Severe Acute Respiratory Infection Patients Research Articles

Combining Procalcitonin and Rapid Multiplex Respiratory Virus Testing for Antibiotic Stewardship in Older Adult Patients With Severe Acute Respiratory Infection

ObjectivesVirus infection is underevaluated in older adults with severe acute respiratory infections (SARIs). We aimed to evaluate the clinical impact of combining point-of-care molecular viral test and serum procalcitonin (PCT) level for antibiotic stewardship in the emergency department (ED). DesignA prospective twin-center cohort study was conducted between January 2017 and March 2018. Setting and ParticipantsOlder adult patients who presented to the ED with SARIs received a rapid molecular test for 17 respiratory viruses and a PCT test. MeasuresTo evaluate the clinical impact, we compared the outcomes of SARI patients between the experimental cohort and a propensity score–matched historical cohort. The primary outcome was the proportion of antibiotics discontinuation or de-escalation in the ED. The secondary outcomes included duration of intravenous antibiotics, length of hospital stay, and mortality. ResultsA total of 676 patients were included, of which 169 patients were in the experimental group and 507 patients were in the control group. More than one-fourth (27.9%) of the patients in the experimental group tested positive for virus. Compared with controls, the experimental group had a significantly higher proportion of antibiotics discontinuation or de-escalation in the ED (26.0% vs 16.1%, P = .007), neuraminidase inhibitor uses (8.9% vs 0.6%, P < .001), and shorter duration of intravenous antibiotics (10.0 vs 14.5 days, P < .001). Conclusions and ImplicationsCombining rapid viral surveillance and PCT test is a useful strategy for early detection of potential viral epidemics and antibiotic stewardship. Clustered viral respiratory infections in a nursing home is common. Patients transferred from nursing homes to ED may benefit from this approach.

2209. Charlson Comorbidity Index Scores and In-hospital Prognosis in Severe Acute Respiratory Infections Patients

BackgroundRespiratory infections are one of the leading causes of mortality, and comorbid conditions play a significant role in the severity and fatality of these infections. The Charlson Comorbidity index (CCI) is the most used comorbidity index, presenting a few updated versions since its establishment. In the present study, we evaluated the CCI score and possible predictors of mortality in hospitalized patients with Severe Acute Respiratory Infection (SARI), aiming to test whether the CCI is a valid in-hospital prognostic indicator.MethodsPatients older than 14 years, hospitalized from 2010 to 2016 due to SARI by viral infection, and who were submitted to respiratory virus testing were included. We assessed comorbidity retrospectively through chart review, and calculated 4 variants of the CCI.ResultsOf the 291 patients assessed, 72.8% (n = 212) presented comorbidities and 24% died (n = 70). The most recurrent comorbidities were Chronic Pulmonary Disease (n = 76/212, 36%) and HIV (n = 50/212, 23.6%). Respiratory virus testing was positive in 38.1% of patients (n = 111), Influenza and Rhinoviruses being the most frequent. The 1994 Age-adjusted CCI predicted in-hospital mortality in SARI patients (P = 0.04), and HIV was independently associated with in-hospital mortality (P = 0.032).ConclusionThe comorbidity scores used to assess mortality risk in hospitalized patients with SARI displayed poor results, but HIV infection was considered a marker of severity. However, other factors should be considered in order to compose a scoring system that allows us to specifically assess the risk of mortality in patients with SARI. Disclosures All authors: No reported disclosures.

Epidemiology of Severe Acute Respiratory Infection (SARI) Cases at a sentinel site in Egypt, 2013-15.

BackgroundSentinel surveillance for severe acute respiratory infection (SARI) in Egypt began in 2006 and occurs at eight sites. Avian influenza is endemic, and human cases of influenza A (H5N1) have been reported annually since 2006. This study aimed to describe the epidemiology of SARI at a major sentinel site in the country.MethodsData included in the study were collected from a major SARI sentinel site in Egypt during three consecutive years (2013–15).ResultsA total of 1254 SARI patients conforming to the WHO case definition were admitted to the sentinel site, representing 5.6% of admitted patients for all causes and 36.6% of acute respiratory infection patients. A total of 99.7% of the patients were tested, and 21.04% tested positive; 48.7% of cases involved influenza A viruses, while 25% involved influenza B. The predominant age group was under 5 years of age, accounting for 443 cases. The seasonality of the influenza data conformed to the Northern Hemisphere pattern.ConclusionsThe present study’s results show that SARI leads to substantial morbidity in Egypt. There is a great need for high-quality data from the SARI surveillance system in Egypt, especially with endemic respiratory threats such as influenza A (H5N1) in Egypt.

