A pooled testing strategy for identifying SARS-CoV-2 at low prevalence.

Suppressing infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will probably require the rapid identification and isolation of individuals infected with the virus on an ongoing basis. Reverse-transcription polymerase chain reaction (RT-PCR) tests are accurate but costly, which makes the regular testing of every individual expensive. These costs are a challenge for all countries around the world, but particularly for low-to-middle-income countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups1-7. A balance must be struck between increasing the group size and retaining test sensitivity, as sample dilution increases the likelihood of false-negative test results for individuals with a low viral load in the sampled region at the time of the test8. Similarly, minimizing the number of tests to reduce costs must be balanced against minimizing the time that testing takes, to reduce the spread of the infection. Here we propose an algorithm for pooling subsamples based on the geometry of a hypercube that, at low prevalence, accurately identifies individuals infected with SARS-CoV-2 in a small number of tests and few rounds of testing. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, largely parallel searches are preferred. We report proof-of-concept experiments in which a positive subsample was detected even when diluted 100-fold with negative subsamples (compared with 30-48-fold dilutions described in previous studies9-11). We quantify the loss of sensitivity due to dilution and discuss how it may be mitigated by the frequent re-testing of groups, for example. With the use of these methods, the cost of mass testing could be reduced by a large factor. At low prevalence, the costs decrease in rough proportion to the prevalence. Field trials of our approach are under way in Rwanda and South Africa. The use of group testing on a massive scale to monitor infection rates closely and continually in a population, along with the rapid and effective isolation of people with SARS-CoV-2 infections, provides a promising pathway towards the long-term control of coronavirus disease 2019 (COVID-19).

Community- and Hospital-Acquired Infections in Surgical patients at a Tertiary Referral Hospital in Rwanda.

BACKGROUND: Extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) are increasing in globally. The aim of this study was to compare community-acquired infections (CAIs) and hospital-acquired infections (HAIs) and determine the rate of third-generation cephalosporin resistance and ESBL-PE at a tertiary referral hospital in Rwanda. METHODS: This was a cross-sectional study of Rwandan acute care surgery patients with infection. Samples were processed for culture and susceptibility patterns using Kirby-Bauer disk diffusion method. Third-generation cephalosporin resistance and ESBL-PE were compared in patients with CAI versus HAI. RESULTS: Over 14 months, 220 samples were collected from 191 patients: 116 (62%) patients had CAI, 59 (32%) had HAI, and 12 (6%) had both CAI and HAI. Most (n = 178, 94%) patients were started on antibiotics with third-generation cephalosporins (ceftriaxone n = 109, 57%; cefotaxime n = 52, 27%) and metronidazole (n = 155, 81%) commonly given. Commonly isolated organisms included Escherichia coli (n = 62, 42%), Staphylococcus aureus (n = 27, 18%), and Klebsiella spp. (n = 22, 15%). Overall, 67 of 113 isolates tested had resistance to third-generation cephalosporins, with higher resistance seen in HAI compared with CAI (74% vs 46%, p value = 0.002). Overall, 47 of 89 (53%) isolates were ESBL-PE with higher rates in HAI compared with CAI (73% vs 38%, p value = 0.001). CONCLUSIONS: There is broad and prolonged use of third-generation cephalosporins despite high resistance rates. ESBL-PE are high in Rwandan surgical patients with higher rates in HAI compared with CAIs. Infection prevention practices and antibiotic stewardship are critical to reduce infection rates with resistant organisms in a low-resource setting.

An Assessment of the Knowledge and Perceptions of Precision Medicine (PM) in the Rwandan Healthcare Setting.

