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Nicholas A Feasey

Publications and source records attributed to Nicholas A Feasey.

5 recordsLinked to original sources
PubMed2025

Prospective characterisation of drug-resistant bloodstream infections in Africa and Asia (ACORN2): a surveillance network assessment.

BACKGROUND: Antimicrobial resistance (AMR) is a major global health threat, but there is scarcity of laboratory surveillance data linked to clinical information to determine burden and inform interventions, especially from low-income and middle-income countries. The ACORN2 study sought to address this through prospective case-based surveillance in 19 hospitals across Africa and Asia to characterise drug-resistant infections by origin, clinical syndrome, patient age, outcome, and geographical location. METHODS: Patients were enrolled on selected wards and clinical data were collected daily for community-acquired infections (CAIs). Point prevalence surveys for hospital-acquired infections (HAIs) were conducted weekly. Mortality was assessed at discharge and after 28 days. Linked microbiology data were extracted from local laboratory databases. Primary descriptive analyses focused on WHO Global Antimicrobial Resistance and Use Surveillance System pathogen (target organism) bloodstream infections (BSIs). Comparisons were adjusted for clustering by site using random effects models. FINDINGS: Over 31 months, 41&#x2009;907 infections were characterised from 41&#x2009;032 admissions. Two-thirds were children (19&#x2009;351; 47&#xb7;2%) or neonates (6649; 16&#xb7;2%). There were marked differences in pathogen incidence and antibiotic resistance when clinical infections were stratified by patient age category and infection origin (CAI/HAI). The highest rates of target organism AMR BSI were third-generation cephalosporin-resistant (3GC-R) Escherichia coli (718&#xb7;56/100&#x2009;000 blood cultured infection episodes), meticillin-resistant Staphylococcus aureus (586&#xb7;89/100&#x2009;000 blood cultured infection episodes), and 3GC-R Klebsiella pneumoniae (364&#xb7;92/100&#x2009;000 blood cultured infection episodes). In-hospital mortality was 13&#xb7;1% (166/1265) in patients with target organism BSI versus 6&#xb7;2% (1357/21&#x2009;845) in those with negative blood cultures, p<0&#xb7;0001. INTERPRETATION: ACORN2 has shown practical implementation of collecting linked clinical-laboratory AMR data in low-income and middle-income countries and identified a significant burden of WHO GLASS BSI. Adoption of the ACORN2 approach at scale might enhance use of diagnostic microbiology and improve the volume of clinical data included in national and global AMR surveillance datasets. FUNDING: Wellcome.

Humans↗
PubMed2025

Transmission of extended spectrum &#x3b2;-lactamase-producing Escherichia coli and antimicrobial resistance gene flow across One Health compartments in eastern Africa: a whole-genome sequence analysis from a prospective cohort study.

