FilmArray Respiratory Panel Integrated in a field Point Of Care dispositive for the diagnosis of respiratory tract infections in rural areas in Senegal

The development of molecular syndrome-based kits for the diagnosis of respiratory infections offers rapid and sensitive detection of common respiratory pathogens and will have a significant impact on the care of patients. In this study, we present the results obtained after the introduction of the FilmArray respiratory panel in a field Point of care (POC) for the diagnosis of virus and bacteria responsible of respiratory tract infections in Senegal rural area. From February to August 2017, we collected nasal swabs from febrile patients that presented symptoms of respiratory tract infections in three health posts located in Niakhar. Specimens were tested on site by multiplex Polymerase Chain Reaction (PCR), using the FilmArray respiratory panel® that targets 20 pathogens, including 17 virus and 3 bacteria (bioMérieux). Nasal swabs were collected from 113 patients. The median age was 4 years (ranging from 4 months to 60 years) and 51 (45%) were males. The prevalence of respiratory pathogens was 37.5% (12/32) during the dry season and 54.3% (44/81) in the rainy season (p=0.16). The prevalence of respiratory pathogen carriage was higher in children under 5 years of age (38/55, 69.1%). The most prevalent micro-organisms detected were influenza B virus (16/113, 14%), human rhinovirus/enterovirus (10/113, 9%), parainfluenzae virus (9/113, 8%), respiratory syncytial virus (8/113, 7%), adenovirus (5/113, 4%), human metapneumovirus (3/113, 3%), Chlamydia pneumoniae (2/113, 2%) and Coronavirus (2/113, 2%). The study has demonstrated that the integration of the FilmArray respiratory panel into a field POC could significantly improve the management of respiratory tract infections in rural areas. Author summary Respiratory tract infections are one of the leading causes of death worldwide. Populations in underdeveloped countries are the most affected, especially children under 5 years of age. Among the pathogens responsible for these infections, bacteria and viruses are the most identified. In poor countries, laboratory diagnosis can only be done in urban areas. They are generally based on bacteriological, immunological or molecular biology techniques. The concept of POC is not developed in underdeveloped countries. Its existence would have made it possible to carry out RDTs to confirm the clinician’s diagnosis and allow rapid management of the patient. In the current situation, the time required to achieve results is often very long for patients. In this study, we sought to demonstrate the significant contribution of the FilmArray respiratory panel in the management of respiratory tract infections in rural areas. We also wanted to reduce the time it takes to deliver results in order to improve patient care. This dispositif was integrated in a field POC which was implemented in Niakhar since 2015, in order to improve the management of emerging diseases. The FilmArray respiratory panel gave us the opportunity to investigate the causes of respiratory tract infections in this area. For each patient, we systematically target 20 pathogens, including 17 viruses and 3 bacteria, with a single multiplex PCR. One of the main results of this study is that children under 5 years of age are the most affected by respiratory tract infections. Then we noted a lack of consultation among adults that could be explained by the banalization of respiratory problems or a preference for traditional care. The fact that children under 5 years of age are the most affected could also serve as a basis for implementing vaccination programmes directly targeting the most vulnerable age groups. It should be noted that for 51% of patients, the result of the diagnosis was negative. It would appear that some pathogens responsible for respiratory tract infections are not targeted by the multiplex PCR. Thus, it would be necessary to screen these pathogens in order to integrate them into a panel that would cover the most pathogens in circulation in this area.