Epidemiology and costs of severe acute respiratory infection and influenza hospitalizations in adults with diabetes in India.

The incidence of diabetes mellitus is increasing rapidly in India. In addition to well-known complications, diabetes increases the risk for hospitalization and death from severe acute respiratory infection (SARI) and influenza. Here we examined the impact of SARI and influenza in Indian adults with diabetes. This was a single-center, active surveillance study conducted in Jammu and Kashmir State, India, during the 2015-2016 and 2016-2017 influenza seasons. Adults hospitalized for SARI and receiving at least one diabetes medication were included. Demographics, health care use, and direct costs were collected from medical records and interviews of patients or caregivers. Indirect costs were estimated based on lost earnings and WHO-CHOICE estimates for hospital costs. The study included 192 patients with type 2 diabetes. Median age was 66 years, median body mass index was 26.6 kg/m2, and most patients had comorbidities, especially hypertension and cardiovascular disease (83.9%). Only 32.2% regularly monitored blood glucose or hemoglobin A1C, and median values at admission indicated poor glycemic control for most. Influenza was detected in 8.9% of cases. The median hospital stay for SARI was 8 days, and 22 patients (11.4%) died. Median total costs associated with hospitalization were US$710 (interquartile range, $539-$1067) for SARI patients and US$716 ($556-$1078) for influenza patients, mostly (~75%) from indirect costs. Adults with diabetes in India hospitalized with SARI or influenza are generally older, in poor health, and suffer from poor glycemic control. The costs for their hospitalization and care are substantial.

The effectiveness of influenza vaccination in preventing hospitalizations in elderly in Beijing, 2016–18

BackgroundInfluenza vaccinations play an important role in preventing influenza related hospitalizations. The objective of this study was to estimate the effectiveness of vaccination in protecting Beijing residents aged ≥60 years from influenza related hospitalizations during the 2016/17 and 2017/18 influenza seasons. MethodsPatients who met the definition of severe acute respiratory infection (SARI) and were hospitalized in the nine sentinel hospitals in Beijing during the 2016/17 and 2017/18 influenza seasons were identified as the study population. The vaccination status of patients was obtained from a vaccination registry. Real-time reversetranscription polymerasechainreaction (RT-PCR) experiments were conducted to test pharyngeal or lower respiratory tract samples collected from SARI patients for influenza A and B viruses. Vaccine effectiveness (VE) was examined using a test-negative design that compare the odds of vaccination among influenza positives and negatives, adjusting for calendar week of illness onset, age, and underlying medical conditions. ResultsWe identified 50,364 patients in the study, in which there were 145 influenza cases and 528 influenza-negative controls aged ≥60 years in 2016/17 season and 149 cases and 358 controls aged ≥60 years in 2017/18 season. The most commonly identified subtype among participants was influenza A(H3N2) in 2016/17 and 2017/18 season (78.5% and 70.6%). Among the adults aged ≥60 years, the adjusted VE of vaccination against any influenza virus for serious acute respiratory infection (SARI) patients was 32.8% (95% confidence interval [CI]: −22.0 to 63.0%) in 2016/17 season. While the adjusted VE in 2017/18 season were 4.6% (95% CI: −72.4 to 47.2%) against any types of influenza, 29.2% (95% CI: −92.9 to 74%) against influenza A(H1N1)pdm09, −37.7% (95% CI: −293.8; 51.9%) against influenza A(H3N2) viruses, and 3.6% (95% CI: −113.8 to 56.5%) against influenza B. ConclusionThe influenza vaccine provided moderate protection in 2016/17 season and mild protection in 2017/18 season for influenza related inpatients of adults aged ≥60 years in Beijing.

Severe Acute Respiratory Infections With Influenza and Noninfluenza Respiratory Viruses: Yemen, 2011-2016.

