Clinical characteristics and outcomes of patients with severe acute respiratory infections (SARI): results from the Egyptian surveillance study 2010–2014

Cairo University Hospital (CUH) is a 5100-beds tertiary referral teaching hospital. Inclusion criteria consisted of hospitalized adults (defined as age ≥ 18 years old), as well as pediatric patients (age < 18 years old), with the diagnosis of SARI, who provided a respiratory sample, from February 2010 to February 2014. Due to an annual review by dedicated investigators and updates to WHO guidelines, the case definition for SARI has evolved over the study period. Before February 2010, as a global-surveillance case definition of SARI did not exist, the definition for SARI was adapted from the WHO protocol on rapid response for persons ≥5 years old [3]. Whereas, for children <5 years old, SARI definition was adapted from the program for Integrated Management of Childhood Illness [4]. After March 2011, the global standards and tools for influenza surveillance developed by the WHO were adopted [5]. As of January 2014, the WHO surveillance case definitions for SARI was implemented [6] as follows, acute respiratory infection with history of fever or measured fever of ≥ 38 C°; and cough; with onset within the last 10 days; and requiring hospitalization [6]. An enrollment form was used to collect data from enrolled eligible patients including patient demographics, medical history, clinical signs and symptoms, comorbidities, reported influenza vaccine status, recent travel history, treatment, clinical course, and outcome. Patients with incomplete medical records were excluded.

Nasopharyngeal (NP) and oropharyngeal (OP) swabs for detecting viruses and blood cultures for detecting bacteria were taken from eligible patients on admission using operating procedures described by the WHO [12]. Specimens were taken an average of 7 days after illness onset (range: 1–66 days).

Total nucleic acid (TNA) was extracted by the automated KingFisher Flex Magnetic Particle Processor (Thermo Scientific, Waltham, MA, USA) using MagMAX Total Nucleic Acid Isolation Kit (Cat No. AM 1840, Applied Biosystems, Foster, CA, USA) according to the manufacturer’s instructions. The viral target was amplified using specific primers and probes produced by the CDC (Atlanta, GA, USA) and following standard protocol for reverse transcription polymerase chain reaction detection. From 2010 to 2012, testing for RSV, adenovirus, human parainfluenza viruses (hPIV) 1, 2 and 3, influenza (A and B) and human metapneumovirus was conducted at CUH laboratory and sent for confirmation by the Naval Medical Research Unit No.3 (NAMRU-3) laboratory. From 2013 to 2014, testing was conducted at CUH laboratory. For all samples, the human RNase P gene (RP) was tested as an internal positive control to ensure proper sample collection and nucleic acid extraction. Samples were considered positive to the viral target if the amplification curve crossed the threshold line before cycle 40. All clinical samples should be positive to RP with cutoff value ≤ 37, as prescribed previously [8]. Blood samples were collected for detection of Mycoplasma pneumonia, Chlamydia pneumonia, and Legionella pneumophila, using RT-qPCR.

Prior to study initiation, the study protocol was reviewed and approved by Institutional Review Board at the NAMRU-3, as well as the ethical committee of CUH, in compliance with all applicable federal U.S. regulations governing the protection of human subjects. An informed written consent was obtained from the patients (in the case of adult patients) or patients’ parent/legal guardian (in the case of pediatric patients).

Data analyses were conducted using the software SPSS (Statistical Package for the Social Science; IBM Corp, NY, USA); version 22. Data were summarized using median (range) for quantitative variables and number and percent for qualitative variables. Comparison between groups was done using the Chi-square test for qualitative variables, independent sample t-test for normally distributed quantitative variables, while the Mann-Whitney U test was used for quantitative variables that are not normally distributed. Indicators of severe disease were assessed for each pathogen of interest using Mantel-Haenszel estimates to calculate odds ratios and confidence intervals and the Mantel-Haenszel chi-squared test to assess statistical significance [13]. Logistic regression was used to examine associations between viral respiratory pathogens and severe outcomes, defined as illness requiring ventilation or intensive care unit (ICU) or resulting in death while controlling for demographic and clinical characteristics. Only variables with statistically significant univariate association with severe outcomes were included in multivariate regression analysis. All tests were two-sided, and differences with p <0.05 were considered significant.

Out of 3,207 participants enrolled in this SARI surveillance, 1,075 (33.5%) had positive results for viral and atypical bacteria tested. They included 569/1,075 (53%) females and 506/1,075 (47%) males. The median age was one year (range 0-85 years). Children less than 18 years had a higher viral etiology (981 patients, 91.2%) compared to 94 (8.8%) ones in adults. Notably, children <5 years represented 83% of patients. The highest rates of viral infections were reported for RSV (485 patients, 45.2%), PIV (125, 11.6%), and adenovirus (105, 9.8%). Other encountered viruses included rhinovirus, hMPV, and BOCA virus (2%,7%, and 1%, respectively). Only 3 cases were positive for Mycoplasma and were co-infected with RSV, while only one case of Chlamydia was co-infected with RSV and hMPV. Neither Coronavirus nor Legionella was detected. Table 1 shows these data.

