Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia
- Darboe, Saffiatou, Bradbury, Richard, Phelan, Jody, Kanteh, Abdoulie, Muhammad, Abdul-Khalie, Worwui, Archibald, Yang, Shangxin, Nwakanma, Davis, Perez-Sepulveda, Blanca, Kariuki, Samuel, Kwambana-Adams, Brenda, Antonio, Martin
- Authors: Darboe, Saffiatou , Bradbury, Richard , Phelan, Jody , Kanteh, Abdoulie , Muhammad, Abdul-Khalie , Worwui, Archibald , Yang, Shangxin , Nwakanma, Davis , Perez-Sepulveda, Blanca , Kariuki, Samuel , Kwambana-Adams, Brenda , Antonio, Martin
- Date: 2022
- Type: Text , Journal article
- Relation: Microbial Genomics Vol. 8, no. 3 (2022), p.
- Full Text:
- Reviewed:
- Description: Non-typhoidal Salmonella associated with multidrug resistance cause invasive disease in sub-Saharan Africa. Specific lineages of serovars Typhimurium and Enteritidis have been implicated. Here we characterized the genomic diversity of 100 clinical non-typhoidal Salmonella collected from 93 patients in 2001 from the eastern, and in 2006–2018 from the western regions of The Gambia respectively. A total of 93 isolates (64 invasive, 23 gastroenteritis and six other sites) representing a single infection episode were phenotypically tested for antimicrobial susceptibility using the Kirby–Bauer disc diffusion technique. Whole genome sequencing of 100 isolates was performed using Illumina, and the reads were assembled and analysed using SPAdes. The Salmonella in Silico Typing Resource (SISTR) was used for serotyping. SNP differences among the 93 isolates were determined using Roary, and phylogenetic analysis was performed in the context of 495 African strains from the European Nucleotide Archive. Salmonella serovars Typhimurium (26/64; 30.6%) and Enteritidis (13/64; 20.3%) were associated with invasive disease, whilst other serovars were mainly responsible for gastroenteritis (17/23; 73.9%). The presence of three major serovar Enteritidis clades was confirmed, including the invasive West African clade, which made up more than half (11/16; 68.8%) of the genomes. Multidrug resistance was confined among the serovar Enteritidis West African clade. The presence of this epidemic virulent clade has potential for spread of resistance and thus important implications for systematic patient management. Surveillance and epidemiological investigations to inform control are warranted. © 2022 The Authors.
- Authors: Darboe, Saffiatou , Bradbury, Richard , Phelan, Jody , Kanteh, Abdoulie , Muhammad, Abdul-Khalie , Worwui, Archibald , Yang, Shangxin , Nwakanma, Davis , Perez-Sepulveda, Blanca , Kariuki, Samuel , Kwambana-Adams, Brenda , Antonio, Martin
- Date: 2022
- Type: Text , Journal article
- Relation: Microbial Genomics Vol. 8, no. 3 (2022), p.
- Full Text:
- Reviewed:
- Description: Non-typhoidal Salmonella associated with multidrug resistance cause invasive disease in sub-Saharan Africa. Specific lineages of serovars Typhimurium and Enteritidis have been implicated. Here we characterized the genomic diversity of 100 clinical non-typhoidal Salmonella collected from 93 patients in 2001 from the eastern, and in 2006–2018 from the western regions of The Gambia respectively. A total of 93 isolates (64 invasive, 23 gastroenteritis and six other sites) representing a single infection episode were phenotypically tested for antimicrobial susceptibility using the Kirby–Bauer disc diffusion technique. Whole genome sequencing of 100 isolates was performed using Illumina, and the reads were assembled and analysed using SPAdes. The Salmonella in Silico Typing Resource (SISTR) was used for serotyping. SNP differences among the 93 isolates were determined using Roary, and phylogenetic analysis was performed in the context of 495 African strains from the European Nucleotide Archive. Salmonella serovars Typhimurium (26/64; 30.6%) and Enteritidis (13/64; 20.3%) were associated with invasive disease, whilst other serovars were mainly responsible for gastroenteritis (17/23; 73.9%). The presence of three major serovar Enteritidis clades was confirmed, including the invasive West African clade, which made up more than half (11/16; 68.8%) of the genomes. Multidrug resistance was confined among the serovar Enteritidis West African clade. The presence of this epidemic virulent clade has potential for spread of resistance and thus important implications for systematic patient management. Surveillance and epidemiological investigations to inform control are warranted. © 2022 The Authors.
Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children
- Nabwera, Helen, Espinoza, Josh, Worwui, Archibald, Betts, Modupeh, Bradbury, Richard
- Authors: Nabwera, Helen , Espinoza, Josh , Worwui, Archibald , Betts, Modupeh , Bradbury, Richard
- Date: 2021
- Type: Text , Journal article
- Relation: EBioMedicine Vol. 73, no. (2021), p.
- Full Text:
- Reviewed:
- Description: Background: The specific roles that gut microbiota, known pathogens, and host energy-regulating hormones play in the pathogenesis of non-edematous severe acute malnutrition (marasmus SAM) and moderate acute malnutrition (MAM) during outpatient nutritional rehabilitation are yet to be explored. Methods: We applied an ensemble of sample-specific (intra- and inter-modality) association networks to gain deeper insights into the pathogenesis of acute malnutrition and its severity among children under 5 years of age in rural Gambia, where marasmus SAM is most prevalent. Findings: Children with marasmus SAM have distinct microbiome characteristics and biologically-relevant multimodal biomarkers not observed among children with moderate acute malnutrition. Marasmus SAM was characterized by lower microbial richness and biomass, significant enrichments in Enterobacteriaceae, altered interactions between specific Enterobacteriaceae and key energy regulating hormones and their receptors. Interpretation: Our findings suggest that marasmus SAM is characterized by the collapse of a complex system with nested interactions and key associations between the gut microbiome, enteric pathogens, and energy regulating hormones. Further exploration of these systems will help inform innovative preventive and therapeutic interventions. Funding: The work was supported by the UK Medical Research Council (MRC; MC-A760-5QX00) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement; Bill and Melinda Gates Foundation (OPP 1066932) and the National Institute of Medical Research (NIMR), UK. This network analysis was supported by NIH U54GH009824 [CLD] and NSF OCE-1558453 [CLD]. © 2021 The Author(s). **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Richard Bradbury" is provided in this record**
- Authors: Nabwera, Helen , Espinoza, Josh , Worwui, Archibald , Betts, Modupeh , Bradbury, Richard
- Date: 2021
- Type: Text , Journal article
- Relation: EBioMedicine Vol. 73, no. (2021), p.
- Full Text:
- Reviewed:
- Description: Background: The specific roles that gut microbiota, known pathogens, and host energy-regulating hormones play in the pathogenesis of non-edematous severe acute malnutrition (marasmus SAM) and moderate acute malnutrition (MAM) during outpatient nutritional rehabilitation are yet to be explored. Methods: We applied an ensemble of sample-specific (intra- and inter-modality) association networks to gain deeper insights into the pathogenesis of acute malnutrition and its severity among children under 5 years of age in rural Gambia, where marasmus SAM is most prevalent. Findings: Children with marasmus SAM have distinct microbiome characteristics and biologically-relevant multimodal biomarkers not observed among children with moderate acute malnutrition. Marasmus SAM was characterized by lower microbial richness and biomass, significant enrichments in Enterobacteriaceae, altered interactions between specific Enterobacteriaceae and key energy regulating hormones and their receptors. Interpretation: Our findings suggest that marasmus SAM is characterized by the collapse of a complex system with nested interactions and key associations between the gut microbiome, enteric pathogens, and energy regulating hormones. Further exploration of these systems will help inform innovative preventive and therapeutic interventions. Funding: The work was supported by the UK Medical Research Council (MRC; MC-A760-5QX00) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement; Bill and Melinda Gates Foundation (OPP 1066932) and the National Institute of Medical Research (NIMR), UK. This network analysis was supported by NIH U54GH009824 [CLD] and NSF OCE-1558453 [CLD]. © 2021 The Author(s). **Please note that there are multiple authors for this article therefore only the name of the first 5 including Federation University Australia affiliate “Richard Bradbury" is provided in this record**
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