Isolation and Epidemiology of Respiratory Bacteria From Unusual Sites: Demographic, Seasonal, and Geographic Distribution in a Laboratory-Based Study From a Tertiary Care Hospital in Karachi, Pakistan

Introduction Respiratory pathogens such as <i>Streptococcus pneumoniae</i>, <i>Haemophilus influenzae</i>, and <i>Haemophilus parainfluenzae</i> primarily infect respiratory and oropharyngeal sites. However, they are increasingly being isolated from unusual anatomic sites, such as urogenital and abdominal sources. These atypical occurrences necessitate an understanding of their epidemiology and clinical implications. Methods This study aimed to evaluate the seasonal prevalence, gender distribution, and clinical characteristics of <i>Streptococcus pneumoniae</i>, <i>Haemophilus influenzae</i>, and <i>Haemophilus parainfluenzae</i> isolated from nonrespiratory, unusual sites. Conducted at the Clinical Microbiology Laboratory of Aga Khan University Hospital in Karachi, Pakistan, the study included data from January 2021 to July 2023. Isolates from the urogenital tract, joints, skin and soft tissue, and other invasive samples from various body sites were included, while specimens from usual sites, such as blood, cerebrospinal fluid (CSF), and respiratory samples, were excluded. Analysis was performed after excluding isolates from unknown sources and duplicate samples from the same medical record number. A descriptive analysis was conducted on a small subset of inpatients with detailed clinical histories. Results Out of 2321 samples, 464 (20.0%) were excluded, and 1857 (80.0%) were analyzed, with 49 (2.6%) isolates from unusual sites. Isolation from unusual sites was significantly associated with female gender, the years 2021 and 2022, elderly age group, and Karachi origin (p < 0.05). <i>Haemophilus</i> species (68.6%) were more prevalent than <i>Streptococcus pneumoniae</i> (31.4%) in unusual sites. Seasonal distribution between usual and unusual sites was not statistically significant. A subset of 12 hospitalized patients with <i>Streptococcus pneumoniae</i> (n = 5), <i>Haemophilus influenzae</i> (n = 3), and <i>Haemophilus parainfluenzae</i> (n = 4) from unusual sites was analyzed. The average age was 44.9 years, with a 1:1 male-to-female ratio, and 75% had comorbidities. Infections involved bones/joints (n = 5), intraabdominal sites (n = 3), abscesses (n = 3), and the vagina (n = 1), with varied clinical presentations and empiric treatments. The average hospital stay was 6.25 days, and only one patient had bloodstream dissemination. Conclusion This study found a 2.6% isolation rate of <i>Streptococcus pneumoniae</i> and <i>Haemophilus</i> species from unusual sites, highlighting their clinical relevance. These findings will help microbiologists anticipate such infections and assist clinicians in optimizing empirical treatment strategies.