Review of phenotypic assays for detection of extended-spectrum \u3b2-lactamases and carbapenemases: a microbiology laboratory bench guide

Background: Infections caused by gram-negative antibiotic-resistant bacteria continue to increase. Despite recommendations by the Clinical Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) with regards to detection of antibiotic degrading enzymes secreted by these bacteria, the true prevalence of extended-spectrum \u3b2-lactamase (ESBL) and carbapenemase producers remains a difficult task to resolve. Describing of previously designed phenotypic detection assays for ESBLs and carbapenemases in a single document avails a summary that allows for multiple testing which increases the sensitivity and specificity of detection. Methods and aims: This review, therefore, defined and classified ESBLs and carbapenemases, and also briefly described how the several previously designed phenotypic detection assays for the same should be performed. Conclusion: Extended-spectrum \u3b2-lactamase and carbapenemase detection assays, once performed correctly, can precisely discriminate between bacteria producing these enzymes and those with other mechanisms of resistance to \u3b2-lactam antibiotics

Investigating the evolution and predicting the future outlook of antimicrobial resistance in sub-saharan Africa using phenotypic data for Klebsiella pneumoniae: a 12-year analysis

Abstract Background Antimicrobial resistance (AMR) is a major public health challenge, particularly in sub-Saharan Africa (SSA). This study aimed to investigate the evolution and predict the future outlook of AMR in SSA over a 12-year period. By analysing the trends and patterns of AMR, the study sought to enhance our understanding of this pressing issue in the region and provide valuable insights for effective interventions and control measures to mitigate the impact of AMR on public health in SSA. Results The study found that general medicine patients had the highest proportion of samples with AMR. Different types of samples showed varying levels of AMR. Across the studied locations, the highest resistance was consistently observed against ceftaroline (ranging from 68 to 84%), while the lowest resistance was consistently observed against ceftazidime avibactam, imipenem, meropenem, and meropenem vaborbactam (ranging from 92 to 93%). Notably, the predictive analysis showed a significant increasing trend in resistance to amoxicillin-clavulanate, cefepime, ceftazidime, ceftaroline, imipenem, meropenem, piperacillin-tazobactam, and aztreonam over time. Conclusions These findings suggest the need for coordinated efforts and interventions to control and prevent the spread of AMR in SSA. Targeted surveillance based on local resistance patterns, sample types, and patient populations is crucial for effective monitoring and control of AMR. The study also highlights the urgent need for action, including judicious use of antibiotics and the development of alternative treatment options to combat the growing problem of AMR in SSA

Genomics and bioinformatics capacity in Africa: no continent is left behind

Despite the poor genomics research capacity in Africa, efforts have been made to empower African scientists to get involved in genomics research, particularly that involving African populations. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, an initiative was set to make genomics research in Africa an African endeavor and was developed through funding from the United States’ National Institutes of Health Common Fund and the Wellcome Trust. H3Africa is intended to encourage a contemporary research approach by African investigators and to stimulate the study of genomic and environmental determinants of common diseases. The goal of these endeavors is to improve the health of African populations. To build capacity for bioinformatics and genomics research, organizations such as the African Society for Bioinformatics and Computational Biology have been established. In this article, we discuss the current status of the bioinformatics infrastructure in Africa as well as the training challenges and opportunities.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Isoniazid preventive therapy completion and factors associated with non-completion among patients on antiretroviral therapy at Kisenyi Health Centre IV, Kampala, Uganda.

BackgroundIsoniazid preventive therapy (IPT) is given to HIV patients to reduce the risk of active tuberculosis (TB). However, treatment completion remains suboptimal among those that are initiated. This study aimed to determine the completion level of IPT and the factors associated with non-completion among patients on antiretroviral therapy (ART) at Kisenyi Health Center IV in Kampala, Uganda.MethodsA mixed-methods facility-based retrospective cohort study utilizing routinely collected data from 341 randomly selected HIV patients initiated on IPT was conducted. Data extracted from the registers was used to determine IPT completion. Robust Poisson regression was conducted to determine the associated factors of IPT non-completion, while in-depth interviews were conducted to explore barriers to IPT completion from the patient's perspective.ResultsA total of 341 patients who started on isoniazid (INH) were retrospectively followed up, with 69% (236/341) being female. Overall IPT completion was 83%. Multivariate analysis revealed the prevalence of IPT non-completion among males was 2.24 times the prevalence among females (aPR 2.24, 95% CI: 1.40-3.58, p = 0.001). The prevalence of IPT non-completion among patients with a non-suppressed HIV viral load was 3.00 times the prevalence among those with a suppressed HIV viral load (aPR 3.00, 95% CI: 1.44-6.65, p = 0.007). The prevalence of IPT non-completion among patients who were married, or cohabiting was 0.31 times the prevalence among those who were single (aPR 0.31, 95% CI: 0.17-0.55, pConclusionIPT completion was found to be 83% among the cohort studied. However, lower completion levels persist among males and HIV-virally non-suppressed patients. Lack of IPT-related health education, pill burden, distance to the health facility, and patient relocation were reported as barriers to IPT completion. Interventions that target these groups of people need to be intensified

