Genome-Based Analysis of Extended-Spectrum β-Lactamase-Producing Escherichia coli in the Aquatic Environment and Nile Perch (Lates niloticus) of Lake Victoria, Tanzania.

Zebedayo Baniga,Anders Dalsgaard,Yaovi M Gildas Hounmanou,Robinson H Mdegela,Egle Kudirkiene,Lughano J M Kusiluka

doi:10.3389/fmicb.2020.00108

Zebedayo Baniga, Anders Dalsgaard + Show 4 more

Open Access

https://doi.org/10.3389/fmicb.2020.00108

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Abstract

Extended-spectrum β-lactamase (ESBL)-producing bacteria constitute an emerging global health issue with food products being vehicles of transmission and the aquatic environments serving as potential reservoirs. This study aimed to characterize ESBL-producing Escherichia coli in Nile perch and water from Lake Victoria in Tanzania. A total of 180 samples of Nile perch and 60 water samples were screened for ESBL-producing E. coli on MacConkey agar supplemented with 2 μg/ml of cefotaxime and confirmed by blaCTX–M and blaTEM PCR. Antimicrobial resistance was determined by the disk diffusion method, and the ESBL-producing isolates were whole genome sequencing (WGS). ESBL-producing E. coli were detected in eight of the 180 analyzed Nile perch samples, and only one water sample was positive (1.7%, n = 60). Isolates were resistant to sulfamethoxazole–trimethoprim (100%), ampicillin/cloxacillin (100%), erythromycin 72.7% (8/11), tetracycline 90.9% (10/11), and nalidixic acid 63.6% (7/11). This mostly corroborates the resistance genes that they carried for sulfonamides (sul1 and sul2), trimethoprim (dfrA and dfrB), aminoglycosides [aac(3)-IId, strA, and strB], tetracycline [tet(B) and tet(D)], and fluoroquinolones (qepA4). They harbored plasmid replicon types IncF, IncX, IncQ, and Col and carried blaCTX–M–15 and blaTEM–1B genes generally found on the same contigs as the IncF plasmid replicon. Although epidemiologically unrelated, the strains formed three separate sequence type–phylogroup–serotype-specific clusters: C1, C2, and C3. Cluster C1 included five strains (3 to 13 SNPs) belonging to ST167, phylogroup A, and serotype O9:H21; the two C2 strains (11 SNPs) belong to ST156, phylogroup B1, and serotype ONT:H28; and C3 was made up of four strains (SNPs ranged from 4 to 17) of ST636, phylogroup B2, and serotype O45:H7. The common virulence gene gad was reported in all strains. In addition, strains in C2 and C3 possessed iss, lpfA, and nfaE virulence genes, and the vat gene was found only in C3. The present study reports the occurrence of multidrug-resistant ESBL-producing E. coli carrying plasmid-mediated ESBL genes in offshore water and Nile perch in Lake Victoria. Strains formed three clonal clusters of unknown origin. This study reveals that the Lake may serve as reservoir for ESBL-producing bacteria that can be transmitted by fish as a food chain hazard of One-Health concern.

Highlights

Escherichia coli and other related bacteria can produce extendedspectrum β-lactamase (ESBL) enzymes that hydrolyze a broad spectrum of β-lactam drugs such as cephalosporins and monobactams, classes of antimicrobials that are critical in human medicine (Lavilla et al, 2008; Shaikh et al, 2015; Adelowo et al, 2018)
Our data suggest that as far as ESBL-producing enteric bacteria are concerned, the consumption of Nile perch represent limited food safety risks compared with other human exposures to ESBL-producing E. coli, for example, through direct humanto-human fecal transmission and consumption of livestock meat products
The grouping of the 11 ESBL-producing E. coli into three clades each showing identical characteristics, for example, STs, phylogroup, antimicrobial resistance, and virulence genes, is surprising, and we are not able to explain the clonal nature of these clades as the E. coli strains were epidemiologically unrelated

Summary

Introduction

Escherichia coli and other related bacteria can produce extendedspectrum β-lactamase (ESBL) enzymes that hydrolyze a broad spectrum of β-lactam drugs such as cephalosporins (e.g., ceftazidime and cefotaxime) and monobactams (e.g., aztreonam and nocardicin), classes of antimicrobials that are critical in human medicine (Lavilla et al, 2008; Shaikh et al, 2015; Adelowo et al, 2018). The β-lactamase enzymes are derived from mutations in temoneira (TEM), sulfhydryl variable (SHV), and CTX-M genes located on bacterial plasmids or chromosomes (Ben Said et al, 2015; Legese et al, 2017; Adelowo et al, 2018). These genes can be horizontally transferred from one bacterial strain to another including across bacterial species (Lavilla et al, 2008). These TEM enzymes have been reported from Klebsiella spp. and Enterobacter spp. isolated in food, clinical, and environmental samples around the world as previously described (Smet et al, 2010; Delgado et al, 2016)

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