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Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs.

ABSTRACT: Fluoroquinolones came into widespread use in African countries in the early 2000s, after patents for the first generation of these drugs expired. By that time, quinolone antibacterial agents had been used intensively worldwide and resistant lineages of many bacterial species had evolved. We sought to understand which Gram negative enteric pandemic lineages have been reported from Africa, as well as the nature and transmission of any indigenous resistant clones. A systematic review of articles indexed in the Medline and AJOL literature databases was conducted. We report on the findings of 43 eligible studies documenting local or pandemic fluoroquinolone-resistant enteric clones in sub-Sahara African countries. Most reports are of invasive non-typhoidal Salmonella and Escherichia coli lineages and there have been three reports of cholera outbreaks caused by fluoroquinolone-resistant Vibrio cholerae O1. Fluoroquinolone-resistant clones have also been reported from commensals and animal isolates but there are few data for non-Enterobacteriaceae and almost none for difficult-to-culture Campylobacter spp. Fluoroquinolone-resistant lineages identified in African countries were universally resistant to multiple other classes of antibacterial agents. Although as many as 972 non-duplicate articles refer to fluoroquinolone resistance in enteric bacteria from Africa, most do not report on subtypes and therefore information on the epidemiology of fluoroquinolone-resistant clones is available from only a handful of countries in the subcontinent. When resistance is reported, resistance mechanisms and lineage information is rarely investigated. Insufficient attention has been given to molecular and sequence-based methods necessary for identifying and tracking resistant clones in Africa and more research is needed in this area.

SUBMITTER: Chattaway MA

PROVIDER: S-EPMC4841292 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs.

Chattaway Marie A MA Aboderin Aaron O AO Fashae Kayode K Okoro Chinyere K CK Opintan Japheth A JA Okeke Iruka N IN

Frontiers in microbiology 20160422

Fluoroquinolones came into widespread use in African countries in the early 2000s, after patents for the first generation of these drugs expired. By that time, quinolone antibacterial agents had been used intensively worldwide and resistant lineages of many bacterial species had evolved. We sought to understand which Gram negative enteric pandemic lineages have been reported from Africa, as well as the nature and transmission of any indigenous resistant clones. A systematic review of articles in ...[more]

PMID: 27148238

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Project description:Background:Antimicrobial resistance (AMR) thwarts the curative power of drugs and is a present-time global problem. We present data on antimicrobial susceptibility and resistance determinants of bacteria the WHO has highlighted as being key antimicrobial resistance concerns in Africa, to strengthen knowledge of AMR patterns in the region. Methods:Blood, stool, and urine specimens of febrile patients, aged between ? 30 days and ? 15 years and hospitalized in Burkina Faso, Gabon, Ghana, and Tanzania were cultured from November 2013 to March 2017 (Patients > 15 years were included in Tanzania). Antimicrobial susceptibility testing was performed for all Enterobacterales and Staphylococcus aureus isolates using disk diffusion method. Extended-spectrum beta-lactamase (ESBL) production was confirmed by double-disk diffusion test and the detection of bla CTX-M, bla TEM and bla SHV. Multilocus sequence typing was conducted for ESBL-producing Escherichia coli and Klebsiella pneumoniae, ciprofloxacin-resistant Salmonella enterica and S. aureus. Ciprofloxacin-resistant Salmonella enterica were screened for plasmid-mediated resistance genes and mutations in gyrA, gyrB, parC, and parE. S. aureus isolates were tested for the presence of mecA and Panton-Valentine Leukocidin (PVL) and further genotyped by spa typing. Results:Among 4,052 specimens from 3,012 patients, 219 cultures were positive of which 88.1% (n = 193) were Enterobacterales and 7.3% (n = 16) S. aureus. The prevalence of ESBL-producing Enterobacterales (all CTX-M15 genotype) was 45.2% (14/31; 95% CI: 27.3, 64.0) in Burkina Faso, 25.8% (8/31; 95% CI: 11.9, 44.6) in Gabon, 15.1% (18/119; 95% CI: 9.2, 22.8) in Ghana and 0.0% (0/12; 95% CI: 0.0, 26.5) in Tanzania. ESBL positive non-typhoid Salmonella (n = 3) were detected in Burkina Faso only and methicillin-resistant S. aureus (n = 2) were detected in Ghana only. While sequence type (ST)131 predominated among ESBL E. coli (39.1%;9/23), STs among ESBL K. pneumoniae were highly heterogenous. Ciprofloxacin resistant nt Salmonella were commonest in Burkina Faso (50.0%; 6/12) and all harbored qnrB genes. PVL were found in 81.3% S. aureus. Conclusion:Our findings reveal a distinct susceptibility pattern across the various study regions in Africa, with notably high rates of ESBL-producing Enterobacterales and ciprofloxacin-resistant nt Salmonella in Burkina Faso. This highlights the need for local AMR surveillance and reporting of resistances to support appropriate action.

