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

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 ESBLproducing 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 bla CTX−M and bla TEM 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 bla CTX−M−15 and bla TEM−1B genes generally found on the same contigs as the IncF plasmid replicon. Although epidemiologically unrelated, the strains formed three separate sequence type-phylogroup-serotypespecific 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 Frontiers in Microbiology | www.frontiersin.org February 2020 | Volume 11 | Article 108 Baniga et al.Genomics of ESBL-E. coli in Lake Victoria 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.

Predominance of blaTEM and tetA genes in antibiotic-resistant Escherichia coli isolates from Laguna Lake, Philippines

“…TEM types are capable of deactivating classes of penicillin drugs such as ampicillin (Bailey et al 2011). Recent reports of TEM harboring E. coli isolates sampled from water sources (Osinśka et al 2017;Baniga et al 2020) were consistent with the findings in this study. However, our findings seem to disagree with the recent report of isolates sampled from selected hospital sewers and rivers in the Philippines, wherein E. coli isolates were found to carry bla CTX-M genes (Suzuki et al 2020).…”

“…Among the ARB, the spread of ESBL-producing Enterobacteriaceae is identified as a primary concern of the World Health Organization (WHO) in 2015 (Ng & Gin 2019). From the ESBL-producing bacteria, the temoneira (TEM) β-lactamases are produced due to mutations in TEM, which are encoded by bla TEM genes (Bailey et al 2011;Baniga et al 2020). TEM types are capable of deactivating classes of penicillin drugs such as ampicillin (Bailey et al 2011).…”

Persistence and Dissemination Capacities of a blaNDM-5-Harboring IncX-3 Plasmid in Escherichia coli Isolated from an Urban River in Montpellier, France

“…They were isolated in different countries (all continents are represented) and in environmental and clinical samples. Other studies reported the occurrence of ST636-producing ESBLs in clinical and environmental samples [ 62 , 63 , 64 ], suggesting a generalist trait for this ST.…”

ESBL and AmpC β-Lactamase Encoding Genes in E. coli From Pig and Pig Farm Workers in Vietnam and Their Association With Mobile Genetic Elements

“…This included annotation of transposons and insertion sequences located around the resistance genes, the phylogenetic relatedness of the plasmid components reconstructed from strains, and genetic relatedness of the strains, all based on whole genome sequences. This approach provides a holistic answer to the transmission of resistance genes between hosts, either by transfer of strains or by spread of mobile genetic elements, and thus it extends the approaches used in most previous studies of spread of resistance genes and mobile genetic element between hosts (Kudirkiene et al, 2018;Zajac et al, 2019;Baniga et al, 2020). Analysis of the plasmids and the genetic contexts along with the strains diversity allow to investigate the diversity, distribution, and transmission dynamics of resistance plasmids in the strains (David et al, 2020).…”