Antimicrobial resistance and antimicrobial stewardship in South Africa: a survey of healthcare workers in academic and nonacademic hospitals.

Objective: Antimicrobial stewardship programmes (ASPs) facilitate appropriate antimicrobial use and require contextualization for optimal functioning. We aimed to investigate perceptions of and antimicrobial resistance (AMR) and ASPs among healthcare workers in academic and nonacademic hospitals. Design: Cross-sectional survey. Setting: Three academic (Charlotte Maxeke Johannesburg Academic, Inkosi Albert Luthuli, Tygerberg) and three nonacademic hospitals (Leratong, Prince Mshiyeni Memorial, and Paarl) in South Africa from January to June 2022. Participants: Doctors, nurses, and pharmacists. Methods: Voluntary questionnaire using Google Forms, encompassing AMR, ASPs, and selected discipline-specific components. Results: Participants comprised 79 doctors (50 academic), 178 nurses (169 academic), and 21 pharmacists (18 academic) and were female predominant. AMR was a problem in academic hospitals (74.7% vs 51.2%, p 0.004); 73.5% overall reported inappropriate antimicrobial use as a major contributor. Adequate education on antimicrobials occurred in only 36.4% overall. Microbiological testing guided therapy more often in nonacademic settings (80.0% vs 50.2%, p <0.001). In both settings, antimicrobial availability drove selection in 48.2%. Overall, ASPs improved patient care (89.8%) and reduced antimicrobial use (86.9%), although felt to override prescriber autonomy in academic settings (29.4% vs 7.5%, p 0.007), mainly among nurses. Only 50.2% reported successful local ASPs. A minority of pharmacists (20.0%) reported sufficient hospital support for ASPs. Education, involvement of infection control staff, and inclusion of nurses in ASPs were most impactful on AMR. Conclusion: Selected healthcare worker perspectives differ by category and setting and can be targeted to improve ASPs. Further studies should target a higher number of clinical staff in both settings.

Evaluating systematic targeted universal testing for tuberculosis in primary care clinics of South Africa: A cluster-randomized trial (The TUTT Trial).

BACKGROUND: The World Health Organization (WHO) recommends systematic symptom screening for tuberculosis (TB). However, TB prevalence surveys suggest that this strategy does not identify millions of TB patients, globally. Undiagnosed or delayed diagnosis of TB contribute to TB transmission and exacerbate morbidity and mortality. We conducted a cluster-randomized trial of large urban and rural primary healthcare clinics in 3 provinces of South Africa to evaluate whether a novel intervention of targeted universal testing for TB (TUTT) in high-risk groups diagnosed more patients with TB per month compared to current standard of care (SoC) symptom-directed TB testing. METHODS AND FINDINGS: Sixty-two clinics were randomized; with initiation of the intervention clinics over 6 months from March 2019. The study was prematurely stopped in March 2020 due to clinics restricting access to patients, and then a week later due to the Coronavirus Disease 2019 (COVID-19) national lockdown; by then, we had accrued a similar number of TB diagnoses to that of the power estimates and permanently stopped the trial. In intervention clinics, attendees living with HIV, those self-reporting a recent close contact with TB, or a prior episode of TB were all offered a sputum test for TB, irrespective of whether they reported symptoms of TB. We analyzed data abstracted from the national public sector laboratory database using Poisson regression models and compared the mean number of TB patients diagnosed per clinic per month between the study arms. Intervention clinics diagnosed 6,777 patients with TB, 20.7 patients with TB per clinic month (95% CI 16.7, 24.8) versus 6,750, 18.8 patients with TB per clinic month (95% CI 15.3, 22.2) in control clinics during study months. A direct comparison, adjusting for province and clinic TB case volume strata, did not show a significant difference in the number of TB cases between the 2 arms, incidence rate ratio (IRR) 1.14 (95% CI 0.94, 1.38, p = 0.46). However, prespecified difference-in-differences analyses showed that while the rate of TB diagnoses in control clinics decreased over time, intervention clinics had a 17% relative increase in TB patients diagnosed per month compared to the prior year, interaction IRR 1.17 (95% CI 1.14, 1.19, p < 0.001). Trial limitations were the premature stop due to COVID-19 lockdowns and the absence of between-arm comparisons of initiation and outcomes of TB treatment in those diagnosed with TB. CONCLUSIONS: Our trial suggests that the implementation of TUTT in these 3 groups at extreme risk of TB identified more TB patients than SoC and could assist in reducing undiagnosed TB patients in settings of high TB prevalence. TRIAL REGISTRATION: South African National Clinical Trials Registry DOH-27-092021-4901.

