Antimicrobial Resistance profiles and genomic analysis of Salmonella enterica from two referral hospitals in Zambia.
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ABSTRACT:
PROVIDER: PRJEB59725 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10869400_1.fastq.gz | Fastqsanger.gz | |||
| ERR10869400_2.fastq.gz | Fastqsanger.gz | |||
| ERR10869401_1.fastq.gz | Fastqsanger.gz | |||
| ERR10869401_2.fastq.gz | Fastqsanger.gz | |||
| ERR10869402_1.fastq.gz | Fastqsanger.gz |
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Project description:ObjectivesThis study investigated antimicrobial susceptibility and genomic profiling of S. enterica isolated from bloodstream infections at a tertiary referral hospital in Lusaka, Zambia, 2018-2019.MethodThis was a prospective hospital-based study involving routine blood culture samples submitted to the microbiology laboratory at the University Teaching Hospital. Identification of S. enterica and determination of antimicrobial susceptibility profiles was achieved through conventional and automated methods. Whole-genome sequencing (WGS) was conducted, and the sequence data outputs were processed for species identification, serotype determination, multilocus sequence typing (MLST) profile determination, identification of antimicrobial resistance determinants, and phylogeny.ResultsSeventy-six Salmonella enterica were isolated and 64 isolates underwent WGS. Salmonella Typhi (72%) was the most prevalent serotype. Notable was the occurrence of invasive non-typhoidal Salmonella Typhimurium ST313 (3%), resistance to cephalosporins (4%) and ciprofloxacin (5%), multidrug resistance (46%), and reduced susceptibility to ciprofloxacin (30%) and imipenem (3%). Phylogenetic cluster analysis showed multiple Salmonella serovars with a wide range of genetic diversity.ConclusionThe genetic diversity of Salmonella Typhi, high prevalence of multidrug resistance, and the emergence of ciprofloxacin and cephalosporin resistance warrants improved hygiene and water and sanitation provision, continued surveillance to apprise antibiograms and inform policy, and the introduction of the typhoid conjugate vaccine.
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Project description:ObjectiveTo delineate the prevalence and factors associated with antimicrobial use across six referral hospitals in Tanzania using WHO point prevalence survey (PPS) methodology to inform hospital-specific antimicrobial stewardship programmes.DesignCross-sectional analytical study.SettingSix referral hospitals in Tanzania.ParticipantsPatients irrespective of age and gender (n=948) admitted in the six referral hospital wards before 8:00 hours on each day of the survey were included in December 2019. Using the WHO PPS methodology, data on hospitals, wards, patients, antibiotics, and indications for antibiotics were collected.Outcome measuresWe analysed the prevalence of antibiotic use by referral hospital, ward, indication and patient characteristics as the main outcomes. We also described adherence to the Tanzania Standard Treatment Guidelines (STG) and WHO's AWaRe categorisation of antibiotics.ResultsApproximately 62.3% of inpatients were prescribed antibiotics, predominantly from the Access group of antibiotics (ceftriaxone, metronidazole or ampicillin-cloxacillin). The overall adherence of antibiotic prescriptions to the Tanzania STG was high (84.0%), with the exception of Sekou Toure Regional Referral Hospital (68.0%) and Maweni Regional Referral Hospital (57.8%). The most common indication for antibiotic prescriptions was community-acquired infections (39.8%). Children less than 2 years of age (OR 1.73, 95% CI 1.02 to 2.92, p=0.039); admission to surgical wards (OR 4.90, 95% CI 2.87 to 8.36, p <0.001); and admission to paediatric wards (OR 3.93, 95% CI 2.16 to 7.15, p <0.001) were associated with increased odds of antibiotic use. Only 2 of 591 patients were prescribed antibiotics based on culture and antimicrobial susceptibility testing results.ConclusionsEmpirical use of antibiotics is common, and the Access group of antibiotics is predominantly prescribed in children less than 2 years and patients admitted to surgical and paediatric wards. Lack of utilisation of antimicrobial susceptibility testing services in these hospitals requires urgent interventions. Routine monitoring of antibiotic use is recommended to be part of antibiotic stewardship programmes in Tanzania.
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Project description:BackgroundImproved knowledge regarding antimicrobial use in Ghana is needed to reduce antimicrobial resistance (AMR). This includes point prevalence studies (PPSs) in hospitals. Objectives were to: (i) provide baseline data in two hospitals [Keta Municipal Hospital (KMH) and Ghana Police Hospital (GPH)] and identify priorities for improvement; (ii) assess the feasibility of conducting PPSs; and (iii) compare results with other studies.MethodsStandard PPS design using the Global PPS paper forms, subsequently transferred to their template. Training undertaken by the Scottish team. Quality indicators included: rationale for use; stop/review dates; and guideline compliance.ResultsPrevalence of antibiotic use was 65.0% in GPH and 82.0% in KMH. Penicillins and other β-lactam antibiotics were the most frequently prescribed in both hospitals, with third-generation cephalosporins mainly used in GPH. Antibiotic treatment was mainly empirical and commonly administered intravenously, duration was generally short with timely oral switching and infections were mainly community acquired. Encouragingly, there was good documentation of the indications for antibiotic use in both hospitals and 50.0%-66.7% guideline compliance (although for many indications no guideline existed). In addition, almost all prescribed antibiotics had stop dates and there were no missed doses. The duration of use for surgical prophylaxis was generally more than 1 day (69.0% in GPH and 77.0% in KMH).ConclusionsThese two hospitals were the first in Ghana to use the Global PPS system. We found the PPS was feasible, relatively rapid and achieved with limited training. Targets for improvement identified included reduction of broad-spectrum antibiotics and duration of treatment.
