Epidemiology of respiratory viral infections in two long-term refugee camps in Kenya, 2007-2010

A Clinical Study on Microbiological Profile in Tracheostomy Wounds

Tracheostomy is a surgical procedure in an emergency setting to relieve the upper airway obstruction by creating an opening in the anterior part of trachea. It can also be done electively to wean off from a ventilator, during an elective surgery and clearance of pulmonary secretions. This study was a retrospective analysis of microbiological profile, antibiotic sensitivity & resistance pattern in patients with a tracheostomized wound. A retrospective review of the microbiological profiles of all adult patients who underwent a tracheostomy was conducted between May 2022 and May 2023 at our hospital. Based on the tracheostomy indications, patients were allocated under obstructed and non-obstructed group. Any patient with at least one positive sample was followed up quarterly for a year. The first culture result obtained was recorded at least one month following the last antibiotic dose in each quarter. Out of the 65 tracheal aspirate results obtained from 58 patients (mean age, 57.5 ± 16.48 years), the most common procedure and indications were surgical tracheostomy (72.4%) and non-obstructed causes (74.1%), respectively. Moreover, 47.7% of the culture results indicated Pseudomonas aeruginosa, which showed significantly different proportions across the quarters (p = 0.006). Among obstructed patients, P. aeruginosa was the most common (35%), followed by methicillin-resistant Staphylococcus aureus (MRSA; 23.5%). The colonization was predominantly by gram negative bacteria Acinetobacter species, P. aeruginosa & Klebsiella pneumoniae and fungal species like Candida albicans followed by Aspergillus niger and non-Albicans candida.

RSV Infection in Refugees and Asylum Seekers: A Systematic Review and Meta-Analysis

Respiratory diseases, including respiratory syncytial virus (RSV) infections, are common reasons for seeking healthcare among refugees and asylum seekers. A systematic review with meta-analysis was designed to appraise all the available evidence on RSV infections among individuals in refugee camps. Three medical databases (PubMed, Embase, and Scopus) as well as the preprint repository medRxiv.org were searched for eligible observational studies, and the collected cases were pooled in a random-effects meta-analysis model. Heterogeneity was assessed using the I2 statistics. Funnel plots and a regression analysis were calculated for analyzing reporting bias. Eventually, six studies were retrieved from three areas (Bangladesh, Thailand, and Kenya), with pooled estimates of 129.704 cases per 1000 samples (95% CI 66.393 to 237.986) for RSV compared to 110.287 per 1000 people for influenza A (95% CI 73.186 to 162.889), 136.398 cases per 1000 people (95% CI 84.510 to 212.741) for human adenovirus (HAdV), 69.553 per 1000 people (95% CI 49.802 to 96.343) for parainfluenzavirus (PIFV), and 60.338 per 1000 people (95% CI 31.933 to 111.109) for human metapneumovirus (hMPV). Using influenza A as a reference group, the risk for a positive specimen was greater for RSV (relative risk [RR] 1.514, 95% CI 1.396 to 1.641) and HAdV (RR 1.984, 95% CI 1.834 to 2.146) and lower for influenza B (RR 0.276, 95% CI: 0.239 to 0.319), PIFV (RR: 0.889, 95% CI 0.806 to 0.981), and hMPV (RR 0.594, 95% CI 0.534 to 0.662). In summary, high rates of RSV infections were documented among individuals sheltered in refugee camps, stressing the importance of specifically designed preventive strategies.

Epidemiology of SARS-CoV-2 in Kakuma Refugee Camp Complex, Kenya, 2020-20211

Understanding SARS-CoV-2 infection in populations at increased risk for poor health is critical to reducing disease. We describe the epidemiology of SARS-CoV-2 infection in Kakuma Refugee Camp Complex, Kenya. We performed descriptive analyses of SARS-CoV-2 infection in the camp and surrounding community during March 16, 2020‒December 31, 2021. We identified cases in accordance with national guidelines.We estimated fatality ratios and attack rates over time using locally weighted scatterplot smoothing for refugees, host community members, and national population. Of the 18,864 SARS-CoV-2 tests performed, 1,024 were positive, collected from 664 refugees and 360 host community members. Attack rates were 325.0/100,000 population (CFR 2.9%) for refugees,150.2/100,000 population (CFR 1.11%) for community, and 628.8/100,000 population (CFR 1.83%) nationwide. During 2020-2021, refugees experienced a lower attack rate but higher CFR than the national population, underscoring the need to prioritize SARS-CoV-2 mitigation measures, including vaccination.

Navigating challenges: a socioecological analysis of sexual and reproductive health barriers among Eritrean refugee women in Ethiopia, using a key informant approach

OBJECTIVES

The study aimed to explore the experiences and perceptions of healthcare providers (HCPs) regarding the sexual and reproductive health (SRH) challenges of Eritrean refugee women in Ethiopia.

DESIGN

A qualitative exploratory design with the key informant approach.

SETTING AND PARTICIPANTS

The study was conducted in the Afar regional state, North East, Ethiopia. The study participants were HCP responsible for providing SRH care for refugee women.

RESULTS

Eritrean refugee women have worse health outcomes than the host population. The SRH needs were found to be hindered at multiple layers of socioecological model (SEM). High turnover and shortage of HCP, restrictive laws, language issues, cultural inconsistencies and gender inequalities were among the main barriers reported. Complex multistructural factors are needed to improve SRH needs of Eritrean refugee women.

CONCLUSIONS

A complex set of issues spanning individual needs, social norms, community resources, healthcare limitations and structural mismatches create significant barriers to fulfilling the SRH needs of Eritrean refugee women in Ethiopia. Factors like limited awareness, cultural taboos, lack of safe spaces, inadequate healthcare facilities and restrictive policies all contribute to the severe limitations on SRH services available in refugee settings. The overlap in findings underscores the importance of developing multilevel interventions that are culturally sensitive to the needs of refugee women across all SEM levels. A bilateral collaboration between Refugees and Returnees Service (RRS) structures and the Asayta district healthcare system is critically important.

Seasonal patterns of communicable disease incidence and antibiotic prescribing in Moria refugee camp, Greece

BACKGROUND

Infectious diseases remain a major risk for refugees living in camps. Limited research has been undertaken into the burden and impact of infections in the current refugee crisis around the Mediterranean.This analysis examines the frequency and incidence rates of common infections, and use of antibiotics at a healthcare facility inside Moria refugee camp on the island of Lesvos, Greece, during the winter and summer seasons of 2019.

METHODS

This is a retrospective analysis of routinely, prospectively collected service data from the main acute healthcare facility inside Moria camp.

RESULTS

Of a total of 9601 consultations, 25.16% were for infections (winter: 31.53%, summer: 19.45%). Respiratory, skin and gastrointestinal infections were the most frequent, with incidence rates up to 3.5 times, 50 times and twice as high as those in Western Europe, respectively. Antibiotic prescribing was high (27.7% of all respiratory infections) with high use of broad-spectrum antibiotics (40.2%), raising concerns about induction of antimicrobial resistance.

CONCLUSIONS

The burden of infectious diseases in refugee camps remains high throughout all seasons. Antimicrobial stewardship programmes should be adapted to refugee camp settings to prevent the development of unnecessary antimicrobial resistance. Improving living conditions and access to healthcare in refugee camps is likely to reduce infection rates and antimicrobial resistance among refugees.

Respiratory Syncytial Virus, Influenza and SARS-CoV-2 in Homeless People from Urban Shelters: A Systematic Review and Meta-Analysis (2023)

Homeless people (HP) are disproportionally affected by respiratory disorders, including pneumococcal and mycobacterial infections. On the contrary, more limited evidence has been previously gathered on influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and very little is known about the occurrence of human respiratory syncytial virus (RSV), a common cause of respiratory tract infections among children and the elderly. The present systematic review was designed to collect available evidence about RSV, influenza and SARS-CoV-2 infections in HP, focusing on those from urban homeless shelters. Three medical databases (PubMed, Embase and Scopus) and the preprint repository medRxiv.org were therefore searched for eligible observational studies published up to 30 December 2023, and the collected cases were pooled in a random-effects model. Heterogeneity was assessed using the I2 statistics. Reporting bias was assessed by funnel plots and a regression analysis. Overall, 31 studies were retrieved, and of them, 17 reported on the point prevalence of respiratory pathogens, with pooled estimates of 4.91 cases per 1000 HP (95%CI: 2.46 to 9.80) for RSV, 3.47 per 1000 HP for influenza and 40.21 cases per 1000 HP (95%CI: 14.66 to 105.55) for SARS-CoV-2. Incidence estimates were calculated from 12 studies, and SARS-CoV-2 was characterized by the highest occurrence (9.58 diagnoses per 1000 persons-months, 95%CI: 3.00 to 16.16), followed by influenza (6.07, 95%CI: 0.00 to 15.06) and RSV (1.71, 95%CI: 0.00 to 4.13). Only four studies reported on the outcome of viral infections in HP: the assessed pathogens were associated with a high likelihood of hospitalization, while high rates of recurrence and eventual deaths were reported in cases of RSV infections. In summary, RSV, influenza and SARS-CoV-2 infections were documented in HP from urban shelters, and their potential outcomes stress the importance of specifically tailored preventive strategies.

Climate Change and Human Health in Africa in Relation to Opportunities to Strengthen Mitigating Potential and Adaptive Capacity: Strategies to Inform an African "Brains Trust"

Background

Africa faces diverse and complex population/human health challenges due to climate change. Understanding the health impacts of climate change in Africa in all its complexity is essential for implementing effective strategies and policies to mitigate risks and protect vulnerable populations. This study aimed to outline the major climate change-related health impacts in Africa in the context of economic resilience and to seek solutions and provide strategies to prevent or reduce adverse effects of climate change on human health and well-being in Africa.