INTRODUCTION: Precision medicine (PM) or personalized medicine is an innovative approach that aims to tailor disease prevention and treatment to consider the differences in people's genes, environments, and lifestyles. Although many efforts have been made to accelerate the universal adoption of PM, several challenges need to be addressed in order to advance PM in Africa. Therefore, our study aimed to establish baseline data on the knowledge and perceptions of the implementation of PM in the Rwandan healthcare setting. METHOD: A descriptive qualitative study was conducted in five hospitals offering diagnostics and oncology services to cancer patients in Rwanda. To understand the existing policies regarding PM implementation in the country, two additional institutions were surveyed: the Ministry of Health (MOH), which creates and sets policies for the overall vision of the health sector, and the Rwanda Biomedical Center (RBC), which coordinates the implementation of health sector policies in the country. The researchers conducted 32 key informant interviews and assessed the functionality of available PM equipment in the 5 selected health facilities. The data were thematically categorized and analyzed. RESULTS: The study revealed that PM is perceived as a complex and expensive program by most health managers and health providers. The most cited challenges to implementing PM included the following: the lack of policies and guidelines; the lack of supportive infrastructures and limited suppliers of required equipment and laboratory consumables; financial constraints; cultural, behavioral, and religious beliefs; and limited trained, motivated, and specialized healthcare providers. Regarding access to health services for cancer treatment, patients with health insurance pay 10% of their medical costs, which is still too expensive for Rwandans. CONCLUSION: The study participants highlighted the importance of PM to enhance healthcare delivery if the identified barriers are addressed. For instance, Rwandan health sector leadership might consider the creation of specialized oncology centers in all or some referral hospitals with all the necessary genomic equipment and trained staff to serve the needs of the country and implement a PM program.

Antimicrobial Resistance Profile of Bacteria Causing Pediatric Infections at the University Teaching Hospital in Rwanda.

Bacterial infections pose a global threat, especially in the pediatric population. Antimicrobials that are used to treat such infections continuously show reduced efficacy, and empirical therapy is a major treatment option in Rwanda. This study aimed to determine the resistance rate of commonly used antibiotics in pediatric patients. The study was conducted from June 1, 2018 to May 30, 2019, and microbiological samples were collected from 712 children with suspected bacterial infections. Antimicrobial sensitivity testing was performed on 177 positive cultures (24%) that were considered for data analysis. The findings show that the major bacterial isolates were Klebsiella pneumoniae (n = 50, 28.2%), Escherichia coli (n = 47, 26.5%), and Staphylococcus aureus (n = 38, 21.4%). In general, the greatest antibiotic resistance rate was observed in ampicillin (n = 125, 86.2%), amoxicillin-clavulanic acid (n = 84, 82.4%), amoxicillin (n = 64, 79%), cefadroxil (n = 83, 69.2%), tetracycline (n = 72, 59.7%), ceftazidime (n = 42, 55.3%), and cefuroxime (n = 14, 53.8%). More specifically, Klebsiella pneumoniae was 100% resistant to amoxicillin-clavulanic acid, cefuroxime, trimethoprim-sulfamethoxazole, ceftazidime, erythromycin, and clindamycin. Staphylococcus aureus was 86.7% resistant to ampicillin, and Escherichia coli was 91.7% resistant to tetracycline, 90.6% resistant to ampicillin, 83.3% resistant to amoxicillin-clavulanic acid, 79.3% resistant to cefadroxil, and 78.6% resistant to ceftazidime. Moreover, Klebsiella pneumoniae from blood and urine was 96.8% and 100% sensitive, respectively, to meropenem. Staphylococcus aureus from blood was 100% sensitive to vancomycin, whereas Escherichia coli from urine was sensitive to clindamycin (100%), nitrofurantoin (80.6%), and ciprofloxacin (72.7%). In conclusion, our findings show a high resistance rate to commonly used antibiotics, which suggests precaution in empirical therapy and continued surveillance of antimicrobial resistance.

Bacteriological Profile and Antimicrobial Susceptibility Patterns of Bloodstream Infection at Kigali University Teaching Hospital.

BACKGROUND: Worldwide, bacterial bloodstream infections (BSIs) constitute an important cause of morbidity and mortality in clinical settings. Due to the limited laboratory facilities in sub-Saharan Africa, poor diagnosis of BSIs results in poor clinical outcomes and leads to a risk of antimicrobial resistance. The present work was carried out to describe the microbiological features of BSIs using the data collected from Centre Hospitalier Universitaire de Kigali (CHUK). METHODS: A retrospective study was carried out at CHUK. The blood culture results of 2,910 cases - from adults, children and infants - were reviewed in the Microbiology service from October 2017 to October 2018. The following variables were considered: age, gender, admitting department, blood culture results, and antimicrobials sensitivity test results. Data were entered and analyzed using Microsoft Excel 2013. RESULTS: Twelve percent (341/2,910) of blood culture results reviewed were positive with 108 (31.7%) Gram positive bacteria and 233 (68.3%) Gram negative bacteria. The most prevalent pathogens were Klebsiella pneumoniae 108 (31.7%) and Staphylococcus aureus 100 (29.3%). This study revealed a high resistance to commonly prescribed antibiotics such as penicillin, trimethoprim sulfamethoxazole, and Ampicillin with 91.8, 83.3, and 81.8% of resistance, respectively. However, bacteria were sensitive to imipenem and vancomycin with 98.1 and 94.3% of sensitivity, respectively. The pediatrics and neonatology departments showed a high number of positive culture with 97/341 (28.4%), and 93/341 (27%) respectively. The overall prevalence of multidrug resistance was 77.1%. CONCLUSION: The prevalence of bacterial pathogens in BSIs was found to be high. The antibiotic resistance to the commonly used antibiotics was high. Appropriate treatment of BSIs should be based on the current knowledge of bacterial resistance pattern. This study will help in formulating management of diagnostic guidelines and antibiotic policy.