Project description:Sub-Saharan Africa represents 69% of the total number of individuals living with HIV infection worldwide and 72% of AIDS deaths globally. Pulmonary infection is a common and frequently fatal complication, though little is known regarding the lower airway microbiome composition of this population. Our objectives were to characterize the lower airway microbiome of Ugandan HIV-infected patients with pneumonia, to determine relationships with demographic, clinical, immunological, and microbiological variables and to compare the composition and predicted metagenome of these communities to a comparable cohort of patients in the US (San Francisco). Bronchoalveolar lavage samples from a cohort of 60 Ugandan HIV-infected patients with acute pneumonia were collected. Amplified 16S ribosomal RNA was profiled and aforementioned relationships examined. Ugandan airway microbiome composition and predicted metagenomic function were compared to US HIV-infected pneumonia patients. Among the most common bacterial pulmonary pathogens, Pseudomonas aeruginosa was most prevalent in the Ugandan cohort. Patients with a richer and more diverse airway microbiome exhibited lower bacterial burden, enrichment of members of the Lachnospiraceae and sulfur-reducing bacteria and reduced expression of TNF-alpha and matrix metalloproteinase-9. Compared to San Franciscan patients, Ugandan airway microbiome were significantly richer, and compositionally distinct with predicted metagenomes that encoded a multitude of distinct pathogenic pathways e.g secretion systems. Ugandan pneumonia-associated airway microbiome is compositionally and functionally distinct from those detected in comparable patients in developed countries, a feature which may contribute to adverse outcomes in this population. Please note that the data from the comparable cohort of patients in the USUS data was published as supplemental material of PMID: 22760045 but not submitted to GEO The 'patient_info.txt' contains 12 clinical, 7 immunological and 3 microbiological variables for each patient.

Project description:BackgroundChildren in Sub-Saharan Africa (SSA) comprise half of the total regional population, yet existing mental health services are severely under-equipped to meet their needs. Although effective interventions for the treatment of disruptive behavioral disorders (DBDs) in youth have been tested in high-poverty and high-stress communities in developed countries, and are relevant for widespread dissemination in low- and middle-income countries (LMICs), most of these evidence-based practices (EBPs) have not been utilized in SSA, a region heavily impacted by poverty, diseases including HIV/AIDS, and violence. Thus, this paper presents a protocol for a scale-up longitudinal experimental study that uses a mixed-methods, hybrid type II, effectiveness implementation design to test the effectiveness of an EBP, called Multiple Family Group (MFG) aimed at improving child behavioral challenges in Uganda while concurrently examining the multi-level factors that influence uptake, implementation, sustainment, and youth outcomes.MethodsThe MFG intervention will be implemented and tested via a longitudinal experimental study conducted across 30 public primary schools located in both semi-urban and rural communities. The schools will be randomly assigned to three study conditions (n = 10 per study condition): (1) MFG delivered by trained family peers; (2) MFG delivered by community health workers; or; (3) comparison: usual care comprising mental health care support materials, bolstered with school support materials. A total of 3000 children (ages 8 to 13 years; grades 2 to 7) and their caregivers (N = 3000 dyads); 60 parent peers, and 60 community health workers will be recruited. Each study condition will comprise of 1000 child-caregiver dyads. Data will be collected at baseline, 8 and 16 weeks, and 6-month follow-up.DiscussionThis project is the first to test the effectiveness of the MFG intervention while concurrently examining multi-level factors that influence overall implementation of a family-based intervention provided in schools and aimed at reaching the large child population with mental health service needs in Uganda. Moreover, the study draws upon an EBP that has already been tested for delivery by parent peers and community facilitators, and hence will take advantage of the advancing science behind task-shifting. If successful, the project has great potential to address global child mental health needs.Trial registrationClinicalTrials.gov, ID: NCT03081195 . Registered on 16 March 2017.

Project description:Background: Emerging data from Africa indicates remarkably low numbers of reported COVID-19 deaths despite high levels of disease transmission. However, evolution of these trends as the pandemic progresses remains unknown. More certain are the devastating long-term impacts of the pandemic on health and development evident globally. Research tailored to the unique needs of African countries is crucial. UKCDR and GloPID-R have launched a tracker of funded COVID-19 projects mapped to the WHO research priorities and research priorities of Africa and less-resourced countries and published a baseline analysis of a living systematic review (LSR) of these projects. Methods: In-depth analyses of the baseline LSR for COVID-19 funded research projects in Africa (as of 15th July 2020) to determine the funding landscape and alignment of the projects to research priorities of relevance to Africa. Results: The limited COVID-19 related research across Africa appears to be supported mainly by international funding, especially from Europe, although with notably limited funding from United States-based funders. At the time of this analysis no research projects funded by an African-based funder were identified in the tracker although there are several active funding calls geared at research in Africa and there may be funding data that has not been made publicly available. Many projects mapped to the WHO research priorities and five particular gaps in research funding were identified, namely: investigating the role of children in COVID-19 transmission; effective modes of community engagement; health systems research; communication of uncertainties surrounding mother-to-child transmission of COVID-19; and identifying ways to promote international cooperation. Capacity strengthening was identified as a dominant theme in funded research project plans. Conclusions: We found significantly lower funding investments in COVID-19 research in Africa compared to high-income countries, seven months into the pandemic, indicating a paucity of research targeting the research priorities of relevance to Africa.

Dataset Information

Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs.

Publications

Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs.

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