Methods

For this narrative review, a literature search was conducted in the Web of Science, Scopus, CAB Abstracts, MEDLINE and EMBASE electronic databases. We also searched the reference lists of retrieved articles for additional records as well as reports. We followed a conceptual framework to ensure all aspects of climate change and health impacts in Africa were identified.

Results

The average temperatures in all six eco-regions of Africa have risen since the early twentieth century, and heat exposure, extreme events, and sea level rise are projected to disproportionately affect Africa, resulting in a larger burden of health impacts than other continents. Given that climate change already poses substantial challenges to African health and well-being, this will necessitate significant effort, financial investment, and dedication to climate change mitigation and adaptation. This review offers African leaders and decision-makers data-driven and action-oriented strategies that will ensure a more resilient healthcare system and safe, healthy populations-in ways that contribute to economic resiliency.

Conclusions

The urgency of climate-health action integrated with sustainable development in Africa cannot be overstated, given the multiple economic gains from reducing current impacts and projected risks of climate change on the continent's population health and well-being. Climate action must be integrated into Africa's development plan to meet the Sustainable Development Goals, protect vulnerable populations from the detrimental effects of climate change, and promote economic development.

The impact of anthropogenic climate change on pediatric viral diseases

The adverse effects of climate change on human health are unfolding in real time. Environmental fragmentation is amplifying spillover of viruses from wildlife to humans. Increasing temperatures are expanding mosquito and tick habitats, introducing vector-borne viruses into immunologically susceptible populations. More frequent flooding is spreading water-borne viral pathogens, while prolonged droughts reduce regional capacity to prevent and respond to disease outbreaks with adequate water, sanitation, and hygiene resources. Worsening air quality and altered transmission seasons due to an increasingly volatile climate may exacerbate the impacts of respiratory viruses. Furthermore, both extreme weather events and long-term climate variation are causing the destruction of health systems and large-scale migrations, reshaping health care delivery in the face of an evolving global burden of viral disease. Because of their immunological immaturity, differences in physiology (e.g., size), dependence on caregivers, and behavioral traits, children are particularly vulnerable to climate change. This investigation into the unique pediatric viral threats posed by an increasingly inhospitable world elucidates potential avenues of targeted programming and uncovers future research questions to effect equitable, actionable change. IMPACT: A review of the effects of climate change on viral threats to pediatric health, including zoonotic, vector-borne, water-borne, and respiratory viruses, as well as distal threats related to climate-induced migration and health systems. A unique focus on viruses offers a more in-depth look at the effect of climate change on vector competence, viral particle survival, co-morbidities, and host behavior. An examination of children as a particularly vulnerable population provokes programming tailored to their unique set of vulnerabilities and encourages reflection on equitable climate adaptation frameworks.

Study of bacterial respiratory infections and antimicrobial susceptibility profile among antibiotics naive outpatients visiting Meru teaching and referral hospital, Meru County, Kenya in 2018

OBJECTIVE

Respiratory tract infections cause significant morbidity and mortality globally and are the most common infectious diseases in humans. This study aims at assessing the presence of bacterial respiratory infections, number of people infected and antimicrobial susceptibility profile among antibiotic naïve outpatients presenting with respiratory tract infections in Meru Teaching and Referral Hospital.

METHODS

The study was conducted in Meru Teaching and Referral Hospital, Meru County from April 2017 to August 2018. Upper respiratory infections were characterized by acute infection of nasal cavity, pharynx and larynx while lower respiratory infections were characterized by chest pains, prolonged cough, productive sputum, difficulty in breathing, fever and weight loss. A total of 384 sputum and throat samples were collected aseptically from patients who were clinically suspected to have respiratory infections and cultured in blood agar, MacConkey agar and chocolate agar. Bacterial isolates were identified by colonial morphology, Gram stain and confirmed by biochemical tests. Antimicrobial susceptibility profile was determined using agar disc diffusion method.

RESULTS

Respiratory bacterial pathogens were isolated in 45.6% of the samples. The prevalence of the bacteria species isolated were as follows Pseudomonas species (36.6%), Klebsiella species (20.6%), Staphylococcus aureus (16.6%), Streptococcus pyogenes (13.7%), Streptococcus pneumoniae (10.3%) and mixed isolates (2.3%). Amoxicillin and ampicillin recorded the highest resistance rate. Most of the isolates displayed high level of resistance to more than two antibiotics. Although multidrug resistance is reported in the study, gentamicin, amikacin and cefuroxime are recommended as the antibiotics of choice against bacterial isolates obtained.

CONCLUSION

Bacterial respiratory infections were prevalent in the study area and the isolates obtained showed resistance to commonly used antibiotics such as amoxicillin, ampicillin, ciprofloxacin piperacillin ciprofloxacin, ceftazidime, piperacillin-tazobactam and cephalexin. Therefore need for a continuous surveillance of antimicrobial resistance in management of respiratory infections in the study area.

Estimates of the national burden of respiratory syncytial virus in Kenyan children aged under 5 years, 2010-2018

BACKGROUND

Respiratory syncytial virus (RSV) is among the leading childhood causes of viral pneumonia worldwide. Establishing RSV-associated morbidity and mortality is important in informing the development, delivery strategies, and evaluation of interventions.

METHODS

Using data collected during 2010-2018 from base regions (population-based surveillance studies in western Kenya and the Kilifi Health and Demographic Surveillance Study), we estimated age-specific rates of acute respiratory illness (ARI), severe acute respiratory illness (SARI-defined as hospitalization with cough or difficulty breathing with onset within the past 10 days), and SARI-associated deaths. We extrapolated the rates from the base regions to other regions of Kenya, while adjusting for risk factors of ARI and healthcare seeking behavior, and finally applied the proportions of RSV-positive cases identified from various sentinel and study facilities to the rates to obtain regional age-specific rates of RSV-associated outpatient and non-medically attended ARI and hospitalized SARI and severe ARI that was not hospitalized (non-hospitalized SARI). We applied age-specific RSV case fatality ratios to SARI to obtain estimates of RSV-associated in- and out-of-hospital deaths.

RESULTS

Among Kenyan children aged < 5 years, the estimated annual incidence of outpatient and non-medically attended RSV-associated ARI was 206 (95% credible interval, CI; 186-229) and 226 (95% CI; 204-252) per 1000 children, respectively. The estimated annual rates of hospitalized and non-hospitalized RSV-associated SARI were 349 (95% CI; 303-404) and 1077 (95% CI; 934-1247) per 100,000 children respectively. The estimated annual number of in- and out-of-hospital deaths associated with RSV infection in Kenya were 539 (95% CI; 420-779) and 1921 (95% CI; 1495-2774), respectively. Children aged < 6 months had the highest burden of RSV-associated severe disease: 2075 (95% CI; 1818-2394) and 44 (95% CI 25-71) cases per 100,000 children for hospitalized SARI and in-hospital deaths, respectively.

CONCLUSIONS

Our findings suggest a substantial disease burden due to RSV infection, particularly among younger children. Prioritizing development and use of maternal vaccines and affordable long-lasting monoclonal antibodies could help reduce this burden.

Etiologies of influenza-like illness and severe acute respiratory infections in Tanzania, 2017-2019

In 2016, Tanzania expanded sentinel surveillance for influenza-like illness (ILI) and severe acute respiratory infection (SARI) to include testing for non-influenza respiratory viruses (NIRVs) and additional respiratory pathogens at 9 sentinel sites. During 2017-2019, respiratory specimens from 2730 cases underwent expanded testing: 2475 specimens (90.7%) were tested using a U.S. Centers for Disease Control and Prevention (CDC)-developed assay covering 7 NIRVs (respiratory syncytial virus [RSV], rhinovirus, adenovirus, human metapneumovirus, parainfluenza virus 1, 2, and 3) and influenza A and B viruses. Additionally, 255 specimens (9.3%) were tested using the Fast-Track Diagnostics Respiratory Pathogens 33 (FTD-33) kit which covered the mentioned viruses and additional viral, bacterial, and fungal pathogens. Influenza viruses were identified in 7.5% of all specimens; however, use of the CDC assay and FTD-33 kit increased the number of specimens with a pathogen identified to 61.8% and 91.5%, respectively. Among the 9 common viruses between the CDC assay and FTD-33 kit, the most identified pathogens were RSV (22.9%), rhinovirus (21.8%), and adenovirus (14.0%); multi-pathogen co-detections were common. Odds of hospitalization (SARI vs. ILI) varied by sex, age, geographic zone, year of diagnosis, and pathogen identified; hospitalized illnesses were most common among children under the age of 5 years. The greatest number of specimens were submitted for testing during December-April, coinciding with rainy seasons in Tanzania, and several viral pathogens demonstrated seasonal variation (RSV, human metapneumovirus, influenza A and B, and parainfluenza viruses). This study demonstrates that expanding an existing influenza platform to include additional respiratory pathogens can provide valuable insight into the etiology, incidence, severity, and geographic/temporal patterns of respiratory illness. Continued respiratory surveillance in Tanzania, and globally, can provide valuable data, particularly in the context of emerging respiratory pathogens such as SARS-CoV-2, and guide public health interventions to reduce the burden of respiratory illnesses.

Implementation, effectiveness and monitoring of telemedicine program in Bhutanese refugees camp in Eastern Nepal

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Spatial-temporal distribution and sequence diversity of group a human respiratory syncytial viruses in Kenya preceding the emergence of ON1 genotype

Background

Human respiratory syncytial virus (HRSV) is a major cause of severe viral acute respiratory illness and contributes significantly to severe pneumonia cases in Africa. Little is known about its spatial–temporal distribution as defined by its genetic diversity.

