Viral etiology of lower respiratory tract infections in adults in the pre-COVID-19 pandemic era: A cross-sectional study in a single center experience from Cameroon.

Background and Aims: Respiratory viruses are responsible for the majority of lower respiratory tract infections (LRTIs) worldwide. However, there is a gap on the epidemiology of viral LRTIs in adults in sub-Saharan African countries. In Cameroon, like in other countries, the role of viral respiratory pathogens in the etiology of LRTIs in adults is helpful for clinical management. This study aimed to determine the viral aetiologies of LRTIs among hospitalized adults in a reference center for respiratory diseases in the town of Yaounde in Cameroon and its surroundings. Methods: A cross-sectional study was conducted from January 2017 to January 2018 at Jamot Hospital in Yaounde (Cameroon). Clinical and demographic information; BAL and sputa were collected from hospitalized patients meeting LRTI case definitions. The clinical samples were investigated for respiratory pathogens with a commercial Reverse Transcriptase Real-Time Polymerase Chain Reaction (RT-PCR) targeting 21 viruses, cultures for bacterial and fungal infections. Results: The 77 included adult patients with LRTIs had an appropriate clinical sample for microbial investigations. A viral agent was detected in 22.1% (17/77) samples. The main viruses detected included rhinovirus (10/77), coronavirus (hCoV-OC43 and hCoV-229E), and influenza A virus (3/77 each). A concomitant viral and bacterial co-infection occurred in 7.8% of patients (6/77) while viral co-infection occurred in one patient (1.3%). No Severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) was detected in clinical samples. Most patients were under antimicrobials before getting diagnosed. Conclusions: Respiratory viruses account for 22.1% of LRTIs in hospitalized patients in this study. Despite prior antimicrobial therapy and delay, rhinovirus, coronavirus and influenza A virus were the most detected in patients in the pre-COVID-19 pandemic era in a single center experience from Cameroon.

Implementation of large-scale pooled testing to increase rapid molecular diagnostic test coverage for tuberculosis: a retrospective evaluation.

In 2021, only 6.4 million of the 10.6 million people with tuberculosis (TB) were diagnosed and treated for the disease. Although the World Health Organization recommends initial diagnostic testing using a rapid sensitive molecular assay, only 38% of people diagnosed with TB benefited from these, due to barriers including the high cost of available assays. Pooled testing has been used as an approach to increase testing efficiency in many resource-constrained situations, such as the COVID-19 pandemic, but it has not yet been widely adopted for TB diagnostic testing. Here we report a retrospective analysis of routine pooled testing of 10,117 sputum specimens using the Xpert MTB/RIF and Xpert MTB/RIF Ultra assays that was performed from July 2020 to February 2022. Pooled testing saved 48% of assays and enabled rapid molecular testing for 4156 additional people as compared to individual testing, with 6.6% of specimens positive for TB. From an in silico analysis, the positive percent agreement of pooled testing in pools of 3 as compared with individual testing for the Xpert MTB/RIF Ultra assay was estimated as 99.4% (95% CI, 96.6% to 100%). These results support the scale-up of pooled testing for efficient TB diagnosis.

A combined effort of 11 laboratories in the WHO African region to improve quality of Buruli ulcer PCR diagnosis: The "BU-LABNET".

Buruli ulcer is one of the 20 neglected tropical diseases in the world. This necrotizing hypodermitis is a chronic debilitating disease caused by an environmental Mycobacterium ulcerans. At least 33 countries with tropical, subtropical and temperate climates have reported Buruli ulcer in African countries, South America and Western Pacific regions. Majority of cases are spread across West and Central Africa. The mode of transmission is unclear, hindering the implementation of adequate prevention for the population. Currently, early diagnosis and treatment are crucial to minimizing morbidity, costs and preventing long-term disability. Biological confirmation of clinical diagnosis of Buruli ulcer is essential before starting chemotherapy. Indeed, differential diagnosis are numerous and Buruli ulcer has varying clinical presentations. Up to now, the gold standard biological confirmation is the quantitative PCR, targeting the insertion sequence IS2404 of M. ulcerans performed on cutaneous samples. Due to the low PCR confirmation rate in endemic African countries (under 30% in 2018) for numerous identified reasons within this article, 11 laboratories decided to combine their efforts to create the network "BU-LABNET" in 2019. The first step of the network was to harmonize the procedures and ship specific reagents to each laboratory. With this system in place, implementation of these procedures for testing and follow-up was easy and the laboratories were able to carry out their first quality control with a very high success rate. It is now time to integrate other neglected tropical diseases to this platform, such as yaws or leprosy.