In 2010, Yemen started the surveillance for severe acute respiratory infections (SARIs) by establishing 2 sentinel sites in Sana’a and Aden city. This study aims to determine the proportions of influenza and noninfluenza viruses among SARI patients and to determine the severity of SARI and its associated factors. The data of SARI patients who were admitted to SARI surveillance sites at Al Johory hospital in Sana’a and Al Wahdah hospital in Aden city during the period 2011-2016 were analyzed. The proportions of positive influenza viruses (type A, B) and noninfluenza viruses (respiratory syncytial, adenovirus, human parainfluenza, and human metapneumovirus), intensive care unit (ICU) admission rate, and fatality rate among SARI patients were calculated. A total of 1811 of SARI patients were admitted during 2011-2016. Of those, 78% were <15 years old. A total of 89 (5%) patients had influenza viruses and 655 (36%) had noninfluenza viruses. The overall ICU admission rate was 40% and the case-fatality rate was 8%. Infection by influenza type (A, B) and mixed (adenovirus, human parainfluenza) was significantly associated with lower ICU admission. Age <15 years old, infection with influenza B, pre-existence of chronic diseases, and admission to Aden site were significantly associated with higher fatality rate among patients. In conclusion; SARI patients in Yemen had a high ICU admission and case-fatality rates. Influenza type B, chronic diseases, and admission to Aden site are associated with higher fatality rate. Expanding surveillance sites and panel of laboratory tests to involve other pathogens will help to provide accurate diagnosis for SARI etiology and give more comprehensive picture. Training staff for SARI case management will help to reduce severe outcomes.

Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013.

BackgroundFew comprehensive data exist regarding the epidemiology of severe acute respiratory infections (SARI) in low income countries. This study aimed at identifying etiologies and describing clinical features of SARI-associated hospitalization in Madagascar.MethodsIt is a prospective surveillance of SARI in 2 hospitals for 3 years. Nasopharyngeal swabs, sputum, and blood were collected from SARI patients enrolled and tested for viruses and bacteria. Epidemiological and clinical information were obtained from case report forms.ResultsOverall, 876 patients were enrolled in the study, of which 83.1% (728/876) were tested positive for at least one pathogen. Viral and bacterial infections occurred in 76.1% (667/876) and 35.8% (314/876) of tested samples, respectively. Among all detected viruses, respiratory syncytial virus (RSV) was the most common (37.7%; 348/924) followed by influenza virus A (FLUA, 18.4%; 170/924), rhinovirus (RV, 13.5%; 125/924), and adenovirus (ADV, 8.3%; 77/924). Among bacteria, Streptococcus pneumoniae (S. pneumoniae, 50.3%, 189/370) was the most detected followed by Haemophilus influenzae type b (Hib, 21.4%; 79/370), and Klebsiella (4.6%; 17/370). Other Streptococcus species were found in 8.1% (30/370) of samples. Compared to patients aged less than 5 years, older age groups were significantly less infected with RSV. On the other hand, patients aged more than 64 years (OR = 3.66) were at higher risk to be infected with FLUA, while those aged 15–29 years (OR = 3.22) and 30–64 years (OR = 2.39) were more likely to be infected with FLUB (influenza virus B).ConclusionThe frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. Amongst young children, the demonstrated burden of RSV should guide clinicians for a better case management of children. These findings reveal the need to develop point-of-care tests to avoid overuse of antibiotics and to promote vaccine that could reduce drastically the RSV hospitalizations.

The burden of influenza-associated respiratory hospitalizations in Bhutan, 2015-2016.

BackgroundInfluenza burden estimates help provide evidence to support influenza prevention and control programs. In this study, we estimated influenza‐associated respiratory hospitalization rates in Bhutan, a country considering influenza vaccine introduction.MethodsUsing real‐time reverse transcription‐polymerase chain reaction laboratory results from severe acute respiratory infection (SARI) surveillance, we estimated the proportion of respiratory hospitalizations attributable to influenza each month among patients aged <5, 5‐49, and ≥50 years in six Bhutanese districts for 2015 and 2016. We divided the sum of the monthly influenza‐attributed hospitalizations by the total of the six district populations to generate age‐specific rates for each year.ResultsIn 2015, 10% of SARI patients tested positive for influenza (64/659) and 18% tested positive (129/736) in 2016. The incidence of influenza‐associated hospitalizations among all age groups was 50/100 000 persons (95% confidence interval [CI]: 45‐55) in 2015 and 118/100 000 persons (95% CI: 110‐127) in 2016. The highest rates were among children <5 years: 182/100 000 (95% CI: 153‐210) in 2015 and 532/100 000 (95% CI: 473‐591) in 2016. The second highest influenza‐associated hospitalization rates were among adults ≥50 years: 110/100 000 (95% CI: 91‐130) in 2015 and 193/100 000 (95% CI: 165‐221) in 2016.ConclusionsInfluenza viruses were associated with a substantial burden of severe illness requiring hospitalization especially among children and older adults. These findings can be used to understand the potential impact of seasonal influenza vaccination in these age groups.

Overview of three influenza seasons in Georgia, 2014-2017.

