Description

Sputum Microbial Profile and Clinical Features of Patients with GeneXpert and AFB Negative in San Lazaro Hospital Manila-Philippines

Ndiabamoh Crespo’o Mbe-cho1,2, Kentaro Sakashita1,3, Motoi Suzuki4, Sharon E. Cox1,5

1School of Tropical Medicine and Global Health Nagasaki University, Japan, 2Biotechnology Center University of Yaoundé I Cameroon; 3Nagasaki-San Lazaro Hospital Research Lab, Manila, the Philippines, 4National Institute of Infectious Diseases Tokyo, Japan; 5Faculty of Population Health, London School of Hygiene and Tropical Medicine, UK

Introduction
The Philippines is amongst the seven countries accounting for 90% of the burden of tuberculosis (TB) in the world in 2019. We sought to investigate the presence of other potentially pathogenic organisms and their clinical features in archived sputum samples from acutely unwell patients admitted to a TB ward in Manila-Philippines and presenting with symptoms consistent with a clinical diagnosis of pulmonary TB, but who were negative  for Xpert(®) MTB/Rif assay and Acid Fast Bacilli (AFB).
Methods
A pilot retrospective analytical cross-sectional study on 82 sputa samples was carried out. DNA was extracted using a QIAGEN kit (Hilden, Germany). Positive controls prepared from blood culture isolates were extracted using the same kit above following manufacturers protocol. Three multiplex Polymerase chain reactions (PCR) for 16S rRNA assays were designed for typical bacteria (Streptococcus pneumoniae, Hemophilus influenzae, Moraxella catarrhalis), atypical bacteria (Chlamydia pneumoniae, Legionella pneumoniae, mycoplasma pneumoniae) and (Burkholderia pseudomallei, Burkholderia thailandensis). Final PCR products were run in Shimadzu MultiNA Microchip Electrophoresis System for DNA analysis. All data were analysed using STATA® 15.
Results
Overall bacteria prevalence was 74/82(90.24%). The most prevalent were Burkholdera pseudomallei 72/82(87.80%) and Hemophilus influenza 22/82(26.83%). A high proportion of patients had a cough of greater than 2 weeks 51/82(76.12%) and chest x-ray findings consistent with TB infection 59/76(86.76%). The odds of having a cough for more than two weeks and weight loss were about five {OR 5.70(CI: 1.79, 18.09)}, p=0.0008 and four times{OR 4.44(95%CI:1.56, 12.62)} p=0.0022 respectively higher in those with positive Xpert/AFB compared to those negative. On the other hand, there was no significant association observed (p= 0.1006) with chest x-ray lesions consistent with TB. 
Conclusion
The prevalence of other bacterial infections is high in patients suspected and/or diagnosed of PTB although this warrants more research on the types and prevalence of each bacteria. 
Most clinical features such as cough of more than 2 weeks, chest x-ray lesions, fever and weight loss can be present in other lung affections/diseases. Having a cough for more than two weeks and a weight loss were the most determining factors in bacteriologically confirmed TB cases. 

Keywords: Acid-fast-bacilli, GeneXpert, negative, sputum, bacteria.