Prevalence of Pneumocystis jirovecii in Smear Negative Sputum Samples at the Coast General Teaching and Referral Hospital in Kenya

Abstract

Pneumocystis jirovecii pneumonia (PJP) is a significant opportunistic fungal infection among tuberculosis (TB) smear-negative and retreatment patients, especially in resource-limited settings. The overlap in clinical symptoms between PJP and tuberculosis can lead to delayed or incorrect diagnosis, resulting in ineffective therapy and poor patient outcomes. The aim of this study was to compare the socio-demographic characteristics and potential risk factors associated with Pneumocystis jirovecii infection, determine the prevalence of PJP, and assess the diagnostic performance of Toluidine blue O staining versus nested polymerase chain reaction (PCR) among TB smear-negative and retreatment patients at Coast General Hospital. A cross-sectional study of 100 TB smear-negative and retreatment patients was performed. Toluidine Blue O staining was used to evaluate sputum samples, followed by nested PCR targeting P. jirovecii's mitochondrial large subunit ribosomal RNA (mtLSU rRNA). The socio-demographic and clinical data were described using frequencies and percentages. Bivariate logistic regression was used to investigate associations between P. jirovecii infection and predictor factors. Odds ratios (ORs), 95% confidence intervals (CIs), and p-values were provided. The diagnostic performance characteristics, including sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), were computed with nested PCR as the reference standard. Of the 100 participants, 41% tested positive for P. jirovecii by nested PCR, while 29% tested positive using Toluidine blue O staining. Nested PCR uncovered an additional 12 positive cases from samples that were negative according to TBO staining. Most participants were male (63%), employed (84%), and aged between 20 and 49 years (23%). Fever was reported in 59% of participants, night sweats in 61%, and reduced EuroQol status in 74%. Bivariate logistic regression analysis showed no statistically significant association between P. jirovecii infection and socio-demographic factors, including age, gender, employment status, environmental factors such as housing type, flooding exposure, and health risk factors such as TB treatment status, fungal growth, fuel type, and smoking habit (p > 0.05). Similarly, clinical risk factors such as fever (OR = 1.63, 95% CI: 0.72–3.77), night sweats (OR = 0.71, 95% CI: 0.31–1.60), and EuroQol status (OR = 0.93, 95% CI: 0.38–2.34) were not significantly associated with P. jirovecii infection. Toluidine blue O staining demonstrated a sensitivity of 70.7% and specificity of 98.3% compared with nested PCR. The study found a rather high prevalence of P. jirovecii (41% among TB smear-negative and retreatment patients). Although no significant socio-demographic or clinical risk factors were identified, toluidine blue O staining demonstrated high sensitivity and acceptable specificity, indicating its potential use as a screening tool in resource-constrained settings where molecular diagnostic methods are not readily available. Using sensitive molecular diagnostic tools and target screening for Pneumocystis jirovecii before starting TB treatment may improve early detection, guide appropriate treatment, and improve patient outcomes in high-risk populations.