Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting.
Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. coli has been extensively investigated in resource-rich settings, in sub-Saharan Africa molecular patterns of AMR are not well described. In this study, we have begun to explore the population structure and molecular determinants of AMR amongst E. coli isolates from Malawi.



Ninety-four E. coli isolates from patients admitted to Queen's Hospital, Malawi, were whole-genome sequenced. The isolates were selected on the basis of diversity of phenotypic resistance profiles and clinical source of isolation (blood, CSF and rectal swab). Sequence data were analysed using comparative genomics and phylogenetics.



Our results revealed the presence of five clades, which were strongly associated with E. coli phylogroups A, B1, B2, D and F. We identified 43 multilocus STs, of which ST131 (14.9%) and ST12 (9.6%) were the most common. We identified 25 AMR genes. The most common ESBL gene was bla CTX-M-15 and it was present in all five phylogroups and 11 STs, and most commonly detected in ST391 (4/4 isolates), ST648 (3/3 isolates) and ST131 [3/14 (21.4%) isolates].



This study has revealed a high diversity of lineages associated with AMR, including ESBL and fluoroquinolone resistance, in Malawi. The data highlight the value of longitudinal bacteraemia surveillance coupled with detailed molecular epidemiology in all settings, including low-income settings, in describing the global epidemiology of ESBL resistance.
Patrick
P
Musicha
Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.|Liverpool School of Tropical Medicine, Liverpool, UK.
Nicholas A
NA
Feasey
Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.|Liverpool School of Tropical Medicine, Liverpool, UK.
Amy K
AK
Cain
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
Teemu
T
Kallonen
Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.|Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
Chrispin
C
Chaguza
Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.
Chikondi
C
Peno
Microbiology Unit, Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi.
Margaret
M
Khonga
Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.
Sarah
S
Thompson
Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.
Katherine J
KJ
Gray
Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
Alison E
AE
Mather
Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.|Division of Infection and Immunity, University College London, London, UK.
Robert S
RS
Heyderman
Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.|Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
Dean B
DB
Everett
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.|Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
Nicholas R
NR
Thomson
Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, Blantyre, Malawi.|Microbiology Unit, Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi.
Chisomo L
CL
Msefula
D000293:Adolescent; D000328:Adult; D002648:Child; D002675:Child, Preschool; D002701:Chloramphenicol / Q000494:pharmacology; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000453:epidemiology / Q000382:microbiology*; D005260:Female; D005798:Genes, Bacterial; D014644:Genetic Variation; D023281:Genomics; D006801:Humans; D008295:Malawi / Q000453:epidemiology; D008297:Male; D008826:Microbial Sensitivity Tests; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D014505:Urban Population / Q000706:statistics & numerical data; D055815:Young Adult; D018440:beta-Lactam Resistance / Q000235:genetics*; D001618:beta-Lactamases / Q000235:genetics*
D002701:Chloramphenicol; D001618:beta-Lactamases