Generalizability of machine learning in predicting antimicrobial resistance in E. coli: a multi-country case study in Africa

[11] Levine MM(2022)Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning Bioinformatics 38 325-90

[12] Kotloff KL(2019)PATRIC as a unique resource for studying antimicrobial resistance Brief Bioinform 20 1094-60

[13] Katyali D(2024)Boosting pathogen genomics and bioinformatics workforce in Africa Lancet Infect Dis 24 e106-9

[14] Kawau G(2017)Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131 Genome Res 27 1437-undefined

[15] Blomberg B(2018)Multidrug resistance among Escherichia coli and Klebsiella pneumoniae carried in the gut of out-patients from pastoralist communities of Kasese district, Uganda PLoS ONE 13 e0200093-undefined

[16] Achi CR(2023)Unraveling virulence determinants in extended-spectrum beta-lactamase-producing Escherichia coli from East Africa using whole-genome sequencing BMC Infect Dis 23 587-undefined

[17] Ayobami O(2022)An ST131 clade and a phylogroup a clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals Microb Genomics 8 000863-undefined

[18] Mark G(2018)Fastp: an ultra-fast all-in-one FASTQ preprocessor Bioinformatics 34 i884-undefined

[19] Zankari E(2009)Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 1754-undefined

[20] Hasman H(2021)Twelve years of SAMtools and BCFtools Gigascience 10 giab008-undefined

[11] Levine MM(2022)Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning Bioinformatics 38 325-90

[12] Kotloff KL(2019)PATRIC as a unique resource for studying antimicrobial resistance Brief Bioinform 20 1094-60

[13] Katyali D(2024)Boosting pathogen genomics and bioinformatics workforce in Africa Lancet Infect Dis 24 e106-9

[14] Kawau G(2017)Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131 Genome Res 27 1437-undefined

[15] Blomberg B(2018)Multidrug resistance among Escherichia coli and Klebsiella pneumoniae carried in the gut of out-patients from pastoralist communities of Kasese district, Uganda PLoS ONE 13 e0200093-undefined

[16] Achi CR(2023)Unraveling virulence determinants in extended-spectrum beta-lactamase-producing Escherichia coli from East Africa using whole-genome sequencing BMC Infect Dis 23 587-undefined

[17] Ayobami O(2022)An ST131 clade and a phylogroup a clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals Microb Genomics 8 000863-undefined

[18] Mark G(2018)Fastp: an ultra-fast all-in-one FASTQ preprocessor Bioinformatics 34 i884-undefined

[19] Zankari E(2009)Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 1754-undefined

[20] Hasman H(2021)Twelve years of SAMtools and BCFtools Gigascience 10 giab008-undefined