Signs Of Respiratory Infection Research Articles

Influence of Microbiota on Clinical Expressions of Respiratory Viral Infections.

Respiratory infections, mainly due to viruses, are among the leading causes of worldwide morbidity and mortality. We investigated the prevalence of viruses and bacteria in a cross-sectional survey conducted in Dielmo, a village in rural Senegal with a population of 481 inhabitants. Nasopharyngeal sampling was performed in 50 symptomatic subjects and 101 asymptomatic subjects. Symptomatic subjects were defined as individuals presenting with clinical signs of respiratory infection, whereas asymptomatic subjects were recruited in the same households. The identification of pathogens was performed by polymerase chain reaction for 18 respiratory viruses and eight respiratory bacteria. The prevalence results for respiratory viruses detected in each study group demonstrated that 83.6% of symptomatic samples were positive for at least one respiratory virus, and 21.8% were detected in asymptomatic samples. Influenza A (P = 0.0001), metapneumovirus (P = 0.04), and enterovirus (P = 0.001) were significantly more prevalent in symptomatic patients. Overall, 82.0% of symptomatic subjects and 26.9% of asymptomatic subjects were positive for at least one respiratory bacterium. The most frequent pathogenic bacteria detected were Moraxella catarrhalis (56%) and Streptococcus pneumoniae (48.0%) among symptomatic individuals, whereas in asymptomatic subjects Corynebacterium propinquum was more prevalent (18%). A principal component analysis showed that parainfluenzas 2 and 4 were associated with asymptomatic subjects, whereas influenza A was associated with the presence of symptoms. Considering these results, a large epidemiological surveillance of the circulation of these respiratory pathogens in the general population should be conducted to provide a better understanding of their carriage and to potentially prevent epidemics.

The Incidence and Factors Affecting the 28-day Hospital Admission Among Adult Ambulatory COVID-19 Patients

Objective: This study aimed to determine the 28-day hospital admission incidence and risk factors related to the hospitalization of COVID-19 patients who were followed as outpatients in a university hospital. Methods: A retrospective cohort study was designed in which the sociodemographic characteristics, symptoms on the first visit, presence of comorbidities, and viral load predictor cycle threshold (Ct) value were defined as independent variables and hospital admission in the first 28 days after the first visit was defined as dependent variable. Factors related to hospital admission were evaluated with univariate and multivariate analyses. Cox regression analysis was used for multivariate analyses, and the effect size was determined with a hazard ratio (HR). Statistical significance was defined as p<0.05. Results: 368 patients were included in this study. The median (25-75th percentile) age was 36 (28-45) years, and 46.1% of the patients were female. Sixty-five patients (17.7%) were hospitalized in the first 28 days. When age ≤29 referenced, age≥50 (HR=4.1, 95% confidence interval [CI]=1.7-9.6), 40-49 (HR=3.0, 95% CI=1.3-6.6) and 30-39 (HR=1.6, 95% CI=0.6-3.6), fever or chills, (HR=2.3, 95% CI=1.3-4.1), dyspnea (HR=2.0, 95% CI=1.1-3.4), fatigue (HR=1.9, 95% CI=1.0-3.5), vomiting (HR=3.0, 95% CI=1.5-5.8), and sore throat (HR=0.4, 95% CI=0.2-0.8) were defined as independent risk factors according to multivariable analysis. Hypertension was the only comorbidity independently predicting hospital admission (HR=2.2, 95% CI=1.0-4.4). Conclusion: Advanced age, systemic and lower respiratory tract infection signs, and hypertension independently increased the 28-day hospital admission. The presence of a sore throat was not a factor for hospital admission. A lower risk of hospital admission in patients with sore throats may indicate that the patient will have a mild upper respiratory tract infection and will not progress to severe disease. Due to missing data, this study could not fully evaluate the hospital admission risk factors. Studies that include clinical, laboratory, and radiological findings are needed to generate a more accurate model predicting hospital admission risk.

