Impact of respiratory viral infections on mortality and critical illness among hospitalized patients with chronic obstructive pulmonary disease.

BACKGROUND: Seasonal respiratory viral infections are associated with exacerbations and morbidity among patients with COPD. The real-world clinical outcomes associated with seasonal viral infections are less well established among hospitalized patients. RESEARCH QUESTION: To estimate the association between seasonal respiratory viral infections, 30-day mortality, and intensive care unit (ICU) admission among hospitalized COPD patients. STUDY DESIGN AND METHODS: We conducted an analysis of a national prospective multicenter cohort of COPD patients hospitalized with acute respiratory illness during winter seasons (2011-2015) in Canada. Nasopharyngeal swabs were performed on all patients at the onset of hospital admission for diagnosis of viral infection. Primary outcomes were 30-day mortality and ICU admissions. Secondary outcomes included invasive/non-invasive ventilation use. RESULTS: Among 3931 hospitalized patients with COPD, 28.5% (1122/3931) were diagnosed with seasonal respiratory viral infection. Viral infection was associated with increased admission to ICU (OR 1.5, 95% CI 1.2-1.9) and need for mechanical ventilation (OR 1.9, 95% CI 1.4-2.5), but was not associated with mortality (OR 1.1, 95% CI 0.8-1.4). Patients with respiratory syncytial virus (RSV) were equally likely to require ICU admission (OR 1.09, 95% CI 0.67-1.78), and more likely to need non-invasive ventilation (OR 3.1; 95% CI 1.8-5.1) compared to patients with influenza. INTERPRETATION: Our results suggest COPD patients requiring hospitalization for respiratory symptoms should routinely receive viral testing at admission, especially for RSV and influenza, to inform prognosis, clinical management, and infection control practices during winter seasons. Patients with COPD will be an important target population for newly developed RSV therapeutics. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov ID: NCT01517191.

In Vitro Investigation of the Impact of Bacterial-Fungal Interaction on Carbapenem-Resistant Klebsiella pneumoniae.

Fungal-bacterial co-culturing is a potential technique for the production of secondary metabolites with antibacterial activity. Twenty-nine fungal species were screened in a co-culture with carbapenem-resistant Klebsiella pneumoniae at different temperatures. A temperature of 37 ° showed inhibition of bacterial growth. Antimicrobial susceptibility testing for K. pneumoniae was conducted to compare antibiotic resistance patterns before and after the co-culture. Genotypic comparison of the K. pneumonia was performed using next generation sequencing (NGS). It was shown that two out of five K. pneumoniae, with sequence type ST 101 isolates, lost bla-OXA48, bla-CTX-M-14, tir, strA and strB genes after the co-culture with Scopulariopsis brevicaulis fungus. The other three isolates (ST 383 and 147) were inhibited in the co-culture but did not show any changes in resistance. The total ethyl acetate extract of the fungal-bacterial co-culture was tested against K. pneumoniae using a disc diffusion method. The concentration of the crude extract was 0.97 mg/µL which resulted in total inhibition of the bacteria. Using chromatographic techniques, the purified compounds were identified as 11-octadecenoic acid, 2,4-Di-tert-butylphenol, 2,3-Butanediol and 9-octadecenamide. These were tested against K. pneumoniae using the well diffusion method at a concentration of 85 µg/µL which resulted in total inhibition of bacteria. The co-culture results indicated that bacteria under chemical stress showed variable responses and induced fungal secondary metabolites with antibacterial activities.

Heterologous immunization with Covishield and Pfizer vaccines against SARS-CoV-2 elicits a robust humoral immune response.