BackgroundInfluenza epidemiological and virologic data from Georgia are limited. We aimed to present Influenza Like Illness (ILI) and Severe Acute Respiratory Infection (SARI) surveillance data and characterize influenza viruses circulating in the country over three influenza seasons.MethodsWe analyzed sentinel site ILI and SARI data for the 2014–2017 seasons in Georgia. Patients’ samples were screened by real-time RT-PCR and influenza viruses isolated were characterized antigenically by haemagglutination inhibition assay and genetically by sequencing of HA and NA genes.Results32% (397/1248) of ILI and 29% (581/1997) of SARI patients tested were positive for influenza viruses. In 2014–2015 the median week of influenza detection was week 7/2015 with B/Yamagata lineage viruses dominating (79%); in 2015–2016—week 5/2016 was the median with A/H1N1pdm09 viruses prevailing (83%); and in 2016–2017 a bimodal distribution of influenza activity was observed—the first wave was caused by A/H3N2 (55%) with median week 51/2016 and the second by B/Victoria lineage viruses (45%) with median week 9/2017. For ILI, influenza virus detection was highest in children aged 5–14 years while for SARI patients most were aged >15 years and 27 (4.6%) of 581 SARI cases died during the three seasons. Persons aged 30–64 years had the highest risk of fatal outcome, notably those infected with A/H1N1pdm09 (OR 11.41, CI 3.94–33.04, p<0.001). A/H1N1pdm09 viruses analyzed by gene sequencing fell into genetic groups 6B and 6B.1; A/H3N2 viruses belonged to genetic subclades 3C.3b, 3C.3a, 3C.2a and 3C.2a1; B/Yamagata lineage viruses were of clade 3 and B/Victoria lineage viruses fell in clade1A.ConclusionIn Georgia influenza virus activity occurred mainly from December through March in all seasons, with varying peak weeks and predominating viruses. Around one third of ILI/ SARI cases were associated with influenza caused by antigenically and genetically distinct influenza viruses over the course of the three seasons.

Preliminary results of official influenza and acute respiratory infection surveillance in two towns of Burkina Faso, 2013\u20132015

BackgroundIn 2010, influenza, influenza-like illness (ILI) and acute respiratory infection (ARI) surveillance was established by the government of Burkina Faso. We provide preliminary descriptive results from this surveillance activity.MethodsThe study period was 2013 through 2015. Two primary healthcare facilities in Bobo-Dioulasso district reported ILI in outpatients. Influenza virology, using reverse transcription-polymerase chain reaction (rRT-PCR), was available for a proportion of ILI patients. One hospital, in the capital Ouagadougou, reported ARI in both outpatients and inpatients (hospitalized). Inpatients admitted with ARI were considered severe ARI (SARI). We estimated the proportion of primary care outpatient visits that were ILI, and the proportion of those that were due to influenza, by age. We estimated the proportion of hospital outpatient visits that were ARI and the proportion of those that were SARI, by age.ResultsAmong combined outpatient visits in the Bobo-Dioulasso facilities, 19.6% were for ILI. One half (49.9%) of outpatient visits in infants and 30.9% in 1–4 year-olds were ILI. Among ILI outpatient visits 14.8% were due to influenza virus and, of these, 58.5% were type A and 41.5% type B. At the Ouagadougou hospital, 6.7% of outpatient visits were ARI, and 22.3% of those were SARI. The highest proportions of ARI were among infants (19.8%) and 1–4 year-olds (16.0%). The proportion of ARI that was SARI was highest among ≥15 year-olds (31.5%) followed by 1–4 year-olds (22.4%). Overall, 4.1% of SARI patients died.ConclusionsThese preliminary data indicate the importance of respiratory infections among health care attendances in Burkina Faso, and influenza may be an important contributor to these.

Comparison of the nasopharynx microbiome between influenza and non-influenza cases of severe acute respiratory infections: A pilot study.

AimsInfluenza A virus (IAV) can cause severe acute respiratory infection (SARI), and disease outcome may be associated with changes in the microbiome of the nasopharynx. This is a pilot study to characterize the microbiome of the nasopharynx in patients hospitalized with SARI, infected and not infected by IAV.Methods and ResultsUsing target sequencing of the 16S rRNA gene, we assessed the bacterial community of nasopharyngeal aspirate samples and compared the microbiome of patients infected with IAV with the microbiome of patients who were negative for IAV. We observed differences in the relative abundance of Proteobacteria and Firmicutes between SARI patients, with Streptococcus being enriched and Pseudomonas underrepresented in IAV patients compared with patients who were not infected with IAV.Conclusion Pseudomonas taxon seems to be in high frequency on the nasopharynx of SARI patients with non‐IAV infection and might present a negative association with Streptococcus taxon. Microbial profile appears to be different between SARI patients infected or not infected with IAV.

