Acute respiratory infections (ARI) are, according to the World Health Organization (WHO), the leading cause of morbidity and mortality due to infection in the world. It is estimated that between 290,000 and 650,000 deaths each year are associated with influenza virus infection. In the last year, the number of ARI cases has increased significantly as a consequence of the SARS CoV-2 (COVID-19) pandemic, which accounts for about 110.7 million cases of infection and more than 2.4 million deaths worldwide. All age groups are susceptible to acute respiratory infections; however, they are more prevalent in children, the elderly, and individuals with immune system disorders. These infections frequently result in the need for medical attention which, during rainy or winter periods, when they are more prevalent, tends to overload emergency and outpatient services, and increases the request for laboratory tests and other diagnostic aids, as well as the prescription and consumption of antibiotics. Although ARI can be viral or bacterial in origin, in most cases they are caused by viruses, agents that cause infections that are generally self-limiting, are not eliminated by antibiotic therapy and can easily be transmitted to others and trigger outbreaks of infection. The most frequent signs and symptoms of ARI are similar, regardless of whether they are caused by viruses or bacteria; therefore, their clinical presentation is not sufficient to reach a definitive microbiological diagnosis. Moreover, in some ARI of bacterial origin, the microorganisms are difficult to isolate and identify using conventional techniques; sometimes there is even co-infection by virus and bacteria, so it is necessary to use combined detection methodologies that allow their correct diagnosis.