Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Sep 7;23(1):587.
doi: 10.1186/s12879-023-08579-0.

Unraveling virulence determinants in extended-spectrum beta-lactamase-producing Escherichia coli from East Africa using whole-genome sequencing

Ivan Sserwadda #  1   2   3 , Benson R Kidenya #  4 , Stephen Kanyerezi  1   3 , Inyasi Lawrence Akaro  5 , Baraka Mkinze  5 , Stephen E Mshana  6 , Suhaila O Hashim  2 , Everlyne Isoe  2 , Jeremiah Seni  6 , Moses L Joloba  1 , Gerald Mboowa  7   8   9
Affiliations

Unraveling virulence determinants in extended-spectrum beta-lactamase-producing Escherichia coli from East Africa using whole-genome sequencing

Ivan Sserwadda et al. BMC Infect Dis. .

Abstract

Escherichia coli significantly causes nosocomial infections and rampant spread of antimicrobial resistance (AMR). There is limited data on genomic characterization of extended-spectrum β-lactamase (ESBL)-producing E. coli from African clinical settings. This hospital-based longitudinal study unraveled the genetic resistance elements in ESBL E. coli isolates from Uganda and Tanzania using whole-genome sequencing (WGS). A total of 142 ESBL multi-drug resistant E. coli bacterial isolates from both Tanzania and Uganda were sequenced and out of these, 36/57 (63.1%) and 67/85 (78.8%) originated from Uganda and Tanzania respectively. Mutations in RarD, yaaA and ybgl conferring resistances to chloramphenicol, peroxidase and quinolones were observed from Ugandan and Tanzanian isolates. We reported very high frequencies for blaCTX-M-15 with 11/18(61.1%), and blaCTX-M-27 with 12/23 (52.1%), blaTEM-1B with 13/23 (56.5%) of isolates originating from Uganda and Tanzania respectively all conferring resistance to Beta-lactam-penicillin inhibitors. We observed chloramphenicol resistance-conferring gene mdfA in 21/23 (91.3%) of Tanzanian isolates. Extraintestinal E. coli sequence type (ST) 131 accounted for 5/59 (8.4%) of Tanzanian isolates while enterotoxigenic E. coli ST656 was reported in 9/34 (26.4%) of Ugandan isolates. Virulence factors originating from Shigella dysenteriae Sd197 (gspC, gspD, gspE, gspF, gspG, gspF, gspH, gspI), Yersinia pestis CO92 (irp1, ybtU, ybtX, iucA), Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (csgF and csgG), and Pseudomonas aeruginosa PAO1 (flhA, fliG, fliM) were identified in these isolates. Overall, this study highlights a concerning prevalence and diversity of AMR-conferring elements shaping the genomic structure of multi-drug resistant E. coli in clinical settings in East Africa. It underscores the urgent need to strengthen infection-prevention controls and advocate for the routine use of WGS in national AMR surveillance and monitoring programs.Availability of WGS analysis pipeline: the rMAP source codes, installation, and implementation manual can free be accessed via https://github.com/GunzIvan28/rMAP .

Keywords: Antimicrobial resistance; East Africa; Extended-spectrum β-lactamase; Virulence factors; Whole-genome sequencing.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Proportions of the ESBL-producing E. coli from the study sites that conformed to initial pre-sequencing (LITE) Illumina protocol
Fig. 2
Fig. 2
Heat map showing Ugandan E. coli predominant genes from ResFinder database
Fig. 3
Fig. 3
Heat map showing Tanzanian E. coli predominant genes from ResFinder database
Fig. 4
Fig. 4
Phylogenetic tree showing the distribution of AMR genes and STs across the two study sites
See this image and copyright information in PMC

References

    1. Mboowa G, Sserwadda I, Bulafu D, Chaplain D, Wewedru I, Seni J, et al. Transmission Dynamics of Antimicrobial Resistance at a National Referral Hospital in Uganda. Am J Trop Med Hyg. 2021;105(2):498–506. doi: 10.4269/ajtmh.20-1522. - DOI - PMC - PubMed
    1. Rossolini GM, Arena F, Pecile P. Pollini SJCoip. Update on the Antibiotic Resistance Crisis. 2014;18:56–60. - PubMed
    1. Nathan C, Cars OJNEJoM. Antibiotic resistance—problems, progress, and prospects. 2014;371(19):1761–3. - PubMed
    1. Pärnänen K, Karkman A, Tamminen M, Lyra C, Hultman J, Paulin L et al. Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics. 2016;6:35790. - PMC - PubMed
    1. McEwen SA, Collignon PJ, Aarestrup FM, Schwarz S, Shen J, Cavaco L. Antimicrob Resistance: One Health Perspective. 2018;6(2):6. doi: 10.1128/microbiolspec.ARBA-0009-2017. - DOI

LinkOut - more resources