Biology subjects

Feasey, N. A.

Publications and source records attributed to Feasey, N. A..

14 recordsLinked to original sources

bioRxiv2026

Whole-genome sequencing reveals inter-household networks of gut-colonising ESBL-producing Escherichia coli in two rural Malawian districts

Infection with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) is a global health concern that disproportionately affects sub-Saharan Africa (SSA). Gut mucosal colonisation is thought to precede invasive infection. Understanding ESBL-Ec colonisation and transmission across communities is therefore essential. We investigated the genomic epidemiology and spatial structure of 159 gut-colonising ESBL-Ec isolates from the faeces of 211 people in two rural Malawian villages using longitudinal sampling (2023-24), whole-genome sequencing and household mapping. Colonisation prevalence rose from 34.1% (95% CI: 27.8-41.0) to 54.2% (95% CI: 46.0-62.3) over one year. Isolates belonged to 33 sequence types (STs), most commonly ST38 and ST131, harbouring 46 distinct antimicrobial resistance gene types. Fifteen strains were identified in [≥]3 households that were typically separated by short geographic distances (<400 m). Of 190 pairwise comparisons between same-strain isolates from different households sampled concurrently within villages, 88.9% differed by [≤]10 single nucleotide polymorphisms, consistent with multi-household involvement in community transmission networks. Lineage-specific ST38 and ST131 network analyses linked rural isolates to urban Malawian isolates collected within the last decade. Our findings provide a transferable framework for inferring ESBL-Ec flow in community settings and highlight the need for One Health surveillance and improved sanitation infrastructure to limit transmission.

microbiology↗

bioRxiv2025

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

BACKGROUNDCiprofloxacin resistant Klebsiella pneumoniae is common or emerging in many geographies, and knowledge of local resistance rates is important for empirical therapy. Whilst there are known K. pneumoniae ciprofloxacin resistance determinants, there is a lack of systematic data on the effect of determinants, alone and in combination, and there are no publicly accessible tools for predicting resistance from whole genome sequence data. METHODSThe KlebNET-GSP AMR Genotype-Phenotype Group aggregated a matched genotype-phenotype dataset of n=12,167 K. pneumoniae species complex (KpSC) isolates from 27 countries between 2001-2021. We developed a rules-based classifier to predict ciprofloxacin resistance by categorizing the number of quinolone resistance determining regions mutations in gyrA and parC, the number of plasmid-mediated quinolone resistance genes, and the presence/absence of aac(6')-Ib-cr (which can acetylate ciprofloxacin). Predictive performance was assessed using the discovery dataset, for which we re-phenotyped discrepant isolates; and validated using externally contributed datasets (n=7,030 KpSC isolates). RESULTSThe rules-based classifier predicted R vs S/I with categorical agreement, sensitivity, and specificity >96%, and major/very major error rates <4%. Performance was similar across diverse KpSC sources (human, animal, other), species, and intra-species lineages. External validation of the classifier yielded overall 93.12% categorical agreement [95% confidence interval (CI), 92.50-93.74%], 8.65% major errors [95% CI, 7.34-9.97%], and 6.20% very major errors [95% CI, 5.51-6.90%]. We implemented the classifier in Kleborate, a command-line tool that is integrated into the Pathogenwatch web platform. Using this to assess the global distribution of ciprofloxacin resistance determinants in KpSC genomes available in Pathogenwatch (n=31,319, from 109 countries between years 2000-2023), we observed a significant positive association between national quinolone consumption rates and predicted ciprofloxacin resistance (R2=0.20, p=0.004). CONCLUSIONS Ciprofloxacin resistance phenotypes can be reasonably predicted from genotypes, which is sufficient for informing surveillance. However, unexplained resistance remains and accuracy is insufficient for clinical applications. We demonstrate the value of aggregating genotype-phenotype data to explore resistance mechanisms and develop predictors, but highlight complexities in combining phenotype data from different assays and standards.

genomics↗

bioRxiv2025

An evaluation of screening methods for the detection of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in environmental samples from healthcare settings