Methods

A retrospective study conducted utilizing archived nasopharyngeal specimens from patients attending outpatient clinics in hospitals located in five demographically and climatically distinct regions of Kenya; Coast, Western, Highlands, Eastern and Nairobi. The viral total RNA was extracted and tested using multiplex real time RT‐PCR (reverse transcriptase polymerase chain reaction). A segment of the G‐gene was amplified using one‐step RT‐PCR and sequenced by Sanger di‐deoxy method. Bayesian analysis of phylogeny was utilized and subsequently median joining methods for haplotype network reconstruction.

Results

Three genotypes of HRSVA were detected; GA5 (14.0%), GA2 (33.1%), and NA1 (52.9%). HRSVA prevalence varied by location from 33% to 13.2% in the Highlands and the Eastern regions respectively. The mean nucleotide diversity (Pi[π]) varied by genotype: highest of 0.018 for GA5 and lowest of 0.005 for NA1. A total of 58 haplotypes were identified (GA5 10; GA2 20; NA1 28). These haplotypes were introduced into the population locally by single haplotypes and additional subsidiary seeds amongst the GA2 and the NA1 haplotypes.

Conclusions

HRSVA was found across all the regions throughout the study period and comprised three genotypes; GA5, GA2, and NA1 genotypes. The genotypes were disproportionately distributed across the regions with GA5 gradually increasing toward the Western zones and decreasing toward the Eastern zones of the country.

Exploring the impact of multidimensional refugee vulnerability on distancing as a protective measure against COVID-19: The case of Syrian refugees in Lebanon and Turkey

•

The conditions of refugee living make distancing an impractical COVID-19 protection measure.

•

Refugees are increasingly susceptible to the biological and socioeconomic effects of COVID-19, due to the decreased ability to practice distancing measures.

•

We suggest an interdisciplinary framework, based on biosocial perspectives on health, to guide more relevant COVID-19 responses in refugee communities.

•

Intervention and protection measures should consider the political, material, spatial, physiological, psychological and sociocultural dimensions of refugee vulnerability to mitigate decreased distancing abilities in settings of refugee life.

Background

The unequal physiological and socioeconomic consequences of the COVID-19 pandemic across the world are revealing the multidimensional components of health and vulnerability. As governments have pushed physical and social distancing as protective strategies, this study explores the extent to which this approach is relevant for Syrian refugees living in Lebanon and Turkey.

Methods

This qualitative study draws on 11 interviews with refugee experts and development practitioners (3) and Syrian refugee families (4 from Turkey, 4 from Lebanon) during the COVID-19 pandemic, as well as a review of recent literature. In addition, it draws on 71 semi-structured interviews with staff at NGOs supporting refugees (48 from Turkey, 23 from Lebanon) collected in 2018. Qualitative data analysis software ATLAS.ti 8 was used to perform content-based thematic analysis using both deductive and inductive coding.

Findings

The study finds that distancing—physically and socially—can be ineffective as a disease protection strategy in Syrian refugee communities. This is influenced by six major interconnected dimensions of refugee vulnerability—political, material, spatial, physiological, psychological and sociocultural—which collectively form an interdisciplinary framework to guide more relevant COVID-19 interventions in refugee communities. The inability to distance is not necessarily rooted in lack of knowledge. Rather, when the inside conditions of living are crowded and unhygienic, but also include cultural expectations of familial care, and the outside conditions of survival-necessitated work are perpetuated through precarious political protections, distancing becomes impractical in application, despite the sense of internalized responsibility to keep one another safe.

Conclusions

The findings suggest that more relevant COVID-19 interventions and protection measures must consider the non-physiological manifestations of disease across multiple dimensions of vulnerability to mitigate decreased distancing abilities in settings of refugee life.

Epidemiology of Human Metapneumovirus-associated Lower Respiratory Tract Infections in African Children: Systematic Review and Meta-analysis

BACKGROUND

Human metapneumovirus (hMPV) has been associated with upper and lower respiratory tract infections (LRTI) in children and adults. This systematic review evaluated the epidemiology of hMPV-associated LRTI, including severe acute respiratory infection (SARI) hospitalization or clinically diagnosed severe pneumonia, in African children under 5 years of age.

METHODS

We searched Science Direct, PubMed, Cochrane Central, Scopus, and WHO regional databases using the terms "("Human metapneumovirus" AND "Africa") OR ("hMPV" AND "Africa")" up to September 17, 2020. Other sources included ClinicalTrials.gov to obtain unpublished data. Studies were included if children were less than 5 years of age and hospitalized with hMPV-associated LRTI, SARI or if clinically diagnosed with severe pneumonia in the community. The main outcomes were prevalence of hMPV identified among children with hospitalized LRTI or SARI. We further calculated odds ratios for hMPV in cases with LRTI compared with non-LRTI controls. Pooled results were calculated using a random-effects model.

RESULTS

Thirty studies were eligible for inclusion in the review. The prevalence of hMPV-LRTI/SARI among hospitalized and severe pneumonia cases was 4.7% [95% confidence interval (CI): 3.9-5.6, I2 = 95.0]. The case-control studies indicated that hMPV was 2.0-fold (95% CI: 0.9-4.4) more likely to be identified in LRTI cases (10.3%) than controls (6.0%). Three of 5 studies reported hMPV-associated LRTI case fatality risk, with a pooled estimate of 1.3% (95% CI: 0.3-2.9; I2 = 49).

CONCLUSIONS

hMPV was associated with approximately 5% of LRTI/SARI hospitalizations or severe pneumonia cases in Africa.

Disease burden in a large cohort of asylum seekers and refugees in Germany

Background

Currently, health care systems worldwide are challenged with providing care to an increasing number of migrants, refugees, and displaced persons. In this article, we report on disease burden and drug prescription patterns in a large refugee cohort in Germany.

Methods

We conducted a cross-sectional study of anonymized medical records including demographic data, diagnoses, and drug prescriptions in two refugee reception centres between 2015 and 2019. Refugees and migrants received medical assistance exclusively through the on-site clinics. Thus, this study represents all medical visits of the housed residents.

Results

In total, n = 15531 diagnoses from n = 4858 patients in a cohort of n = 10431 accommodated refugees were recorded. N = 11898 medications were prescribed. Overall, 29.8% of all refugees sought medical attention. Half of the patients were female (49.6%), the average age was 23.8 years (SD [standard deviation] 17.0, min 0, max 81), and 41.5% were minors (<18 years). Most patients had Middle Eastern or Northern African origin (63.9%). The largest proportion of diagnoses belonged to the ICD (International Statistical Classification of Diseases and Related Health Problems) category “R” (miscellaneous, 33.5%), followed by diseases of the respiratory system (category “J”, 16.5%), or the musculoskeletal system (category “M”, 7.1%). Non-steroidal anti-inflammatory drugs were most frequently prescribed.

Conclusions

This analysis in two large refugee centres in Germany shows that about one third of refugees seek medical attention upon initial arrival. Complaints are manifold, with a high prevalence of respiratory infections.

A spatial queuing model for the location decision of emergency medical vehicles for pandemic outbreaks: the case of Za'atari refugee camp

Purpose

Refugee camps can be severely struck by pandemics, like potential COVID-19 outbreaks, due to high population densities and often only base-level medical infrastructure. Fast responding medical systems can help to avoid spikes in infections and death rates as they allow the prompt isolation and treatment of patients. At the same time, the normal demand for emergency medical services has to be dealt with as well. The overall goal of this study is the design of an emergency service system that is appropriate for both types of demand.

Design/methodology/approach

A spatial hypercube queuing model (HQM) is developed that uses queuing-theory methods to determine locations for emergency medical vehicles (also called servers). Therefore, a general optimization approach is applied, and subsequently, virus outbreaks at various locations of the study areas are simulated to analyze and evaluate the solution proposed. The derived performance metrics offer insights into the behavior of the proposed emergency service system during pandemic outbreaks. The Za'atari refugee camp in Jordan is used as a case study.

Findings

The derived locations of the emergency medical system (EMS) can handle all non-virus-related emergency demands. If additional demand due to virus outbreaks is considered, the system becomes largely congested. The HQM shows that the actual congestion is highly dependent on the overall amount of outbreaks and the corresponding case numbers per outbreak. Multiple outbreaks are much harder to handle even if their cumulative average case number is lower than for one singular outbreak. Additional servers can mitigate the described effects and lead to enhanced resilience in the case of virus outbreaks and better values in all considered performance metrics.

Research limitations/implications

Some parameters that were assumed for simplification purposes as well as the overall model should be verified in future studies with the relevant designers of EMSs in refugee camps. Moreover, from a practitioners perspective, the application of the model requires, at least some, training and knowledge in the overall field of optimization and queuing theory.

Practical implications

The model can be applied to different data sets, e.g. refugee camps or temporary shelters. The optimization model, as well as the subsequent simulation, can be used collectively or independently. It can support decision-makers in the general location decision as well as for the simulation of stress-tests, like virus outbreaks in the camp area.

Originality/value

The study addresses the research gap in an optimization-based design of emergency service systems for refugee camps. The queuing theory-based approach allows the calculation of precise (expected) performance metrics for both the optimization process and the subsequent analysis of the system. Applied to pandemic outbreaks, it allows for the simulation of the behavior of the system during stress-tests and adds a further tool for designing resilient emergency service systems.