Evaluation of three protocols for direct susceptibility testing for gram negative-Enterobacteriaceae from patient samples in Uganda with SMS reporting

Abstract In Uganda, the challenge of generating and timely reporting essential antimicrobial resistance (AMR) data has led to overreliance on empirical antibiotic therapy, exacerbating the AMR crisis. To address this issue, this study aimed to adapt a one-step AMR testing protocol alongside an SMS (Short Message Service) result relay system (SRRS), with the potential to reduce the turnaround time for AMR testing and result communication from 4 days or more to 1 day in Ugandan clinical microbiology laboratories. Out of the 377 samples examined, 54 isolates were obtained. Notably, E. coli (61%) and K. pneumoniae (33%) were the most frequently identified, majority testing positive for ESBL. Evaluation of three AMR testing protocols revealed varying sensitivity and specificity, with Protocol A (ChromID ESBL-based) demonstrating high sensitivity (100%) but no calculable specificity, Protocol B (ceftazidime-based) showing high sensitivity (100%) and relatively low specificity (7.1%), and Protocol C (cefotaxime-based) exhibiting high sensitivity (97.8%) but no calculable specificity. ESBL positivity strongly correlated with resistance to specific antibiotics, including cefotaxime, ampicillin, and aztreonam (100%), cefuroxime (96%), ceftriaxone (93%), and trimethoprim sulfamethoxazole (87%). The potential of integrating an SRRS underscored the crucial role this could have in enabling efficient healthcare communication in AMR management. This study underscores the substantial potential of the tested protocols for accurately detecting ESBL production in clinical samples, potentially, providing a critical foundation for predicting and reporting AMR patterns. Although considerations related to specificity warrant careful assessment before widespread clinical adoption

Source-tracking ESBL-producing bacteria at the maternity ward of Mulago hospital, Uganda.

IntroductionEscherichia coli, Klebsiella pneumoniae and Enterobacter (EKE) are the leading cause of mortality and morbidity in neonates in Africa. The management of EKE infections remains challenging given the global emergence of carbapenem resistance in Gram-negative bacteria. This study aimed to investigate the source of EKE organisms for neonates in the maternity environment of a national referral hospital in Uganda, by examining the phenotypic and molecular characteristics of isolates from mothers, neonates, and maternity ward.MethodsFrom August 2015 to August 2016, we conducted a cross-sectional study of pregnant women admitted for elective surgical delivery at Mulago hospital in Kampala, Uganda; we sampled (nose, armpit, groin) 137 pregnant women and their newborns (n = 137), as well as health workers (n = 67) and inanimate objects (n = 70 -beds, ventilator tubes, sinks, toilets, door-handles) in the maternity ward. Samples (swabs) were cultured for growth of EKE bacteria and isolates phenotypically/molecularly investigated for antibiotic sensitivity, as well as β-lactamase and carbapenemase activity. To infer relationships among the EKE isolates, spatial cluster analysis of phenotypic and genotypic susceptibility characteristics was done using the Ridom server.ResultsGram-negative bacteria were isolated from 21 mothers (15%), 15 neonates (11%), 2 health workers (3%), and 13 inanimate objects (19%); a total of 131 Gram-negative isolates were identified of which 104 were EKE bacteria i.e., 23 (22%) E. coli, 50 (48%) K. pneumoniae, and 31 (30%) Enterobacter. Carbapenems were the most effective antibiotics as 89% (93/104) of the isolates were susceptible to meropenem; however, multidrug resistance was prevalent i.e., 61% (63/104). Furthermore, carbapenemase production and carbapenemase gene prevalence were low; 10% (10/104) and 6% (6/104), respectively. Extended spectrum β-lactamase (ESBL) production occurred in 37 (36%) isolates though 61 (59%) carried ESBL-encoding genes, mainly blaCTX-M (93%, 57/61) implying that blaCTX-M is the ideal gene for tracking ESBL-mediated resistance at Mulago. Additionally, spatial cluster analysis revealed isolates from mothers, new-borns, health workers, and environment with similar phenotypic/genotypic characteristics, suggesting transmission of multidrug-resistant EKE to new-borns.ConclusionOur study shows evidence of transmission of drug resistant EKE bacteria in the maternity ward of Mulago hospital, and the dynamics in the ward are more likely to be responsible for transmission but not individual mother characteristics. The high prevalence of drug resistance genes highlights the need for more effective infection prevention/control measures and antimicrobial stewardship programs to reduce spread of drug-resistant bacteria in the hospital, and improve patient outcomes