Detection of infectious bronchitis virus in chicken in Kerala by real time Taqman RT-PCR assay

Chickens with signs of respiratory infection were screened for the presence of infectious bronchitis virus (IBV). Tissue samples were collected from dead and ailing chickens and were propagated intra-allantoically in embryonated chicken eggs and the allantoic fluid was harvested. The tissue samples and harvested allantoic fluid were probed with reverse transcriptase polymerase chain reaction (RT-PCR) with primers targeting 5’UTR of IBV. A total of 95 samples were tested, by RT-PCR. A Taqman probe labelled real time PCR assay targeting the 5’ UTR and Nucleocapsid (N) gene of IBV was standardised for the detection of IBV in all the 95 tissue and allantoic fluid samples to assess its efficiency. The real time PCR could detect IBV in all the 95 allantoic fluid and tissue samples including the samples, which were negative in preliminary detection. Hence, in the present study, the real time PCR assay was found to have equal efficacy on clinical samples and allantoic fluid and with a sensitivity of 100% and specificity of 90.90% in comparison with the conventional RT-PCR assay.

Changes in serotype distribution of <i>Streptococcus pneumonia</i> circulating among children in the Russian Federation after 13-valent pneumococcal conjugate vaccine introduction.

During a prospective multicenter non-interventional observational study, a comparative assessment was made of the serotype structure of pneumococci circulating among healthy children under the age of 5 years and children of the same age group with signs of respiratory infections in the periods 2016-2018 and 2020-2022. Data on the serotype structure of pneumococci in the period from 2016-2018 were obtained from our previous works. In 2020-2022 the study included 2066 healthy children and 603 children with respiratory infections. Streptococcus pneumoniae and their DNA were detected in nasopharyngeal swabs by classical culture and molecular methods. Typing was carried out by molecular methods. On the territory of the Russian Federation, pneumococci belonging to the serotypes included in the 13-valent vaccine are being forced out of circulation and replaced by non-vaccine serotypes. Before the introduction of mass antipneumococcal vaccination (until 2015), the 13-valent conjugate vaccine covered from 66.2% to 92% of pneumococci, after the start of mass anti-pneumococcal vaccination in the period 2016-2018, coverage decreased to 57.3%. Between 2020 and 2022, coverage was less than 40%. The main “non-vaccine” serotypes/serogroups circulating in the Russian Federation are 15AF, 11AD, 23A, 9LN and 16F.

Aetiology of Acute Undifferentiated Fever Among Children Under the Age of Five in Vietnam: A Prospective Study

BackgroundTo investigate the aetiology of acute undifferentiated fever (AUF) among children under the age of five in Vietnam.MethodsThis prospective study was conducted in the Thai Binh paediatric hospital, between July 2020 and July 2021 among children with AUF at admission. Real-time PCR testing 18 microbial pathogens were done on blood samples.Results286 children were included, with median age of 16 months. 64.7% were male. 53.9% were positive for at least one pathogen by PCR. Enterovirus, human herpesvirus 6, adenovirus, and varicella zoster virus PCR were positive for 31.1, 12.6, 1.4, and 1.0% patients, respectively. Other pathogens tested negative by PCR. During the hospital stay, based on clinical criteria 47.2% children secondarily presented with signs of respiratory tract infections, 18.9% had hand, foot and mouth disease, 4.6% had chickenpox. 4.2% presented signs of central nervous system infections, 1.0% had dengue (antigenic test) and 1.0% had signs of gastrointestinal infection. Finally, 23.1% patients presented a fever with or without a rash and no other symptoms and ultimately received a diagnosis of AUF.ConclusionReal-time PCR of blood is useful for detecting pathogens and diagnosing infectious causes of AUF. Further prospective studies with blood and urine culture testing and PCR investigation of not only blood but also cerebrospinal fluid, throat, and skin samples according to symptoms would be of interest to confirm the predominance of viral infections in children with AUF and to guide therapeutic options.

