Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities

Throughout the COVID-19 pandemic, extensive research has been conducted on SARS-COV-2 to elucidate its genome, prognosis, and possible treatments. However, few looked at the microbial markers that could be explored in infected patients and that could predict possible disease severity. The aim of this study is to compare the nasopharyngeal microbiota of healthy subjects, moderate, under medication, and recovered SARS-COV-2 patients. In 2020, 38 nasopharyngeal swabs were collected from 6 healthy subjects, 14 moderates, 10 under medication and 8 recovered SARS-COV-2 patients at King Fahad Medical city. Metatranscriptomic sequencing was performed using Minion Oxford nanopore sequencing. No significant difference in alpha as well as beta diversity was observed among all four categories. Nevertheless, we have found that Streptococcus spp including Streptococcus pneumoniae and Streptococcus thermophilus were among the top 15 most abundant species detected in COVID-19 patients but not in healthy subjects. The genus Staphylococcus was found to be associated with COVID-19 patients compared to healthy subjects. Furthermore, the abundance of Leptotrichia was significantly higher in healthy subjects compared to recovered patients. Corynebacterium on the other hand, was associated with under-medication patients. Taken together, our study revealed no differences in the overall microbial composition between healthy subjects and COVID-19 patients. Significant differences were seen only at specific taxonomic level. Future studies should explore the nasopharyngeal microbiota between controls and COVID-19 patients while controlling for confounders including age, gender, and comorbidities; since these latter could affect the results and accordingly the interpretation.IMPORTANCEIn this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including Leptotrichia, Staphylococcus, and Corynebacterium were only observed. Leptotrichia was significantly higher in healthy subjects, whereas Staphylococcus and Corynebacterium were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.

Clinical Characteristics, Laboratory Findings, Management, and Outcome of Severe Coronavirus Disease 2019 in Children at a Tertiary Care Center in Riyadh, Saudi Arabia: A Retrospective Study

BACKGROUND

Numerous studies worldwide have reported COVID-19 in children; however, the clinical symptoms and consequences of COVID-19 in children have only been reported in a few studies in Saudi and gulf region. Therefore, we aimed to investigate the clinical features and outcomes of COVID-19 infection in children and the therapeutic interventions used.

METHODS

This retrospective cohort study included 96 patients with confirmed severe acute respiratory syndrome coronavirus 2 infection aged ≤14 years who were admitted to a tertiary governmental care hospital in Riyadh, Saudi Arabia between March 2020 and November 2020. Data on children with COVID-19, including demographics, comorbidities, symptoms, imaging and laboratory results, therapies, and clinical outcomes, were analyzed.

RESULTS

Of 96 children admitted with a confirmed diagnosis of COVID-19, 63.8% were aged ≤ 3 years, 52.1% were male, 56.2% had an unknown source of infection, and 51% had no comorbidities. Most cases had severe infection (71.88%) as they required oxygen, 10.42% of whom were critical. The most common symptoms were respiratory-related (98%), and the common physical sign was fever (49%). High D-dimer (90.7%) and C-reactive protein (72.09%) levels were found in most cases. Oxygen (71.88%) was the most commonly used treatment. Most patients were discharged home and fully recovered (97.92%). We reported two deaths (2.08%).

CONCLUSIONS

Our findings showed that the majority of the admitted children with COVID-19 were ≤3 years of age (52.1%) and infected with an unknown source (56.2%). Moreover, the majority of the cases had severe COVID-19 infection as they required oxygen (71.88%), although they had favorable outcomes. However, some cases were critical and resulted in death. Future studies will be crucial to better understand the disease spectrum and potential therapeutic options for COVID-19 in children.

Willingness, beliefs, and barriers regarding the COVID-19 vaccine in Saudi Arabia: a multiregional cross-sectional study

Background

The coronavirus disease 2019 (COVID-19) has spread worldwide, and the vaccine remains the ultimate cornerstone to overcoming its long-term impact. Vaccine hesitancy might obstruct the effort to achieve herd immunity and eradicate the virus. We assessed Saudi Arabian individuals’ willingness, beliefs, and barriers regarding the COVID-19 vaccine and their adherence to preventive measures during and after the pandemic.