Adherence to malaria treatment guidelines among health care workers in private health facilities in Kampala's informal settlements, Uganda.

Poor adherence to malaria treatment guidelines among healthcare workers (HCWs) is a major contribution to diagnostic challenges, treatment failure, and non-rational use of antimalarial medicines. However, there is limited information about adherence to malaria treatment guidelines among HCWs in private health facilities in informal settlements in Uganda. This study therefore assessed the level of adherence to malaria treatment guidelines and associated factors among HCWs in private health facilities in Kampala's informal settlements. A cross-sectional study was conducted among 339 HCWs from private health facilities in slums of 4 selected divisions in Kampala, Uganda. Quantitative data was collected using a semi-structured questionnaire, cleaned in MS Excel 2016 and analyzed using STATA 15.0 statistical software. Bivariate and multivariate analysis were conducted using a generalized linear model of modified Poisson regression to obtain factors associated with adherence to malaria treatment guidelines. The study revealed that majority of respondents 71.1%(241/339) were aged 30 years and below, and 50.1%(170/339) of the were female. Almost all of the respondents 98.8%(335/339) reported that they had malaria diagnostic equipment (microscopy or rapid diagnostic tests) at their facilities, 47.5%(161/339) had non-recommended anti-malarial drugs present in stock and 36.0% reported that they did not refer severely ill patients to higher health facilities in the previous 3 months. Although 92.6%(314/339) of the respondents had heard about the national malaria treatment guidelines, 63.1%(214/339) of them adhered to these guidelines. Having a bachelors degree (APR 1.54, (CI: 1.13-2.10)P 0.006), and having high levels of knowledge (APR 1.44, (CI: 1.13-1.60)P 0.001) were positively associated with high adherence to malaria treatment guidelines. In conclusion, adherence to malaria treatment guidelines was suboptimal and less than the national target of 90%. Enforcement, supervision, trainings, and continuous medical education should be enhanced in private healthcare facilities to improve adherence to malaria treatment guidelines in informal settlements

Increasing Antimicrobial Resistance in Surgical Wards at Mulago National Referral Hospital, Uganda, from 2014 to 2018—Cause for Concern?

Antimicrobial Resistance (AMR) and Healthcare Associated Infections (HAIs) are major global public health challenges in our time. This study provides a broader and updated overview of AMR trends in surgical wards of Mulago National Referral Hospital (MNRH) between 2014 and 2018. Laboratory data on the antimicrobial susceptibility profiles of bacterial isolates from 428 patient samples were available. The most common samples were as follows: tracheal aspirates (36.5%), pus swabs (28.0%), and blood (20.6%). Klebsiella (21.7%), Acinetobacter (17.5%), and Staphylococcus species (12.4%) were the most common isolates. The resistance patterns for different antimicrobials were: penicillins (40–100%), cephalosporins (30–100%), β-lactamase inhibitor combinations (70–100%), carbapenems (10–100%), polymyxin E (0–7%), aminoglycosides (50–100%), sulphonamides (80–100%), fluoroquinolones (40–70%), macrolides (40–100%), lincosamides (10–45%), phenicols (40–70%), nitrofurans (0–25%), and glycopeptide (0–20%). This study demonstrated a sustained increase in resistance among the most commonly used antibiotics in Uganda over the five-year study period. It implies ongoing hospital-based monitoring and surveillance of AMR patterns are needed to inform antibiotic prescribing, and to contribute to national and global AMR profiles. It also suggests continued emphasis on infection prevention and control practices (IPC), including antibiotic stewardship. Ultimately, laboratory capacity for timely bacteriological culture and sensitivity testing will provide a rational choice of antibiotics for HAI