Epidemiology and molecular characterization of influenza viruses in Burkina Faso, sub‐Saharan Africa

BackgroundThe importance of influenza viruses in respiratory infections in sub‐Saharan Africa has been historically overlooked, including in Burkina Faso.ObjectivesThis study therefore aimed at evaluating the prevalence and seasonal occurrence of influenza viruses in children under 5 years old, at risk of influenza‐related complications, presenting with influenza‐like illness (ILI) or severe acute respiratory infection (SARI). The study also aimed at identifying the periods with increased influenza transmission for vaccination recommendations in Burkina Faso.MethodsFrom January 2014 to December 2015, ILI and SARI (2015 only) patients were recruited in six healthcare centers in Burkina Faso. Influenza A and B molecular detection and subtyping were performed. Clade clustering of a subset of A(H1N1)pdm09 and A(H3N2) strains was deduced by performing phylogenetic analyses on hemagglutinin gene sequences. Weekly surveillance data from FluNet (2011‐2013; 2016) and this study (2014‐2015) were used to identify periods of increased influenza activity.ResultsInfluenza A and B viruses were detected in 15.1% (112 of 743) of ILI and 6.6% (12 of 181) of SARI patients. Overall, influenza A viruses were largely predominant (81 of 124, 65.3%), with 69.1% of A(H3N2) and 30.9% of A(H1N1)pdm09 strains. Four waves of increased transmission were identified in 2014‐2015, each dominated by different influenza subtypes and clades. Between 2011 and 2016, periods of increased influenza activity varied in their frequency, duration, and timing.ConclusionInfluenza A and B viruses were detected in a substantial number of ILI and SARI cases in Burkina Faso. Vaccination in September‐October would likely protect the highest number of patients.

Hospitalization costs due to severe acute respiratory infection (SARI) in three Central American countries

Objective: To estimate the direct medical costs of severe acute respiratory infection (SARI) in children and adults from three Central American countries with a bottom-up costing approach.Methods: The costs of inpatients treatment were estimated through the retrospective bottom-up costing in a randomized sample of clinical records from SARI patients treated in teaching tertiary hospitals during 2009 - 2011 period. Activities incurred per patient were registered and a setting-specific cost per activity was acquired. Average cost per patient in the group of children and elderly adults was estimated for each country. In Nicaragua, only the pediatric population was included. Costs were expressed in local currency (2011), American dollars, and international dollars (2005) for country comparison.Results: The care cost per case in children in Guatemala was the cheaper (I$971.95) compared to Nicaragua (I$1,431.96) and Honduras (I$1,761.29). In adults, the treatment cost for Guatemala was the more expensive: I$4,065.00 vs. I$2,707.91 in Honduras.Conclusion: Bottom-up costing of SARI cases allowed the mean estimates per treated case that could have external validity for the target population diagnosed in hospitals with similar epidemiological profiles and level of complexity for the study countries. This information is very relevant for the decision-making.

Mortality estimates among adult patients with severe acute respiratory infections from two sentinel hospitals in southern Arizona, United States, 2010\u20132014

BackgroundFrom October 2010 through February 2016, Arizona conducted surveillance for severe acute respiratory infections (SARI) among adults hospitalized in the Arizona-Mexico border region. There are few accurate mortality estimates in SARI patients, particularly in adults ≥ 65 years old.The purpose of this study was to generate mortality estimates among SARI patients that include deaths occurring shortly after hospital discharge and identify risk factors for mortality.MethodsPatients admitted to two sentinel hospitals between 2010 and 2014 who met the SARI case definition were enrolled. Demographic data were used to link SARI patients to Arizona death certificates. Mortality within 30 days after the date of admission was calculated and risk factors were identified using logistic regression models.ResultsAmong 258 SARI patients, 47% were females, 51% were white, non-Hispanic and 39% were Hispanic. The median age was 63 years (range, 19 to 97 years) and 80% had one or more pre-existing health condition; 9% died in hospital. Mortality increased to 12% (30/258, 30% increase) when electronic vital records and a 30-day post-hospitalization time frame were used. Being age ≥ 65 years (OR = 4.0; 95% CI: 1.6–9.9) and having an intensive care unit admission (OR = 7.4; 95% CI: 3.0–17.9) were independently associated with mortality.ConclusionThe use of electronic vital records increased SARI-associated mortality estimates by 30%. These findings may help guide prevention and treatment measures, particularly in high-risk persons in this highly fluid border population.