BACKGROUND: The One Health paradigm considers interdependence of human, animal, and environmental health. However, there is little evidence from high-income countries to support the importance of a One Health approach to addressing spread of antimicrobial resistance (AMR). Given AMR is a global threat, understanding how the close interactions of humans with animals and the environment in low-income settings affect the spread of AMR is important. We aimed to investigate diversity and transmission of extended spectrum &#x3b2;-lactamase (ESBL)-producing Escherichia coli across household-linked One Health compartments using genomic data. METHODS: We sequenced whole genomes of ESBL-producing E coli isolates from humans, animals, and the environment from a prospective, longitudinal cohort study conducted in Malawi (April 29, 2019, to Dec 3, 2020) and Uganda (July 16, 2020, to Aug 6, 2021). In the cohort study, 259 households were enrolled at baseline in Malawi and 92 in Uganda from a mix of urban, peri-urban, and rural areas. Households were followed up at months 1, 3, and 6 in Malawi and at months 1, 2, and 4 in Uganda. Samples collected at each visit included human and animal stool, environmental samples from hand-contact areas, food, and water, and broader environmental samples such as river water. Samples were cultured in buffered peptone water and then ESBL chromogenic agar to isolate ESBL-producing E coli. ESBL-producing E coli isolates underwent whole-genome sequencing. We performed phylogenetic analyses, and in-silico multi-locus sequence typing, characterised AMR determinants and linked genotypes with sample location, ecological source, and other covariates. We performed fine-scale single nucleotide polymorphism (SNP) and network analysis to infer strain and plasmid transmission across ecological compartments. The primary outcome was colonisation with ESBL-producing E coli. Secondary outcomes were genomic clusters and ESBL genomic determinants within and between One Health compartments. FINDINGS: We found high diversity of ESBL-producing E coli, with 170 sequence types and 166 genomic clusters identified from 2344 genomes, including 1814 genomes from Malawi (907 human, 221 animal, and 686 environmental) and 530 genomes from Uganda (380 human, 147 animal, and three environmental). Sequence type (ST)131 dominated in Malawi (209 [11&#xb7;5%] of 1814 genomes), and ST10 dominated in Uganda (45 [8&#xb7;5%] of 530 genomes). Common ESBL genes blaCTX-M-15 (1604 [68&#xb7;4%] of 2344 genomes) and blaCTX-M-27 (336 [14&#xb7;3%] of 2344 genomes) were carried on a complex network of 55 and 30 different plasmids. This diversity of plasmids presented multiple pathways for dissemination and revealed high force of selection. Phylogenetic analyses revealed common intermixing of isolates between humans, animals, and the environment. SNP transmission analysis revealed ecologically overlapping clusters, suggesting ESBL-producing E coli co-circulation both within and between compartments with frequent spillover events. Applying a five-SNP threshold, we inferred 463 human-environment transmission events, 146 human-animal events, and 142 animal-environment events. INTERPRETATION: Our work suggests that a One Health approach is crucial to addressing AMR in eastern Africa. Improving water, sanitation, and hygiene systems will create a safer environment, reduce spillovers of AMR bacteria between compartments, and eventually reduce AMR reservoirs in the environment and in animals. FUNDING: Medical Research Council, National Institute for Health and Care Research, and Wellcome Trust.

Humans↗
PubMed2025

Factors associated with positive blood cultures in children in nine African and Asian countries: the ACORN2 surveillance network.

BACKGROUND: Blood culture (BC) in children has relatively low diagnostic yield and high contamination rates, limiting cost-effectiveness. We aimed to determine readily available baseline characteristics to identify hospitalised children with a likelihood of higher diagnostic yield in low- and middle-income countries. METHODS: We used data from ACORN2, a prospective clinical surveillance network including 19 hospitals across Africa and Asia. We included participants <18 years, hospitalised for a suspected infection, prescribed parenteral antibiotics and with a BC sample. Sociodemographic and clinical data were recorded for each infection episode and linked to routine microbiology data. We described true pathogen (non-contaminant) BC positivity proportion and performed mixed-effects logistic regression, with study site and patient as the random effect, to identify factors associated with BC positivity. RESULTS: Of the 26 407 paediatric infection episodes, 17 815 (67%) had a BC sample and 15 384 were included in the analysis. BC results were: true pathogens in 689 (4.5%), contaminants in 1399 (9%) and uncertain pathogens in 143 (0.9%). In the multivariable model, factors associated with a positive BC were age (29 days-12-month-olds OR 1.33, 95% CI 1.06 to 1.66 and 5-18 year-olds OR 1.62, 95% CI 1.30 to 2.01 vs 1-4 year-olds), number of clinical severity signs (OR 1.29, 95% CI 1.18 to 1.40 per one sign) and hospital acquired infection (OR 3.05, 95% CI 2.30 to 4.06 vs community-acquired). Suspected diagnosis of sepsis (OR 2.09, 95% CI 1.67 to 2.61), gastrointestinal/abdominal (OR 2.36, 95% CI 1.78 to 3.13), skin and soft tissue or bone (OR 3.64, 95% CI 2.57 to 5.14) and genitourinary infection (OR 2.22, 95% CI 1.39 to 3.56) were more likely to have a positive BC, compared with respiratory infections. CONCLUSION: We confirmed the low BC yield among hospitalised children. We identified groups for which diagnostic stewardship efforts to increase BC uptake should be prioritised and others in which it could be limited in times of financial or logistic constraints.