Postpasteurization Testing of Human Milk Sterility at Human Milk Banks in Resource-Limited Settings: An Alternative to Standard Microbiological Quality Testing.

Introduction: Pasteurized donor human milk provides nutrition and bioactive factors for infant growth and health when a mother's own milk is not available. Bacteriological testing is recommended for each pasteurized batch of donor milk before distribution to ensure that the milk is safe for use. Charm Peel Plates (CPPs) are a simplified, easy-to-use culture method for detecting microorganisms in milk and milk products. This study investigates the feasibility of using CPPs as an alternative test for current standard postpasteurization screening by human milk banks (HMBs), particularly those in resource-limited settings. Aim: The aim of this study was to evaluate the feasibility of using the CPP versus the 5% horse blood agar (HBA) plate (standard South African National Health Laboratory Service method) for detecting bacterial growth in pasteurized human milk samples. Methods: For each of the 50 pasteurized donor milk samples, 100-µL aliquots were cultured on routine HBA and 1 mL on CPPs for the total bacterial colony count. Any positive growth was identified using VITEK® 2 (bioMérieux). To demonstrate the ability of CPPs to support bacterial growth, four spiked samples were tested. Results: Concurrent negative test results were reported for 49/50 (98%) samples with only one positive test with HBA. Conclusions and Recommendations: The CPP is equivalent to HBA for detection of bacterial growth. Additional advantages of CPPs are ease of use and cost-effectiveness. The CPP is therefore recommended as a point-of-care, bacteriological screening method for donor human milk by HMBs, particularly those in resource-limited settings.

Low prevalence of macrolide resistance in Mycoplasma genitalium infections in a cohort of pregnant women living with human immunodeficiency virus.

OBJECTIVE: Macrolide resistance in Mycoplasma genitalium (M. genitalium) is increasing as a result of the widespread use of azithromycin in the treatment of sexually transmitted infections (STIs). To date, there are few published studies on macrolide resistance patterns in South African pregnant women. This study now contributes to the growing body of knowledge. METHODS: This study included 385 pregnant women living with HIV. Vaginal swabs were collected from consenting pregnant women and used for the detection of M. genitalium using the TaqMan assay. Macrolide resistance-associated mutations in the 23S rRNA gene were determined for all samples that tested positive for M. genitalium using the AllplexTM MG & AziR assay (Seegene) which allows for the simultaneous detection and identification of M. genitalium and six mutations (A2058C, A2058G, A2058T, A2059C, A2059G and A2059T) responsible for azithromycin resistance. The correlation between the TaqMan assay and AllplexTM MG & AziR assay (Seegene) for the detection of M. genitalium was also performed in a subset of 121 samples. RESULTS: Of the 385 samples tested in this study, 14 samples were positive for M. genitalium estimating a prevalence of 3.6%. The same 14 samples also tested positive on the AllplexTM assay indicating a good correlation between the TaqMan Assay and the AllplexTM. Of the 14 positive samples, one sample carried a mutation at position A2059G denoting macrolide resistance in this pathogen. Mutations in the other regions of the 23S rRNA were not detected. All assay controls used in the mutation scanning produced the desired results showing the validity of the assay. CONCLUSION: In this study, macrolide resistance in M. genitalium was detected. Despite the low prevalence of resistance determinants ongoing antimicrobial resistance surveillance is vital considering that azithromycin is used in the syndromic management for the treatment of vaginal discharge syndrome.

Assessment of Antibiotic Resistance and Efflux Pump Gene Expression in Neisseria Gonorrhoeae Isolates from South Africa by Quantitative Real-Time PCR and Regression Analysis.