Quantitative PCR for the Diagnosis of HCMV Pneumonia in HSCT Recipients and Other Immunocompromised Hosts

Pneumonia is among the most serious manifestations of HCMV infection, with high morbidity and mortality. Probable pneumonia is defined as the detection of HCMV in bronchoalveolar lavage (BAL) by viral isolation or DNA quantification (qPCR) combined with symptoms and/or signs of respiratory infection. However, currently, there is no reproducible and well-defined viral load (VL) from BAL that can reliably differentiate patients with pneumonia from the much more common detection of viral DNA in seropositive patients without true HCMV pneumonia. Several studies have been published with the aim of establishing an optimal VL for differentiating pneumonia from viral lung shedding. The aim of this review is to collect and analyze the methodology and the conclusions obtained in studies whose objectives included the correlation between HCMV VL in BAL and/or the plasma and the occurrence of HCMV pneumonia. For this purpose, a total of 14 articles have been included. There are some conclusions on which they all agree. PCR techniques were more sensitive and had a higher NPV than culture techniques but were less specific and had a low PPV. The mean HCMV loads in both BAL and the plasma were significantly higher in patients with pneumonitis than in those without. The HCMV load in patients with pneumonitis was higher in BAL than in the plasma, making qPCR in BAL a better predictor of HCMV pneumonitis than in the plasma. Nevertheless, this review highlights the difficulty of establishing a universal VL value, both in BAL and in the blood, to differentiate patients with HCMV pneumonia from those without. To complete the information available in these studies, prospective multicentre studies would be required. Methodologically, a large number of patients with HCMV pneumonitis would have to be included, and a subclassification of the type of immunosuppression of each patient should be made in order to obtain an optimal VL threshold in different host groups.

Covid-19-Pandemie: Empfehlungen zur Infektionsprävention in Optometriepraxen

Purpose. The recommendations justify infection control measures to minimize SARS-CoV-2 transmission in optometry practices. Material and Methods. During January 2020 to September 2022, a literature search on infection control of COVID-19 was conducted in NCBI PubMed, Web of Science, Cochrane COVID-19 study register, WHO COVID-19 Global Literature on Coronavirus linked to the keywords SARS-CoV-2 and COVID-19 with the following links: Transmission, tenacity, risk assessment, screening, protective measures, vaccination, virucidal disinfection, virucidal antisepsis and post-exposure prophylaxis. Results. While the primary vector of transmission of SARS- CoV-2 is the inhalation of virus particles via the oro-naso- pharyngeal path, ocular means of transmission also have to be considered. Especially hand to eye contacts present a danger. Vaccination proves to be effective for decreasing difficult disease progressions and transmission. Surgical masks are effective tools for slowing the spread of SARS-CoV-2, especially when considered as “source-control” when worn by potentially infectious persons. Hand antiseptics, mucous membrane antiseptics and surface disinfectants declared as “limited virucidal” are effective against SARS-CoV-2. Since viral particles remain potentially infectious for up to several days, proper surface disinfection is crucial. Conclusion. Infection control concepts in optometry practic- es have to incorporate interruption of all transmission path- ways of SARS-CoV-2 in this professional field. Professionals and patients should wear surgical masks. Staff should wear masks with a higher protective standard (for example CN95/ FFP2) when treating patients with symptoms of respiratory infections. Personnel should be vaccinated and trained in hand antisepsis. The indications for surface disinfection of critical surfaces and equipment must be maintained. Any staff showing signs of respiratory infections is to be tested immediately; contacts to COVID-19 positive persons have to be tested for 5 d daily. After contact with possibly or definitely infectious person virucidal gargling and virucidal nose spray may prove beneficial. Keywords SARS-CoV-2, tenacity, anamnestic risk assessment, infection control, personal protective equipment, disinfection, antisepsis, screening, post-exposure prophylaxis

Highlighting the Treatment Regimens used in COVID-19 epidemic in Iraq with Special Regards to Vitamin D

