A prospective observational study of community acquired pneumonia in Kenya: the role of viral pathogens.

BACKGROUND: Lower respiratory tract infections continue to contribute significantly to morbidity and mortality across all age groups globally. In sub-Saharan Africa, many studies of community acquired pneumonia in adults have focused on HIV-infected patients and little attention has been given to risk factors and etiologic agents in an urban area with a more moderate HIV prevalence. METHODS: We prospectively enrolled 77 patients admitted to a 280 bed teaching hospital in Kenya with radiographically confirmed community acquired pneumonia from May 2019 to March 2020. The patients were followed for etiology and clinical outcomes. Viral PCR testing was performed using the FTD respiratory pathogen-21 multiplex kit on nasopharyngeal or lower respiratory samples. Additional microbiologic workup was performed as determined by the treating physicians. RESULTS: A potential etiologic agent(s) was identified in 57% including 43% viral, 5% combined viral and bacterial, 5% bacterial and 4% Pneumocystis. The most common etiologic agent was Influenza A which was associated with severe clinical disease. The most common underlying conditions were cardiovascular disease, diabetes and lung disease, while HIV infection was identified in only 13% of patients. Critical care admission was required for 24, and 31% had acute kidney injury, sometimes in combination with acute respiratory distress or sepsis. CONCLUSION: Viruses, especially influenza, were commonly found in patients with CAP. In contrast to other studies from sub-Saharan Africa, the underlying conditions were similar to those reported in high resource areas and point to the growing concern of the double burden of infectious and noncommunicable diseases.

HIV Prevalence and Characteristics Among Patients With AIDS-Defining and Non-AIDS-Defining Cancers in a Tertiary Hospital in Kenya.

PURPOSE: Antiretroviral therapy (ART) has resulted in a higher life expectancy of persons living with HIV. This has led to an aging population at risk for both non-AIDS-defining cancers (NADCs) and AIDS-defining cancers (ADCs). HIV testing among patients with cancer in Kenya is not routinely performed, making its prevalence undefined. The aim of our study was to determine the prevalence of HIV and the spectrum of malignancies among HIV-positive and HIV-negative patients with cancer attending a tertiary hospital in Nairobi, Kenya. MATERIALS AND METHODS: We conducted a cross-sectional study between February 2021 and September 2021. Patients with a histologic cancer diagnosis were enrolled. Demographic data and HIV- and cancer-related clinical variables were obtained. HIV pretest counseling and consent were done, and testing was performed using a fourth-generation assay. Positive results were confirmed using a third-generation assay. RESULTS: We enrolled 301 patients with cancer; 67.8% (204 of 301) were female; the mean age was 50.7 ± 12.5 years. From our cohort, 10.6% (95% CI, 7.4 to 14.7, n = 32 of 301) of patients were HIV-positive with the prevalence of a new HIV diagnosis of 0.7% (n = 2 of 301). Of the HIV-positive patients, 59.4% (19 of 32) had a NADC. The commonest NADC was breast cancer (18.8%; 6 of 32), whereas non-Hodgkin lymphoma (18.8%; 6 of 32) and cervical cancer (18.8%; 6 of 32) were the most prevalent ADCs among HIV-positive patients. CONCLUSION: The prevalence of HIV infection among patients with cancer was twice the Kenya national HIV prevalence. NADCs comprised a larger percentage of the cancer burden. Universal opt-out HIV testing of patients attending for cancer care regardless of cancer type may facilitate early recognition of HIV-infected patients and aid in appropriate selection of ART and cancer therapies and preventive strategies.

Prevalence of Antimicrobial Resistance and Association with Patient Outcomes in a Rural Kenyan Hospital.

Data on antimicrobial resistance (AMR) and association with outcomes in resource-variable intensive care units (ICU) are lacking. Data currently available are limited to large, urban centers. We attempted to understand this locally through a dual-purpose, retrospective study. Cohort A consisted of adult and pediatric patients who had blood, urine, or cerebrospinal fluid cultures obtained from 2016 to 2020. A total of 3,013 isolates were used to create the Kijabe Hospital's first antibiogram. Gram-negative organisms were found to be less than 50% susceptible to third- and fourth-generation cephalosporins, 67% susceptible to piperacillin-tazobactam, 87% susceptible to amikacin, and 93% susceptible to meropenem. We then evaluated the association between AMR and clinical characteristics, management, and outcomes among ICU patients (Cohort B). Demographics, vital signs, laboratory results, management data, and outcomes were obtained. Antimicrobial resistance was defined as resistance to one or more antimicrobials. Seventy-six patients were admitted to the ICU with bacteremia during this time. Forty complete paper charts were found for review. Median age was 34 years (interquartile range, 9-51), 26 patients were male (65%), and 28 patients were older than 18 years (70%). Septic shock was the most common diagnosis (n = 22, 55%). Six patients had AMR bacteremia; Escherichia coli was most common (n = 3, 50%). There was not a difference in mortality between patients with AMR versus non-AMR infections (P = 0.54). This study found a prevalence of AMR. There was no association between AMR and outcomes among ICU patients. More studies are needed to understand the impact of AMR in resource-variable settings.

A Case Report of Concurrent Cryptococcal and Tuberculous Meningitis in an Immunosuppressed Renal Transplant Patient.