Methods

A self-administered electronic validated questionnaire was distributed among the five major regions in Saudi Arabia between November and December 2020. The questionnaire addressed the sociodemographic data, beliefs, potential barriers, parents’ acceptance of COVID-19 vaccination for their children, and adherence to protective measures during and after the pandemic.

Results

Of 8,056 participants, 4,218 (52.4%) of a non-representative sample were willing to be vaccinated against COVID-19. Being a young adult, male, having less than a high school degree, being a smoker, having a chronic disease, and having a history of seasonal influenza vaccine uptake were positive predictors of COVID-19 vaccine acceptance. Hesitant participants reported concerns about vaccine side effects and safety as the main barriers to accepting the COVID-19 vaccine. Some refusers (26.1%) declared that they would reconsider vaccination only if the safety and effectiveness of the vaccine were reported by more studies.

Conclusions

Our study revealed a promising willingness to accept the vaccine among the population, with positive beliefs and attitudes toward COVID-19 vaccination. However, a considerable proportion of the population was reluctant to accept the vaccine. Thus, publicly providing information about vaccine safety and implementing health education programs is crucial for increasing the public’s confidence in the vaccine.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12875-021-01606-6.

Diagnosis and management of community-acquired urinary tract infection in infants and children: Clinical guidelines endorsed by the Saudi Pediatric Infectious Diseases Society (SPIDS)

Urinary tract infection (UTI) is the most common bacterial disease in childhood worldwide and may have significant adverse consequences, particularly for young children. In this guideline, we provide the most up-to-date information for the diagnosis and management of community-acquired UTI in infants and children aged over 90 days up to 14 years. The current recommendations given by the American Academy of Pediatrics Practice guidelines, Canadian Pediatric Society guideline, and other international guidelines are considered as well as regional variations in susceptibility patterns and resources. This guideline covers the diagnosis, therapeutic options, and prophylaxis for the management of community-acquired UTI in children guided by our local antimicrobial resistance pattern of the most frequent urinary pathogens. Neonates, infants younger than three months, immunocompromised patients, children recurrent UTIs, or renal abnormalities should be managed individually because these patients may require more extensive investigation and more aggressive therapy and follow up, so it is considered out of the scope of these guidelines. Establishment of children-specific guidelines for the diagnosis and management of community-acquired UTI can reduce morbidity and mortality. We present a clinical statement from the Saudi Pediatric Infectious Diseases Society (SPIDS), which concerns the diagnosis and management of community-acquired UTI in children.

Gut Hormones in Health and Obesity: The Upcoming Role of Short Chain Fatty Acids

We are currently facing an obesity pandemic, with worldwide obesity rates having tripled since 1975. Obesity is one of the main risk factors for the development of non-communicable diseases, which are now the leading cause of death worldwide. This calls for urgent action towards understanding the underlying mechanisms behind the development of obesity as well as developing more effective treatments and interventions. Appetite is carefully regulated in humans via the interaction between the central nervous system and peripheral hormones. This involves a delicate balance in external stimuli, circulating satiating and appetite stimulating hormones, and correct functioning of neuronal signals. Any changes in this equilibrium can lead to an imbalance in energy intake versus expenditure, which often leads to overeating, and potentially weight gain resulting in overweight or obesity. Several lines of research have shown imbalances in gut hormones are found in those who are overweight or obese, which may be contributing to their condition. Therefore, this review examines the evidence for targeting gut hormones in the treatment of obesity by discussing how their dysregulation influences food intake, the potential possibility of altering the circulating levels of these hormones for treating obesity, as well as the role of short chain fatty acids and protein as novel treatments.

Severity of Salmonella infection among sickle cell diseases pediatric patients: Description of the infection pattern

Introduction

Sickle cell disease (SCD) affects millions worldwide. It has a spectrum of clinical manifestations. However, SCD is more prone to have invasive infection compared with normal individual, and one of the main pathogen of concern is salmonella, where the individual with SCD is more susceptible to salmonella infection. Furthermore, several distinct clinical syndromes can develop in children infected with salmonella, depending on both host factors and the specific serotype involved

Objectives

We aim to describe the infection patterns and whole range of potential complications in children with SCD exposed to invasive salmonella infection.