Coronavirus disease 2019 (COVID-19) is a flu-like infection caused by a novel virus known as Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). After the widespread around the world, it was announced by the World Health Organization (WHO) as a global pandemic. The symptoms of COVID-19 may arise within 2 weeks and the severity ranged from mild with signs of respiratory infection to severe cases of organ failure and even death. Management of COVID-19 patients includes supportive treatment and pharmacological medications expected to be effective with no definitive cure of the disease. The aims of this study are highlighting the management protocol and supportive therapy especially vitamin D and manifesting the clinical symptoms by patients in Iraq. An observational study was conducted on 200 patients and descriptive parameters for data were calculated to analyze the results. The mean age was 42.56±17.49 years and the majority of patients were presented with mild to moderate symptoms (78%). There were many different pharmacological treatment regimens and random doses and duration of vitamin D were taken by the patients. In conclusion, a non-specific treatment protocol was used for the patients without compliance to the national guidelines for management and treatment of COVID-19 patients in Iraq with the administration of a wide range of pharmaceutical agents that required monitoring for their safety and efficacy. Vitamin D is administered in different doses and duration without depending on the basal serum concentration.

Impact of Streptococcus pneumoniae colonization in upper airway on the clinical manifestations of children with respiratory syncytial virus infection

Objective: To investigate the effects of Streptococcus pneumoniae (Spn) colonization and the change of upper airway microbiome on the clinical manifestations in children with respiratory syncytial virus (RSV) infection. Methods: A retrospective cohort included 508 RSV-infected children with pneumonia and hospitalized in Respiratory Department of Children's Hospital of Chongqing Medical University from July 2009 to July 2018. A total of 508 cases of RSV-infected children (RSV non-sequencing group) were divided into 2 groups: children with Spn airway colonization (RSV+Spn group) and children without with Spn airway colonization (RSV group) according to the detection for virus and bacteria in nasopharyngeal aspirate, and these 2 groups were compared in terms of clinical manifestations by chi-square test in different age groups. In addition, in RSV pandemic season from November 2018 to February 2020, nasopharyngeal aspirates were collected from 20 children hospitalized in Respiratory Department of Children's Hospital of Chongqing Medical University and infected with RSV but without any positive detection of bacteria (RSV 16 S-sequencing group) and from children undergoing surgery without any sign of respiratory infection (control group). The difference of microbiome detected by 16 S RNA sequencing was compared using rank sum test between RSV 16 S-sequencing group and control group, and also between children with severe and mild pneumonia in RSV 16 S-sequencing group. Results: A total of 508 RSV non-sequencing group included 346 males and 162 females, and the visiting age was 6 (2, 12) months. RSV group included 443 cases and RSV+Spn group included 65 cases. In the study 244 cases were aged <6 months and 264 cases were aged ≥6 months. In children aged ≥6 months of RSV non-sequencing group, the proportion of cases presenting fever over 38 ℃ and cases with severe pneumonia in RSV+Spn group were higher than those in RSV group (53.2% (25/47) vs. 34.6% (72/217), 38.3% (18/47) vs. 21.2% (46/217), χ²=5.70,6.15, both P<0.05). RSV 16 S-sequencing group included 16 males and 4 females and the visiting age was 3.0 (1.9, 8.0) months. Airway microbiome diversity in RSV 16 S-sequencing group was lower than that in control group (alpha index: 0.93 (0.42, 2.51) vs. 3.05 (2.88, 3.61), U=60.00, P=0.001). Conclusions: RSV infection is associated with the changes of the upper airway microbiome. When the balance of airway microbiome is broken and the presence of the dominant colonization of Spn follows, it may aggravate the severity of RSV infection in children aged ≥6 months.

The Effects of the 'Catabolic Crisis' on Patients' Prolonged Immobility after COVID-19 Infection.