Introduction: Treatment of gonorrhoea infection is limited by the increasing prevalence of multidrug-resistant strains. Cost-effective molecular diagnostic tests can guide effective antimicrobial stewardship. The aim of this study was to correlate mRNA expression levels in Neisseria gonorrhoeae antibiotic target genes and efflux pump genes to antibiotic resistance in our population. Methods: This study investigated the expression profile of antibiotic resistance-associated genes (penA, ponA, pilQ, mtrR, mtrA, mtrF, gyrA, parC, parE, rpsJ, 16S rRNA, and 23S rRNA) and efflux pump genes (macAB, norM, and mtrCDE), by quantitative real-time PCR, in clinical isolates from KwaZulu-Natal, South Africa. Whole-genome sequencing was used to determine the presence or absence of mutations. Results: N. gonorrhoeae isolates, from female and male patients presenting for care at clinics in KwaZulu-Natal, South Africa, were analysed. As determined by binomial regression and ROC analysis, the most significant (p ≤ 0.05) markers for resistance prediction in this population, and their cutoff values, were determined to be mtrC (p = 0.024; cutoff <0.089), gyrA (p = 0.027; cutoff <0.0518), parE (p = 0.036; cutoff <0.0033), rpsJ (p = 0.047; cutoff <0.0012), and 23S rRNA (p = 0.042; cutoff >7.754). Conclusion: Antimicrobial stewardship includes exploring options to conserve currently available drugs for gonorrhoea treatment. There is the potential to predict an isolate as either susceptible or nonsusceptible based on the mRNA expression level of specific candidate markers, to inform patient management. This real-time qPCR approach, with few targets, can be further investigated for use as a potentially cost-effective diagnostic tool to detect resistance.

Pyrazinamide resistance in rifampicin discordant tuberculosis.

INTRODUCTION: Mycobacterium tuberculosis strains with phenotypically susceptible rpoB mutations (rifampicin discordant) have emerged following implementation of rapid molecular drug resistance testing for tuberculosis. Whilst rifampicin resistance is known to be associated with resistance to other rifamycins (rifapentine and rifabutin) as well as isoniazid and pyrazinamide, rifampicin discordant strains have shown high rates of susceptibility to isoniazid and rifabutin. However, pyrazinamide susceptibly testing results have not been reported. MATERIALS AND METHODS: We evaluated pyrazinamide resistance in 80 rifampicin discordant and 25 rifampicin and isoniazid susceptible isolates from KwaZulu-Natal in South Africa using Mycobacteria Growth Indicator Tube method and sequencing of the pncA. We also compared susceptibility of pyrazinamide with that of isoniazid. RESULTS: Pyrazinamide resistance was found in 6/80 (7.5%) rifampicin discordant isolates. All pyrazinamide resistant isolates were also resistant to isoniazid and pyrazinamide resistance was found to be associated with isoniazid resistance. No pyrazinamide resistance was found among the isoniazid susceptible isolates. CONCLUSION: Given the low prevalence of pyrazinamide resistance in rifampicin discordant TB, this anti-TB drug still has a significant role in the treatment of these patients. Performing pyrazinamide susceptibility testing remains a challenge, our findings show that isoniazid susceptible isolates are unlikely to be resistant to pyrazinamide among the discordant TB isolates.

Neonatal sepsis in a tertiary unit in South Africa.

BACKGROUND: Antimicrobial resistance (AMR) has emerged as a global threat to healthcare resulting in an increase in morbidity and mortality. Neonatal sepsis is ranked as the third highest cause of neonatal demise globally, in which AMR accounted for 31.0% of deaths. AMR in neonates has been poorly characterised in Durban, South Africa. Thus, the resultant effect of AMR on empiric regimens for neonatal sepsis is uncertain in this setting. Therefore, this study analysed the aetiology and antimicrobial susceptibility patterns of bloodstream infections within the neonatal intensive care unit at a tertiary hospital in Durban, with the aim of establishing an effective empiric regimen for the unit. METHODS: A retrospective data review on positive blood cultures from the neonatal intensive care unit at Inkosi Albert Luthuli Central Hospital was conducted. Three time periods were analysed: 2014, 2016 and 2018. Culture data from neonates aged 0-30 days were included and repeat cultures were de-duplicated. The frequency of common organisms and their antimicrobial susceptibilities were analysed. Fischer's exact test was used for subgroup analysis. Poisson and logistic regressions were used to assess significant trends in organisms and antimicrobial susceptibilities over time. RESULTS: Late-onset sepsis (86.8%) predominated over early-onset sepsis (13.2%). A preponderance of gram-positive organisms (68.7%) over gram-negatives (26.8%) and fungi (4.5%) was detected. Common pathogens included coagulase-negative staphylococci (53.5%), Klebsiella pneumoniae (11.6%), enterococci (9.3%), and Acinetobacter baumannii (7.7%). Despite the small contribution of fungi to the microbial profile, fluconazole-resistant Candida parapsilosis predominated within that group. High rates of resistance to first- and second-line antibiotics were also noted among gram-positive and gram-negative organisms. Multidrug resistant organisms included extended-spectrum beta-lactamase (ESBL) K. pneumoniae (7.6%) and extensively-drug resistant A. baumannii (7.0%). However, a statistically significant decrease in ESBL-producing organisms was documented during the entire study period (p = 0.005). CONCLUSIONS: It was determined that first-line antimicrobials, advocated by the World Health Organization for treatment of neonatal sepsis, proved ineffective in this unit due to high levels of AMR. Therefore, this study advises that meropenem with or without vancomycin provides optimal empiric cover. Amphotericin B is advocated for empiric antifungal therapy. Ongoing surveillance is necessary.

