southern Arizona. Monitoring respiratory illness in border populations will help better understand the etiologies. Improving influenza vaccination coverage may help prevent some SARI cases.
| S-EPMC4814863 | biostudies-literature
Project description:BACKGROUND:Estimates of influenza-associated hospitalization are limited in low- and middle-income countries, especially in Africa. OBJECTIVE:To estimate the national number of influenza-associated severe acute respiratory illness (SARI) hospitalization in Zambia. METHODS:We conducted active prospective hospital-based surveillance for SARI at the University Teaching Hospital (UTH) situated in Lusaka Province during 2011-2014. Upper respiratory tract samples were tested for influenza virus using a reverse transcriptase polymerase chain reaction assay. We estimated age-specific rates of influenza-associated SARI hospitalizations for the UTH using census and secondary data on respiratory hospitalizations following estimation approaches recommended by the World Health Organization. We used the UTH hospitalization rates as a proxy for Lusaka Province. These rates were adjusted for each of the remaining 9 provinces based on their prevalence of risk factors for pneumonia and healthcare-seeking behavior. Rates were expressed per 100,000 population. RESULTS:SARI cases accounted for 77.1% (13 389/17 354) of respiratory admissions at the UTH; 82.7% (11 859/14 344) and 50.8% (1530/3010) among individuals aged <5 and ?5 years, respectively. Among SARI cases tested, the influenza virus detection rate was 5.5% (152/2734), 4.8% (48/998), and 6.0% (104/1736) among individuals aged <5 and ?5 years, respectively. The mean annual national number of influenza-associated SARI hospitalizations was 6181 (95% CI: 4321-8041-rate: 43.9; 95% CI: 30.7-57.1); 4669 (95% CI: 3287-6051-rate: 187.7; 95% CI: 132.1-243.3) among children aged <5 years; and 1512 (95% CI: 1037-1987-rate: 13.1; 95% CI: 9.0-17.2) among individuals aged ?5 years. CONCLUSIONS:The burden of influenza-associated SARI hospitalizations was substantial and was highest among children aged <5 years.
| S-EPMC5818337 | biostudies-literature
Project description:ObjectiveTo assess virus-specific hospitalisation rates, risk factors for illness severity and seasonal trends in children hospitalised with acute respiratory infections (ARI).DesignProspective cohort study.SettingA government hospital serving low-income and middle-income population in Amman, Jordan.ParticipantsChildren under 2?years of age hospitalised with fever and/or respiratory symptoms (n=3168) from 16 March 2010 to 31 March 2013. Children with chemotherapy-associated neutropenia and newborns who had never been discharged after birth were excluded from the study.Outcome measuresHospitalisation rates and markers of illness severity: admission to intensive care unit (ICU), mechanical ventilation (MV), oxygen therapy, length of stay (LOS) and death.ResultsOf the 3168 subjects, 2581 (82%) had at least one respiratory virus detected, with respiratory syncytial virus (RSV) being the most predominant pathogen isolated. During admission, 1013 (32%) received oxygen therapy, 284 (9%) were admitted to ICU, 111 (4%) were placed on MV and 31 (1%) children died. Oxygen therapy was higher in RSV-only subjects compared with human rhinovirus-only (42%vs29%, p<0.001), adenovirus-only (42%vs21%, p<0.001) and human parainfluenza virus-only (42%vs23%,?p<0.001) subjects. The presence of an underlying medical condition was associated with oxygen therapy (adjusted OR (aOR) 1.95, 95%?CI 1.49 to 2.56), ICU admission (aOR 2.51, 95%?CI 1.71 to 3.68), MV (aOR 1.91, 95%?CI 1.11 to 3.28) and longer LOS (aOR1.71, 95%?CI 1.37 to 2.13). Similarly, younger age was associated with oxygen therapy (0.23, 95%?CI 0.17 to 0.31), ICU admission (aOR 0.47, 95%?CI 0.30 to 0.74), MV (0.28, 95%?CI 0.15 to 0.53) and longer LOS (aOR 0.47, 95%?CI 0.38 to 0.59). Pneumonia was strongly associated with longer LOS (aOR 2.07, 95%?CI 1.65 to 2.60), oxygen therapy (aOR 2.94, 95%?CI 2.22 to 3.89), ICU admission (aOR 3.12, 95%?CI 2.16 to 4.50) and MV (aOR 3.33, 95%?CI 1.85 to 6.00). Virus-specific hospitalisation rates ranged from 0.5 to 10.5 per 1000 children.ConclusionRespiratory viruses are associated with severe illness in Jordanian children hospitalised with ARI. Prevention strategies such as extended breast feeding, increased access to palivizumab and RSV vaccine development could help decrease hospitalisation rates and illness severity, particularly in young children with underlying medical conditions.
