Microbial profile and antimicrobial sensitivity patterns in patients hospitalised in the six regional/provincial hospitals in the free state and northern cape from 2018 to 2022

Abstract

Background: Bacterial infections are the major cause of morbidity and mortality in an immune-compromised subset of patients. Over 1.4 million people worldwide suffer from nosocomial infections that are associated with microorganisms. Hospital acquired infections are an increasing problem across Sub-Saharan Africa, while bacterial contamination of indoor hospitals, particularly in Intensive-Care Units is a serious global health hazard with high morbidity and mortality rates. Many patient factors influence the acquisition of microbial infections in patients. This includes age, immune status, pre-existing disease and diagnostic or therapeutic interventions. Patients with chronic diseases such as HIV or TB are vulnerable to infections, especially to opportunistic organisms. Only the bacteria that are sensitive to antibiotics are suppressed or killed, while the resistant strains survive and become endemic and spread easily within the hospital environment.

Objectives

1. Determine microbial profile prevalence in immunocompromised patients who

were hospitalized in the different hospitals having TB or are HIV positive.

2. Determine the risk factors that are associated with microbial infections in

immunocompromised patients.

3. Compare the microbial prevalence rate in HIV-positive patients compared to

HIV-negative patients.

4. Determine the antibiotic susceptibility pattern of the identified microorganisms.

5. Assess the impact of microbial infections on the mortality rate of

immunocompromised patients from other studies globally.

Methods: This was a retrospective, cross-sectional study. The data included in the

study was from 1 January 2018 to 31 December 2022. All patients who were admitted at the selected sites having underlying diseases such as TB and HIV from 1 January 2018 to 31 December 2022 were selected. Results: The study consisted of 48 597 participants and most of the participants in the study were from the Frances Baard District Municipality in Kimberley in the Northern Cape Province (58.4%), followed by the Mangaung Metropolitan Municipality in the Free State Province (37.9%). The majority of the patients in the study (58.4%) were treated at the Robert Mangaliso Sobukwe Provincial Hospital (Northern Cape Province), followed by 20.9% patients treated at the Universitas Academic hospital (Free State Province). The highest age group percentage in the study was 27.1%, which fell between 28 and 37 years, followed by 26.4% between the ages of 38 and 47 years, with the lowest population (0.8%) was found between 78 and 87 years. The study showed that fewer patients were admitted to hospital from the age of 58 years and above and most participants in the study were recorded to be female 49.9%). There was a slight difference among male (49.4%). The study also recorded that 0.7% of the patients’ gender was unknown. The study showed that 89.4% of patients tested negatively for TB across all six hospitals. 6.8% patients tested positively for TB, while 1.6% and 1.8% patients’ TB results were unknown or not tested, respectively. The National District Hospital recorded the highest number of patients who tested positively for TB at a rate of n=169 (9.7%), followed by Bongani Regional Hospital at a rate of n=119 (8.3%). Robert Mangaliso Sobukwe Provincial Hospital had n=2 226 (7.8%) TB-positive cases, Mofumahafi Manapo Mopeli Regional Hospital recorded n=23 (7.1%) TB-positive cases, Pelonomi Regional Hospital had n=409 (6.3%) positive cases and Universitas Academic hospital recorded n=362 (3.6%) TB-positive cases, which is the lowest. The majority of the participants in the patients in the study were not tested for HIV using the HIV-1/2 rapid screen test and of those who were tested, only 1.2% were reported to be HIV positive and 4.2% were negative. 70.9% of the patients did not have HIV- 1/2 AB/AG screen results, while 24.4% tested negative and 4.3% tested positive. The data show that only 0.6% of the patients had equivocal HIV results. The study showed that 7.9% (n=3 862/48 597) patients’ HIV viral load were undetectable, which means that the patients were compliant with Antiretroviral Therapy (ART) treatment. The undetectable HIV viral load was <20-50 copies/mL, 6.9% patients had a low HIV viral load of 50-10 000 copies/mL and a population of n=3 299 (6.8%) was found to have a high HIV viral load >100 000 copies/mL. The study showed that 74.9% patients were not tested for HIV viral load. 68.9% of patients monitored. 23.4% of the patients displayed a low immune system (<350 cells/mm3), which means that they were not complying with ART treatment. 3.6% of the patients had mild immunosuppression (350–499 cells/mm3) and 4.2% of the patients had a strong immune system, which means that they are complying with to ART treatment. The study also evaluated the prevalence testing method for all the specimens submitted to the laboratory for microbes and antimicrobial testing. Automated culture was the method mostly used in the laboratory and it was reported to be at the rate of 42.8%, followed by culture urine (25.4%), culture pus (23.3%). Culture catheter tip was the least frequently used test method, displaying a rate of 8.5%. 48 597 specimens were reported to have been tested in the laboratory. In the study, the type of specimen collected from patients and sent to the laboratory for testing was also analysed. 48 597 specimens were collected. Blood culture (38.4%) was the most frequently collected specimen as the patients might have been suspected of having a bloodstream infection and urine was the second-most frequently collected specimen (16.5%), as the patients might have been suspected for having UTI. The study observed a prevalence of microorganisms in hospitals that are located in urban facilities, compared to facilities located in rural areas and the top 10 prevalent microorganisms from the sample isolates were Escherichia Coli (16.9%), staphylococcus aureus (14.5%), Coagulase Negative staphylococcus (11.9%), Klebsiella Pneumoniae subsp Pneumonia (9.4%), Staphylococcus Epidermidis (5.2%), Streptococcus Pneumoniae (4%), Proteus Mirabilis (4%), Acinetobacter Baumannii (3.7%), Pseudomonas Aeruginosa (3.2%), Enterobacter Cloacae subsp. Cloacae (2.9%). The study showed that Trimethoprimsulfamethoxazole antibiotic showed high resistance to both gram-negative and grampositive bacteria, 68.3% and 42.2%, respectively. Gentamicin showed high antibiotic resistance in gram-positive bacteria Enterococcus faecalis at 31.8% and Enterococcus Faecium at 69.8%). The study showed that Streptococcus Pneumoniae had high sensitivity (50.7%) to Ceftriaxone antibiotic. The study proved that the ward type where patients were admitted to plays a huge risk factor in antibiotic treatment. Most patients who were admitted to Medical wards showed a very high prevalence of antimicrobial resistance. Resistance was observed in all the antibiotics. The same trend was observed in both ICUs, in the A6 Intensive Care Unit and Multidisciplinary unit. Nitrofurantoin antibiotic displayed high sensitivity in most wards. A systematic review of previous studies found that opportunistic microorganisms cause a high mortality rate in immunocompromised patients. Conclusion: Majority of patients had a high HIV viral load and low CD4 count, which show non-compliance with ART. The majority of male patients had a detectable viral load and a low CD4 count, which is a risk factor for acquiring microbial infections. There was a high prevalence of antimicrobial resistance from different wards in the study and Trimethoprim-sulfamethoxazole antibiotic showed high resistance to both gram-negative and gram-positive bacteria, 68.3% and 42.2%, respectively.