Drug-resistant infections with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) are increasingly problematic, especially in healthcare settings. ESBL-E infections lead to a worse treatment outcome and often require escalating antibiotic treatment to reserve antibiotics such as carbapenems. Understanding how these bacteria are transmitted within healthcare settings is complex and not well understood, but it is a requirement for effective infection prevention and control strategies. To what extent environmental ESBL-E reservoirs contribute to transmission is unclear. To accurately capture these reservoirs, laboratory processing of environmental samples needs to be optimised to reliably detect ESBL-E, which is challenging because they can be scarce and part of complex microbial communities. Here, we assessed screening methods for the detection of ESBL-producing Escherichia coli (ESBL-Ec) and Klebsiella pneumoniae (ESBL-Kp) from environmental swabs taken from healthcare settings, testing different swab types, pre-enrichment conditions and selective agars. We show that a pre-enrichment of 18 hours significantly increased the recovery of 3GC-resistant gram-negatives. The choice of selective agar impacted the number of ESBL-Ec and ESBL-Kp detected. This also affected the number of samples requiring additional species confirmation, which is costly and time-consuming. For our use case and by considering additional factors such as cost and practical aspects, Membrane Lactose Glucuronide Agar supplemented with cefotaxime performed best for the combined detection of ESBL-Ec and ESBL-Kp. Our work will guide environmental surveillance of ESBL-E by providing optimised methods for laboratory processing of environmental samples from healthcare settings.

microbiology↗

bioRxiv2024

One Health in Eastern Africa: No barriers for ESBL producing E. coli transmission or independent antimicrobial resistance gene flow across ecological compartments

The One Health paradigm considers the interdependence of human, animal and environmental health. In high-income countries, limited evidence has been found from recent studies to support the importance of a One Health approach to addressing spread of antimicrobial resistance (AMR). Given AMR is a global threat, and we are all interconnected it would be important to know if closer interaction of humans with animals and the environment in low-income present a contrasting picture. We used whole genome sequencing to investigate the genomic diversity and to infer transmission of extended spectrum beta-lactamase producing Escherichia coli (ESBL-Ec) between different ecological niches (humans, animals and the environment). We found high diversity of ESBL-Ec with 172 genomic clusters and 167 sequence types identified from 2,344 genomes. Common ESBL genes, blaCTX-M-15 (67.6%) and blaCTX-M-27 (14.2%) were carried on a complex network of different plasmids, presenting multiple pathways for dissemination and revealing the high force of selection. Using fine-scale genomic clustering across multiple thresholds ranging from 0 to 20 single nucleotide polymorphisms, we found that genomes isolated from humans, animals and the environment formed overlapping clusters, indicating recent ESBL-Ec transmission and co-circulation both within and between ecological compartments. These findings demonstrate that the One Health approach is highly relevant to tackling AMR in low-income settings, and therefore critical to consider if we are to address the rise of AMR globally.

genomics↗

bioRxiv2024

An exploration of unusual antimicrobial resistance phenotypes in Salmonella Typhi from Blantyre, Malawi reveals the ongoing role of IncHI1 plasmids

Typhoid fever is a significant public health problem endemic in Southeast Asia and Sub- Saharan Africa. Antimicrobial treatment of typhoid is however threatened by the increasing prevalence of antimicrobial resistant (AMR) S. Typhi, especially in the globally successful lineage (4.3.1) which has rapidly spread in East and Southern Africa. AMR elements can be found either on plasmids or in one of the three chromosomal integration sites, and there is variability of this across the lineage. Several previous studies with Malawian isolates indicated a clonal, locally spreading lineage with chromosomally integrated resistance genes. In a recent study however we noted three isolates with unusual predicted resistance profiles, and we here present the resolved genomes of these isolates using long- and short-read sequencing. Our work shows that these isolates are potentially imported cases, most closely related to the recently described sub-lineage 4.3.1.EA1, and encode IncHI1 plasmids with reduced resistance profiles compared to the major reference sequence of these plasmids spreading in East Africa. Similar reduced resistance plasmids were reported in a recent large-scale study in five isolates from Tanzania, highlighting the urgency for better coverage of the African continent in genome studies to better understand the dynamics of these potentially co-circulating plasmids.

genomics↗

bioRxiv2023

Molecular mechanisms of re-emerging chloramphenicol susceptibility in extended-spectrum beta-lactamase producing Enterobacterales

Infections with Enterobacterales (E) are increasingly difficult to treat due to antimicrobial resistance. After ceftriaxone replaced chloramphenicol (CHL) as empiric therapy for suspected sepsis in Malawi in 2004, ESBL-E rapidly emerged. Concurrently, resistance to CHL in Escherichia coli and Klebsiella spp. decreased, raising the possibility of CHL re-introduction. However, many phenotypically susceptible isolates still carry CHL acetyltransferase (CAT) genes. We used a combination of genomics, phenotypic susceptibility assays, experimental evolution and functional assays for CAT activity to understand the molecular mechanisms and stability of this re-emerging CHL susceptibility. Of 840 Malawian isolates, 31% had discordant CHL susceptibility genotype-phenotype, and we selected 42 isolates for in-depth analysis. Stable degradation of cat genes by insertion sequences led to re-emergence of CHL susceptibility. Our study suggests CHL could be reintroduced as reserve agent for critically ill patients with ESBL-E infections in Malawi and similar settings and highlights the ongoing challenges in inferring antimicrobial resistance from sequence data.