Respiratory Viruses in Invasively Ventilated Critically Ill Patients—A Prospective Multicenter Observational Study

The presence of respiratory viruses and the association with outcomes were assessed in invasively ventilated ICU patients, stratified by admission diagnosis. Prospective observational study. Five ICUs in the Netherlands. Between September 1, 2013, and April 30, 2014, 1,407 acutely admitted and invasively ventilated patients were included. None. Nasopharyngeal swabs and tracheobronchial aspirates were collected upon intubation and tested for 14 respiratory viruses. Out of 1,407 patients, 156 were admitted because of a severe acute respiratory infection and 1,251 for other reasons (non-severe acute respiratory infection). Respiratory viruses were detected in 28.8% of severe acute respiratory infection patients and 17.0% in non-severe acute respiratory infection (p < 0.001). In one third, viruses were exclusively detected in tracheobronchial aspirates. Rhinovirus and human metapneumovirus were more prevalent in severe acute respiratory infection patients (9.6% and 2.6% vs 4.5 and 0.2%; p = 0.006 and p < 0.001). In both groups, there were no associations between the presence of viruses and the number of ICU-free days at day 28, crude mortality, and mortality in multivariate regression analyses. Respiratory viruses are frequently detected in acutely admitted and invasively ventilated patients. Rhinovirus and human metapneumovirus are more frequently found in severe acute respiratory infection patients. Detection of respiratory viruses is not associated with worse clinically relevant outcomes in the studied cohort of patients.

Detection of Viruses and Mycoplasma pneumoniae in Hospitalized Patients with Severe Acute Respiratory Infection in Northern China, 2015-2016.

Severe acute respiratory infection (SARI) presents a huge disease and economic burden worldwide. The present study described the frequency and types of different infectious etiologies among hospitalized patients with SARI in Tianjin, China, during 2015 and 2016. Basic information, in addition to a throat or serum sample, was collected from SARI patients. Nine viruses were detected using reverse transcription polymerase chain reaction, and Mycoplasma pneumoniae was detected using the Serodia Myco II gelatin particle agglutination test. A total of 585 specimens from 2,290 SARI cases were collected. The most common infection (19.66%, 115/585) was M. pneumoniae, followed by influenza virus A/B (6.15%, 36/585), and respiratory syncytial virus (4.96%, 29/585). Identification of viral or M. pneumoniae infections was the highest in the pediatric medicine ward (74.84%, 119/159), followed by the intensive care unit (37.04%, 80/216) and respiratory medicine ward (34.29%, 72/210). M. pneumoniae was highest (38.71%, 24/62) in the 5-14-year age group. Influenza was the main infection in January 2015 and March 2016. The correlation coefficient for the proportion of hospitalized cases of SARI and the positive detection rate within the same week was 0.25. M. pneumoniae and influenza were the leading pathogens among hospitalized SARI patients. A continued surveillance of hospitalized cases of SARI can detect emerging diseases, such as avian influenza A (H7N9) virus and other respiratory disease outbreaks.

Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007-2014.

IntroductionLittle is known about the role of viral respiratory pathogens in the etiology, seasonality or severity of severe acute respiratory infections (SARI) in the Eastern Mediterranean Region.MethodsSentinel surveillance for SARI was conducted from December 2007 through February 2014 at 20 hospitals in Egypt, Jordan, Oman, Qatar and Yemen. Nasopharyngeal and oropharyngeal swabs were collected from hospitalized patients meeting SARI case definitions and were analyzed for infection with influenza, respiratory syncytial virus (RSV), adenovirus (AdV), human metapneumovirus (hMPV) and human parainfluenza virus types 1–3 (hPIV1-3). We analyzed surveillance data to calculate positivity rates for viral respiratory pathogens, describe the seasonality of those pathogens and determine which pathogens were responsible for more severe outcomes requiring ventilation and/or intensive care and/or resulting in death.ResultsAt least one viral respiratory pathogen was detected in 8,753/28,508 (30.7%) samples tested for at least one pathogen and 3,497/9,315 (37.5%) of samples tested for all pathogens–influenza in 3,345/28,438 (11.8%), RSV in 3,942/24,503 (16.1%), AdV in 923/9,402 (9.8%), hMPV in 617/9,384 (6.6%), hPIV1 in 159/9,402 (1.7%), hPIV2 in 85/9,402 (0.9%) and hPIV3 in 365/9,402 (3.9%). Multiple pathogens were identified in 501/9,316 (5.4%) participants tested for all pathogens. Monthly variation, indicating seasonal differences in levels of infection, was observed for all pathogens. Participants with hMPV infections and participants less than five years of age were significantly less likely than participants not infected with hMPV and those older than five years of age, respectively, to experience a severe outcome, while participants with a pre-existing chronic disease were at increased risk of a severe outcome, compared to those with no reported pre-existing chronic disease.ConclusionsViral respiratory pathogens are common among SARI patients in the Eastern Mediterranean Region. Ongoing surveillance is important to monitor changes in the etiology, seasonality and severity of pathogens of interest.

