Co-detection of respiratory pathogens among ILI patients: characterization of samples collected during the 2018/19 and 2019/20 pre-pandemic seasons

• Published in: BMC infectious diseases Vol. 24; no. 1; pp. 881 - 10
• Main Authors: Ferrari, Allegra, Schiavetti, Irene, Ogliastro, Matilde, Minet, Carola, Sibilio, Raffaella, Giberti, Irene, Costa, Elisabetta, Massaro, Elvira, Lai, Piero Luigi, Mosca, Stefano, Bruzzone, Bianca, Orsi, Andrea, Panatto, Donatella, Icardi, Giancarlo
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 29.08.2024; BioMed Central; BMC
• Subjects: Adenoviruses; Adolescent; Adult; Aged; Aged, 80 and over; Algorithms; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria, Pathogenic; Bacterial infections; Bacterial Infections - diagnosis; Bacterial Infections - epidemiology; Bacterial Infections - microbiology; Causes of; Chi-square test; Child; Child, Preschool; Chronic illnesses; Co-infection; Coinfection - epidemiology; Coinfection - microbiology; Coinfection - virology; Comorbidity; Correlation; COVID-19; Datasets; Diagnosis; Epidemiology; Female; Haemophilus influenzae; Health aspects; Humans; Identification and classification; Immunization; Infant; Infant, Newborn; Infection; Influenza; Influenza A; Influenza B; Influenza, Human - epidemiology; Influenza, Human - virology; Italy - epidemiology; Laboratories; LRI; Male; Middle Aged; Mortality; Oropharynx - microbiology; Oropharynx - virology; Pandemics; Pathogenic microorganisms; Pathogens; Pertussis; Primary care; Respiratory diseases; Respiratory pathogens; Respiratory syncytial virus; Respiratory tract diseases; Respiratory tract infection; Respiratory tract infections; Respiratory Tract Infections - diagnosis; Respiratory Tract Infections - epidemiology; Respiratory Tract Infections - microbiology; Respiratory Tract Infections - virology; Rhinovirus; Seasons; Severe acute respiratory syndrome coronavirus 2; Streptococcus infections; Streptococcus pneumoniae; Syndromic surveillance; URI; Viral diseases; Viruses; Viruses - classification; Viruses - genetics; Viruses - isolation & purification; Young Adult; Italy; United States > US; LRI; Co-infection; Respiratory pathogens; Respiratory tract infection; Syndromic surveillance; URI
• ISSN: 1471-2334; 1471-2334
• DOI: 10.1186/s12879-024-09687-1

Influenza-like illness (ILI) patients co-detected with respiratory pathogens exhibit poorer health outcomes than those with single infections. To address the paucity of knowledge concerning the incidence of concurrent respiratory pathogens, their relationships, and the clinical differences between patients detected with single and multiple pathogens, we performed an in-depth characterization of the oropharyngeal samples of primary care patients collected in Genoa (Northwest Italy), during winter seasons 2018/19-2019/20.The apriori algorithm was employed to evaluate the incidence of viral, bacterial, and viral-bacterial pairs during the study period. The grade of correlation between pathogens was investigated using the Phi coefficient. Factors associated with viral, bacterial or viral-bacterial co-detection were assessed using logistic regression.The most frequently identified pathogens included influenza A, rhinovirus, Haemophilus influenzae and Streptococcus pneumoniae. The highest correlations were found between bacterial-bacterial and viral-bacterial pairs, such as Haemophilus influenzae-Streptococcus pneumoniae, adenovirus-Haemophilus influenzae, adenovirus-Streptococcus pneumoniae, RSV-A-Bordetella pertussis, and influenza B Victoria-Bordetella parapertussis. Viruses were detected together at significantly lower rates. Notably, rhinovirus, influenza, and RSV exhibited significant negative correlations with each other. Co-detection was more prevalent in children aged < 4, and cough was shown to be a reliable indicator of viral co-detection.Given the evolving epidemiological landscape following the COVID-19 pandemic, future research utilizing the methodology described here, while considering the circulation of SARS-CoV-2, could further enrich the understanding of concurrent respiratory pathogens.