Association of Staphylococcus nasal colonization and HIV in end-stage renal failure patients undergoing peritoneal dialysis.

INTRODUCTION: Staphylococcal infections can cause significant morbidity in patients undergoing dialysis. This study evaluated the effects of HIV infection on nasal carriage of Staphylococcus aureus, staphylococcal peritonitis, and catheter infection rates in patients with end-stage renal failure managed with continuous ambulatory peritoneal dialysis (CAPD). METHODS: Sixty HIV-positive and 59 HIV-negative CAPD patients were enrolled and followed up for up to 18 months. S. aureus nasal carriage (detected by nasal swab culture), Staphylococcal peritonitis (diagnosed by clinical presentation, and CAPD effluent Staphylococcal culture and white blood cell count ≥100 cells/µL), and catheter infections (including exit site and tunnel infections) were assessed monthly. RESULTS: At 18 months, S. aureus nasal carriage rates were 43.3% and 30.5% (p = 0.147) and the methicillin-resistant S. aureus (MRSA) nasal carriage rates were 31.7% and 13.6% (p = 0.018) for the HIV-positive and HIV-negative cohorts, respectively. The HIV-positive cohort was associated with increased hazards for staphylococcal peritonitis, (adjusted hazard ratio [AHR] 2.85, 95% confidence interval [CI] 1.19-6.84, p = 0.019) due to increased coagulase-negative staphylococcal (CNS) peritonitis rate in the HIV-positive cohort compared with the HIV-negative cohort (0.435 vs. 0.089 episodes/person-years; AHR 7.64, CI 2.18-26.82, p = 0.001). On multivariable analysis, CD4+ cell count <200 cells/µL, diabetes, and S. aureus nasal carriage were found to be independent predictors of S. aureus peritonitis. CONCLUSIONS: These findings suggest that HIV infection may be a risk factor for MRSA nasal colonization and may increase the risks of CNS peritonitis, while a CD4+ cell count <200 cells/µL and S. aureus nasal carriage may be important predictors of S. aureus peritonitis.

Antimicrobial stewardship approach: Prevalence of antimicrobial resistant bacteria at a regional hospital in South Africa.

INTRODUCTION: Antimicrobial stewardship practices are crucial for the regular surveillance to change the antimicrobial policy. This study was conducted to decide the prevalence of common bacteria and their antibiogram regarding antimicrobial stewardship program within one year, at the regional and district, Stanger hospital in South Africa. METHODOLOGY: It was based the study on clinical data and laboratory records of the patients. It reviewed the clinical and laboratory data. The prevalence/proportion rate was calculated and correlated with the majority of microorganism vs empirical therapy. RESULTS: The prevalence of MRSA, MRSE, VRSA, ESBL+ K. pneumoniae; E. coli cultured from the blood was 25%, 49%, 2%, 62% and 27% respectively. Similarly, we analysed for other targeted MDROs organisms (Acinetobacter species and P. aeruginosa, CRE, CPE) isolated from blood culture and endotracheal aspirate. The prevalence of MDR Acinetobacter species exceeded 61%, 33% from the blood and ETA respectively. The prevalence of MDR P. aeruginosa was 10% from ETA. The MRSA, MRSE, VRSA, VRE were observed in blood specimen. The majority of the microorganisms cultured from the CSF was Cryptococcus neoformans and followed by bacteria: Streptococcus pneumonia, Streptococcus group B and Haemorphilus influenza. CONCLUSION: The selection of empirical antimicrobial therapy relates not only the institutions or unit-specific antibiogram but also the site of infection. We can further suggest continuing to do surveillance of antibiogram and prevalence of MDR organisms for infection control as well as for empirical therapy, part of the antimicrobial  stewardship program based on yearly records to change the local hospital antibiotic policy.