Method

This is a retrospective observational cohort study which was conducted at King Fahad Medical City (KFMC), Riyadh, Saudi Arabia between 2012 and 2018. All sickle cell patients who are exposed to invasive salmonella infections and treated in our hospital over the last 6 years were included in our study.

Results

Six patients were enrolled in the study, five males and one female with ratio of (M: F) 5:1, age range from 20 months–14 years, and the diagnosis at admission were as follows: (three as vasooclusive crisis, three as infection) with different kind of infections (three sepsis, three septic arthritis, four osteomyelitis, one meningitis, one myositis, one periorbital cellulitis, one diskitis), where three (50%) suffered multiple sites of infections and the other three (50%) with one site of infection, two (50%) of osteomyelitis patients suffered multifocal infection. Species identification is as follows: (three group D, one group C, and two were not specified), only two occasions where resistant to ciprofloxacin while all others were pan sensitive. Fever was prolonged (take more than seven days to subside even with appropriate therapy and intervention) in five out of six.

Conclusions

Multiple site of infection, sever osteomylitis, and delay in fever response consolidated the fact of high virulence of salmonella in SCD patients. We did not encounter significant resistant rate to both quinolone and cephalosporin.

Invasive Candidiasis in pediatric patients at King Fahad Medical City in Central Saudi Arabia. A 5-year retrospective study

Objectives:

To identify predisposing factors, species distribution, antifungal susceptibility, and outcome.

Methods:

This study is a retrospective chart review that was conducted at a children’s hospital at King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia. One hundred twenty-nine children with invasive candidiasis who were admitted between January 2010 and January 2015.

Results:

The statistical analysis results have revealed a group of risk factors; prematurity in 37 (28.7%) of patients, low birth weight in 42 (32.6%), central venous catheter in 59 (45.7%), malignancy in 21 (16.3%), immunotherapy in 20 (15.5%), and ventilator support in 60 (46.5%). More than 2-fold mortality rate in patients who had heart vegetation (odds ratio [OR]: 2.9) and patients who had Candida isolated from their blood were more than twice as likely to die as patients with Candida isolated from other sites (OR: 2.2). A total of 48.3% of patients on ventilator died versus 26.1% who were not on ventilator (p=0.009); and 43.8% of patients in the ICU died versus only 24.5% of patients who were not in the ICU (p=0.03). Candida parapsilosis exhibited the highest mortality rate (56.2%).

Conclusion:

Candida albicans is the most common isolate among all Candida species. Gender, low birth weight, prolonged ICU stay, presence of vegetation, positive blood culture, and mechanical ventilation as a strong predictive risk factors for death in children with invasive candidiasis, a finding that could be applied as prophylactic indicator in critically ill children especially neonates.

Acute viral respiratory infections among children in MERS-endemic Riyadh, Saudi Arabia, 2012-2013

The emergence of the Middle East Respiratory Syndrome (MERS) in Saudi Arabia has intensified focus on Acute Respiratory Infections [ARIs]. This study sought to identify respiratory viruses (RVs) associated with ARIs in children presenting at a tertiary hospital. Children (aged ≤13) presenting with ARI between January 2012 and December 2013 tested for 15 RVs using the Seeplex^R RV15 kit were retrospectively included. Epidemiological data was retrieved from patient records. Of the 2235 children tested, 61.5% were ≤1 year with a male: female ratio of 3:2. Viruses were detected in 1364 (61.02%) children, 233 (10.4%) having dual infections: these viruses include respiratory syncytial virus (RSV) (24%), human rhinovirus (hRV) (19.7%), adenovirus (5.7%), influenza virus (5.3%), and parainfluenzavirus-3 (4.6%). Children, aged 9-11 months, were most infected (60.9%). Lower respiratory tract infections (55.4%) were significantly more than upper respiratory tract infection (45.3%) (P < 0.001). Seasonal variation of RV was directly and inversely proportional to relative humidity and temperature, respectively, for non MERS coronaviruses (NL63, 229E, and OC43). The study confirms community-acquired RV associated with ARI in children and suggests modulating roles for abiotic factors in RV epidemiology. However, community-based studies are needed to elucidate how these factors locally influence RV epidemiology. J. Med. Virol. 89:195-201, 2017. © 2016 Wiley Periodicals, Inc.