Environmental health conditions in protracted displacement: A systematic scoping review

Adequate environmental health services are critical for human rights, health, and development, especially in the context of forced displacement. There are more than 70 million forcibly displaced persons worldwide, most in protracted situations, having been displaced for more than two years. Some live in camps or informal settlements, but most live in urban areas. Environmental health services are important in the transition from emergency response to sustainable development in these settings, but evidence on environmental health in displaced populations is disparate and of variable quality. We conducted a systematic scoping review of environmental conditions, exposures, and outcomes in protracted displacement settings; obstacles to improvement in environmental health services; and recommendations made for improvement. We included 213 publications from peer-reviewed and grey literature databases. Data were extracted on environmental health topics including water, sanitation, hygiene, overcrowding, waste management, energy supply, vector control, menstrual hygiene, air quality, and food safety. Most studies present data from low- and lower-middle income countries. Northern Africa and Western Asia and Sub-Saharan Africa are the most-represented regions. There is substantial evidence on water, sanitation, and crowding, but few studies report findings on other environmental health topics. Water-related disease, parasites, and respiratory infections are frequently cited and studies report that services often fail to meet international standards for humanitarian response. The most frequent obstacles and recommendations are institutional, political, or implementation-related, but few studies provide concrete recommendations for improvement. Our review compiles and characterizes the research on environmental health in protracted displacement. We recommend including displaced populations in international environmental health policy and monitoring initiatives, and bridging from humanitarian response to sustainable development by preparing for long-term displacement from the early stages of a crisis.

Acute respiratory infections among under-five children from households using biomass fuel in Ethiopia: systematic review and meta-analysis

Acute respiratory infections are a serious public health concern across the globe, they are, however, prominently present in Sub-Saharan Africa. In Ethiopia, different primary studies were conducted in regard to the link between household biomass fuel use and acute respiratory infections among under-five children. However, there is no national study on the association between household biomass fuel use and acute respiratory is infections among under-five children. Thus, the aim of this systematic review and meta-analysis to estimate the pooled prevalence of acute respiratory infections and their predictors among under-five children in Ethiopia.

The systematic review was reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guideline. We systematically searched the databases: PubMed/Medline, Cochrane library, Google Scholar, Web of Science, and Scopus were searched to access potentially relevant articles conducted in Ethiopia about acute respiratory infections among under five children. Stata/SE 14.00 statistical software was used for analysis and the pooled prevalence with 95% confidence interval (CI) were presented using tables and forest plots. To assess the heterogeneity among studies, I square (I2) tests were used. Publication bias was checked by Begg’s and Egger’s regression test. The random effects meta-analysis model was employed to estimate the pooled prevalence and predictors of under-five acute respiratory infections A total of 7 studies with 8, 529 study participants were included in this meta-analysis. The pooled prevalence of acute respiratory infection among under five children was 17.75% (95% CI: 16.95, 18.55). Child holding during cooking (OR: 2.84, 95% CI: 1.48, 5.47) and using unclean sources of energy for cooking (OR: 0.38, 95% CI: 0.21, 0.70) were identified predictors of under-five children acute respiratory infection.

In the current study, the pooled prevalence of acute respiratory infection among under-five children was relatively high. Child holding during cooking and using unclean sources of energy for cooking were significantly associated with under-five acute respiratory infections. Therefore, the policies and regulations enacted should address the barriers that impede the development of clean and efficient energy sources.

Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia

BACKGROUND

Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences.

RESULTS

We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes.

CONCLUSION

This is the first genomic characterization of HMPV genomes from African patients.

The burden of anaemia among displaced women and children in refugee settings worldwide, 2013-2016

Introduction

Displaced persons have a unique risk for developing anaemia due to often limited diets, overcrowding, new infections and inadequate sanitation and hygiene. The lack of anaemia prevalence estimates among the displaced inhibit global planning for anaemia reduction.

Methods

We analysed population representative, cross-sectional nutrition surveys from 2013 to 2016 conducted by the United Nations High Commissioner for Refugees and partner agencies. Included surveys measured haemoglobin concentration among children 6–59 months, non-pregnant women 15–49 years, or both groups. For each survey, we calculated mean haemoglobin and prevalence of total anaemia (<110 g/L in children, <120 g/L in women), and classified public health severity following WHO guidelines. Pearson correlations between indicators from women and children surveys were calculated where both subpopulations were measured.

Results

Analysis included 196 surveys among children and 184 surveys among women from 121 unique refugee settings in 24 countries. The median prevalence of total anaemia in children and women was 44% and 28%, respectively. Sixty-one per cent of child surveys indicated a problem of severe public health importance compared with 25% of surveys in women. The prevalence of total anaemia in children and women was strongly correlated (ρ=0.80). Median prevalence of total anaemia was approximately 55% greater and mean haemoglobin was 6 g/L lower among children age 6–23 months compared with children 24–59 months. West and Central Africa region had the highest median prevalence of anaemia both in women and children.

Conclusion

While the burden of anaemia is high among the displaced, it mirrors that of the general population. Haemoglobin should continue to be measured in nutrition surveys in refugee settings. Sustained, multisectoral efforts to reduce anaemia are needed, with specific focus on children under 2 years of age and refugee settings in the West and Central Africa region.

The Epidemiology and Burden of Influenza B/Victoria and B/Yamagata Lineages in Kenya, 2012-2016

Background

The impact of influenza B virus circulation in Sub-Saharan Africa is not well described.

Methods

We analyzed data from acute respiratory illness (ARI) in Kenya. We assessed clinical features and age-specific hospitalization and outpatient visit rates by person-years for influenza B/Victoria and B/Yamagata and the extent to which circulating influenza B lineages in Kenya matched the vaccine strain component of the corresponding season (based on Northern Hemisphere [October–March] and Southern Hemisphere [April–September] vaccine availability).

Results

From 2012 to 2016, influenza B represented 31% of all influenza-associated ARIs detected (annual range, 13–61%). Rates of influenza B hospitalization and outpatient visits were higher for <5 vs ≥5 years. Among <5 years, B/Victoria was associated with pneumonia hospitalization (64% vs 44%; P = .010) and in-hospital mortality (6% vs 0%; P = .042) compared with B/Yamagata, although the mean annual hospitalization rate for B/Victoria was comparable to that estimated for B/Yamagata. The 2 lineages co-circulated, and there were mismatches with available trivalent influenza vaccines in 2/9 seasons assessed.

Conclusions

Influenza B causes substantial burden in Kenya, particularly among children aged <5 years, in whom B/Victoria may be associated with increased severity. Our findings suggest a benefit from including both lineages when considering influenza vaccination in Kenya.

The epidemiology and severity of respiratory viral infections in a tropical country: Ecuador, 2009-2016

BACKGROUND

Respiratory viral infections (RVI) are a leading cause of mortality worldwide. We compared the epidemiology and severity of RVI in Ecuador during 2009-2016.

METHODS

Respiratory specimens collected within the national surveillance system were tested for influenza viruses, respiratory syncytial virus (RSV), adenovirus, parainfluenza virus, and human metapneumovirus. Overall and virus-specific positive detection rate (PDR) were calculated and compared the timing of epidemics caused by the different viruses. Logistic regression models were used to compare the age distribution and risk of death across respiratory viruses.

RESULTS

A total of 41,172 specimens were analyzed: influenza (PDR=14.3%) and respiratory syncytial virus (RSV) (PDR=9.5%) were the most frequently detected viruses. Influenza epidemics typically peaked in December-January and RSV epidemics in March; seasonality was less evident for the other viruses. Compared to adults, children were more frequently infected with RSV, adenovirus, parainfluenza, and influenza B, while the elderly were less frequently infected with influenza A(H1N1)p. The age-adjusted risk of death was highest for A(H1N1)p (odds ratio [OR] 1.73, 95% confidence intervals [CI] 1.38-2.17), and lowest for RSV (OR 0.75, 95%CI 0.57-0.98).

CONCLUSIONS

Whilst influenza and RSV were the most frequently detected pathogens, the risk of death differed by RVI, being highest for pandemic influenza and lowest for RSV.

Prevalence of human respiratory syncytial virus infection in people with acute respiratory tract infections in Africa: A systematic review and meta-analysis

AIM

The epidemiology of human respiratory syncytial virus (HRSV) infection has not yet been systematically investigated in Africa. This systematic review and meta-analysis are to estimate the prevalence of HRSV infections in people with acute respiratory tract infections (ARTI) in Africa.

METHOD

We searched PubMed, EMBASE, Africa Journal Online, and Global Index Medicus to identify observational studies published from January 1, 2000, to August 1, 2017. We used a random-effects model to estimate the prevalence across studies. Heterogeneity (I2 ) was assessed via the chi-square test on Cochran's Q statistic. Review registration: PROSPERO CRD42017076352.

RESULTS

A total of 67 studies (154 000 participants) were included. Sixty (90%), seven (10%), and no studies had low, moderate, and high risk of bias, respectively. The prevalence of HRSV infection varied widely (range 0.4%-60.4%). The pooled prevalence was 14.6% (95% CI 13.0-16.4, I2  = 98.8%). The prevalence was higher in children (18.5%; 95% CI 15.8-21.5) compared to adults (4.0%; 95% CI 2.2-6.1) and in people with severe respiratory tract infections (17.9%; 95% CI 15.8-20.1) compared to those with benign forms (9.4%; 95% CI 7.4-11.5); P-values <0.0001. The HRSV prevalence was not associated with sex, subregion in Africa, setting, altitude, latitude, longitude, and seasonality.

CONCLUSION

This study suggests a high prevalence of HRSV in people with ARTI in Africa, particularly among children and people with severe clinical form. All innovative strategies to curb the burden should first focus on children which present the highest HRSV-related burden.

