Incidence and etiology of hospitalized acute respiratory infections in the Egyptian Delta.

INTRODUCTION: Acute Respiratory Infections (ARI) are responsible for nearly two million childhood deaths worldwide. A limited number of studies have been published on the epidemiology of viral respiratory pathogens in Egypt. METHODS: A total of 6113 hospitalized patients >1 month of age with suspected ARI were enrolled between June 23, 2009 and December 31, 2013. Naso- and oropharyngeal specimens were collected and tested for influenza A and B, respiratory syncytial virus, human metapneumovirus, adenovirus, and parainfluenza viruses 1-3. Blood specimens from children 1-11 months were cultured and bacterial growth was identified by polymerase chain reaction. Results from a healthcare utilization survey on the proportion of persons seeking care for ARI was used to calculate adjusted ARI incidence rates in the surveillance population. RESULTS: The proportion of patients with a viral pathogen detected decreased with age from 67% in patients age 1-11 months to 19% in patients ≥65 years of age. Influenza was the dominant viral pathogen detected in patients ≥1 year of age (13.9%). The highest incidence rates for hospitalized ARI were observed in children 1-11 months (1757.9-5537.5/100 000 population) and RSV was the most commonly detected pathogen in this age group. CONCLUSION: In this study population, influenza is the largest viral contributor to hospitalized ARIs and children 1-11 months of age experience a high rate of ARI hospitalizations. This study highlights a need for surveillance of additional viral pathogens and alternative detection methods for bacterial pathogens, which may reveal a substantial proportion of as yet unidentified etiologies in adults.

Influenza hospitalization epidemiology from a severe acute respiratory infection surveillance system in Jordan, January 2008-February 2014.

BACKGROUND: Acute respiratory infections (ARIs) are a major cause of morbidity and mortality worldwide. Influenza typically contributes substantially to the burden of ARI, but only limited data are available on influenza activity and seasonality in Jordan. METHODS: Syndromic case definitions were used to identify individuals with severe acute respiratory infections (SARI) admitted to four sentinel hospitals in Jordan. Demographic and clinical data were collected. Nasopharyngeal and oropharyngeal swabs were tested for influenza using real-time reverse transcription polymerase chain reaction and typed as influenza A or B, with influenza A further subtyped. RESULTS: From January 2008-February 2014, 2891 SARI cases were tested for influenza, and 257 (9%) were positive. While 73% of all SARI cases were under 5 years of age, only 57% of influenza-positive cases were under 5 years of age. Eight (3%) influenza-positive cases died. An annual seasonal pattern of influenza activity was observed. The proportion of influenza-positive cases peaked during November-January (14-42%) in the non-pandemic years. CONCLUSIONS: Influenza is associated with substantial morbidity and mortality in Jordan. The seasonal pattern of influenza aligns with known Northern Hemisphere seasonality. Further characterization of the clinical and financial burden of influenza in Jordan will be critical in supporting decisions regarding disease control activities.

The Burden of Influenza-Associated Hospitalizations in Oman, January 2008-June 2013.

INTRODUCTION: Acute respiratory infections (ARI), including influenza, comprise a leading cause of morbidity and mortality worldwide. Influenza surveillance provides important information to inform policy on influenza control and vaccination. While the epidemiology of influenza has been well characterized in western countries, few data exist on influenza epidemiology in the Eastern Mediterranean Region. We describe the epidemiology of influenza virus in Oman. METHODS: Using syndromic case definitions and protocols, patients from four regional hospitals in Oman were enrolled in a descriptive prospective study to characterize the burden of severe acute respiratory infections (SARI) and influenza. Eligible patients provided demographic information as well as oropharyngeal (OP) and nasopharyngeal (NP) swabs. Specimens were tested for influenza A and influenza B; influenza A viruses were subtyped using RT-PCR. RESULTS: From January 2008 through June 2013, a total of 5,147 cases were enrolled and tested for influenza. Influenza strains were detected in 8% of cases for whom samples were available. Annual incidence rates ranged from 0.5 to 15.4 cases of influenza-associated SARI per 100,000 population. The median age of influenza patients was 6 years with children 0-2 years accounting for 34% of all influenza-associated hospitalizations. By contrast, the median age of non-influenza SARI cases was 1 year with children 0-2 years comprising 59% of SARI. Compared to non-influenza SARI cases, a greater proportion of influenza cases had pre-existing chronic conditions and underwent ventilation during hospitalization. CONCLUSIONS: Influenza virus is associated with a substantial proportion of SARI in Oman. Influenza in Oman approximately follows northern hemisphere seasonality, with major peaks in October to December and a lesser peak around April. The burden of influenza was greatest in children and the elderly. Future efforts should examine the burden of influenza in other potential risk groups such as pregnant women to inform interventions including targeted vaccination.

Risk factors of prolonged hospital stay in children with viral severe acute respiratory infections.