Seasonal influenza vaccine effectiveness against laboratory-confirmed influenza hospitalizations – Latin America, 2013

BackgroundDespite widespread utilization of influenza vaccines, effectiveness (VE) has not been routinely measured in Latin America. MethodsWe used a case test-negative control design to estimate trivalent inactivated influenza VE against laboratory-confirmed influenza among hospitalized children aged 6months-5years and adults aged ≥60years which are age-groups targeted for vaccination. We sought persons with severe acute respiratory infections (SARI), hospitalized at 71 sentinel hospitals in Argentina, Brazil, Chile, Colombia, Costa Rica, El Salvador, Honduras, Panama, and Paraguay during January–December 2013. Cases had an influenza virus infection confirmed by real-time reverse transcription PCR (rRT-PCR); controls had a negative rRT-PCR result for influenza viruses. We used a two-stage random effects model to estimate pooled VE per target age-group, adjusting for the month of illness onset, age and preexisting medical conditions. ResultsWe identified 2620 SARI patients across sites: 246 influenza cases and 720 influenza-negative controls aged ≤5years and 448 cases and 1206 controls aged ≥60years. The most commonly identified subtype among participants (48%) was the influenza A(H1N1)pdm09 virus followed by influenza A(H3N2) (34%) and influenza B (18%) viruses. Among children, the adjusted VE of full vaccination (one dose for previously vaccinated or two if vaccine naïve) against any influenza virus SARI was 47% (95% confidence interval [CI]: 14–71%); VE was 58% (95% CI: 16–79%) against influenza A(H1N1)pdm09, and 65% (95% CI: −9; 89%) against influenza A(H3N2) viruses associated SARI. Crude VE of full vaccination against influenza B viruses associated SARI among children was 3% (95% CI: −150; 63). Among adults aged ≥60years, adjusted VE against any influenza SARI was 48% (95% CI: 34–60%); VE was 54% (95% CI: 37–69%) against influenza A(H1N1)pdm09, 43% (95% CI: 18–61%) against influenza A(H3N2) and 34% (95% CI: −4; 58%) against B viruses associated SARI. ConclusionInfluenza vaccine provided moderate protection against severe influenza illness among fully vaccinated young children and older adults, supporting current vaccination strategies.

ICD-9 code reporting among patients from the Minnesota SARI surveillance program

IntroductionThe ICD-9 codes for acute respiratory illness (ARI) andpneumonia/influenza (P&amp;I) are commonly used in ARI surveillance;however, few studies evaluate the accuracy of these codes or theimportance of ICD-9 position. We reviewed ICD-9 codes reportedamong patients identified through severe acute respiratory infection(SARI) surveillance to compare medical record documentation withmedical coding and evaluated ICD-9 codes assigned to patients withinfluenza detections.MethodsThe Minnesota Department of Health (MDH) conducted SARIsurveillance at three hospitals. All hospitalized patients withsubmission of a physician-ordered upper respiratory specimens(e.g., sputum, throat or nasopharyngeal swabs) were enrolled.A medical chart review was conducted to identify those meetingSARI criteria, defined as patients admitted to an inpatient ward withnew onset of respiratory symptoms or acute exacerbation of chronicrespiratory conditions. Enrolled patients who did not meet the SARIcriteria were categorized as non-SARI. Residual material from theupper respiratory specimens were submitted to MDH for influenzatesting by RT-PCR. Demographic and clinical data, including upto eight ICD-9 codes, were collected through the medical recordreview. Patients with an ICD-9 code indicating ARI (460 to 466)or P&amp;I (480 to 488) were defined as having an ARI/P&amp;I code. Wecompared the frequency of ARI/P&amp;I codes by SARI clinical criteriaand influenza detection and evaluated the position of the reportedARI/P&amp;I code.ResultsFrom May 2013 through August 2015, we enrolled 5,950patients, of which 4,449 (75%) met SARI criteria and 1501 did not(non-SARI). An ARI/P&amp;I code in any position was found in 61%(2705) of SARI vs. 16% (241) of non-SARI patients (odds ratio [OR]8.1, 95% confidence interval [CI] 7.0-9.4); an ARI/P&amp;I code in thefirst position was found in 40% of SARI vs 7% of non-SARI patients(OR=8.6, 95% CI 7.0-10.5). Among SARI patients with at least oneARI/P&amp;I code, 66% had their first or only ARI/P&amp;I code in the 1stposition, 25% in the 2ndposition, and 6% in the 3rdposition. Foridentification of SARI, sensitivity/specificity was 61%/84% for ARI/P&amp;I codes in any position and 40%/93% for ARI/P&amp;I codes in the 1stposition. Among SARI patients, codes for pneumonia (486) and acutebronchiolitis (466.11, 466.19) were commonly reported. The mostfrequent codes among SARI patients without an ARI/P&amp;I code werefever (780.6), acute respiratory failure (518.81), and asthma (493.92)(Table). Influenza was detected among 8% (351) of SARI patients.An ARI/P&amp;I code in any position was more common in influenza-positive vs. influenza-negative SARI patients (77% vs 59%, OR 2.4,95% CI 1.8-3.1). An ARI/P&amp;I code in the 1stposition was slightlymore common in influenza-positive vs -negative patients though notsignificant (44% vs 40%).ConclusionsAmong patients from whom a respiratory specimen was collected,administrative data identified those meeting SARI with moderatesensitivity and high specificity, and with lower sensitivity but greaterspecificity when limited to the 1stICD-9 position. Pneumonia andacute bronchiolitis ICD-9 codes were frequent ARI/P&amp;I codes amongSARI patients. Further investigation is needed to determine the valueof including additional ICD-9 codes, such as respiratory distress andacute asthma exacerbation, in identifying SARI.