Integrating human rights approaches into public health practices and policies to address health needs amongst Rohingya refugees in Bangladesh: a systematic review and meta-ethnographic analysis

Background

The Rohingya people of Myanmar are one of the most persecuted communities in the world and are forced to flee their home to escape conflict and persecution. Bangladesh receives the majority of the Rohingya refugees. On arrival they experience a number of human rights issues and the extent to which human rights approaches are used to inform public health programs is not well documented. The aim of this systematic review was to document human rights- human rights-related health issues and to develop a conceptual human rights framework to inform current policy practice and programming in relation to the needs of Rohingya refugees in Bangladesh.

Methods

This systematic review was conducted using the 2015 Preferred Reporting Items for Systematic reviews and Meta-Analysis guidelines. Eight computerized databases were searched: Academic Search complete, Embase, CINAHL, JStor, Pubmed, Scopus, SocIndex, and Proquest Central along with grey literature and Google Scholar. Of a total of 752 articles retrieved from the eight databases and 17 studies from grey literature, 31 studies met our inclusion criteria.

Results

Using meta-ethnographic synthesis, we developed a model that helps understand the linkages of various human rights and human rights-related health issues of Rohingya refugees. The model highlights how insufficient structural factors, poor living conditions, restricted mobility, and lack of working rights for extended periods of time collectively contribute to poor health outcomes of Rohingya refugees.

Conclusion

This review provides a human-rights approach to frame actions both at program and policy level in a sustained way to address the health needs of Rohingya refugees in Bangladesh. Such policy actions will focus on finding long term solutions for integrating the Rohingya population while addressing their immediate rights issue.

Trial registration

This systematic review has not been registered.

Contemporaneous data on the prevalence of Human Respiratory Syncytial Virus infection in people with acute respiratory tract infections in Africa (2000-2017)

Availability of accurate data on the burden of the Human Respiratory Syncytial Virus (HRSV) can help to implement better strategies to curb this burden in Africa continent among people with acute respiratory tract infections (ARTI). We summarize here available contemporaneous data published from January 1, 2000 to August 31, 2017 on the prevalence of HSRV infection among people with ARTI in the continent.

Reassessment of high prevalence human adenovirus detections among residents of two refugee centers in Kenya under surveillance for acute respiratory infections

Human adenoviruses (HAdVs) were previously detected at high prevalence by real-time reverse transcription-polymerase chain reaction (rRT-PCR) in the upper respiratory tract of residents of two Kenyan refugee camps under surveillance for acute respiratory infection (ARI) between October 2006 and April 2008. We sought to confirm this finding and characterize the HAdVs detected. Of 2148 respiratory specimens originally tested, 511 (23.8%) screened positive for HAdV and 510 were available for retesting. Of these, 421 (82.4%) were confirmed positive by repeat rRT-PCR or PCR and sequencing. Other respiratory viruses were codetected in 55.8% of confirmed HAdV-positive specimens. Species B and C viruses predominated at 82.8%, and HAdV-C1, -C2, and -B3 were the most commonly identified types. Species A, D, and F HAdVs, which are rarely associated with ARI, comprised the remainder. Viral loads were highest among species B HAdVs, particularly HAdV-B3. Species C showed the widest range of viral loads, and species A, D, and F were most often present at low loads and more often with codetections. These findings suggest that many HAdV detections were incidental and not a primary cause of ARI among camp patients. Species/type, codetections, and viral load determinations may permit more accurate HAdV disease burden estimates in these populations.

Sexual and reproductive healthcare for women asylum seekers in Switzerland: a multi-method evaluation

BACKGROUND

Forced migration significantly endangers health. Women face numerous health risks, including sexual violence, lack of contraception, sexually transmitted disease, and adverse perinatal outcomes. Therefore, sexual and reproductive healthcare is a significant aspect of women asylum seekers' health. Even when healthcare costs of asylum seekers are covered by the government, there may be strong barriers to healthcare access and specific needs may be addressed inadequately. The study's objectives were a) to assess the accommodation and healthcare services provided to women asylum seekers in standard and specialised health care, b) to assess the organisation of healthcare provision and how it addresses the sexual and reproductive healthcare needs of women asylum seekers.

METHODS

The study utilised a multi-method approach, comprising a less-dominant quantitative component and dominant qualitative component. The quantitative component assessed accommodation conditions for women in eight asylum centres using a survey. The qualitative component assessed healthcare provision on-site, using semi-structured interviews with health and social care professionals (n = 9). Asylum centres were selected to cover a wide range of characteristics. Interview analysis was guided by thematic analysis.

RESULTS

The accommodation in the asylum centres provided gender-separate rooms and sanitary infrastructure. Two models of healthcare were identified, which differed in the services they provided and in their organisation: 1) a standard healthcare model characterised by a lack of coordination between healthcare providers, unavailability of essential services such as interpreters, and fragmented healthcare, and 2) a specialised healthcare model specifically tailored to the needs of asylum-seekers. Its organisation is characterised by a network of closely collaborating health professionals. It provided essential services not present in the standard model. We recommend the specialised healthcare model as a guideline for best practise.

CONCLUSIONS

The standard, non-specialised healthcare model used in some regions in Switzerland does not fully meet the healthcare needs of women asylum seekers. Specialised healthcare services used in other regions, which include translation services as well as gender and culturally sensitive care, are better suited to address these needs. More widespread use of this model would contribute significantly toward protecting the sexual and reproductive integrity and health of women asylum seekers.

Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya: baseline epidemiological observations

Background: Endemic and seasonally recurring respiratory viruses are a major cause of disease and death globally. The burden is particularly severe in developing countries. Improved understanding of the source of infection, pathways of spread and persistence in communities would be of benefit in devising intervention strategies. Methods: We report epidemiological data obtained through surveillance of respiratory viruses at nine outpatient health facilities within the Kilifi Health and Demographic Surveillance System, Kilifi County, coastal Kenya, between January and December 2016. Nasopharyngeal swabs were collected from individuals of all ages presenting with acute respiratory infection (ARI) symptoms (up to 15 swabs per week per facility) and screened for 15 respiratory viruses using real-time PCR. Paediatric inpatient surveillance at Kilifi County Hospital for respiratory viruses provided comparative data. Results: Over the year, 5,647 participants were sampled, of which 3,029 (53.7%) were aged <5 years. At least one target respiratory virus was detected in 2,380 (42.2%) of the samples; the most common being rhinovirus 18.6% (1,050), influenza virus 6.9% (390), coronavirus 6.8% (387), parainfluenza virus 6.6% (371), respiratory syncytial virus (RSV) 3.9% (219) and adenovirus 2.7% (155). Virus detections were higher among <5-year-olds compared to older children and adults (50.3% vs 32.7%, respectively; χ 2(1) =177.3, P=0.0001). Frequency of viruses did not differ significantly by facility (χ 2(8) =13.38, P=0.072). However, prevalence was significantly higher among inpatients than outpatients in <5-year-olds for RSV (22.1% vs 6.0%; χ 2(1) = 159.4, P=0.0001), and adenovirus (12.4% vs 4.4%, χ 2(1) =56.6, P=0.0001). Conclusions: Respiratory virus infections are common amongst ARI outpatients in this coastal Kenya setting, particularly in young children. Rhinovirus predominance warrants further studies on the health and socio-economic implications. RSV and adenovirus were more commonly associated with severe disease. Further analysis will explore epidemiological transmission patterns with the addition of virus sequence data.

DETECTION OF NON-INFLUENZA VIRUSES IN ACUTE RESPIRATORY INFECTIONS IN CHILDREN UNDER FIVE-YEAR-OLD IN COTE D'IVOIRE (JANUARY - DECEMBER 2013)

BACKGROUND

Influenza sentinel surveillance in Cote d'Ivoire showed that 70% of Acute Respiratory Infections (ARI) cases remained without etiology. This work aims to describe the epidemiological, clinical, and virological pattern of ARI that tested negative for influenza virus, in children under five years old.

MATERIALS AND METHODS

one thousand and fifty nine samples of patients presenting influenza Like Illness (ILI) or Severe Acute Respiratory Infections (SARI) symptoms were tested for other respiratory viruses using multiplex RT-PCR assays targeting 10 respiratory viruses.

RESULTS

The following pathogens were detected as follows, hRV 31,92% (98/307), hRSV 24.4% (75/329), PIV 20.5% (63/307), HCoV 229E 12,05% (37/307), hMPV 6.2% (19/307), HCoVOC43 1.0% (3/307) and EnV 1.0% (3/307). Among the 1,059 specimens analyzed, 917 (86.6%) were ILI samples and 142 (23.4%) were SARI samples. The proportion of children infected with at least one virus was 29.8% (273/917) in ILI cases and 23.9% (34/142) in SARI cases. The most prevalent viruses, responsible for ILI cases were hRV with 35.89% (98/273) and hRSV in SARI cases with 41.2% (14/34) of cases. Among the 1,059 patients, only 22 (2.1%) children presented risk factors related to the severity of influenza virus infection.

CONCLUSION

This study showed that respiratory viruses play an important role in the etiology of ARI in children. For a better understanding of the epidemiology of ARI and improved case management, it would be interesting in this context to expand the surveillance of influenza to other respiratory viruses.