| S-EPMC5961648 | biostudies-literature
Project description:BACKGROUND:An epidemic of severe acute respiratory syndrome (SARS) has been associated with an outbreak of atypical pneumonia originating in Guangdong Province, People's Republic of China. We aimed to identify the causative agent in the Guangdong outbreak and describe the emergence and spread of the disease within the province. METHODS:We analysed epidemiological information and collected serum and nasopharyngeal aspirates from patients with SARS in Guangdong in mid-February, 2003. We did virus isolation, serological tests, and molecular assays to identify the causative agent. FINDINGS:SARS had been circulating in other cities of Guangdong Province for about 2 months before causing a major outbreak in Guangzhou, the province's capital. A novel coronavirus, SARS coronavirus (CoV), was isolated from specimens from three patients with SARS. Viral antigens were also directly detected in nasopharyngeal aspirates from these patients. 48 of 55 (87%) patients had antibodies to SARS CoV in their convalescent sera. Genetic analysis showed that the SARS CoV isolates from Guangzhou shared the same origin with those in other countries, and had a phylogenetic pathway that matched the spread of SARS to the other parts of the world. INTERPRETATION:SARS CoV is the infectious agent responsible for the epidemic outbreak of SARS in Guangdong. The virus isolated from patients in Guangdong is the prototype of the SARS CoV in other regions and countries.
| S-EPMC7112415 | biostudies-literature
Project description:ObjectiveThe aim of this study was to estimate the proportion of rubella disease in a measles case-based surveillance in Cameroon prior to rubella vaccine introduction into the national immunisation programme.DesignThis was a cross-sectional study for rubella infection in Cameroon for the period 2008 to 2014.SettingPatients suspected with measles from the 10 regions of Cameroon were recruited according to the WHO measles case definition and were tested for rubella IgM antibodies accompanied with the case report/investigation forms.ParticipantsAll persons with rash and fever within 14 days of onset of rash according to the standard WHO African Regional Office (WHO/AFRO) case definition for a suspected measles case.Outcome measuresDescriptive analyses and simple logistic regressions were performed. OR were estimated.ResultsA total of 9907 serum samples from people with fever and rash were received in the laboratory from 2008 to 2014. A total of 7489 (75.59%) measles-negative samples were tested for rubella; 699 (9.3%) were positive for rubella IgM antibodies. Logistic regression analysis was done using IgM antibodies detection as the outcome variable. Age, sex and setting were explanatory variables. Logistic regression analysis revealed that, comparing the proportion of rubella IgM seropositivity status by age, the association to a positive rubella IgM increased with age from 1 to 4 years (OR 7.11; 95% CI 4.35 to 12.41; p<0.0001), through 5 to 9 years (OR 13.07; 95% CI 7.93 to 22.93; p<0.001), to 10 to 14 years of age (OR 13.86; 95% CI 8.06 to 25.12; p<0.001). Persons aged ?15 years were also more likely to have rubella infection than children under one (OR 3.69; 95% CI 1.85 to 7.48; p=0.0001). There were also significant associations with sex, with males being less associated to a positive rubella serology than females (OR 1.33; 95% CI 1.14 to 1.56; p=0.0001). No statistically significant difference in proportion of rubella cases was observed between urban and rural populations (OR 1.11; 95% CI 0.94 to 1.31; p=0.208).ConclusionsThis study reveals that rubella virus circulates in Cameroon, with important number of cases in children under 15 years. This finding supports the planned introduction of rubella-containing vaccines into the Expanded Program on Immunization.
| S-EPMC5594209 | biostudies-literature
Project description:We performed whole-genome sequencing on 170 clinical carbapenemase-producing Enterobacter spp. isolates collected globally during 2008-2014. The most common carbapenemase was VIM, followed by New Delhi metallo-β-lactamase (NDM), Klebsiella pneumoniae carbapenemase, oxacillin 48, and IMP. The isolates were of predominantly 2 species (E. xiangfangensis and E. hormaechei subsp. steigerwaltii) and 4 global clones (sequence type [ST] 114, ST93, ST90, and ST78) with different clades within ST114 and ST90. Particular genetic structures surrounding carbapenemase genes were circulating locally in various institutions within the same or between different STs in Greece, Guatemala, Italy, Spain, Serbia, and Vietnam. We found a common NDM genetic structure (NDM-GE-U.S.), previously described on pNDM-U.S. from Klebsiella pneumoniae ATCC BAA-214, in 14 different clones obtained from 6 countries spanning 4 continents. Our study highlights the importance of surveillance programs using whole-genome sequencing in providing insight into the molecular epidemiology of carbapenemase-producing Enterobacter spp.