Understanding the efficacy and durability of heterologous immunization schedules against SARS-CoV-2 is critical, as supply demands and vaccine choices become significant issues in the global vaccination strategy. Here we characterize the neutralizing antibodies produced in two subjects who received combination immunizations against SARS-CoV-2, first with Covishield (Oxford-AstraZeneca) vaccine, followed 33 days later with a second dose (booster) shot of the Pfizer-BioNTech vaccine. Serum samples were collected 25 days following the primary vaccination and 13 days after the secondary Pfizer vaccination. Both subjects exhibited increased levels of isotype IgG and IgM antibodies directed against the entire spike protein following immunizations. These antibodies also exhibited increased reactivity with the receptor binding domain (RBD) in the spike protein and neutralized the infectivity of replicating vesicular stomatitis virus (VSV) that contains the COVID-19 coronavirus S protein gene in place of its normal G glycoprotein. This VSV pseudovirus also contains the reporter gene for enhanced green fluorescent protein (eGFP). Antibody titers against the spike protein and serum neutralization titers against the reporter virus are reported for the 2 heterologous vaccinated individuals and compared to a positive control derived from a convalescent patient and a negative control from an unexposed individual. The Pfizer-BioNTech vaccine increased antibody binding to the spike protein and RBD, and approached levels found in the convalescent positive control. Neutralizing antibodies against the VSV-S pseudovirus in the 2 subjects also approached levels in the convalescent sera. These results firmly validate the value of the Pfizer-BioNTech vaccine in boosting immunity following initial Covishield inoculation.

Whole-genome sequencing of Egyptian multidrug-resistant Klebsiella pneumoniae isolates: a multi-center pilot study.

Multidrug-resistant (MDR) Klebsiella pneumoniae is a common infectious pathogen. We performed whole-genome sequencing (WGS) of 39 randomly selected, geographically diverse MDR K. pneumoniae from nine Egyptian hospitals. Clinical sources, phenotypic antibiotic resistance, and hyper-mucoviscosity were documented. WGS data were epidemiologically interpreted and tested for the presence of antibiotic resistance and virulence genes. Based on WGS data, we identified 18 classical multi-locus sequence types (MLST), the most common type being ST101 (23.1%) followed by ST147 (17.9%). Phylogenetic analyses identified small numbers of closely related isolates in a few of the centers, so we mostly documented independent nosocomial acquisition or import from public sources. The most common acquired resistance gene found was blaCTX-M-15, detected in 27 isolates (69.2%). Carbapenemase genes encountered were blaNDM-1 (n = 13), blaNDM-5 (n = 1), blaOXA-48 (n = 12), blaOXA-181 (n = 2), and blaKPC2 (n = 1). Seven strains (18%) contained more than a single carbapenemase gene. While searching for virulence-associated genes, sixteen wzi alleles were identified with wzi137, wzi64, and wzi50 most commonly found in ST101, ST147, and ST16, respectively. Yersiniabactin was the most common virulence factor (69.2%). Hyper-mucoviscosity was documented for 6 out of 39 isolates.This is the first genomic study of MDR K. pneumoniae from Egypt. The study revealed a clear spread of well-known international clones and their associated antimicrobial resistance and (hyper)virulence traits. The clinical situation in Egypt seems to reflect the scenario documented in many other countries and requires close attention.

The use of multiplex PCR for the detection of atypical pathogens in Egyptian children with CAP: a high rate of Bordetella pertussis in early infancy.

BACKGROUND: Atypical pathogen infections played an important role in community-acquired pneumonia (CAP) in children. Pathogen-specific clinical symptoms are often lacking, and it is difficult to detect atypical pathogens by culture methods. The use of multiplex polymerase chain reaction (PCR) methods enables testing for many pathogens simultaneously in a single analysis. AIM: To determine the role of atypical pathogens in children hospitalized with CAP. PATIENTS AND METHODS: This cross-sectional study was conducted throughout a 2-year period from August 2015 to September 2017. It included 400 Egyptian children hospitalized with clinical diagnosis of CAP at a tertiary hospital in Cairo, Egypt. Sputum samples were collected from lower respiratory tract of all enrolled patients by mucus trap catheter for identification of Bordetella pertussis, Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella pneumophilia by using multiplex real-time PCR. RESULTS: Among the 400 CAP patients enrolled in this study, atypical pathogens were detected in 12/400 (3%) patients. Bordetella pertussis was detected in 2% of cases, and it was responsible for CAP in 8/104 (7.69%) infants in the age stratum ≤ 4 months; compared with pertussis-negative cases, pertussis-positive cases were younger and incompletely vaccinated (P values were 0.001 and 0.007, respectively). Mycoplasma pneumoniae was detected in 1% of cases, all were among the age stratum > 4 months ≤ 59 months in 4/272 (1.47%) children. CONCLUSION: In early infancy, Bordetella pertussis causes a significant proportion of hospitalized CAP cases; all were ≤ 4 months old and incompletely vaccinated. This finding could suggest the role of maternal immunization in developing countries.

