Molecular Testing for Respiratory Viruses

Respiratory pathogens carriage in guinea pigs raised as livestock in Ecuador: A proxy to study a neglected reservoir for zoonotic transmission in the Andean Region

In the Andean region of South America, guinea pigs (Cavia porcellus) are raised as livestock in close contact with other domestic animals and humans. Although the susceptibility of guinea pigs to being affected by a wide range of diseases is well known as a laboratory animal model, there are a few reports about the potential role of zoonotic pathogens in livestock guinea pigs. In this work, we analyzed the nasopharyngeal carriage of respiratory pathogenic viruses and bacteria in guinea pigs from farms in Ecuador. We isolated streptococci and aerococci cultures that were analyzed for species identification by MALDI-TOF MS. Several species, including Streptococcus pneumoniae, S. pseudopneumoniae, S. oralies, and S. mitis were found. Moreover, strains resistant to antibiotics like levofloxacin, erythromycin, and sulfamethoxazole-trimethoprim were also found. Our results suggest the role of guinea pigs as a zoonotic reservoir for occupational exposure to respiratory pathogens in the Andean region of South America, where guinea pig farming is an important industry.

Guidelines for Antibiotics Prescription in Critically Ill Patients

How to cite this article: Khilnani GC, Tiwari P, Mittal S, Kulkarni AP, Chaudhry D, Zirpe KG, et al. Guidelines for Antibiotics Prescription in Critically Ill Patients. Indian J Crit Care Med 2024;28(S2):S104-S216.

Epidemiologic and clinical updates on viral infections in Saudi Arabia

In the past two decades, the world has witnessed devastating pandemics affecting the global healthcare infrastructure and disrupting society and the economy worldwide. Among all pathogens, viruses play a critical role that is associated with outbreaks due to their wide range of species, involvement of animal hosts, easily transmitted to humans, and increased rates of infectivity. Viral disease outbreaks threaten public health globally due to the challenges associated with controlling and eradicating them. Implementing effective viral disease control programs starts with ongoing surveillance data collection and analyses to detect infectious disease trends and patterns, which is critical for maintaining public health. Viral disease control strategies include improved hygiene and sanitation facilities, eliminating arthropod vectors, vaccinations, and quarantine. The Saudi Ministry of Health (MOH) and the Public Health Authority (also known as Weqayah) in Saudi Arabia are responsible for public health surveillance to control and prevent infectious diseases. The notifiable viral diseases based on the Saudi MOH include hepatitis diseases, viral hemorrhagic fevers, respiratory viral diseases, exanthematous viral diseases, neurological viral diseases, and conjunctivitis. Monitoring trends and detecting changes in these viral diseases is essential to provide proper interventions, evaluate the established prevention programs, and develop better prevention strategies. Therefore, this review aims to highlight the epidemiological updates of the recently reported viral infections in Saudi Arabia and to provide insights into the recent clinical treatment and prevention strategies.

Practice of non-pharmaceutical interventions against COVID-19 and reduction of the risk of influenza-like illness: a cross-sectional population-based study

Introduction

While the widespread implementation of the non-pharmaceutical interventions was intended to contain the COVID-19 pandemic, such measures could be also effective in limiting the spread of other respiratory infections. This study aimed to examine the association between the implementation of personal protective measures and the occurrence of influenza-like illnesses (ILI) in the general population.

Methods

An online retrospective cross-sectional observational study was conducted in April 2021 to assess cases of ILI among Lebanese adults aged 18 years and above, from all Lebanese governorates during the 2020–2021 flu season. Data were collected using a convenience sampling method. In addition to their socio-demographic information, participants were asked about their frequency of implementing personal protective measures and if they have experienced symptoms of ILI in the previous 6 months. The overall score of the personal protective measures was computed. Multivariable logistic regression was performed to examine the association between participants’ level of adoption of personal protective measures against COVID-19 and the occurrence of ILI.

Results

Among the 1019 Lebanese adults participating in this study, 352 (34.54%) of them reported symptoms of ILI between October 2020 and March 2021. Lebanese adults who wore their facemasks frequently or always were less likely to suffer from symptoms of ILI than others who did not wear the mask (aOR = 0.452, 95% CI = 0.349–0.693, p < 0.001). Similarly, adults who adopt the following protective measures washing hands (aOR = 0.608, 95% CI = 0.524–0.922, p < 0.001), respecting cough etiquette (aOR = 0.763, 95% CI = 0.598–0.918, p < 0.001), disinfecting surface (aOR = 0.892, 95% CI = 0.632–0.911, p = 0.012), avoiding crowded places (aOR = 0.739, 95% CI = 0.688–0.903, p = 0.049), respecting physical distancing (aOR = 0.646, 95% CI = 0.482–0.833, p = 0.031) on a regular basis (frequently/always) were less likely to report symptoms of influenza-like illnesses when compared with those who did not adhere at all to these measures.

Conclusion

Our study highlighted the potential of personal protective measures against COVID-19 in reducing the transmission of respiratory infections such as ILI. Such findings might be invested during influenza season, particularly among groups at high risk of developing severe complications. Exploring trends detected by the national severe acute respiratory infection surveillance system is recommended to confirm the utility of these measures.