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Project description:BackgroundAntimicrobial stewardship (AMS) programs are critical in combating antimicrobial resistance (AMR). In Zambia, there is little information regarding the capacity of hospitals to establish and implement AMS programs. The objective of this study was to conduct a baseline assessment of WHO core elements for an AMS program implementation in eight hospitals in Zambia.Materials and methodsWe conducted an exploratory cross-sectional study from September 2023 to December 2023 using a self-scoring Periodic National and Healthcare Facility Assessment Tool from the World Health Organization (WHO) policy guidance on integrated AMS activities in human health. Eight public hospitals were surveyed across the five provinces of Zambia. Data was analyzed using the WHO self-scoring tool and thematic analysis.ResultsOverall, 62.5% (6/8) of the facilities scored low (below 60%) in implementing AMS programs. Most facilities had challenges with reporting AMS feedback within the hospital (average score = 46%), Drugs and Therapeutics Committee (DTC) functionality (average score = 49%), AMS actions (average score = 50%), education and training (average score = 54%), and leadership commitment to AMS activities (average score = 56%). The overall score for all AMS core elements was average (56%). All the hospitals (100%) did not have an allocated budget for AMS programs. Finally, there were neither antibiograms to guide antimicrobial utilization nor AMS-trained staff in more than 50% of the hospitals surveyed.ConclusionThis study found low AMS implementation in these public hospitals, especially where DTCs were non-functional. The identified challenges and gaps require urgent attention for sustainable multidisciplinary AMS programs.
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Project description:BackgroundNeisseria gonorrhoeae, the causative agent for sexually transmitted infection (STI) gonorrhoea, has emerged with a significant public health impact on acquiring resistance to antimicrobials available for treatment. The resistance of N. gonorrhoeae limit treatment options and contributed to high morbidity associated with gonorrhoea. Data on antimicrobial resistance (AMR) profiles in N. gonorrhoeae is scares in Zambia. This study aimed to determine the antibiotic susceptibilities in N. gonorrhoeae isolates from Lusaka, Zambia.MethodsA prospective cross-sectional study was conducted on 630 STI patients who presented with urethral or vaginal discharge from 2019 to 2020. Urethral and endocervical secretions were cultured on Modified Thayer Martin agar and incubated at 36 °C ± 1 °C in 5% CO2 for 24 h. Identification of N. gonorrhoeae isolates was achieved by Gram stain, oxidase, nitrocefin disk, BactiCard Neisseria, and Viteck® Compact. The AMR profiles were determined using E-test. Statistical significant was determined by Pearson's Chi-square test, Mann-Whitney U test, or logistic regression with p-values of < 0.05 indicating significance.ResultsA total of 630 patients were recruited of which 46% (290/630) with the median of 29 years and interquartile range (IQR) of 19-39 years were male. The median of the females was 26 years and IQR of 15-37 years. Neisseria gonorrhoeae was isolated from 19.4% (122/630) patients of which 72.9% (89/122) were male, with highest prevalence of isolation in the age category of 25-34 years. The prevalence of resistance was high to penicillin (85.2%), tetracycline (68.9%) and ciprofloxacin (59.8%) with MIC90 of 32 µg/mL, 8 µg/mL, and 8 µg/mL respectively. The isolates had reduced susceptibility to cefixime (1.6%), spectinomycin (4.9%) and (4.9%) for azithromycin. All isolates were susceptible to ceftriaxone. Risk factors associated with AMR were douching in females (AOR 6.69, 95% CI; 1.11-40.31, p = 0.039), female gender (AOR 7.64, 95% CI; 1.11-52.33, p = 0.048), HIV-positivity (AOR 26.59, 95% CI; 3.67-192.7, p = 0.005), no condom use or unprotected sex (AOR 5.48, 95% CI; 1.17-22.75 p = 0.026), sex trading (AOR 4.19, 95% CI; 1.55-11.33, p = 0.010), and over-counter treatment of ciprofloxacin (AOR 3.44, 95% CI; 1.17-22.75, p = 0.023).ConclusionThe N. gonorrhoeae resistance to penicillin, tetracycline and ciprofloxacin was high necessitating revision of the treatment guidelines. However, no resistance to ceftriaxone was detected. Therefore, monitoring of antibiotic resistance remains critical in Zambia.
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