Prematurity, a significant predictor for worse outcome in viral bronchiolitis: a comparative study in infancy.

BACKGROUND: The rate of admissions to hospital with bronchiolitis has increased over the past years. The reasons for this are likely to be multifactorial including improved survival of preterm infants. AIM: To assess the severity of viral bronchiolitis in preterm compared to term infants admitted at a tertiary hospital in Cairo, Egypt, based on the outcome. PATIENTS AND METHODS: This prospective study was conducted throughout a 3-year period from September 2011 to October 2014. It included 153 infants, 74 healthy preterm, and 79 healthy term infants admitted with clinical diagnosis of bronchiolitis at a tertiary hospital in Cairo, Egypt. Bronchiolitis severity score (BSS) was recorded, and nasopharyngeal swabs were obtained from each patient at the time of presentation. Viruses were identified using reverse transcription polymerase chain reaction (RT-PCR). The clinical course and patient's outcome were recorded. RESULTS: This study recorded a significantly more severe BSS for preterm compared to term infants. The preterm group had an increased mean length of hospital stay and oxygen therapy and was more likely to need intensive care unit admission and mechanical ventilation (MV) compared to the term group. The mean (± SD) BSS for infections with h-MPV, RSV, and para-influenza 3 was more significantly severe in preterm compared to term infants. Bacterial co-infection was significantly correlated with severity scoring in both groups. CONCLUSION: Prematurity significantly affects the severity of bronchiolitis, and this underscores the importance of early categorization as a high-risk group on their first visit. The physician should be aware that their illness runs a more severe course, even if they have no underlying disorders.

High Prevalence of VIM, KPC, and NDM Expression among Surgical Site Infection Pathogens in Patients Having Emergency Surgery.

BACKGROUND: The rate of surgical site infection (SSI) in patients who undergo emergency operations is higher than in other patients. Previous studies showed an increasing role of gram- negative pathogens (GNP) in SSI. We aimed to identify GNP causing SSIs after emergency surgery, to characterize the carbapenemase-resistance genes in carbapenem-resistant pathogens (CRPs), and to identify the risk factors for SSI caused by CRP. METHOD: We conducted a one-year prospective study from September 2014 in the Emergency Hospital of Cairo University Hospitals. Surveillance for SSIs was conducted according to the case definitions of the U.S. Centers for Disease Control and Prevention. Clinical specimens from patients suspected of having SSI were collected; pathogens were identified by Bruker matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectometry. Antimicrobial susceptibility was tested by the VITEK-2 and E-test. Carbapenem-resistant GNPs were characterized by multiplex polymerase chain reaction for IMP, VIM, SPM, OXA-48, NDM, KPC, BIC, AIM, GIM, SIM, and DIM. Clinical data for patients with SSI infected with CRP were compared with the non-infected patients for detection of risk factors. RESULTS: Surgical site infection affected 6.7% of patients who had emergency operations, and GNP represented 85% of these pathogens. Carbapenem-resistant pathogens caused 61% of the SSI, including all those caused by Acinetobacter baumannii, 70% of those caused by Pseudomonas aeruginosa, and 67% of those caused by Klebsiella pneumoniae. The PCR revealed that VIM, KPC, and NDM were the most common resistance genes. Risk factors for SSI were previous hospitalization, longer hospital stay, type of surgical incision, and abundant drainage; whereas previous hospitalization and infection by non-enteric environmental GNP were the risk factors for SSI caused by CRP. CONCLUSION: The rate of SSIs caused by CRP was high after emergency surgery. VIM, KPC, and NDM were the most commonly found genes. Prior hospitalization and infection by non-enteric GNP were risk factors, which can be mitigated by eradication of bacterial populations in environmental reservoirs and control of transmission.

Prematurity is a significant predictor of worse outcomes in viral bronchiolitis: A comparative study in infancy.