microbiology↗

bioRxiv2023

Household geckos as a potential vector for Salmonella transmission in Malawi

Salmonella was isolated from 23/79 (29.1%) gecko stool samples from households in southern Malawi. Whole genome sequencing of 47 isolates revealed 27 Salmonella serovars spanning two subspecies. Our results demonstrate that geckos play an important role in the carriage and potentially, transmission of Salmonella within households.

ecology↗

bioRxiv2021

Genomic and antigenic diversity of carried Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi

Klebsiella pneumoniae is an antimicrobial resistance (AMR) associated pathogen of global importance, and polyvalent vaccines targeting K. pneumoniae O-antigens are in development. Genomes from sub-Saharan Africa (sSA) are underrepresented in global sequencing efforts. We therefore carried out a genomic analysis of extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae complex isolates colonising adults in Blantyre, Malawi, placed these isolates in a global genomic context, and compared colonising to invasive isolates from the main public hospital in Blantyre. 203 isolates from stool and rectal swabs from adults were whole-genome sequenced and compared to a publicly available multicountry collection of 484 K. pneumoniae genomes sampled to cover maximum diversity of the species, 150 previously sequenced Malawian and 66 Kenyan isolates from blood or sterile sites. We inferred phylogenetic relationships and analysed the diversity of genetic loci linked to AMR, virulence, capsule (K-) and LPS O-antigen (O-types). We find that the diversity of Malawian Klebsiella isolates is representative of the species population structure, but with local success and expansion of sequence types (STs) ST14, ST15, ST340 and ST307. Siderophore and hypermucoidy genes were more frequent in invasive versus carriage isolates (present in 13% vs 1%, p < 0.001) but still generally lacking in most invasive isolates. The population structure and distribution of O-antigen types was similar in Malawian invasive and carriage isolates, with O4 being more common in Malawian isolates (14%) than in previously published studies (2-5%). We conclude that host factors, pathogen opportunity or alternate virulence loci not linked to invasive disease elsewhere are likely to be the major determinants of invasive disease in Malawi. Distinct ST and O-type distributions in Malawi highlights the need for geographically aware sampling to robustly define secular trends in Klebsiella diversity. Colonising and invasive isolates in Blantyre are similar and hence O-typing of colonising Klebsiella isolates may be a rapid and cost-effective approach to describe global diversity and guide vaccine development. Data SummaryAll data and code to replicate this analysis is available as the blantyreESBL v1.0.0 R package (https://doi.org/10.5281/zenodo.5554082) available at https://github.com/joelewis101/blantyreESBL. Reads from all isolates sequenced as part of this study have been deposited in the European Nucleotide Archive, and accession numbers (as well as accession numbers of publicly available genomes used in this analysis) are provided in the R package.

microbiology↗

bioRxiv2021

Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity.