Humans↗
PubMed2025

Diversity of Salmonella enterica isolates from urban river and sewage water in Blantyre, Malawi.

BACKGROUND: Salmonella enterica encompasses over 2,600 serovars, including several commonly associated with severe infection in humans. Salmonella is a major cause of sepsis in Africa; however, diagnosis requires clinical microbiology facilities. Environmental surveillance has the potential to play a role in Salmonella surveillance. METHODS: We undertook water-based environmental surveillance in Blantyre, Malawi, from 2018-2020, taking samples from rivers (87.9%), a sewage plant (8.85%) and other water sources (3.24%), isolating and storing 1,042 non-typhoidal Salmonella (NTS) isolates in this period. Of these, 341 NTS isolates were whole genome sequenced, genome quality was checked, duplicate genomes from any given sample were removed and core genome phylogeny was reconstructed. AMRFinder, PathogenWatch and SISTR were used to further investigate serovar, sequence type and antimicrobial resistance determinants. RESULTS: After quality checks, and removal of duplicate genomes, 270 NTS genomes remained for further analysis. Multiple Salmonella serovars associated with human infection were detected, of which S. Typhimurium (55/270 isolates) was the most common, including 44 of Sequence Type (ST) 313, a serovar commonly associated with severe invasive disease (iNTS). Six lineage 2 ST313 genomes possessed AMR genes predicting multidrug resistance (MDR), while 29 lineage 3 isolates contained no AMR predictive genes. PCR based detection of staG has been proposed as a diagnostic marker of S. Typhi; however, all eight genomes that contained staG identified as Salmonella enterica serovar Orion, raising concerns about the specificity of this marker as a monoplex for environmental surveillance of S. Typhi. DISCUSSION: The study identified diverse Salmonella serovars in the environment, including those reported to cause invasive disease, emphasizing the complex but potentially valuable contribution of implementing environmental surveillance for Salmonella in high burden areas lacking diagnostic microbiology capacity.

Sewage↗
PubMed2024

Optimized methods for the targeted surveillance of extended-spectrum beta-lactamase-producing Escherichia coli in human stool.

Understanding transmission pathways of important opportunistic, drug-resistant pathogens, such as extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli, is essential to implementing targeted prevention strategies to interrupt transmission and reduce the number of infections. To link transmission of ESBL-producing E. coli (ESBL-EC) between two sources, single-nucleotide resolution of E. coli strains, as well as E. coli diversity within and between samples, is required. However, the microbiological methods to best track these pathogens are unclear. Here, we compared different steps in the microbiological workflow to determine the impact different pre-enrichment broths, pre-enrichment incubation times, selection in pre-enrichment, selective plating, and DNA extraction methods had on recovering ESBL-EC from human stool samples, with the aim to acquire high-quality DNA for sequencing and genomic epidemiology. We demonstrate that using a 4-h pre-enrichment in Buffered Peptone Water, plating on cefotaxime-supplemented MacConkey agar and extracting DNA using Lucigen MasterPure DNA Purification kit improves the recovery of ESBL-EC from human stool and produced high-quality DNA for whole-genome sequencing. We conclude that our optimized workflow can be applied for single-nucleotide variant analysis of an ESBL-EC from stool.IMPORTANCEDrug-resistant infections are increasingly difficult to treat with antibiotics. Preventing infections is thus highly beneficial. To do this, we need to understand how drug-resistant bacteria spread to take action to stop infection and transmission. This requires us to accurately trace these bacteria between different sources. In this study, we compared different laboratory methods to see which worked best for detecting extended-spectrum beta-lactamase (ESBL)-producing E. coli, a common cause of urinary tract or bloodstream infections, from human stool samples. We found that enriching stool in a nutrient broth for 4 h, then plating the bacterial suspension on antibiotic-selective MacConkey agar, and finally extracting DNA from the bacteria using a specific DNA purification kit resulted in improved recovery of ESBL E. coli and high-quality DNA. Sequencing multiple isolates from stool allowed us to distinguish unambiguously and at high resolution between different variants of ESBL E. coli present in stool.

Humans↗