BACKGROUND: The rate of admissions to hospital with bronchiolitis has increased over the past years. The reasons for this are likely to be multifactorial including improved survival of preterm infants. AIM: To assess the severity of viral bronchiolitis in preterm compared with term infants admitted at a tertiary hospital in Cairo, Egypt, based on the outcome. MATERIALS AND METHODS: This prospective study was conducted throughout a 3-year period from September 2011 to October 2014. It included 153 infants, 74 healthy preterm and 79 healthy term infants, admitted with clinical diagnosis of bronchiolitis at a tertiary hospital in Cairo, Egypt. Bronchiolitis severity score (BSS) was recorded, and nasopharyngeal swabs were obtained from each patient at the time of presentation. Viruses were identified using reverse transcription PCR. The clinical course and patient's outcome were recorded. RESULTS: This study recorded a significantly more severe BSS for preterm compared with term infants. The preterm group had an increased mean length of hospital stay and oxygen therapy and were more likely to need ICU admission and mechanical ventilation compared with the term group. The mean ±SD BSS for infections with human metapneumovirus, respiratory syncytial virus, parainfluenza 3 was more significantly severe in preterm compared with term infants. Bacterial co-infection was significantly correlated with severity scoring in both groups. CONCLUSION: Prematurity significantly affects the severity of bronchiolitis, and this underscores the importance of early categorization of these infants as a high-risk group on their first visit. Physician should be aware that their illness runs a more severe course, even if they have no underlying disorders.

Viral causes of acute respiratory infection among Egyptian children hospitalized with severe acute asthma exacerbation.

BACKGROUND: Viral respiratory infections are associated with nearly 80% of asthma exacerbation episodes. These can have severe adverse outcomes in patients with established asthma. AIM: The aim of the study was to identify the viral causes of acute respiratory infection that precipitate acute asthma exacerbation in Egyptian asthmatic children. PATIENTS AND METHODS: The current prospective study was conducted in Cairo University Children's Hospitals from December 2010 to December 2011. All asthmatic children (n=130) aged 2-12 years admitted with asthma exacerbation due to severe lower respiratory tract infection were included. All cases were subjected to nasopharyngeal or throat swabs that were analyzed for common respiratory viruses, including respiratory syncytial virus (RSV), human metapneumovirus (hMPV), influenza B (Flu B), human parainfluenza virus (hPIV), influenza A (H1N1), and adenovirus (ADV) using the real-time PCR technique. All patients were followed up to record the outcome. RESULTS: PCR analysis was positive for one respiratory virus in 54 asthmatic patients (41.5%) and was negative in 76 patients (58.5%), with a high predominance of RSV (51.9%) and hMPV (25.9%) especially in winter and early spring months. Hypoxia was detected in all patients with RSV infection; of these patients, 21.4% were admitted to the ICU, 14.3% required mechanical ventilation, and 14.3% died. In contrast, among those with hMPV infection, hypoxia was detected in 71.4%; none required ICU admission or mechanical ventilation. CONCLUSION AND RECOMMENDATIONS: Viral etiology of lower respiratory tract infections constitutes an important cause of acute asthma exacerbation in asthmatic children admitted to children's hospitals in Cairo, supporting the need for large-scale multicentric studies on asthmatic patients over multiple years using a wider-panel PCR for detection of respiratory viruses.

Detection of the first G6P[14] human rotavirus strain from a child with diarrhea in Egypt.

We report the first detection of a G6P[14] rotavirus strain in Egypt from the stool of a child participating in a hospital-based diarrhea surveillance study conducted throughout the year 2004. Rotavirus infection was initially detected using a rotavirus group A VP6 enzyme immunoassay; the P (VP4) and G (VP7) genotypes of the strain were identified by RT-PCR. We sequenced the VP7 gene and the VP8* portion of the VP4 gene and the strain displayed the strongest identity to the VP7 [>94% nucleotides (nt), >97% amino acids (aa)] and VP4 (>93% nt, >98% aa) sequences of PA169, a novel G6P[14] strain first isolated from a child in Italy during the winter of 1987. Additional sequencing and analysis of the other remaining structural (VP1-VP3, VP6) and non-structural (NSP1-NSP5) proteins support this animal-to-human reassortment theory. According to the full genome classification system, the G6P[14] strain (EGY3399) was assigned to G6-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3 genotypes. The greatest similarity of EGY3399 NSP4 and NSP5 gene sequences were to those of ovine and simian origin, respectively. Coupled with other observations, our results suggest G6P[14] isolates rarely cause severe diarrhea in Egyptian children, and support other studies that indicate animal rotavirus contribute to the genetic diversity of rotavirus detected from humans through interspecies transmission and single or multiple segments reassortment.