Escherichia coli is a ubiquitous bacterium and one of the most prevalent Gram-negative species associated with drug resistant infections. The large number of sequenced genomes available have provided us with a consistently growing knowledge base to further understand pathogenesis and epidemiology of this organism. However, data from sub-Saharan Africa (sSA) are underrepresented in global sequencing efforts and E. coli genetic diversity from this region is poorly described. To reduce this gap, we investigated extended-spectrum beta-lactamase (ESBL)-producing E. coli colonising adults in Blantyre, Malawi to assess the bacterial diversity and AMR determinants and to place these isolates in the context of the wider population structure. We performed short-read whole-genome sequencing of 473 colonising ESBL E. coli isolated from human stool and contextualised the genomes with a previously curated multi-country species wide collection of 10,146 genomes. The most frequently identified sequence types (STs) in our collection were the globally successful ST131, ST410 and ST167, and the dominant ESBL genes were blaCTX-M, mirroring global trends. However, 37% of Malawian isolates did not cluster with any isolates in the curated multicountry collection and a core gene phylogeny was consistent with locally spreading subclades within globally dominant clones, including in ST410 and ST167. We also found Carbapenemase genes in our collection at low frequency; we used long read sequencing to characterise selected ESBL and carbapenemase-associated plasmids, demonstrating the presence of globally distributed carbapenemase carrying plasmids. Increased genomic surveillance of E. coli from Malawi and sSA is necessary to understand local, regional and global transmission of both E. coli and the AMR genes they commonly carry. Impact StatementDrug-resistant Escherichia coli producing extended-spectrum beta lactamase (ESBL) or carbapenemase enzymes have been identified by the World Health Organisation as priority pathogens of global concern, and whole genome sequencing has provided insight into mechanisms of virulence, antimicrobial resistance, and the spread of high-risk clones. However, studies analysing large numbers of E. coli using whole-genome data often focus on opportunistic use of hospital diagnostic collections in high-income settings. Understanding how the genomic epidemiology of E. coli in low- and middle-income countries (including many of the nations of sub-Saharan Africa) differs is essential to provide insight into local, and global drivers of transmission. We therefore sequenced 473 ESBL-producing E. coli genomes colonising adults in Blantyre, Malawi. We analyse determinants of antimicrobial resistance and virulence and place the isolates in wider context using a previously published global E. coli collection that was generated to represent the whole species diversity of sequences publicly available at the time of generation. We find that there is diversity in Malawian isolates not reflected in the curated global collection: widely successful antimicrobial-resistance associated E. coli sequence types are represented in Blantyre, but locally circulating subclades are apparent. Furthermore, given the high number of ESBL producing pathogens causing infections there is an unmet need for carbapenem antimicrobials which are still active against ESBL-producers but are not yet widely available in our setting. We find that carbapenemases (enzymes that can render bacteria resistant to carbapenems) in our collection are unusual but present and carried on globally disseminated plasmids. So too are globally successful, stably carbapenemase-associated E. coli lineages. Although the Malawian isolates analysed typically lacked carbapenemases, carbapenem use is increasing in Malawi and their unstewarded use will accelerate selection for carbapememases in E. coli in the future. Our study highlights the need for robust stewardship protocols and ongoing genomic surveillance as these agents are introduced. Data SummaryAll data and code to replicate this analysis are available as the blantyreESBL v1.3 R package (https://doi.org/10.5281/zenodo.5554081) available at https://github.com/joelewis101/blantyreESBL. Reads from all isolates sequenced as part of this study have been deposited in the European Nucleotide Archive, under PRJEB26677, PRJEB28522 and PRJEB36486 (short reads) and PRJNA869071 (Nanopore reads and hybrid assemblies). Accession numbers (as well as accession numbers of publicly available genomes used in this analysis) linked to sample metadata are provided in the R package and as supplementary data to this manuscript.

microbiology↗

bioRxiv2021

Isolation and characterisation of bacteriophages with activity against invasive non-typhoidal Salmonella causing bloodstream infection in Malawi

In recent years, novel lineages of invasive non-typhoidal Salmonella (iNTS) serovars Typhimurium and Enteritidis have been identified in patients with bloodstream infection in sub-Saharan Africa. Here, we isolated and characterised 32 phages capable of infecting S. Typhimurium and S. Enteritidis, from water sources in Malawi and the UK. The phages were classified in three major phylogenetic clusters that were geographically distributed. In terms of host range, Cluster 1 phages were able to infect all bacterial hosts tested, whereas Clusters 2 and 3 had a more restricted profile. Cluster 3 contained two sub-clusters, and 3.b contained the most novel isolates. This study represents the first exploration of the potential for phages to target the lineages of Salmonella that are responsible for bloodstream infections in sub-Saharan Africa.

microbiology↗

bioRxiv2020

An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes

We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium. By optimising a logistics pipeline that collected isolates as thermolysates, permitting shipment in ambient conditions, the project assembled a diverse collection of 10,419 clinical and environmental isolates from low- and middle-income countries in less than one year. The bacteria were obtained from 51 countries/territories dating from 1949 to 2017, with a focus on Africa and Latin-America. All isolates were collected in barcoded tubes and genome sequenced using an optimised DNA extraction method and the LITE pipeline for library construction. After Illumina sequencing, the total reagent cost was less than USD$10 per genome. Our method can be applied to genome-sequence other large bacterial collections at a relatively low cost, within a limited timeframe, to support global collaborations.

