Abstract:
Antibiotic resistance (AR) remains a major threat to public and animal
health globally. However, AR ramifications in developing countries are worsened by
limited molecular diagnostics, expensive therapeutics, inadequate numbers of skilled
clinicians and scientists, and unsanitary environments. The epidemiology of Gramnegative
bacteria, their AR genes, and geographical distribution in Africa are described
here. Data were extracted and analyzed from English-language articles published
between 2015 and December 2019. The genomes and AR genes of the
various species, obtained from the Pathosystems Resource Integration Center
(PATRIC) and NCBI were analyzed phylogenetically using Randomized Axelerated
Maximum Likelihood (RAxML) and annotated with Figtree. The geographic location
of resistant clones/clades was mapped manually. Thirty species from 31 countries
and 24 genera from 41 countries were analyzed from 146 articles and 3,028 genomes,
respectively. Genes mediating resistance to -lactams (including blaTEM-1,
blaCTX-M, blaNDM, blaIMP, blaVIM, and blaOXA-48/181), fluoroquinolones (oqxAB, qnrA/B/
D/S, gyrA/B, and parCE mutations, etc.), aminoglycosides (including armA and rmtC/
F), sulfonamides (sul1/2/3), trimethoprim (dfrA), tetracycline [tet(A/B/C/D/G/O/M/39)],
colistin (mcr-1), phenicols (catA/B, cmlA), and fosfomycin (fosA) were mostly found in
Enterobacter spp. and Klebsiella pneumoniae, and also in Serratia marcescens, Escherichia
coli, Salmonella enterica, Pseudomonas, Acinetobacter baumannii, etc., on mostly
IncF-type, IncX3/4, ColRNAI, and IncR plasmids, within IntI1 gene cassettes, insertion
sequences, and transposons. Clonal and multiclonal outbreaks and dissemination
of resistance genes across species and countries and between humans,
animals, plants, and the environment were observed; Escherichia coli ST103, K.
pneumoniae ST101, S. enterica ST1/2, and Vibrio cholerae ST69/515 were common
strains. Most pathogens were of human origin, and zoonotic transmissions were relatively limited.
IMPORTANCE Antibiotic resistance (AR) is one of the major public health threats
and challenges to effective containment and treatment of infectious bacterial diseases
worldwide. Here, we used different methods to map out the geographical hot
spots, sources, and evolutionary epidemiology of AR. Escherichia coli, Klebsiella pneumoniae,
Salmonella enterica, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter
spp., Neisseria meningitis/gonorrhoeae, Vibrio cholerae, Campylobacter jejuni,
etc., were common pathogens shuttling AR genes in Africa. Transmission of the
same clones/strains across countries and between animals, humans, plants, and the
environment was observed. We recommend Enterobacter spp. or K. pneumoniae as
better sentinel species for AR surveillance.