Exploring Perceptions and Acceptance of Minimally Invasive Tissue Sampling among Bereaved Relatives and Health-Care Professionals in Rwanda.

PURPOSE: In most low- and lower middle-income countries (LMICs), minimally invasive tissue sampling (MITS) is a relatively new procedure for identifying the cause of death (CoD). This study aimed to explore perceptions and acceptance of bereaved families and health-care professionals regarding MITS in the context of MITS initiation in Rwanda as an alternative to clinical autopsy. METHODS: This was a qualitative phenomenological study with thematic analysis. Participants were bereaved relatives (individual interviews) and health-care professionals (focus-group discussions) involved in MITS implementation. It was conducted in the largest referral and teaching hospital in Rwanda. RESULTS: Motivators of MITS acceptance included eagerness to know the CoD, noninvasiveness of MITS, trust in medics, and the fact that it was free. Barriers to consent to MITS included inadequate explanations from health-care professionals, high socioeconomic status, lack of power to make decisions, and lack of trust in medics. Health-care professionals perceived both conventional autopsy and MITS as gold-standard procedures in CoD determination. They recommended including MITS among hospital services and commended the post-MITS multidisciplinary discussion panel in CoD determination. They pointed out that there might be reticence in approaching bereaved relatives to obtain consent for MITS. Both groups of participants highlighted the issue of delay in releasing MITS results. CONCLUSION: Both health-care professionals and bereaved relatives appreciate that MITS is an acceptable procedure to include in routine hospital services. Dealing with barriers met by either group is to be considered in the eventual next phases of MITS implementation in Rwanda and similar sociocultural contexts.

Widespread antimicrobial resistance among bacterial infections in a Rwandan referral hospital.

BACKGROUND: Resistance among bacterial infections is increasingly well-documented in high-income countries; however, relatively little is known about bacterial antimicrobial resistance in low-income countries, where the burden of infections is high. METHODS: We prospectively screened all adult inpatients at a referral hospital in Rwanda for suspected infection for seven months. Blood, urine, wound and sputum samples were cultured and tested for antibiotic susceptibility. We examined factors associated with resistance and compared hospital outcomes for participants with and without resistant isolates. RESULTS: We screened 19,178 patient-days, and enrolled 647 unique participants with suspected infection. We obtained 942 culture specimens, of which 357 were culture-positive specimens. Of these positive specimens, 155 (43.4%) were wound, 83 (23.2%) urine, 64 (17.9%) blood, and 55 (15.4%) sputum. Gram-negative bacteria comprised 323 (88.7%) of all isolates. Of 241 Gram-negative isolates tested for ceftriaxone, 183 (75.9%) were resistant. Of 92 Gram-negative isolates tested for the extended spectrum beta-lactamase (ESBL) positive phenotype, 66 (71.7%) were ESBL positive phenotype. Transfer from another facility, recent surgery or antibiotic exposure, and hospital-acquired infection were each associated with resistance. Mortality was 19.6% for all enrolled participants. CONCLUSIONS: This is the first published prospective hospital-wide antibiogram of multiple specimen types from East Africa with ESBL testing. Our study suggests that low-resource settings with limited and inconsistent access to the full range of antibiotic classes may bear the highest burden of resistant infections. Hospital-acquired infections and recent antibiotic exposure are associated with a high proportion of resistant infections. Efforts to slow the development of resistance and supply effective antibiotics are urgently needed.