Genomic surveillance and antimicrobial resistance determinants in Neisseria gonorrhoeae isolates from Uganda, Malawi, and South Africa, 2015-2020
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ABSTRACT:
PROVIDER: PRJEB59971 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR11676100_1.fastq.gz | Fastqsanger.gz | |||
| ERR11676100_2.fastq.gz | Fastqsanger.gz | |||
| ERR11677400_1.fastq.gz | Fastqsanger.gz | |||
| ERR11677400_2.fastq.gz | Fastqsanger.gz | |||
| ERR11677500_1.fastq.gz | Fastqsanger.gz |
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Project description:Genomic surveillance of Neisseria gonorrhoeae isolates from Uganda
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Project description:Antibiotic resistance and its mechanisms have been known for over six decades, but global efforts to characterize its routine drivers have only gained momentum in the recent past. Drivers of clinical and community resistance go beyond just clinical practice, which is why one-health approaches offer the most realistic option for controlling antibiotic resistance. It is noteworthy that the emergence of resistance occurs naturally in the environment, but akin to climate change, the current accelerated emergence and spread bears hallmarks of anthropomorphic influence. If left unchecked, this can undo the medical and agricultural advancements of the last century. The WHO recommends that nations develop, adopt, and implement strategies that track the changing trends in antibiotic resistance levels to tackle this problem. This article examines efforts and progress in developing and implementing a human health antimicrobial resistance surveillance strategy in Uganda. We do so within the context of the National Action Plan for tackling antimicrobial resistance (AMR-NAP) launched in 2018. We discuss the technical milestones and progress in implementing surveillance of GLASS priority pathogens under this framework. The preliminary output of the framework examines the performance and compares AMR and AMU surveillance data to explain observed trends. We conclude that Uganda is making progress in developing and implementing a functional AMR surveillance strategy for human health.
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Project description:A systematic chart review was performed to estimate the frequency of pregnancy outcomes, pregnancy complications and neonatal outcomes at facilities in Blantyre, Malawi; Johannesburg, South Africa; Kampala, Uganda; and Chitungwiza and Harare, Zimbabwe to provide comparisons with estimates from an ongoing clinical trial evaluating the safety of two biomedical HIV prevention interventions in pregnancy. A multi-site, cross-sectional chart review was conducted at Maternal Obstetric Units and hospitals where women participating in the ongoing clinical trial would be expected to deliver. All individuals delivering at the designated facilities or admitted for postpartum care within seven days of a delivery elsewhere (home, health clinic, etc.) were included in the review. Data were abstracted for pregnancy outcomes, pregnancy complications, maternal and neonatal death, and congenital anomalies. Data from 10,138 records were abstracted across all four sites (Blantyre n = 2,384; Johannesburg n = 1,888; Kampala n = 3,708; Chitungwiza and Harare n = 2,158), which included 10,426 pregnancy outcomes. The prevalence of preterm birth was 13% (range across sites: 10.4-20.7) and 4.1% of deliveries resulted in stillbirth (range: 3.1-5.5). The most commonly noted pregnancy complication was gestational hypertension, reported among 4.4% of pregnancies. Among pregnancies resulting in a live birth, 15.5% were low birthweight (range: 13.8-17.4) and 2.0% resulted in neonatal death (range:1.2-3.2). Suspected congenital anomalies were noted in 1.2% of pregnancies. This study provides systematically collected data on background rates of pregnancy outcomes, pregnancy complications and neonatal outcomes that can be used as a reference in support of ongoing HIV prevention studies. In addition, estimates from this study provide important background data for future studies of investigational products evaluated in pregnancy in these urban settings.
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Project description:As South Africa transitions from endemic to intermediate endemicity, hepatitis A surveillance needs strengthening to monitor trends in disease incidence and to identify outbreaks. We used passive laboratory-based surveillance data from the National Health Laboratory Services to calculate national hepatitis A incidence and to establish thresholds for outbreaks. Incidence was calculated by age and geographic location. The static threshold used two or three standard deviations (SDs) above the mean hepatitis A incidence in 2017-2019, and a cumulative summation (CuSum2) threshold used three SDs above the mean of the preceding seven months. These thresholds were applied to hepatitis A data for 2020. From 2017 to 2020, the mean incidence of hepatitis A IgM was 4.06/100,000 and ranged from 4.23 to 4.85/100,000 per year. Hepatitis A incidence was highest in the Western Cape province (WCP) (7.00-10.92/100,000 per year). The highest incidence was in the 1-9-year-olds. The incidence of hepatitis A in 2020 exceeded the static threshold in two districts of the WCP: Cape Winelands in January and Overberg district in August. The provincial incidence did not exceed the static and CuSum2 thresholds. District-level analysis using either threshold was sensitive enough to monitor trends and to alert district health authorities, allowing early outbreak responses.