INTRODUCTION: Severe acute lower respiratory infections (SARIs) are one of the major causes of morbidity and mortality in young children, especially in developing countries. The present study focused on detection of risk factors for prolonged hospital stays among children with viral SARIs. METHODOLOGY: A sentinel surveillance study was conducted at Cairo University Hospital (CUH) between February 2010 and May 2011. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from all children admitted with SARIs. Viruses were identified using reverse transcription polymerase chain reaction (RT-PCR). RESULTS: Out of 1,046 children, 380 (36%) were positive for one or more viruses; these included respiratory syncytial virus (RSV) (22.9%), adenovirus (6.2%), parainfluenza viruses (PIVs1-3) (5.1%), human metapneumovirus (HMPV) (4.5%), influenza A (1.4%), and influenza B (0.6%). Viral etiology was mainly detected in children under one year of age (88.9%). Prolonged length of stay was independently associated with the presence of cyanosis and underlying chronic illness (OR 7.4, CI: 1.8-30.32 [p = 0.005], OR 2.5, CI: 1.36-4.64 [p = 0.004], respectively). Virus type did not affect the length of hospital stay (p > 0.05). Oxygen therapy was required in 91% of the patients. A total of 43 patients (11.6%) required intensive care admission. Twenty-one patients (5.5%) died, and 15 of them (71.4%) had an underlying chronic illness. CONCLUSIONS: The study demonstrated the important burden of respiratory viruses as a cause of SARI in hospitalized children in a tertiary Egyptian hospital. Cyanosis and underlying chronic illness were significantly associated with prolonged length of stay.

Evaluation of a newly developed ELISA against Widal, TUBEX-TF and Typhidot for typhoid fever surveillance.

INTRODUCTION: Typhoid fever is endemic in many parts of the world and represents a major cause of acute febrile illness (AFI). Rapid and accurate laboratory methods for diagnosis of this disease are needed for both patient care and surveillance situations. METHODOLOGY: Serum samples were collected from AFI patients and used to evaluate the performance of a newly developed ELISA assay that uses a mixture of somatic and flagellar antigens to detect the total antibody response against Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) infection. The levels of Ig isotype response (IgG, IgM and IgA) were also evaluated, and results were compared to those of TUBEX-TF and Typhidot commercial kits.  RESULTS: Of 234 culture-confirmed typhoid patients, the total Ig ELISA diagnosed 93% compared to 71% using Widal test. This sensitivity level (93%) is higher than that observed for the individual Ig ELISAs (IgG 75%; IgM 79%; IgA 57%) and the commercial tests TUBEX-TF (75%), Typhidot IgM (63%) and Typhidot IgG (28%). An agreement of 78% was achieved between the total Ig ELISA and Widal test. The average specificity of the ELISA was 96%. Using ELISA, up to 200 samples can be tested per run with cost per test at US$0.20. CONCLUSIONS: The developed ELISA shows superior sensitivity and specificity, when compared to Widal, TUBEX-TF and Typhidot assays, is more cost effective and allows higher throughput. This method is highly recommended for active surveillance studies or outbreak investigations of typhoid fever.

Detection of gyrA mutation among clinical isolates of Campylobacter jejuni isolated in Egypt by MAMA-PCR.

INTRODUCTION: Campylobacter spp are the major cause of enteritis in humans and more than 90% of reported infections are caused by Campylobacter jejuni. Fluoroquinolones such as ciprofloxacin are the antibiotics of choice for treatment. An increase in the frequency of ciprofloxacin-resistant Campylobacter has been reported globally due to a single base mutation (C-257 to T) in codon 86 of the quinolone resistance determining region (QRDR) of the gyrA gene altering the amino acid sequence from threonine at position 86 to isoleucine (Thr-86 to Ile). METHODOLOGY: Campylobacter spp (n = 118) were selected from a collection of Egyptian isolates spanning 1998 to 2005. The presence of C. jejuni gyrA gene was confirmed in each isolate by a PCR assay amplifying 368 bp portion of the gyrA gene. C to T alteration was detected by the mismatch amplification mutation assay MAMA PCR. The MIC of nalidixic acid (NA) and ciprofloxacin (CIP) was determined by E-test. RESULTS: C. jejuni gyrA gene was detected in 100 of the Campylobacter spp studied; the other 18 isolates were found to be Campylobacter coli by lpxA PCR. The mutation was detected in 89 C. jejuni resistant isolates with MIC values (NA; 8 - >256 µg/ml) and (CIP; 4 - >32 µg/ml). The other 11 sensitive C. jejuni isolates with MIC values (NA; 0.38 - 3 µg/ml) and (CIP; 0.03 - 0.125 µg/ml) were not amplified by the MAMA primers. There was 100% congruence with MAMA PCR, MIC results and gyrA gene sequence analysis. CONCLUSIONS: In Egypt the main mechanism for resistance to fluoroquinolones is an alteration in the gyrA QRDR. MAMA PCR provides an economical and rapid means for screening fluoroquinolone resistance.