Infections after renal transplant are a common cause of morbidity and are commonly due to Cytomegalovirus (CMV), Cryptococcus, Mycobacterium tuberculosis, and Aspergillus. Concurrent infections with both cryptococcal and tuberculous aetiologies are rare within the central nervous system (CNS). We present a case of a 67-year-old male patient who presented with three weeks of headaches, confusion, unsteady gait, and seizures. He had type 2 diabetes mellitus and hypertension. He had a kidney transplant three years prior and was on three immunosuppressive agents. He was HIV-negative. He was evaluated and found to have cryptococcal meningitis and received appropriate treatment with liposomal amphotericin B, flucytosine, and serial lumbar punctures. He also had treatment for CMV viremia with valganciclovir. Three weeks later, after an initial good clinical response, he deteriorated with worsening confusion and persistent seizures. We re-evaluated him and found him to have brain imaging suggestive of tuberculosis. We started him on anti-tuberculous medication, and he improved significantly and was alert and seizure free at discharge home one month later. This case highlights that concurrent CNS infections with cryptococcus and tuberculosis do occur especially in patients who are severely immunosuppressed such as after a renal transplant. Failure to improve while on treatment for one CNS opportunistic infection should prompt one to investigate for other concurrent causes.

Intestinal Tuberculosis Presenting with Gastrointestinal Bleeding in Patient on Warfarin Therapy.

Background: Intestinal tuberculosis (ITB) constitutes less than 5% of overall cases of extrapulmonary disease and mostly affects the ileocecal region. The presentation and radiologic findings in enteric tuberculosis can mimic Crohn's disease (CD). Case Presentation. We present a case report of an African woman who presented to a Kenyan hospital with lower gastrointestinal bleeding while on anticoagulation for valvular atrial fibrillation, and was diagnosed with intestinal tuberculosis after colonoscopy, biopsy, and positive staining for tuberculous bacilli. Conclusion: Intestinal tuberculosis causing gastrointestinal bleeding is rare but should be suspected in patients living in TB endemic regions.

Assessment of Cardiac, Vascular, and Pulmonary Pathobiology In Vivo During Acute COVID-19.

Background Acute COVID-19-related myocardial, pulmonary, and vascular pathology and how these relate to each other remain unclear. To our knowledge, no studies have used complementary imaging techniques, including molecular imaging, to elucidate this. We used multimodality imaging and biochemical sampling in vivo to identify the pathobiology of acute COVID-19. Specifically, we investigated the presence of myocardial inflammation and its association with coronary artery disease, systemic vasculitis, and pneumonitis. Methods and Results Consecutive patients presenting with acute COVID-19 were prospectively recruited during hospital admission in this cross-sectional study. Imaging involved computed tomography coronary angiography (identified coronary disease), cardiac 2-deoxy-2-[fluorine-18]fluoro-D-glucose positron emission tomography/computed tomography (identified vascular, cardiac, and pulmonary inflammatory cell infiltration), and cardiac magnetic resonance (identified myocardial disease) alongside biomarker sampling. Of 33 patients (median age 51 years, 94% men), 24 (73%) had respiratory symptoms, with the remainder having nonspecific viral symptoms. A total of 9 patients (35%, n=9/25) had cardiac magnetic resonance-defined myocarditis. Of these patients, 53% (n=5/8) had myocardial inflammatory cell infiltration. A total of 2 patients (5%) had elevated troponin levels. Cardiac troponin concentrations were not significantly higher in patients with and without myocarditis (8.4 ng/L [interquartile range, IQR: 4.0-55.3] versus 3.5 ng/L [IQR: 2.5-5.5]; P=0.07) or myocardial cell infiltration (4.4 ng/L [IQR: 3.4-8.3] versus 3.5 ng/L [IQR: 2.8-7.2]; P=0.89). No patients had obstructive coronary artery disease or vasculitis. Pulmonary inflammation and consolidation (percentage of total lung volume) was 17% (IQR: 5%-31%) and 11% (IQR: 7%-18%), respectively. Neither were associated with the presence of myocarditis. Conclusions Myocarditis was present in a third patients with acute COVID-19, and the majority had inflammatory cell infiltration. Pneumonitis was ubiquitous, but this inflammation was not associated with myocarditis. The mechanism of cardiac pathology is nonischemic and not attributable to a vasculitic process. Registration URL: https://www.isrctn.com; Unique identifier: ISRCTN12154994.

Microbial coinfections and superinfections in critical COVID-19: a Kenyan retrospective cohort analysis.

Objectives: The aim of our study was to outline the burden, risk factors, and outcomes for critical COVID-19 patients with coinfections or superinfections. Methods: This was a retrospective descriptive study of adults who were admitted with critical COVID-19 for ≥ 24 hours. Data collected included demographic profiles and other baseline characteristics, laboratory and radiological investigations, medical interventions, and clinical outcomes. Outcomes of interest included the presence or absence of coinfections or superinfections, and in-hospital mortality. Differences between those with and without coinfections or superinfections were compared for statistical significance. Results: In total, 321 patient records were reviewed. Baseline characteristics included a median age (IQR) of 61.4 (51.4-72.9) years, and a predominance of male (71.3%) and African/black (66.4%) patients. Death occurred in 132 (44.1%) patients, with a significant difference noted between those with added infections (58.2%) and those with none (36.6%) (p = 0.002, odds ratio (OR) = 2.41). One patient was coinfected with pulmonary tuberculosis. Approximately two-thirds of patients received broad-spectrum antimicrobial therapy. Conclusion: Added infections in critically ill COVID-19 patients were relatively uncommon but, where present, were associated with higher mortality. Empiric use of broad-spectrum antimicrobials was common, and may have led to the selection of multidrug-resistant organisms. More robust local data on antimicrobial susceptibility patterns may help in appropriate antibiotic selection, in order to improve outcomes without driving up rates of drug-resistant pathogens.