In comparison to non-viral infected individuals, viral-infected SARI ones had significantly predominant signs and symptoms at presentation. Particularly, they had significant viral prodromal symptoms, as well as tachypnea, wheezes, and convulsions (p=0.000 each). Among individual viral pathogens, SARI patients with influenza had more significant tachypnea (p= 0.038), wheezes (p=0.000), and abnormal breath sounds (p= 0.023), than those with non-influenza viral infections. Patients whose specimens were collected within 5 days of the onset of symptoms were more likely to have a viral pathogen detected than those whose specimens were collected later (73% versus 36%, p = 0.047).

Fifty-three percent of patients had at least one underlying medical condition. These comorbidities included chronic respiratory disorders (asthma, COPD, bronchiectasis, and immotile cilia syndrome), cardiac disorders (heart failure congenital heart diseases, and cardiomyopathy), neuromuscular disorders (epilepsy, cerebral palsy, and myopathies), hematological disorders (thalassemia), endocrine disorders (diabetes mellitus, hypothyroidism, and morbid obesity), renal disorders (end-stage renal disease), and liver disorders (liver cirrhosis and hepatic failure).

In terms of comorbidities, patients with and without viral detection differed significantly in the frequencies of chronic respiratory (p=0.002), endocrine (p=0.000), hepatic (p=0.002), and neuromuscular disorders (p=0.001). Among individual viral pathogens, SARI patients with para-influenza virus had significant endocrine (p= 0.004), and neuromuscular disorders (p=0.012), than those with non-para-influenza viral infections.

For influenza vaccination history; 832/1,075 (77.4%) cases did not receive the vaccine within the 12 months prior to hospital admission, while 243/1,075 (22.6%) were reported as unknown for an influenza vaccination status. Table 1 details these results.

In comparison to non-viral infected individuals, viral-infected SARI ones had significantly lower rates of pneumonia (p=0.004) and admission to the ICU (p=0.000). Patients with influenza virus tended to have significantly different rates of admission to the ICU (p=0.045), and mechanical ventilation (p=0.001), in comparison to those with non-influenza infections. With regards to complications, viral-infected SARI patients had significant differences for developing respiratory failure (p=0.033), and acute respiratory distress syndrome; ARDS (p=0.011), in comparison to those without viral infections.

Overall mortality in SARI-positive patients was 24/1,075 (2.2%) and peaked at 1% in 2014. Overall, only 2(8%) were adults, while 22 (92%) were children. Among children, 18(75%) were aged <5 years. Overall, two-thirds (16/24) had comorbidities. All patients who died were admitted to the ICU and mechanically ventilated. Notably, all patients who died tested positive for a viral pathogen; twelve were positive for RSV, four for influenza virus, two for adenovirus, one for hMPV, one for PIV and four for mixed viral infections, respectively. Among those who died, there was a significant difference between those with (2.2%) and without (5%) viral detection (p = 0.005). Among individual viral pathogens, SARI patients with RSV and influenza had significant deaths (p= 0.045 and 0.006), in comparison to those with non-RSV and non-influenza viral infections. No mortality was reported for patients with atypical bacteria (Table 1).

No infections were independently associated with increased severity of SARI, as indicated by illness requiring mechanical ventilation and/or ICU and/or resulting in death. There was strong evidence that individuals with RSV and influenza were less likely to experience a severe outcome than those not infected with each of these pathogens (RSV OR 1.433, 95% CI 4.698-6.132. p=0.021, influenza OR 3.937, 95% CI 2.447-6.3340, p=0.000). Individuals with multiple infections were no more likely than those with infection with a single pathogen to experience severe outcomes (OR 0.232, 95% CI 0.155-0.619, p = 0.240).

When analyses were stratified by age, neither significant differences in severe outcomes could be encountered between viral-infected and non-infected individuals (OR 0.983, 95% CI 0.503-1.924, p=0.961 and OR 1.100, 95% CI 0.704-1.718, p=0.675) nor between individual viral infections, among children and adults. Table 2 shows these details (Data for PIV, hMPV, Boca virus, rhino-, and enterovirus are not shown in the table).

Logistic regression was used to further examine associations with severe outcomes in SARI-positive individuals with complete demographic data and clinical risk factors. By univariate analysis, individuals with positive results for rhinovirus and adults >18 years were more likely to experience a severe outcome than those not infected with rhinovirus (OR 4.975, 95% CI 2.431-17.812, p=0.024) and children <18 years (OR 10.357, 95% CI 5.895-18.197, p=0.000), respectively.

Multivariate analysis confirmed these results where individuals with positive results for rhinovirus and adults >18 years were more likely to experience a severe outcome than those not infected with rhinovirus (OR 4.807, 95% CI 2.981-16.112, p=0.025) and children <18 years (OR 11.716, 95% CI 7.225-18.998, p=0.000), respectively.

Table 3 shows these results.

Being the most commonly detected virus among our cohort, clinical characteristics and outcomes of RSV-positive patients were compared to those with other respiratory positive cases as well as viral-negative patients.

While patients with RSV-positive infections had significant differences with those with no respiratory viruses identified, with regards to clinical signs and symptoms, comorbidities, and outcomes (ICU admission and deaths); they had no differences with those tested positive for other viral pathogens, with regards to the same parameters. (Table 4 shows these details)

Logistic regression was used to examine associations with severe outcomes in RSV-positive patients with complete demographic data and clinical risk factors. By univariate analysis, individuals with RSV and associated comorbidities were more likely to experience severe outcomes (OR 4.703, 95% CI 0.803-9.672, p=0.001) than those with RSV and no comorbidities (Table 5).