Dietary genistein supplementation for breeders and their offspring improves the growth performance and immune function of broilers

Genistein (GEN) is mainly extracted from soy plants and has potential functions as an antioxidant and in promoting immune function and growth. This study evaluated the effects of feeding breeders and their offspring dietary GEN on the immune function and growth performance of broiler chicks. Breeders were assigned to a control diet or GEN diet (control diet +400 mg/kg GEN), and their offspring were fed a control diet or GEN diet (control diet +40 mg/kg GEN). GEN treatment increased the body weight gain, tibial length, tibial width and slaughter performance of broilers and decreased the feed conversion ratio. The treatment also affected skeletal muscle myosin assembly and growth and increased growth hormone levels and IGF-I and IGFBP1 expression. Following GEN treatment, antigen processing and presentation, macrophage activation, B lymphocyte, NK cell and helper T cell proliferation, and CD4+ T lymphocyte differentiation all increased significantly. Increases were also observed in IgM and IgG concentrations, antibody titers, and antioxidant capacity. In addition, GEN treatment activated the Toll-like receptor signaling pathway and MAPK cascade signaling pathway. In summary, dietary GEN supplementation for breeders and their offspring can improve the growth performance and immune function of broiler chicks.

Viruses causing severe acute respiratory infections (SARI) in children ≤5 years of age at a tertiary care hospital in Rajasthan, India

BACKGROUND & OBJECTIVES

Severe acute respiratory infection (SARI) is one of the leading causes of death among children worldwide. As different respiratory viruses exhibit similar symptoms, simultaneous detection of these viruses in a single reaction mixture can save time and cost. The present study was done in a tertiary care children's hospital for rapid identification of viruses causing SARI among children less than or equal to five years of age using multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) kit.

METHODS

A total of 155 throat swabs were collected from equal number of children suspected to have SARI and processed for extraction of nucleic acids using automated extraction system. Multiplex real-time RT-PCR was done to identify the viruses in the samples.

RESULTS

The overall positivity for viruses in the study was found to be 72.9 per cent with a co-infection rate of 19.5 per cent. Human metapneumovirus (HMPV) was the predominant virus detected in 25.7 per cent children followed by influenza A (H1N1)pdm09, human rhinovirus (HRV) and human adenovirus (HAdV) in 19.9, 11.0 and 8.8 per cent children, respectively. The HMPV was at its peak in February 2013, HAdV showed two peaks in March-April, 2012 and November 2012-March 2013 while HRV was detected throughout the year.

INTERPRETATION & CONCLUSIONS

Multiplex real-time PCR helped in rapid identification of viruses. Seventeen viruses were detected in SARI cases with overall positivity of 72.9 per cent. HMPV was the most predominant virus. However, for better clinico-virological correlation, studies are required with complete work up of all the aetiological agents, clinical profile of patients and treatment outcome.

National burden of hospitalized and non-hospitalized influenza-associated severe acute respiratory illness in Kenya, 2012-2014

BACKGROUND

Influenza-associated respiratory illness was substantial during the emergence of the 2009 influenza pandemic. Estimates of influenza burden in the post-pandemic period are unavailable to guide Kenyan vaccine policy.

OBJECTIVES

To update estimates of hospitalized and non-hospitalized influenza-associated severe acute respiratory illness (SARI) during a post-pandemic period (2012-2014) and describe the incidence of disease by narrow age categories.

METHODS

We used data from Siaya County Referral Hospital to estimate age-specific base rates of SARI. We extrapolated these base rates to other regions within the country by adjusting for regional risk factors for acute respiratory illness (ARI), regional healthcare utilization for acute respiratory illness, and the proportion of influenza-positive SARI cases in each region, so as to obtain region-specific rates.

RESULTS

The mean annual rate of hospitalized influenza-associated SARI among all ages was 21 (95% CI 19-23) per 100 000 persons. Rates of non-hospitalized influenza-associated SARI were approximately 4 times higher at 82 (95% CI 74-90) per 100 000 persons. Mean annual rates of influenza-associated SARI were highest in children <2 years of age with annual hospitalization rates of 147 (95% CI of 134-160) per 100 000 persons and non-hospitalization rates of 469 (95% CI 426-517) per 100 000 persons. For the period 2012-2014, there were between 8153 and 9751 cases of hospitalized influenza-associated SARI and 31 785-38 546 cases of non-hospitalized influenza-associated SARI per year.

CONCLUSIONS

The highest burden of disease was observed among children <2 years of age. This highlights the need for strategies to prevent influenza infections in this age group.

Respiratory syncytial and influenza viruses in children under 2 years old with severe acute respiratory infection (SARI) in Maputo, 2015

Introduction

Although respiratory syncytial virus (RSV) and influenza virus (influenza) infections are one of the leading causes of Severe Acute Respiratory Infections (SARI) and death in young children worldwide, little is known about the burden of these pathogens in Mozambique.

Material and methods

From January 2015 to January 2016, nasopharyngeal swabs from 450 children, aged ≤2 years, who had been admitted to the Pediatric Department of the Maputo Central Hospital (HCM) in Mozambique, suffering with SARI were enrolled and tested for influenza and RSV using a real-time PCR assay.

Results

Influenza and RSV were detected in 2.4% (11/450) and 26.7% (113/424) of the participants. Children with influenza were slightly older than those infected with RSV (10 months in influenza-infected children compared to 3 months in RSV-infected children); male children were predominant in both groups (63.6% versus 54.9% in children with influenza and RSV, respectively). There was a trend towards a higher frequency of influenza (72.7%) and RSV (93.8%) cases in the dry season. Bronchopneumonia, bronchitis and respiratory distress were the most common diagnoses at admission. Antibiotics were administered to 27,3% and 15,9% of the children with influenza and RSV, respectively. Two children, of whom, one was positive for RSV (aged 6 months) and another was positive for Influenza (aged 3 months) died; both were children of HIV seropositive mothers and had bronchopneumonia.

Conclusions

Our data demonstrated that RSV, and less frequently influenza, occurs in children with SARI in urban/sub-urban settings from southern Mozambique. The occurrence of deaths in small children suspected of being HIV-infected, suggests that particular attention should be given to this vulnerable population. Our data also provide evidence of antibiotics prescription in children with respiratory viral infection, which represents an important public health problem and calls for urgent interventions.

Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses

Background

Human adenoviruses (HAdVs) are highly contagious pathogens that are associated with a wide spectrum of human illnesses involving the respiratory tract. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases.

Methodology and results

From January 2012 to December 2015 swabs were collected from consenting ILI outpatients. Adenoviral detection is performed by rRT-PCR with the Anyplex^™ II RV16 Detection kit (Seegene) and molecular characterization was performed using a partial hexon gene sequence. 6381 samples were collected. More than half of patients (51.7%; 3297/6381) were children of ≤ 5 years. 1967 (30.8%) were positive for HAdV with 1561 (79.4%) found in co-infection with at least one another respiratory virus. The most common co-detections were with influenza viruses (53.1%; 1045/1967), rhinoviruses (30%; 591/1967), enteroviruses (18.5%; 364/1967) and RSV (13.5%; 266/1967). Children under 5 were the most infected group (62.2%; 1224/1967; p <0.05). We noted that HAdV was detected throughout the year at a high level with detection peaks of different amplitudes without any clear seasonality. Phylogenetic analysis revealed species HAdV-C in majority, species HAdV-B and one HAdV- 4 genome type. The 9 HAdV-B species like strains from Senegal grouped with genome types HAdV-7, HAdV-55 and HAdV-11 as shown by a phylogenetic branch with a high bootstrap value of (88%).

Conclusion

In conclusion, the results of the present study suggest strong year-round HAdV activity in Senegal, especially in children up to 5 years of age. Molecular studies revealed that the dominant species in circulation in patients with ILI appears to be HAdV-C and HAdV-B species. The circulation of though HAdV-7 and HAdV-55 genome types is of note as these serotypes are recognized causes of more severe and even fatal acute respiratory infections.

Etiology of Acute Respiratory Infections in Infants: A Prospective Birth Cohort Study

BACKGROUND

There is paucity of studies on etiology of acute respiratory infections (ARI) in infants. The objective of this study is to document incidence and etiology of ARI in infants, their seasonal variability and association of clinical profile with etiology.

METHODS

A birth cohort was followed for the first year of life; for each episode of ARI, nasopharyngeal aspirates were collected to identify the causative respiratory virus(es) using multiplex real-time polymerase chain reaction assay. For lower respiratory tract infections blood culture, serum procalcitonin, serum antibodies to Mycoplasma and Chlamydia and urinary Streptococcus pneumoniae antigen were also assayed.

RESULTS

A total of 503 ARI episodes were documented in 310 infants for an incidence rate of 1.8 episodes per infant per year. Of these, samples were processed in 395 episodes (upper respiratory tract infection: 377; lower respiratory tract infection: 18). One or more viruses were detected in 250 (63.3%) episodes and viral coinfections in 72 (18.2%) episodes. Rhinovirus was the most common virus [105 (42%)] followed by respiratory syncytial virus [50 (20%)], parainfluenza virus [42 (16.8%)] and coronavirus [44 (17.6%)]. In lower respiratory tract infections, viral infections were detected in 12 (66.7%) episodes, bacterial infections in 17 (94.4%) episodes and mixed bacterial-viral infections in 8 (44.4%) episodes. Peak incidence of viruses was observed during February-March and September-November. There was no significant difference in symptom duration with virus types.

CONCLUSION

In this cohort of infants, ARI incidence was 1.8 episodes per year per infant; 95% were upper respiratory tract infections. Viruses were identified in 63.3% episodes, and the most common viruses detected were rhinovirus, respiratory syncytial virus and parainfluenza virus.