Background and Objectives: Quarantine, isolation and bed rest associated with COVID-19 infection favored the loss of muscle and bone mass, especially in elderly patients. The current study aims to compare the presence of sarcopenia and osteoporosis in patients with a recent (one month) history of SARS-CoV-2 infection versus the general population. Materials and Methods: A cross-sectional study was conducted in which 157 patients were enrolled, divided into two groups, comparable in structure. The COVID-19 group (group C) consisted of 86 patients who were diagnosed with SARS-CoV-2 respiratory infection within the last 30 days. The non-COVID-19 group (group NC) consists of 71 patients who had no clinical signs of respiratory infection and were not quarantined/hospitalized in the last 3 months. Muscle strength, incidence of sarcopenia (using SARC-F score) and osteoporosis (DEXA determination) and physical performance (SPPB score) in the two groups were assessed and compared. Results: No statistically significant differences were found between the SPPB scores of the C group versus the NC group. Statistically significant differences were found in the evaluation of three parameters included in the SARC-F score. Patients in the C group had difficulties in standing up from a chair (p = 0.009) and climbing stairs (p = 0.030) due to lower muscle strength (p = 0.002) compared with patients in the NC group. No correlation of the SARC F and SPPB scores with the T score values obtained by osteo-densitometry was found. Conclusions: The sudden and significant reduction in physical activity, through various measures taken in the general population during the pandemic, led to an increased incidence of sarcopenia, both in patients who did not have COVID-19 infection and among those quarantined/hospitalized for this condition.

Clinical Outcome of Viral Respiratory Tract Infections in Hospitalized Adults in Norway: High Degree of Inflammation and Need of Emergency Care for Cases With Respiratory Syncytial Virus.

BackgroundThe clinical features and outcomes of viral respiratory tract infections (RTIs) in adults have not been thoroughly studied, especially the respiratory syncytial virus (RSV) disease burden. It has become apparent that outbreaks of RSV in the elderly are associated with increased hospitalization rates. However, little data exists on the severity of such viral RTIs in adults, particularly the need for hospitalization, respiratory support and intensive care.MethodsWe conducted a retrospective observational single-center study at Østfold Hospital Trust, Norway, during three winter seasons 2015–2018. Patients ≥18 years with either influenza A, influenza B, RSV A/B, human metapneumovirus, parainfluenza virus 1–4 or adenovirus detected in respiratory specimens were included, if they were hospitalized 14 days prior or following the detection date, with signs of RTI. Hospital records on treatment and outcome were investigated, as well as mortality of all causes up to 30 days from discharge.ResultsOf the 1222 infection events that were included, influenza A was the most frequent virus detected (39%), while 179 infection events (14.6%) were due to RSV. Influenza B counted for 24% of the infection events, human metapneumovirus 13%, parainfluenza virus 9% and adenovirus 1%. Patients admitted with RSV more often suffered from COPD and congestive heart failure than patients with influenza A. In addition, RSV patients were overrepresented in the urgent response NEWS score (National Early Warning Score) category ≥5. RSV patients also showed signs of more severe inflammation, with WBC ≥11.1 × 109/L and CRP >100 mg/L, and they were more often treated with antibiotic agents during their hospital stay. However, we found no differences in the need for ICU admission or mortality.ConclusionPatients with RSV had more often high values for markers of inflammation and elevated NEWS score when compared to patients hospitalized with other common respiratory viruses. Taken into account that they suffered more frequently from comorbidities like COPD, these patients needed hospitalization more urgently. These findings highlight the need for further investigations on RSV disease in adults and the elderly.

A Narrative Review on the Approach to Antimicrobial Use in Ventilated Patients with Multidrug Resistant Organisms in Respiratory Samples-To Treat or Not to Treat? That Is the Question.

Multidrug resistant organisms (MDRO) are commonly isolated in respiratory specimens taken from mechanically ventilated patients. The purpose of this narrative review is to discuss the approach to antimicrobial prescription in ventilated patients who have grown a new MDRO isolate in their respiratory specimen. A MEDLINE and PubMed literature search using keywords “multidrug resistant organisms”, “ventilator-associated pneumonia” and “decision making”, “treatment” or “strategy” was used to identify 329 references as background for this review. Lack of universally accepted diagnostic criteria for ventilator-associated pneumonia, or ventilator-associated tracheobronchitis complicates treatment decisions. Consideration of the clinical context including signs of respiratory infection or deterioration in respiratory or other organ function is essential. The higher the quality of respiratory specimens or the presence of bacteremia would suggest the MDRO is a true pathogen, rather than colonization, and warrants antimicrobial therapy. A patient with higher severity of illness has lower safety margins and may require initiation of antimicrobial therapy until an alternative diagnosis is established. A structured approach to the decision to treat with antimicrobial therapy is proposed.