Enhancement of the Influenza Surveillance System in the Russian Federation: the Main Results of the Sentinel Surveillance for Influenza and other Acute Respiratory Viral Infections

Existing influenza surveillance system is constantly improved to obtain comprehensive information for understanding of continuously changing situation with the influenza, which is a consequence of the highest variability of the pathogen, its ability to reassortment and the imminence of emergence a new shift-variants of the virus that could cause the next pandemic events. For this purpose, since the 2010 - 2011 epidemic season, in addition to the traditional surveillance system (TS) a new well standardized sentinel surveillance system (SS) for rapid clinical and epidemiological data obtaining was introduced in Russia. A total 7812 hospitalized patients with severe acute respiratory infection (SARI) and 9854 outpatients with influenza-like illness and acute respiratory infection (ILI/ARI) were investigated during the 6-year period in SS. Percent of SARI among all hospitalized patients ranged from 1.7 to 3.1%; about 5.3 - 7.5% SARI patients were placed in the Intensive Care Unit. Etiological monitoring using PCR showed influenza spread trends in SS similar to those registered in the TS: a clear predominance of influenza A (H1N1) pdm09 among SARI and ILI/ARI in 2010 - 2011 and 2015 - 2016 epidemic seasons, influenza A (H3N2) in the epidemic seasons 2011 - 2012 and 2014 - 2015, the co-circulation of these pathogens in 2012 - 2013, 2013 - 2014 seasons in Russia. SARI caused by influenza B virus were detected less frequently than influenza A but increased influenza B activity was registered in the epidemic of 2014 -2015, when Yamagata lineage changed suddenly for the Victorian one. The average frequency of influenza diagnosis among SARI between the seasons varied in the range 12.5 - 27.1%, at the peak of the epidemic it reached 44.8 - 73.5% and was the highest during the season with active circulation of influenza A (H1N1) pdm09 virus. The rate of influenza diagnosis among ILI/ARI has always been lower than that among SARI. Studies have also shown the importance of rhinovirus, RS-virus and parainfluenza infections in SARI development. The frequency of registration of coronaviruses, metapneumovirus and bocavirus infection was very low in SARI and ILI/ARI. It was found that in all studied seasons most of SARI patients with influenza have not been vaccinated. Among ILI/ARI outpatients with influenza, the frequency of vaccinated individuals for the entire period of the study was estimated as 10.1%, which was 4.2 times higher than that in SARI, where only 2.4% of patients were vaccinated. In addition, it was found that for all six seasons the SARI patients with influenza were treated with antivirals drugs 2 times less often compared to outpatients. Analysis of data on concomitant diseases and conditions in SARI patients with influenza confirmed the leading role of pregnancy as a risk factor for hospitalization in all influenza epidemics, irrespective of their etiology. In addition, diabetes and cardiovascular disease were recognized as risk factors for influenza associated SARI development.