Clinical characteristics and viral load of respiratory syncytial virus and human metapneumovirus in children hospitaled for acute lower respiratory tract infection

Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are two common viral pathogens in acute lower respiratory tract infections (ALRTI). However, the association of viral load with clinical characteristics is not well‐defined in ALRTI. To explore the correlation between viral load and clinical characteristics of RSV and HMPV in children hospitalized for ALRTI in Lanzhou, China. Three hundred and eighty‐seven children hospitalized for ALRTI were enrolled. Nasopharyngeal aspirates (NPAs) were sampled from each children. Real‐time PCR was used to screen RSV, HMPV, and twelve additional respiratory viruses. Bronchiolitis was the leading diagnoses both in RSV and HMPV positive patients. A significantly greater frequency of wheezing (52% vs. 33.52%, P = 0.000) was noted in RSV positive and negative patients. The RSV viral load was significant higher in children aged <1 year (P = 0.003), children without fever and wheezing (P = 0.015 and P = 0.000), days of illness <14 days (P = 0.002), children with bronchiolitis (P = 0.012) and children with RSV single infections (P = 0.000). No difference was found in the clinical features of HMPV positive and negative patients. The HMPV viral load had no correlation with any clinical characteristics. The incidences of severe disease were similar between single infection and coinfection for the two viruses (RSV, P = 0.221; HMPV, P = 0.764) and there has no statistical significance between severity and viral load (P = 0.166 and P = 0.721). Bronchiolitis is the most common disease caused by RSV and HMPV. High viral load or co‐infection may be associated with some symptoms but neither has a significant impact on disease severity for the two viruses. J. Med. Virol. 89:589–597, 2017. © 2016 Wiley Periodicals, Inc.

Population-based Surveillance for Medically Attended Human Parainfluenza Viruses From the Influenza Incidence Surveillance Project, 2010-2014

BACKGROUND

Parainfluenza viruses (PIV) have been shown to contribute substantially to pediatric hospitalizations in the United States. However, to date, there has been no systematic surveillance to estimate the burden among pediatric outpatients.

METHODS

From August 2010 through July 2014, outpatient health care providers with enumerated patient populations in 13 states and jurisdictions participating in the Influenza Incidence Surveillance Project conducted surveillance of patients with influenza-like illness (ILI). Respiratory specimens were collected from the first 10 ILI patients each week with demographic and clinical data. Specimens were tested for multiple respiratory viruses, including PIV1-4, using reverse transcriptase-polymerase chain reaction assays. Cumulative incidence was calculated using provider patient population size as the denominator.

RESULTS

PIVs 1-3 were detected in 8.0% of 7716 ILI-related outpatient specimens: 30% were PIV1, 26% PIV2 and 44% PIV3. PIV circulation varied noticeably by year and type, with PIV3 predominating in 2010-2011 (incidence 110 per 100,000 children), PIV1 in 2011-2012 (89 per 100,000), dual predominance of PIV2 and PIV3 (88 and 131 per 100,000) in 2012-2013 and PIV3 (100 per 100,000) in 2013-2014. The highest incidence of PIV detections was among patients aged <5 years (259-1307 per 100,000). The median age at detection for PIV3 (3.4 years) was significantly lower than the median ages for PIV1 (4.5 years) and PIV2 (7.0 years; P < 0.05).

CONCLUSIONS

PIVs 1-3 comprise a substantial amount of medically attended pediatric ILI, particularly among children aged <5 years. Distinct seasonal circulation patterns as well as significant differences in rates by age were observed between PIV types.

Human metapneumovirus epidemiological and evolutionary patterns in Coastal Kenya, 2007-11

BACKGROUND

Human metapneumovirus (HMPV) is an important global cause of severe acute respiratory infections in young children and the elderly. The epidemiology of HMPV in sub-Saharan Africa is poorly described and factors that allow its recurrent epidemics in communities not understood.

METHODS

We undertook paediatric inpatient surveillance for HMPV in Kilifi County Hospital (KCH) of Coastal Kenya between 2007 and 2011. Nasopharyngeal samples collected from children aged 1 day-59 months admitted with severe or very severe pneumonia, were tested for HMPV using real-time polymerase chain reaction (RT-PCR). Partial nucleotide sequences of the attachment (G) and fusion (F) surface proteins of positive samples were determined and phylogenetically analyzed.

RESULTS

HMPV was detected in 4.8 % (160/3320) of children [73.8 % (118/160) of these less than one year of age], ranging between 2.9 and 8.8 % each year over the 5 years of study. HMPV infections were seasonal in occurrence, with cases predominant in the months of November through April. These months frequently coincided with low rainfall, high temperature and low relative humidity in the location. Phylogenetic analysis of partial F and G sequences revealed three subgroups of HMPV, A2 (74 %, 91/123), B1 (3.2 %, 4/123) and B2 (22.8 %, 28/123) in circulation, with subgroup A2 predominant in majority of the epidemic seasons. Comparison of G sequences (local and global) provided a greater phylogenetic resolution over comparison of F sequences and indicated presence of probable multiple G antigenic variants within the subgroups due to differences in amino acid sequence, encoded protein length and glycosylation patterns.

CONCLUSION

The present study reveals HMPV is an important seasonal contributor to respiratory disease hospitalization in coastal Kenya, with an evolutionary pattern closely relating to that of respiratory syncytial virus.

Maternal vaccination for the prevention of influenza: current status and hopes for the future

Influenza is an important cause of morbidity and mortality among pregnant women and young infants, and influenza infection during pregnancy has also been associated with adverse obstetric and birth outcomes. There is substantial evidence - from randomized trials and observational studies - that maternal influenza immunization can protect pregnant women and their infants from influenza disease. In addition, there is compelling observational evidence that prevention of influenza in pregnant women can also protect against certain adverse pregnancy outcomes, including stillbirth and preterm birth. In this article we will review and evaluate the literature on both the burden of influenza disease in pregnant women and infants, as well as the multiple potential benefits of maternal influenza immunization for mother, fetus, and infant. We will also review key clinical aspects of maternal influenza immunization, as well as identify remaining knowledge gaps, and discuss avenues for future investigation.

Solid fuel in kitchen and acute respiratory tract infection among under five children: evidence from Nepal demographic and health survey 2011

This study assessed the association between use of solid fuel in kitchen and ARI among under five children in Nepal. The latest data from the Nepal Demographic and Health Survey 2011 were used. A total of 4,802 under 5 de-jure children were included in this analysis. Cough accompanied by short/rapid breath and chest problem within 2 weeks before survey was considered as the symptoms of ARI. Logistic regression analysis was performed to calculate the odds of being suffered from ARI among the children from households using solid fuel in comparison to the children from households using cleaner fuel. About 84.6% of the families used solid fuel as a primary fuel. Approximately 4.5% children had symptoms of ARI within 2 weeks before the survey. About 3.4 and 4.9% of children from the families using cleaner fuel and solid fuel respectively had symptoms of ARI within 2 weeks preceding survey. After adjusting for age, sex, birth order, urban/rural residence, ecological zone, development region, economic status, number of family members, mother's smoking status and mother's education, odds of suffering from ARI was 1.79 times higher among the children from the households using solid fuel in comparison to the children from households using cleaner fuel (95% CI 1.02, 3.14). This study found the use of solid fuel in the kitchen has as a risk factor for ARI among under five children in Nepal. Longitudinal studies with direct measurement of indoor air pollution and clinical ARI cases can be future research priority.

Management of septic shock and severe infections in migrants and returning travelers requiring critical care

During the past decade, global human movement created a virtually "borderless world". Consequently, the developed world is facing "forgotten" and now imported infectious diseases. Many infections are observed upon travel and migration, and the clinical spectrum is diverse, ranging from asymptomatic infection to severe septic shock. The severity of infection depends on the etiology and timeliness of diagnosis. While assessing the etiology of severe infection in travelers and migrants, it is important to acquire a detailed clinical history; geography, dates of travel, places visited, type of transportation, lay-overs and intermediate stops, potential exposure to exotic diseases, and activities that were undertaken during travelling and prophylaxis and vaccines either taken or not before travel are all important parameters. Tuberculosis, malaria, pneumonia, visceral leishmaniasis, enteric fever and hemorrhagic fever are the most common etiologies in severely infected travelers and migrants. The management of severe sepsis and septic shock in migrants and returning travelers requires a systematic approach in the evaluation of these patients based on travel history. Early and broad-spectrum therapy is recommended for the management of septic shock comprising broad spectrum antibiotics, source control, fluid therapy and hemodynamic support, corticosteroids, tight glycemic control, and organ support and monitoring. We here review the diagnostic and therapeutic routing of severely ill travelers and migrants, stratified by the nature of the infectious agents most often encountered among them.

Sendai virus as a backbone for vaccines against RSV and other human paramyxoviruses

Human paramyxoviruses are the etiological agents for life-threatening respiratory virus infections of infants and young children. These viruses, including respiratory syncytial virus (RSV), the human parainfluenza viruses (hPIV1-4) and human metapneumovirus (hMPV), are responsible for millions of serious lower respiratory tract infections each year worldwide. There are currently no standard treatments and no licensed vaccines for any of these pathogens. Here we review research with which Sendai virus, a mouse parainfluenza virus type 1, is being advanced as a Jennerian vaccine for hPIV1 and as a backbone for RSV, hMPV and other hPIV vaccines for children.

