PMID- 33234606
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20201218
IS  - 2379-5077 (Print)
IS  - 2379-5077 (Electronic)
IS  - 2379-5077 (Linking)
VI  - 5
IP  - 6
DP  - 2020 Nov 24
TI  - Genomic and Resistance Epidemiology of Gram-Negative Bacteria in Africa: a 
      Systematic Review and Phylogenomic Analyses from a One Health Perspective.
LID - 10.1128/mSystems.00897-20 [doi]
LID - e00897-20
AB  - 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 Gram-negative 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 beta-lactams (including bla (TEM-1), bla 
      (CTX-M), bla (NDM), bla (IMP), bla (VIM), and bla (OXA-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, 
      IncX(3/4), 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.
CI  - Copyright (c) 2020 Osei Sekyere and Reta.
FAU - Osei Sekyere, John
AU  - Osei Sekyere J
AUID- ORCID: 0000-0002-9508-984X
AD  - Department of Medical Microbiology, School of Medicine, Faculty of Health 
      Sciences, University of Pretoria, Pretoria, South Africa jod14139@yahoo.com.
FAU - Reta, Melese Abate
AU  - Reta MA
AD  - Department of Medical Microbiology, School of Medicine, Faculty of Health 
      Sciences, University of Pretoria, Pretoria, South Africa.
LA  - eng
PT  - Journal Article
DEP - 20201124
PL  - United States
TA  - mSystems
JT  - mSystems
JID - 101680636
PMC - PMC7687029
OTO - NOTNLM
OT  - Africa
OT  - One Health
OT  - antibiotic resistance
OT  - diagnostics
OT  - genomics
OT  - mobilome
OT  - molecular epidemiology
OT  - resistome
EDAT- 2020/11/26 06:00
MHDA- 2020/11/26 06:01
PMCR- 2020/11/24
CRDT- 2020/11/25 05:37
PHST- 2020/11/25 05:37 [entrez]
PHST- 2020/11/26 06:00 [pubmed]
PHST- 2020/11/26 06:01 [medline]
PHST- 2020/11/24 00:00 [pmc-release]
AID - 5/6/e00897-20 [pii]
AID - mSystems00897-20 [pii]
AID - 10.1128/mSystems.00897-20 [doi]
PST - epublish
SO  - mSystems. 2020 Nov 24;5(6):e00897-20. doi: 10.1128/mSystems.00897-20.