Covid-19 analysis using chest X-rays and CT-scan

COVID-19 is commonly known as a novel coronavirus disease, which is a highly contagious disease that emerged in China in late 2019. This disease is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is a virus belonging to the large family of coronaviruses. The disease first emerged in Wuhan, China in 2019 and then quickly developed into a global pandemic, spreading to more than 213 countries. The well-known symptoms of COVID-19 are fever, shortness of breath, dry cough, and other symptoms. Pain or difficulty breathing may occur. Most of these symptoms point to signs of respiratory infections and lung abnormalities that can be detected by radiologists. So, chest xray and computed tomography images can be used with machine learning algorithms to find the disease.

The effect of standard-dose wintertime vitamin D supplementation on influenza infection in immunized nursing home elderly residents

AimTo investigate whether three-month oral vitamin D supplementation (800 IU in drops) reduces the risk of influenza infection in elderly nursing home residents vaccinated against influenza.MethodsThis cross-sectional observational study enrolled 97 participants (73.2% women) who received one dose of seasonal trivalent 2016-2017 influenza vaccine. The patients were randomized into an experimental group, which received vitamin D supplementation for three months starting on the day of vaccination, and a control group, which did not receive vitamin D supplementation. The primary outcome was the number of influenza infections laboratory-confirmed using a rapid point-of-care test based on nasal swabs collected during vitamin D supplementation. The secondary outcome was serum 25-hydroxyvitamin D level at the end of the study.ResultsThe mean age ±standard deviation was 78.5± 8.8 years. All participants had vitamin D deficiency at baseline. Twenty-three participants who developed signs of respiratory infections during the study were tested for influenza virus. Although the number of influenza-positive participants was lower in the group receiving vitamin D supplementation as compared with the control group (5 vs 12), this difference was not significant. Vitamin D supplementation failed to increase 25(OH)D levels after three months of supplementation.ConclusionElderly nursing home residents in Zagreb County have a significant vitamin D deficiency. The recommended national supplementation of 800 IU daily failed to lead to vitamin D sufficiency and did not reduce the risk of influenza infection among the vaccinated elderly.

Assessment of aerosolized Colistin and Gentamicin in mechanically ventilated patient

Abstract Background and Objectives ineffective parental antibiotic use in treatment of Ventilator associated pneumonia (VAP) open the window for using inhaled antibiotic formula to achieve higher local concentration of antibiotics and subsequently good recovery response, the aim of that work was evaluation of aerosolized antibiotics (Colistin and Gentamicin) efficacy in improving the mechanically ventilated patient as adjunctive to intravenous systemic antibiotics Methods 30 mechanically ventilated patients classified equally in to 3 groups; Group I 10 patients received aerosolized Colistin along with systematic antibiotics (SA). Group II: 10 patients received aerosolized Gentamicin along with systematic antibiotics (SA) and Group III (Control): 10 patients received only systematic antibiotics (SA). All patients were followed up for clinical response by bacteriological culture (after 5 days of aerosolized antibiotics), development of VAP, days of mechanical ventilation, length of stay in the ICU, and mortality. Results The incidence of VAP was 10%; in group I no cases had VAP, while in group II and control group, just (20%) and (10%) of cases had VAP respectively, with insignificant association of VAP with particular group, (P = 0.3). Clinically; only group I showed significant lower degree of temperature in comparison with control group, (P = 0.01). The mean days of MV and ICU in each groups were (6.8±2.15; 8.9±3.11, 5.9±2.23; 7.2±2.7, 5.1±1.1; 6.1±1.85) respectively, with insignificant statistical difference between the treatment groups, (P = 0.2 and 0.07) respectively. Finally, the survival rate in group I was 90%, and was slightly lower in group II and control group; 60% and 50% respectively, with insignificant association of survival status in particular group, (P = 0.1) Conclusion the empirical treatment by AA (Colistin) was effective as an adjuvant to systemic antibiotics for protection of VAP than aerosolized Gentamicin, it had rapid resolution of respiratory infection signs, and subsequently the mechanical ventilation days, ICU stay days, and probably the cost of ICU admission, but did not affect mortality.