Laboratory based antimicrobial resistance surveillance for Pseudomonas aeruginosa blood isolates from South Africa.

INTRODUCTION: Antimicrobial resistant bacterial infections are widespread globally and increases in antimicrobial resistance presents a major threat to public health. Pseudomonas aeruginosa is an opportunistic healthcare-associated pathogen with high rates of morbidity and mortality and an extensive range of resistance mechanisms. This study describes the antibiotic susceptibility profiles of P. aeruginosa isolates from patients with bacteraemia submitted by sentinel laboratories in South Africa from 2014 to 2015. METHODOLOGY: Organism identification and antimicrobial susceptibility testing were done using automated systems. Molecular methods were used to detect common resistance genes and mechanisms. RESULTS: Overall the susceptibility was high for all antibiotics tested with a decrease over the two-year period. There was no change in the MIC50 and MIC90 breakpoints for all antibiotics from 2014 to 2015. The MIC50 was within the susceptible breakpoint range for most antibiotics and the MIC90 was within the susceptible breakpoint range for colistin only. Phenotypically carbapenem non-susceptible isolates harboured the following plasmid-mediated genes: blaVIM (n = 81, 12%) and blaGES (n = 6, 0.9%); blaNDM (n = 4, 0.6%) and blaOXA-48 and variants (n = 3, 0.45%). Porin deletions were observed in one meropenem non-susceptible isolate only, and multi-drug resistance efflux pumps were expressed in the majority of the non-susceptible isolates investigated. BlaVEB-1, blaIMP and blaKPC were not detected. CONCLUSION: The prevalence of resistance to commonly used antibacterial agents was low for P. aeruginosa isolates and similarly, tested resistance mechanisms were detected in a relatively small proportion of isolates. Findings in this study represent baseline information for understanding antimicrobial susceptibility patterns in P. aeruginosa isolates from blood. Our surveillance report may assist in contributing to hospital treatment guidelines.

Analysis of clinical and microbiological data on Acinetobacter baumannii strains assist the preauthorization of antibiotics at the patient level for an effective antibiotic stewardship program.

Drug resistant Acinetobacter baumannii (A. baumannii) poses serious treatment challenges and is on the rise worldwide. The Infectious Diseases Society of America/Society for Healthcare Epidemiology of America recommends preauthorization of antibiotics to ensure successful antibiotic stewardship programs (ASWPs). This study estimates and analyzes the microbiological and clinical characteristics of A. baumanii strains with differentiating criteria for sepsis versus colonization, in order to support preauthorization and assist ASWPs at the patient level. A retrospective observational study was performed from 2008 to 2014. The clinical and microbiological characteristics of A. baumannii strains were correlated to assess pathogenic status and antibiotic resistance patterns. A flow chart was produced to differentiate between sepsis and colonization amongst patient groups. A. baumannii was cultured in 2656 cases, with a prevalence of 0.9-2.4% during 7 years study periods. There was a statistically significant difference between the sepsis and colonization groups (P=0.02). Sepsis accounted for 37-51% of A. baumanii isolates and colonisation for 49-63% (P=<0.01). Multidrug resistant (MDR), extensive drug resistant (XDR) and pandrug resistant (PDR) A. baumannii was detected in 53-60%, 1-19% and 1% of cultures in the sepsis group, and 75%, 8-23% and 1% in the colonized group. There was a high percentage of polymicrobial infection in the sepsis group and pure growth was not always significant for sepsis. Cases of MDR and XDR A. baumannii increased over the seven-year study, while PDR strains emerged. For a successful ASWP, both clinical and microbiological information should be interpreted when establishing preauthorization/decision to treat.