| S-EPMC6004858 | biostudies-literature
Project description:BackgroundInfluenza and respiratory syncytial virus (RSV) infections are responsible for substantial global morbidity and mortality in young children and elderly individuals. Estimates of the burden of influenza- and RSV-associated hospitalization are limited in Africa.MethodsWe conducted hospital-based surveillance for laboratory-confirmed influenza- and RSV-associated severe acute respiratory illness (SARI) among patients of any age at one hospital and a retrospective review of SARI hospitalizations in five hospitals situated in Antananarivo during 2011-2016. We estimated age-specific rates (per 100 000 population) of influenza- and RSV-associated SARI hospitalizations for the Antananarivo region and then extrapolated these rates to the national level.ResultsOverall, the mean annual national number of influenza-associated SARI hospitalizations for all age groups was 6609 (95% CI: 5381-7835-rate: 30.0; 95% CI: 24.4-35.6), 4468 (95% CI: 3796-5102-rate: 127.6; 95% CI: 108.4-145.7), 2141 (95% CI: 1585-2734-rate: 11.6; 95% CI: 8.6-14.8), and 339 (95% CI: 224-459-rate: 50.0; 95% CI: 36.3-74.4) among individuals aged <5, ?5, and ?65 years, respectively. For these same age groups, the mean annual number of RSV-associated SARI hospitalizations was 11 768 (95% CI: 10 553-12 997-rate: 53.4; 95% CI: 47.9-59.0), 11 299 (95% CI: 10 350-12 214-rate: 322.7; 95% CI: 295.6-348.8), 469 (95% CI: 203-783-rate: 2.5;95% CI: 1.1-4.2), and 36 (95% CI: 0-84-rate: 5.8; 0.0-13.5), respectively.ConclusionThe burden of influenza- and RSV-associated SARI hospitalization was high among children aged <5 years. These first estimates for Madagascar will enable government to make informed evidence-based decisions when allocating scarce resources and planning intervention strategies to limit the impact and spread of these viruses.
| S-EPMC6379640 | biostudies-literature
Project description:BackgroundLeptospirosis is a zoonosis usually transmitted through contact with water or soil contaminated with urine from infected animals. Severe flooding can put individuals at greater risk for contracting leptospirosis in endemic areas. Rapid testing for the disease and large-scale interventions are necessary to identify and control infection. We describe a leptospirosis outbreak following severe flooding and a mass chemoprophylaxis campaign in Guyana.Methodology/principal findingsFrom January-March 2005, we collected data on suspected leptospirosis hospitalizations and deaths. Laboratory testing included anti-leptospiral dot enzyme immunoassay (DST), immunohistochemistry (IHC) staining, and microscopic agglutination testing (MAT). DST testing was conducted for 105 (44%) of 236 patients; 52 (50%) tested positive. Four (57%) paired serum samples tested by MAT were confirmed leptospirosis. Of 34 total deaths attributed to leptospirosis, postmortem samples from 10 (83%) of 12 patients were positive by IHC. Of 201 patients interviewed, 89% reported direct contact with flood waters. A 3-week doxycycline chemoprophylaxis campaign reached over 280,000 people.ConclusionsA confirmed leptospirosis outbreak in Guyana occurred after severe flooding, resulting in a massive chemoprophylaxis campaign to try to limit morbidity and mortality.
| S-EPMC3392270 | biostudies-literature
Project description:Encephalitis and meningitis (EM) are severe infections of the central nervous system associated with high morbidity and mortality. The etiology of EM in Kazakhstan is not clearly defined, so from February 1, 2017 to January 31, 2018 we conducted hospital-based syndromic surveillance for EM at the Shymkent City Hospital, in the South Kazakhstan region. All consenting inpatients meeting a standard case definition were enrolled. Blood and cerebrospinal fluid (CSF) samples were collected for bacterial culture, and CSF samples were additionally tested by PCR for four bacterial species and three viruses using a cascading algorithm. We enrolled 556 patients. Of these, 494 were of viral etiology (including 4 probable rabies cases), 37 were of bacterial etiology, 19 were of unknown etiology and 6 were not tested. The most commonly identified pathogens included enterovirus (73%, n = 406 cases), herpes simplex virus (12.8%, n = 71), and Neisseria meningitidis (3.8%, n = 21). The incidence rates (IRs) for enteroviral and meningococcal EM were found to be 14.5 and 0.7 per 100,000 persons, respectively. The IR for bacterial EM using both PCR and culture results was 3-5 times higher compared to culture-only results. Antibacterial medicines were used to treat 97.2% (480/494) of virus-associated EM. Incorporation of PCR into routine laboratory diagnostics of EM improves diagnosis, pathogen identification, ensures IRs are not underestimated, and can help avoid unnecessary antibacterial treatment.
| S-EPMC8121361 | biostudies-literature