Autopsy Characterization of Lung Microbiome of Hiv-Positive Patients in A Tertiary Referral Hospital in Ghana

Abstract

Pulmonary infections are the underlying cause of high morbidity and mortality among Human Immunodeficiency Virus (HIV) infected persons. Notwithstanding, there is limited data on pulmonary co-infecting pathogens and their susceptibility to commonly used antibiotics. Knowledge on these pathogens is therefore critical for implementing effective interventions and treatment guidelines especially, in highly burdened countries with scarce diagnostic facilities. The aim of this study was to characterize the lung microbiome of post-mortem biopsy samples of HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome) patients in Ghana. A total of 102 lung biopsies from HIV/AIDS decedents from the Korle-Bu Teaching Hospital in Ghana were examined for mycobacteria, other bacteria, fungi and viruses. The techniques utilized included; culture, Gram/Ziehl Neelsen (ZN) staining, Matrix Assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) mass spectrometry and Polymerase Chain Reaction (PCR). The drug susceptibility pattern of Mycobacterium tuberculosis complex (MTBC) isolates and other bacteria were subsequently determined using Genotype MTBDRplus and disc diffusion assays respectively. Clinical data and autopsy causes of death were also retrieved for 86 cases and inferences were made by correlating the data to that of the laboratory investigations. From the clinical data, 42 (48.8%) of the cases were males and 42 (48.8%) were females with the mean ages of 40.4 (±10.6) and 37.1 (±11.5) respectively. HIV type was defined in 39 (45.3%) cases and co-infections with tuberculosis (TB), pneumonia, oesophageal candidiasis and/or cryptococcal disease occurred in 12 (14.3%) cases. Characterization of mycobacterial isolates yielded, 25 MTBC and 5 M. abscessus. In addition, an acid-fast isolate was identified as Norcardia farcinica. Drug susceptibility testing of the MTBC isolates showed 1 isoniazid mono-resistance and 3 rifampicin mono-resistance. Other bacteria isolated were 217 (83.8%) with Enterococcus species (61), Staphylococcus species (35), Escherichia coli (28) and Klebsiella pneumoniae (23) dominating. Of the 217, 75 Gram-negatives and 117 Gram-positives were profiled for drug sensitivity. Gram-negative isolates were most susceptible to cefoxitin and gentamicin (45.3% each) but highly resistant to cefuroxime sodium (84.0%). The Gram-positives were also fairly susceptible to levofloxacin (58.0%) but highly resistant to oxacillin (81.2%) and flucloxacillin (75.2%). Also, nine (9) culturable fungi; Candida species (6), Cryptococcus neoformans (1), Pichia occidentalis (1) and Yarrowia lipolytica (1) were identified whereas PCR detected Pneumocystis jiroveci in 43 samples. Viruses detected in the samples included Cytomegalovirus (67); a DNA virus and RNA viruses; Parainfluenza-2 (1) and Enterovirus (1). Findings from this study calls for the introduction of comprehensive definitive laboratory investigation rather than empirical clinical diagnosis to identifying the exact underlying pathogens that cause pulmonary infections in managing HIV patients in Ghana.