Etiology and Incidence of Viral Acute Respiratory Infections Among Refugees Aged 5 Years and Older in Hagadera Camp, Dadaab, Kenya

We used the Centers for Disease Control and Prevention-Kenya Medical Research Institute Acute Respiratory Infection (ARI) Surveillance System data to estimate severe acute respiratory infection (SARI) hospitalization rates, viral etiology, and associated complaints of influenza-like illnesses (ILI) and SARI conditions among those aged 5 years and older in Hagadera, Dadaab refugee camp, Kenya, for 2010-2012. A total of 471 patients aged ≥ 5 years met the case definition for ILI or SARI. SARI hospitalization rates per 10,000 person-years were 14.7 (95% confidence interval [CI] = 9.1, 22.2) for those aged 5-14 years; 3.4 (95% CI = 1.6, 7.2) for those aged 15-24 year; and 3.8 (95% CI = 1.6, 7.2) for those aged ≥ 25 years. Persons between the ages of 5 and 14 years had 3.5 greater odds to have been hospitalized as a result of SARI than those aged ≥ 25 years (odds ratio [OR] = 3.5, P < 0.001). Among the 419 samples tested, 169 (40.3%) were positive for one or more virus. Of those samples having viruses, 36.9% had influenza A; 29.9% had adenovirus; 20.2% had influenza B; and 14.4% had parainfluenza 1, 2, or 3. Muscle/joint pain was associated with influenza A (P = 0.002), whereas headache was associated with influenza B (P = 0.019). ARIs were responsible for a substantial disease burden in Hagadera camp.

Influenza-Associated Disease Burden in Kenya: A Systematic Review of Literature

Background

In Kenya data on the burden of influenza disease are needed to inform influenza control policies.

Methods

We conducted a systematic review of published data describing the influenza disease burden in Kenya using surveillance data collected until December 2013. We included studies with laboratory confirmation of influenza, well-defined catchment populations, case definitions used to sample patients for testing and a description of the laboratory methods used for influenza testing. Studies with or without any adjustments on the incidence rates were included.

Results

Ten studies reporting the incidence of medically-attended and non-medically attended influenza were reviewed. For all age groups, the influenza positive proportion ranged from 5–10% among hospitalized patients, and 5–27% among all medically-attended patients (a combination of in- and outpatients). The adjusted incidence rate of hospitalizations with influenza among children <5 years ranged from 2.7–4.7 per 1,000 [5.7 per 1,000 in children <6 months old], and were 7–10 times higher compared to persons aged ≥5 years. The adjusted incidence of all medically-attended influenza among children aged <5 years ranged from 13.0–58.0 per 1,000 compared to 4.3–26.0 per 1,000 among persons aged ≥5 years.

Conclusions

Our review shows an expanding set of literature on disease burden associated with influenza in Kenya, with a substantial burden in children under five years of age. Hospitalizations with influenza in these children were 2–3 times higher than reported in the United States. These findings highlight the possible value of an influenza vaccination program in Kenya, with children <5 years and pregnant women being potentially important targets.

Prevalence of human respiratory syncytial virus circulating in Iran

Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infection during early childhood and is associated with a great burden on patients, parents, and society. While no treatment is yet available, results from recent phase 2 clinical trials of cell-entry inhibitors and RSV vaccines are promising. To prepare for introduction of these novel therapeutics, good understanding of its molecular epidemiology and continuous RSV surveillance data are necessary. This paper provides an overview of RSV prevalence and genotype distribution in Iran from 1996 to 2013. This meta-analysis includes 21 published studies. In total, 775 (18.7%) of 4140 respiratory specimens were positive for RSV infection. The male-female ratio of RSV-positive patients was 1.5:1. Significant peaks of RSV infection were detected during the cold season (November-March). RSV infection was mainly observed in patients <2 years of age. Phylogenetic studies showed that genotypes GA1, GA2, GA5, and BA co-circulated in Iran in 2007-2013. This review highlights the necessity of introducing standard molecular surveillance programs to inform the epidemiological, clinical, and pathological characteristics of various RSV genotypes. Improved understanding of the molecular epidemiology will be useful for development of novel RSV therapeutics.

Viral coinfection in acute respiratory infection in Mexican children treated by the emergency service: A cross-sectional study

Background

Acute respiratory infections (ARIs) cause illness. Children under five years of age are highly vulnerable to these infections. Viral coinfection or multiple viral infection is a variable that can have a significant impact on the evolution of these diseases.

Methods

This cross-sectional study was carried out in Mexican children (under five years of age) who had an ARI and who were treated by an emergency service in a hospital in Guadalajara, Jalisco, Mexico. The viral etiology, as well as the presence of multiple viral infections, was determined. A structured questionnaire was used to obtain demographic and clinical information. Odds ratio (OR) was calculated, and univariate and multivariate analyses using logistic regression were performed.

Results

In the study population, metapneumovirus (hMPV) was the most frequent virus (22%), followed by adenovirus (hAD) (16%), respiratory syncytial virus (RSV) (14%), rhinovirus (hRV) (12%), bocavirus (hBoV) (9%), influenza virus (IF) (7%), and parainfluenza (PIF) (4%). The frequency of viral coinfections was 31.62%, and multiple logistic regression analysis revealed that hMPV, RSV, PIF, and hBoV were independently associated with multiple viral infection. No difference was found in the clinical manifestation of children with simple and multiple infections. Simple hMPV infection was associated with patients who presented with severe ARI. Using a multivariate analysis, we found that overcrowding is associated with coinfection when the viral etiology was hRV (OR = 2.56, 95% confidence interval (CI) 1.07 to 6.13), IF (OR = 2.56, 95% CI 1.07 to 6.13), PIF (OR = 2.96, 95% CI 1.15 to 7.65), hAD (OR = 2.56, 95% CI 1.07 to 6.13), and hBoV (OR = 2.9, 95% CI 1.14 to 7.34).

Conclusions

Viral coinfections are frequent in children requiring treatment by an emergency service. However, the severity of ARI is similar to that of children with a simple infection. The hMPV is common and may confer a significant disease burden in the Mexican population. Finally, overcrowding is a housing characteristic that favors the development of coinfections.

Electronic supplementary material

The online version of this article (doi:10.1186/s13052-015-0133-7) contains supplementary material, which is available to authorized users.

Identification of viral and bacterial pathogens from hospitalized children with severe acute respiratory illness in Lusaka, Zambia, 2011-2012: a cross-sectional study

BACKGROUND

Morbidity and mortality from respiratory infections are higher in resource-limited countries than developed countries, but limited studies have been conducted in resource-limited settings to examine pathogens from patients with acute respiratory infections. Influenza surveillance has been conducted in Zambia since 2008; however, only 4.3% of patients enrolled in 2011-2012 were positive for influenza. Therefore, we examined non-influenza respiratory pathogens in children with severe acute respiratory illness (SARI) in Zambia, to estimate the scope of disease burden and determine commonly-identified respiratory pathogens.

METHODS

Two reverse transcriptase polymerase chain reaction (rRT-PCR) methods (single and multiplex) were used to analyze nasopharyngeal and throat swabs collected from SARI cases under five years of age from January 2011 through December 2012. All specimens were negative for influenza by rRT-PCR. The panel of singleplex reactions targeted seven viruses, while the multiplex assay targeted thirty-three bacteria, fungi, and viruses.

RESULTS

A set of 297 specimens were tested by singleplex rRT-PCR, and a different set of 199 were tested by multiplex rRT-PCR. Using the singleplex assay, 184/297 (61.9%) specimens were positive for one or more viruses. The most prevalent viruses were human rhinovirus (57/297; 19.2%), human adenovirus (50/297; 16.8%), and respiratory syncytial virus (RSV) (45/297; 15.2%). Using multiplex PCR, at least one virus was detected from 167/199 (83.9%) specimens, and at least one bacteria was detected from 197/199 (99.0%) specimens. Cytomegalovirus (415/199; 208.5%) and RSV (67/199; 33.7%) were the most commonly detected viruses, while Streptococcus pneumonie (109/199; 54.8%) and Moraxella catarrhalis (92/199; 46.2%) were the most commonly detected bacteria.

CONCLUSIONS

Single infections and co-infections of many viruses and bacteria were identified in children with SARI. These results provide an estimate of the prevalence of infection and show which respiratory pathogens are commonly identified in patients. Further studies should investigate causal associations between individual pathogens and SARI.

Influenza pneumonia surveillance among hospitalized adults may underestimate the burden of severe influenza disease

Background

Studies seeking to estimate the burden of influenza among hospitalized adults often use case definitions that require presence of pneumonia. The goal of this study was to assess the extent to which restricting influenza testing to adults hospitalized with pneumonia could underestimate the total burden of hospitalized influenza disease.

Methods

We conducted a modelling study using the complete State Inpatient Databases from Arizona, California, and Washington and regional influenza surveillance data acquired from CDC from January 2003 through March 2009. The exposures of interest were positive laboratory tests for influenza A (H1N1), influenza A (H3N2), and influenza B from two contiguous US Federal Regions encompassing the study area. We identified the two outcomes of interest by ICD-9-CM code: respiratory and circulatory hospitalizations, as well as critical illness hospitalizations (acute respiratory failure, severe sepsis, and in-hospital death). We linked the hospitalization datasets with the virus surveillance datasets by geographic region and month of hospitalization. We used negative binomial regression models to estimate the number of influenza-associated events for the outcomes of interest. We sub-categorized these events to include all outcomes with or without pneumonia diagnosis codes.

Results

We estimated that there were 80,834 (95% CI 29,214–174,033) influenza-associated respiratory and circulatory hospitalizations and 26,760 (95% CI 14,541–47,464) influenza-associated critical illness hospitalizations. When a pneumonia diagnosis was excluded, the estimated number of influenza-associated respiratory and circulatory hospitalizations was 24,816 (95% CI 6,342–92,624). The estimated number of influenza-associated critical illness hospitalizations was 8,213 (95% CI 3,764–20,799). Around 30% of both influenza-associated respiratory and circulatory hospitalizations, as well as influenza-associated critical illness hospitalizations did not have pneumonia diagnosis codes.

Conclusions

Surveillance studies which only consider hospitalizations that include a diagnosis of pneumonia may underestimate the total burden of influenza hospitalizations.