Decline in pneumococcal nasopharyngeal carriage in children 6–23 months with respiratory illnesses following pneumococcal conjugate vaccine implementation

BackgroundFollowing pneumococcal conjugate vaccines (PCVs) implementation, worldwide, pneumococcal carriage rates remained stable, indicating full replacement of vaccine-serotypes (VT) with non-VT. However, data are scarce regarding PCV impact on pneumococcal carriage rates in healthy vs. sick children. We assessed pneumococcal carriage rates dynamics in healthy and sick children 6–23 months, following PCV introduction. MethodsThis is a prospective, population-based surveillance conducted during the years 2009–2017, in southern Israel. Three groups were defined as follows: Children without respiratory infection signs (the healthy/non-respiratory group); Children who had a chest radiography at the hospital (the Hosp-CXR group); and children with community-acquired alveolar pneumonia (CAAP).Rate ratios (RRs; 95% CI) were calculated, comparing between late-13-valent PCV (PCV13) period (2016–2017) and early-PCV period (2009–2010). Rate ratios were adjusted for antibiotic administration, seasonality and ethnicity, and separate calculations were performed for 6–11 and 12–23 month old children. ResultsOverall, 51% of 8627 nasopharyngeal cultures were positive.In 2009–2010 (early-PCV period), the overall carriage rate was 55%; serotypes included in the PCV13 carriage rates were 28%, 31% and 38% in the healthy/non-respiratory, Hosp-CXR, and CAAP groups, respectively.Overall carriage rates in healthy/non-respiratory episodes were stable (~54%) when comparing between 2016 and 17 and 2009–10 (RR = 0.98; 0.84–1.15). In contrast, rates significantly declined for Hosp-CXR (RR = 0.78; 0.63–0.98) and CAAP (RR = 0.65; 0.47–0.89). These trends were driven by ~ 80% VT reductions, coupled with non-VT increase. ConclusionsFollowing 7-valent PCV/ PCV13 introduction, pneumococcal carriage rates declined in respiratory diseases, but not in healthy children and children without respiratory infections. These trends suggest that a reduction in pneumococcal carriage rates during respiratory infections indicates a decline in respiratory infections caused by VT, while carriage rates in non-respiratory cases reflect non-VT predominance, that have low disease potential for respiratory disease.

COVID-19 Pandemic and Hemodialysis: Disease Parameters and Outcome: Single Center Study

Background: Coronavirus disease 2019 (COVID-19) has significantly affected the provision of medical services. The hemodialysis (HD) facilities together with other medical facilities faced challenges in safely providing clinical care to patients and staff during the pandemic. Objective: To describe our experience during the COVID-19 pandemic as regard infection, mortality rate, clinical manifestations, illness duration and the efficacy of our local infection control measures in our Hemodialysis Unit, Ain Shams University Hospital, Cairo, Egypt. Patients and Methods: followed the interim guidance provided by the US Centers for Disease Control and Prevention (CDC) together with the European Renal Association– European Dialysis Transplantation Association (ERA-EDTA) for dealing with the emerging COVID19 pandemic in HD centers. The study included 238 patients on regular HD from Dialysis Unit in Ain Shams University Hospitals. We monitored all patients and staff members for any symptoms or signs of respiratory tract infection and those confirmed to have COVID-19 infection were followed up through their illness. Results: 42 out of total 238 patients were diagnosed to have COVID19 infection by combination of symptoms, chest imaging and SARS COV PCR. Their mean age was 49.8 ± 8.9 years, 19 were males, the mean ± SD total illness duration for all COVID-19 positive patients was 17 ± 8.7. Patients were further subdivided based on survival into cure group (34 patients) and death group (8 patients). CRP and D-dimer were all significantly higher in death group while O2% were significantly lower in death group compared to cure group. Conclusion: COVID 19 pandemic still a major health problem worldwide with significant morbidity and mortality among hemodialysis patients. © 2021, Ain Shams University Faculty of Medicine. All rights reserved.