From February to August 2017, we collected nasal swabs from febrile patients that presented 23 symptoms of respiratory tract infections in three health posts located in Niakhar. Specimens 24 were tested on site by multiplex Polymerase Chain Reaction (PCR), using the FilmArray 25 respiratory panel® that targets 20 pathogens, including 17 virus and 3 bacteria (bioMérieux). 26 Nasal swabs were collected from 113 patients. The median age was 4 years (ranging from 4 27 months to 60 years) and 51 (45%) were males. The prevalence of respiratory pathogens was of the patient. In the current situation, the time required to achieve results is often very long 48 for patients. In this study, we sought to demonstrate the significant contribution of the 49 FilmArray respiratory panel in the management of respiratory tract infections in rural areas. 50 We also wanted to reduce the time it takes to deliver results in order to improve patient care. 51 This dispositif was integrated in a field POC which was implemented in Niakhar since 2015,52 in order to improve the management of emerging diseases. The FilmArray respiratory panel 53 gave us the opportunity to investigate the causes of respiratory tract infections in this area. For 54 each patient, we systematically target 20 pathogens, including 17 viruses and 3 bacteria, with 55 a single multiplex PCR. One of the main results of this study is that children under 5 years of 56 age are the most affected by respiratory tract infections. Then we noted a lack of consultation 57 among adults that could be explained by the banalization of respiratory problems or a 58 preference for traditional care. The fact that children under 5 years of age are the most 59 affected could also serve as a basis for implementing vaccination programmes directly 60 targeting the most vulnerable age groups. It should be noted that for 51% of patients, the 61 result of the diagnosis was negative. It would appear that some pathogens responsible for 62 respiratory tract infections are not targeted by the multiplex PCR. Thus, it would be necessary 63 Introduction 67 Infectious diseases represent a major public health problem in the world. In the poorest 68 countries, they continue to deeply impact economies and paralyze health systems. Progress 69 remains uneven, and millions of people do not benefit from prevention and treatment. In

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Several diagnostic methods could be used for the identification of suspected respiratory 84 pathogens. For a long time, it mainly relied on culture but during the last decades, the 85 development of qPCR has revolutionized diagnostic strategies and largely contributed to 86 expand the knowledge on the epidemiology of respiratory diseases, especially for viruses (6).

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PCR is a method that has a good sensitivity and specificity and allows the concomitant 88 detection of several microorganisms by multiplexing. In addition, the delivery time of results 89 is shorter than for other techniques (7). The best approach could be to target several pathogens 90 in a single run, in order to reduce detection costs, to increase the speed of the diagnosis and  to the laboratory for analysis. The following age categories (<1, 1-5, 6-21, 22-65 and >65 125 years) were adopted to study the prevalence rates.  highest detection rate for respiratory pathogens (11/12, 92%) was noted in infants (< 1 year 177 category), followed by the 1-5 years category (27/49, 55%) ( Table 1). The difference between 178 these two categories was significant (ᵡ 2 = 4.04, p<0.05). No pathogen was identified in the 22-179 65 years category. Infections in the 1-5 category was more diversified, 11 pathogens were 180 identified, more than in the other categories.   Pathogens were identified throughout the study, but the fact that the prevalence was higher 219 during the rainy season suggests seasonality in the transmission of pathogens. However, in 220 this study, the collection of specimens during a limited period constitutes a limit, because

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Results confirm that among the population, children under 5 years of age are more susceptible 227 for respiratory infection (Table 1). For many infectious diseases, the 0-5 years of age group is 228 more exposed than other groups. It should also be noted that the 22-65 age group was not 229 diagnosed as being infected with tested pathogens. One of the explanations could be the low

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The prevalence of this pathogen was higher during the winter season but the difference 263 observed in our results was not significant. We noticed seasonal differences in the apparition 264 of this pathogen, as described by previous studies (16). As expected, RSV was essentially 265 identified in the 0-5 years group, suggesting that this group is more susceptible to infection.  The study has demonstrated an important burden of respiratory pathogens and the high 278 prevalence of respiratory pathogens in the study area. The integration of the FilmArray 279 respiratory panel into the field POC has been very beneficial to the population. Respiratory 280 tract infections were diagnosed on site and results were obtained in a shorter amount of time.

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Health personnel were able to receive considerable support for the diagnosis of respiratory 282 tract infections. Before the installation of BioFire, it was impossible to identify the respiratory 283 pathogens circulating in this area, with the exception of influenza viruses diagnosed by RDTs.

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The people who consulted in the three health posts were able to benefit from adequate The autors would like to thank bioMérieux that provided all the BioFire FilmArray ® material 292 and the Respiratory Panel reagents that were used for the molecular diagnosis.