microbiology↗

bioRxiv2018

rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree

The ability to distinguish between pathogens is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances, remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this program was demonstrated using genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically-confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.\n\nDATA SUMMARYO_LISource code for rPinecone is available on GitHub under the open source licence GNU GPL 3; (url: https://github.com/alexwailan/rpinecone).\nC_LIO_LINewick format files for both phylogenetic trees have been deposited in Figshare; (url: https://doi.org/10.6084/m9.figshare.7022558)\nC_LIO_LIGeographical analysis of the S. Typhi Dataset using Microreact is available at https://microreact.org/project/r1IqkrN1X.\nC_LIO_LIAccession numbers, meta data and sample lineage results of both datasets used in this paper are listed in the supplementary tables.\nC_LI\n\nI/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. {boxtimes}\n\nIMPACT STATEMENTWhole genome sequence data from bacterial pathogens is increasingly used in the epidemiological investigation of infectious disease, both in outbreak and endemic situations. However, distinguishing bacterial species which are both very similar and which are likely to come from a small geographical and temporal range presents a major technical challenge for epidemiologists. rPinecone was designed to address this challenge and utilises phylogenetic data to define lineages within bacterial populations that have limited variation. This approach is therefore of great interest to epidemiologists as it adds a further level of clarity above and beyond that which is offered by existing approaches which have not been designed to consider bacterial isolates containing variation that only transiently exist, but which is epidemiologically informative. rPinecone has the flexibility to be applied to multiple pathogens and has direct application for investigations of clinical outbreaks and endemic disease to understand transmission dynamics or geographical hotspots of disease.

genomics↗

bioRxiv2018

Evolutionary trajectories to amoxicillin-clavulanic acid resistance in Escherichia coli are affected by growth media.

In the face of an accelerating global antimicrobial resistance crisis, the determination of bacterial fitness following acquisition of resistance is an expanding area of research, and increased understanding of this process will be crucial to translate in vitro fitness data to successful therapies. Given that crucial clinical treatment situations are guided by in vitro diagnostic testing in an artificial environment far removed from human physiological niches, we used Escherichia coli and amoxicillin-clavulanic acid (AMC) resistance as a model to understand how such environments could affect the emergence of resistance, associated fitness costs and the predictive value of this data when strains were grown in the more physiologically relevant environments of urine and urothelial organoids. Resistant E. coli isolates were selected for following 24-hour exposure to sub-inhibitory concentrations of AMC in either M9, ISO or LB broth, followed by growth on LB agar containing AMC. No resistant colonies emerged following growth in M9, whereas resistant isolates were detected from cultures grown in ISO and LB broth. We observed both within and between media-type variability in the levels of resistance and fitness of the resistant mutants grown in LB. MICs and fitness of these resistant strains in different media (M9, ISO, LB, human urine and urothelial organoids) showed considerable variation. Media can therefore have a direct effect on the isolation of mutants that confer resistance to AMC and these mutants can exhibit unpredictable MIC and fitness profiles under different growth conditions. This study highlights the risks in relying on a single culture protocol to predict the behaviour and treatment response of bacteria in vivo and highlights the importance of developing comprehensive experimental designs to ensure effective translation of diagnostic procedures to successful clinical outcomes.

microbiology↗

bioRxiv2017

The role of a single non-coding nucleotide in the evolution of an epidemic African clade of Salmonella

Introductory ParagraphSalmonella enterica serovar Typhimurium ST313 is a relatively newly emerged sequence type that is causing a devastating epidemic of bloodstream infections across sub-Saharan Africa. Analysis of hundreds of Salmonella genomes has revealed that ST313 is closely-related to the ST19 group of S. Typhimurium that cause gastroenteritis across the world. The core genomes of ST313 and ST19 vary by just 1000 single-nucleotide polymorphisms (SNPs). We hypothesised that the phenotypic differences that distinguish African Salmonella from ST19 are caused by certain SNPs that directly modulate the transcription of virulence genes.\n\nHere we identified 3,597 transcriptional start sites (TSS) of the ST313 strain D23580, and searched for a gene expression signature linked to pathogenesis of Salmonella. We identified a SNP in the promoter of the pgtE gene that caused high expression of the PgtE virulence factor in African S. Typhimurium, increased the degradation of the factor B component of human complement, contributed to serum resistance and modulated virulence in the chicken infection model. The PgtE protease is known to mediate systemic infection in animal models. We propose that high levels of expression PgtE of by African S. Typhimurium ST313 promotes bacterial survival and bacterial dissemination during human infection.\n\nOur finding of a functional role for an extra-genic SNP shows that approaches used to deduce the evolution of virulence in bacterial pathogens should include a focus on non-coding regions of the genome.

molecular biology↗