A host transcriptomic signature for identification of respiratory viral infections in the community.

Fever-7 is a test evaluating host mRNA expression levels of IFI27, JUP, LAX, HK3, TNIP1, GPAA1 and CTSB in blood able to detect viral infections. This test has been validated mostly in hospital settings. Here we have evaluated Fever-7 to identify the presence of respiratory viral infections in a Community Health Center. A prospective study was conducted in the "Servicio de Urgencias de Atención Primaria" in Salamanca, Spain. Patients with clinical signs of respiratory infection and at least one point in the National Early Warning Score were recruited. Fever-7 mRNAs were profiled on a Nanostring nCounter® SPRINT instrument from blood collected upon patient enrolment. Viral diagnosis was performed on nasopharyngeal aspirates (NPAs) using the Biofire-RP2 panel. A respiratory virus was detected in the NPAs of 66 of the 100 patients enrolled. Median National Early Warning Score was 7 in the group with no virus detected and 6.5 in the group with a respiratory viral infection (P>.05). The Fever-7 score yielded an overall AUC of 0.81 to predict a positive viral syndromic test. The optimal operating point for the Fever-7 score yielded a sensitivity of 82% with a specificity of 71%. Multivariate analysis showed that Fever-7 was a robust marker of viral infection independently of age, sex, major comorbidities and disease severity at presentation (OR [CI95%], 3.73 [2.14-6.51], P<.001). Fever-7 is a promising host immune mRNA signature for the early identification of a respiratory viral infection in the community.

Genotypes of rhinovirus detected among children in two communities of South-West Nigeria.

Rhinoviruses (RVs) are the most common etiological agent implicated in respiratory infections among infants and children. There are currently no approved antivirals and vaccine for use against the virus; hence, the need for information on the genotypes of rhinovirus from developing countries of the world with high burden of the infection. This study determined the genotypes of rhinovirus circulating among children in selected cities in Nigeria. Nasopharyngeal and oropharyngeal samples were carefully collected from children showing signs of respiratory infection in two communities in South-west Nigeria. Polymerase Chain Reaction was used to amplify the hypervariable part of the 5'- non-coding region, the entire viral protein gene 4 and the 5' terminus of the VP2 gene of RV. Nucleotide BLAST and phylogenetic analyses were used to genotype the isolates. Of the samples analysed, 12.7% showed rhinovirus positivity. All the three genotypes of rhinovirus were detected with genotype C (71.4%), being the predominant. Multiple strains of rhinovirus were found circulating. We showed for the first time the genotypes and strains of rhinovirus circulating in Nigeria. Further studies are required to highlight transmission patterns and disease severity among rhinovirus species in Nigeria.

High \u03b2-lactam resistance in Gram-negative bacteria associated with kennel cough and cat flu in Egypt

Antimicrobial resistance within pets has gained worldwide attention due to pets close contact with humans. This report examined at the molecular level, the antimicrobial resistance mechanisms associated with kennel cough and cat flu. 1378 pets in total were assessed for signs of respiratory infection, and nasal and conjunctival swabs were collected across 76 diseased animals. Phenotypically, 27% of the isolates were characterized by multidrug resistance and possessed high levels of resistance rates to β-lactams. Phenotypic ESBLs/AmpCs production were identified within 40.5% and 24.3% of the isolates, respectively. Genotypically, ESBL- and AmpC-encoding genes were detected in 33.8% and 10.8% of the isolates, respectively, with blaSHV comprising the most identified ESBL, and blaCMY and blaACT present as the AmpC with the highest levels. qnr genes were identified in 64.9% of the isolates, with qnrS being the most prevalent (44.6%). Several antimicrobial resistance determinants were detected for the first time within pets from Africa, including blaCTX-M-37, blaCTX-M-156, blaSHV-11, blaACT-23, blaACT25/31, blaDHA-1, and blaCMY-169. Our results revealed that pets displaying symptoms of respiratory illness are potential sources for pathogenic microbes possessing unique resistance mechanisms which could be disseminated to humans, thus leading to the development of severe untreatable infections in these hosts.