Multiplex polymerase chain reaction detection of Streptococcus pneumoniae and Haemophilus influenzae and their antibiotic resistance in patients with community-acquired pneumonia from southwest Iran

• Published in: BMC microbiology 2021-12, Vol.21 (1), p.343-343, Article 343
• Main Authors: Farajzadeh Sheikh, Ahmad, Rahimi, Robab, Meghdadi, Hossein, Alami, Ameneh, Saki, Morteza
• Format: Article
• Language: English
• Subjects: Amoxicillin; Anti-Bacterial Agents - pharmacology; Antibacterial agents; Antibiotic resistance; Antibiotics; CAP; Care and treatment; Ceftriaxone; Clarithromycin; Codification; Community-Acquired Infections - diagnosis; Community-Acquired Infections - microbiology; Community-acquired pneumonia; Control; Cotrimoxazole; Cross-Sectional Studies; DNA polymerase; Dosage and administration; Drug resistance; Drug resistance in microorganisms; Drug Resistance, Bacterial; Genes; Gentamicin; Haemophilus influenzae; Haemophilus influenzae - drug effects; Haemophilus influenzae - genetics; Haemophilus influenzae - isolation & purification; Hemophilus infections; Humans; Identification and classification; Iran; Laboratories; Microbial Sensitivity Tests; Molecular Diagnostic Techniques; Morphology; Multiplex Polymerase Chain Reaction; Multiplexing; Pathogens; Patients; Pneumonia; Pneumonia, Bacterial - diagnosis; Pneumonia, Bacterial - microbiology; Polymerase chain reaction; Prevention; Risk factors; Sensitivity; Sensitivity and Specificity; Sputum; Sputum - microbiology; Strains (organisms); Streptococcus infections; Streptococcus pneumoniae; Streptococcus pneumoniae - drug effects; Streptococcus pneumoniae - genetics; Streptococcus pneumoniae - isolation & purification; Testing
• ISSN: 1471-2180; 1471-2180
• DOI: 10.1186/s12866-021-02408-7

This study aimed to evaluate the occurrence of Streptococcus pneumoniae and Haemophilus influenzae in sputum of patients with community-acquired pneumonia (CAP) using culture and multiplex polymerase chain reaction (M-PCR) methods and to survey the antibiotic resistance patterns of aforesaid isolates. In total, 23.9 % (n = 22/92) of sputum samples showed positive results in the culture method. S. pneumoniae and H. influenzae were isolated from 15 (16.3 %) and 7 (7.6%) samples, respectively. Using M-PCR, 44 (47.8 %) samples were positive for S. pneumoniae and H. influenzae. Of these, S. pneumoniae and H. influenzae were detected in 33 (35.8%) and 11 (11.9%) of the sputum samples, respectively. The sensitivity, specificity, and accuracy rates of PCR in detection of S. pneumoniae in comparison with culture method were 100, 76.6, and 83.6%, respectively. While, the sensitivity, specificity, and accuracy rates of PCR in detection of H. influenzae in comparison with culture method were 100, 95.3, and 95.8%, respectively. Out of 11 isolates of H. influenzae, two strains confirmed as H. influenzae type b (Hib) and 3 isolates were type f. However, 6 isolates were non-typable. The co-trimoxazole and amoxicillin/clavulanate were the less effective antibiotics against S. pneumonia and H. influenzae, respectively. Ceftriaxone with 13.3% resistance rates was the most effective antibiotic against S. pneumoniae, while, clarithromycin, ceftriaxone, and gentamicin with resistance rates of 28.6% for each one were the most effective chemicals against H. influenzae isolates. In this study, the prevalence of S. pneumoniae was more than H. influenzae using culture and M-PCR methods. The M-PCR provided better efficiency in detecting the bacterial agents in CAP patients compared to culture method. This method can improve the early detection of pathogens contributed to CAP. The drug resistant S. pneumoniae and H. influenzae indicated the need to develop a codified monitoring program to prevent further spread of these strains.