| S-EPMC8704411 | biostudies-literature
Project description:BackgroundAntimicrobial resistance (AMR) data in the pediatric population are limited, particularly in developing countries. This study assessed the AMR profile and key resistance phenotypes and genotypes for Gram-negative bacteria (GNB) isolates collected as part of the Antimicrobial Testing Leadership and Surveillance program from pediatric patients in Latin America, Africa-Middle East, and Asia in 2016-2020 versus 2011-2015.MethodsMinimum inhibitory concentrations by broth microdilution methodology were interpreted per the Clinical and Laboratory Standards Institute. European Committee on Antimicrobial Susceptibility Testing breakpoints were used for interpreting colistin activity. β-lactamase genes were screened by polymerase chain reaction and sequencing.ResultsFor Acinetobacter baumannii, low susceptibility (<60.0%) was observed for all antimicrobials, except colistin (≥92.9%), across regions and year periods. Ceftazidime-avibactam, amikacin, colistin, and meropenem were mostly active (78.6%-100.0%) against Enterobacter cloacae, Escherichia coli, and Klebsiella pneumoniae. For Pseudomonas aeruginosa, susceptibility to ceftazidime-avibactam, amikacin, and colistin was ≥85.9%. Among resistance phenotypes, carbapenem-resistant (CR, ≥44.8%) and difficult-to-treat resistant (DTR, ≥37.1%) rates were the highest in A. baumannii. A consistent increase in CR and DTR K. pneumoniae was noted across regions over time. Extended-spectrum β-lactamases (ESBL)-producing K. pneumoniae (32.6%-55.6%) were more frequent than ESBL-producing E. coli (25.3%-37.1%). CTX-M was the dominant ESBL among Enterobacterales. NDM-positive Enterobacterales species and VIM-positive P. aeruginosa were identified across regions.ConclusionsThis study identified high susceptibility to few agents for key GNB in pediatric patients. Continued surveillance of resistance phenotypes and genotypes at regional levels may help to guide appropriate treatment decisions.
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Project description:The aim of this study was to compare the transcriptional response to TB in regions of different incidence / prevalence.
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Project description:OBJECTIVE:This study aimed to characterise antibiotics resistance of Escherichia coli isolates from the formal meat sector (FMS) and informal meat sectors (INMS). METHOD:A total of 162 and 102 E. coli isolates from the FMS, and INMS respectively were isolated by standard culture-based, and biochemical reactions. The isolates were further confirmed by polymerase chain reaction (PCR). The disc diffusion method was used to screen for antimicrobial susceptibility against 19 different antibiotics. The presence of class 1-2 integrons in each E. coli isolates was assessed using 3'-CS and 5'-CS regions specific primers. RESULT:Among the 19 antimicrobials, resistance to tetracyclines, aminoglycosides, cephalosporins, and nitrofurans were found to be more frequent than carbapenems and chloramphenicol. The number of multi-drug resistance ranged from three to ten antimicrobials. The resistant determinants with the highest prevalence in the FMS and INMS were; [aminoglycosides: aadA (40.6%; 31.9%), and strA (6.5%; 9.4%)], [?-lactams: ampC (20%; 45%),], [Chloramphenicol: catI (1.7%; 1.7%), and [tetracyclines: tetB (11.5%; 24%),], and [sulfonamides: sul1 (22.2%; 26.7%),]. CONCLUSION:Higher phenotypic resistance to cephalosporins and carbapenems were found in the FMS than in INMS. The multiple antibiotic resistance (MAR) indexes for FMS and INMS ranged from 0.2-0.5. The results reveal a high prevalence of multidrug-resistant E. coli isolates and resistance determinants, suggesting that consumers and handlers of such meat are at risk of contracting antibiotic-resistant E. coli-related foodborne disease.
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