Sentinel surveillance for influenza A viruses in Lahore District Pakistan in flu season 2015-2016

Background

Influenza A virus (IAV) remains an important global public health threat with limited epidemiological information available from low-and-middle-income countries. The major objective of this study was to describe the proportions, temporal and spatial distribution, and demographic and clinical characteristics of IAV positive patients with influenza like illness (ILI) and severe acute respiratory illness (SARI) in Lahore, Pakistan.

Methods

Prospective surveillance was established in a sentinel hospital from October 2015 to May 2016. All eligible outpatients and inpatients with ILI or SARI were enrolled in the study. Nasal and/or throat swabs were collected along with clinico-epidemiological data. Samples were tested by real-time RT-PCR (rRT-PCR) to identify IAV and subtype. The descriptive analysis of data was done in R software.

Results

Out of 311 enrolled patients, 284 (91.3%) were ILI and 27 (8.7%) were SARI cases. A distinct peak of ILI and SARI activity was observed in February. Fifty individuals (16%) were positive for IAV with peak positivity observed in December. Of 50 IAV, 15 were seasonal H3N2, 14 were H1N1pdm09 and 21 were unable to be typed. The majority of IAV positive cases (98%) presented with current or history of fever, 88% reported cough and 82% reported sore throat. The most common comorbidities in IAV positive cases were hepatitis C (4%), obesity (4%) and tuberculosis (6%). The highest incidence of patients reporting to the hospital was seen three days post symptoms onset (66/311) with 14 of these (14/66) positive for IAV.

Conclusion

Distinct trends of ILI, SARI and IAV positive cases were observed which can be used to inform public health interventions (vaccinations, hand and respiratory hygiene) at appropriate times among high-risk groups. We suggest sampling from both ILI and SARI patients in routine surveillance as recommended by WHO.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-07021-7.

Practice of COVID-19 preventive measures and risk of acute respiratory infections: a longitudinal study in students from 95 countries

Objectives

We aimed to investigate whether the implementation of personal protective measures against COVID-19 reduced the transmission of influenza-like illnesses.

Methods

We followed 758 international students from 95 countries located in 5 continents from October 2020 to March 2021. Their frequency of wearing masks, physical distancing, washing hands, and avoiding crowded places, as well as their reported cases of influenza-like illnesses, were examined. We used Kaplan-Meier analysis to compare the occurrence of symptoms of influenza-like illnesses among participants who adhered with those who did not adhere to the personal protective measures.

Results

From October 2020 to March 2021, 139 (18%) students reported symptoms of influenza-like illnesses. The survival analysis showed that students who frequently wore face masks, exercised physical distancing, and disinfected their hands had a reduced risk of influenza-like illnesses. We found a two-fold increased risk of influenza-like illnesses among participants who did not implement all the personal protective measures compared with those who adhered to the measures (hazard ratio=2.16, 95% CI=1.53-3.05, P<0.001).

Conclusions

Our findings suggest that personal protective measures with high feasibility and acceptability could be implemented during influenza epidemics to reduce transmission.

Pre-clinically evaluated visual lateral flow platform using influenza A and B nucleoprotein as a model and its potential applications

A visual colorimetric rapid screening system based on a lateral flow device for simultaneous detection and differentiation between influenza A and B nucleoprotein as a model was developed. Monoclonal antibodies, specific for either influenza A or B nucleoproteins, were evaluated for their reactivities and were used as targeting ligands. With the best antibody pairs selected, the system exhibited good specificity to both viruses without cross reactivity to other closely related respiratory viruses. Further semi-quantitative analysis using a strip reader revealed that the system is capable of detecting influenza A and B protein content as low as 0.04 and 1 ng per test, respectively, using a sample volume as low as 100 μL, within 10 minutes (R² = 0.9652 and 0.9718). With a performance comparison to the commercial tests, the system demonstrated a four-to-eight-fold higher sensitivity. Pre-clinical evaluation with 101 nasopharyngeal swabs reveals correlated results with a standard molecular approach, with 89% and 83% sensitivity towards influenza A and B viruses, and 100% specificity for both viruses.

Visual colorimetric rapid screening system based on lateral flow device for influenza A and B virus detection as a model and its pre-clinical evaluation.

The Drift in Molecular Testing for Influenza: Mutations Affecting Assay Performance

Influenza is associated with rapid evolution due to lack of RNA polymerase proofreading, immunogenic selection, and frequent rearrangement of gene segments. Evolutionary changes affecting the performance of diagnostic testing have long been recognized. Hence, it is not surprising that such challenges apply to nucleic acid amplification tests, even though they are designed to target highly conserved regions. Initially, case reports involved single isolates of A(H1N1)pdm09. Over the past 4 years, subtype H3N2 viruses evolved to viral clades with mutations in the WHO-recommended target region, such that almost all isolates worldwide have significantly reduced sensitivities with many commercial reverse transcription-PCR tests.