The epidemiology of rotavirus diarrhea in countries in the Eastern Mediterranean Region.

OBJECTIVE: Rotavirus is the leading cause of severe diarrhea among children worldwide, killing approximately 600,000 children annually, including 64,800 in the Eastern Mediterranean Region. Safe, effective rotavirus vaccines will be available soon, and accurate disease burden data will be needed to assess the burden of rotavirus and the value of new vaccines and monitor vaccine program impact. METHODS: To identify epidemiologic studies in which rotavirus diagnostics were applied to children with acute gastroenteritis, we performed a systematic literature review. We selected studies that met 4 criteria and extracted rotavirus data on prevalence estimates, strain identification, age distribution of patients, and seasonal trends. RESULTS: Of the 63 published studies with some rotavirus detection data, 29 met inclusion criteria. Among patients with diarrhea, rotavirus was detected in 40% of inpatients and 23% of outpatients. By 3 years of age, 75% of children experienced a documented rotavirus infection. Circulation of rotavirus occurred year-round, and no clear relationship between the timing of the rotavirus peak with either season or latitude was observed. Comparison of country-specific rotavirus detection rates indicated that the proportion of hospitalizations for rotavirus infection increased with income. CONCLUSION: This systematic review of studies of rotavirus diarrhea among children in the countries of the Eastern Mediterranean Region documents that rotavirus is one of the most significant causes of childhood diarrhea in the region. The findings of this review will be used to establish sentinel hospital surveillance in these countries, estimate disease burden, and characterize its epidemiology using common protocols and diagnostics.

Sensitivity and specificity of various tests for the diagnosis of Helicobacter pylori in Egyptian children.

OBJECTIVES: Many noninvasive methods (using breath, blood, and stool samples) are available to diagnose Helicobacter pylori. However, because the noninvasive tests are proxy measures of the infection, they need validation before use. Factors that may affect test validity include patient age, gender, and geographic location. Because no data were available on the validation of noninvasive tests for the diagnosis of H. pylori among children in the Middle East, this study was performed. METHODS: Children between 2 and 17 years of age evaluated at the Cairo University School of Medicine pediatric gastroenterology clinic who were already scheduled for upper endoscopy were eligible for enrollment in the study. At the time of endoscopy, 3 biopsies were collected and used for rapid urease, histology, and culture, respectively. All children also donated a sample of stool and blood and had a urea breath test performed. Stool and serum samples were tested for the presence of H. pylori by using commercially available enzyme-linked immunosorbent assay-based technology. The sensitivity, specificity, and positive and negative predictive values were calculated for each noninvasive test used in the study. Receiver operating curves also were charted to determine optimal cut points for the various tests when used in the current study cohort. RESULTS: One hundred eight children were enrolled in the study, with 52 children being under 6 years of age. The urea breath test and HpStar (DakoCytomation, Norden, Denmark) stool enzyme-linked immunosorbent assay kit had the highest sensitivity and specificity (sensitivity and specificity: 98 and 89 [urea breath test] and 94 and 81 [HpStar], respectively), whereas the serologic kit had an unacceptably low sensitivity (50%). The sensitivity of neither the urea breath test nor the HpStar tests was affected by subject age, but specificity of the HpStar test, although still high, was significantly lower among children under 6 years. Receiver operating curves found optimal cut points of the urea breath test at 6.2 delta over baseline and of the HpStar at 0.25 enzyme-linked immunosorbent assay units. CONCLUSION: The urea breath test and HpSTAR stool antigen kit are reliable tests for the noninvasive diagnosis of H. pylori among children living in the Middle East.

Universal high-level primary metronidazole resistance in Helicobacter pylori isolated from children in Egypt.

Antimicrobial susceptibility testing was performed on 48 isolates of Helicobacter pylori recovered from Egyptian children undergoing routine endoscopies. The isolates were universally highly resistant to metronidazole, but resistance to other tested antimicrobial agents was rare (4% for clarithromycin, erythromycin, and azithromycin resistance versus 2% for ciprofloxacin and ampicillin resistance). Use of metronidazole for the treatment of H. pylori in Egypt should be avoided.