Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Summary

The feasibility of whole-genome sequencing (WGS) strategies using benchtop instruments has simplified the genome interrogation of every microbe of public health relevance in a lab setting. A methodological adaptation of the workflow for bacterial WGS is described and a bioinformatics pipeline for analysis is also presented.

Abstract

Aquaculture is one of the fastest-growing food-producing sectors worldwide and tilapia (Oreochromis spp.) farming constitutes the major freshwater fish variety cultured. Because aquaculture practices are susceptible to microbial contamination derived from anthropogenic sources, extensive antibiotic usage is needed, leading to aquaculture systems becoming an important source of antibiotic-resistant and pathogenic bacteria of clinical relevance such as Escherichia coli (E. coli). Here, the antimicrobial resistance, virulence, and mobilome features of a pathogenic E. coli strain, recovered from inland farmed Oreochromis spp., were elucidated through whole-genome sequencing (WGS) and in silico analysis. Antimicrobial susceptibility testing (AST) and WGS were performed. Furthermore, phylogenetic group, serotype, multilocus sequence typing (MLST), acquired antimicrobial resistance, virulence, plasmid, and prophage content were determined using diverse available web tools. The E. coli isolate only exhibited intermediate susceptibility to ampicillin and was characterized as ONT:H21-B1-ST40 strain by WGS-based typing. Although only a single antimicrobial resistance-related gene was detected [mdf(A)], several virulence-associated genes (VAGs) from the atypical enteropathogenic E. coli (aEPEC) pathotype were identified. Additionally, the cargo of plasmid replicons from large plasmid groups and 18 prophage-associated regions were detected. In conclusion, the WGS characterization of an aEPEC isolate, recovered from a fish farm in Sinaloa, Mexico, allows insights into its pathogenic potential and the possible human health risk of consuming raw aquacultural products. It is necessary to exploit next-generation sequencing (NGS) techniques for studying environmental microorganisms and to adopt a one health framework to learn how health issues originate.

Introduction

Aquaculture is one of the fastest-growing food-producing sectors worldwide, and its production practices are intended to satisfy the rising food demand for human consumption. Global aquaculture production has tripled from 34 million tonnes (Mt) in 1997 to 112 Mt in 2017¹. The main species groups, contributing to nearly 75% of the production, were seaweed, carps, bivalves, catfish, and tilapia (Oreochromis spp.)¹. However, the appearance of diseases caused by microbial entities is unavoidable because of intensive fish farming, leading to potential economic losses².

Protocol

NOTE: The E. coli strain ACM5 was recovered by processing and culturing the fish sample for fecal coliform (FC) determination¹². During the fish sampling, fish did not show clinical signs of disease, bacterial, or fungal infection, and a mean temperature of 22.3 °C prevailed. After isolation, the E. coli isolate was subjected to biochemical testing and cryopreserved in brain heart infusion (BHI) broth with DMSO (8% v/v) as a cryoprotective agent.

1. Reactivation of frozen E. coli ACM5 stock culture

1. From the frozen bacterial stock, open the tube and use a st....

Results

The antimicrobial susceptibility was determined by the disk diffusion method and interpreted by CLSI breakpoint criteria for 12 antibiotics spanning six distinct antimicrobial classes, that is, aminoglycosides, β-lactams, fluoroquinolones, nitrofurans, phenicols, and folate pathway antagonists. The E. coli ACM5 exhibited sensitivity to all antibiotics except one β-lactam drug. Four β-lactam drugs were tested: ampicillin, carbenicillin, cephalothin, and cefotaxime. Among these, a 14 mm inhibition h.......

Discussion

This study presents an adaptation of the bacterial WGS workflow using a benchtop sequencer and a pipeline for genomic characterization of a pathogenic E. coli variant. Depending on the sequencing platform used, the turnaround times (TATs) for wet laboratory procedures (bacterial culturing, gDNA extraction, library preparation, and sequencing) and sequence analysis could vary, particularly if slow-growing bacteria are studied. Following the protocol for WGS described above, the TAT was within 4 days, which is com.......

Materials

Name	Company	Catalog Number	Comments
Accublock Mini digital dry bath	Labnet	D0100	Dry bath for incubation of tubes
Agencourt AMPure XP	Beckman Coulter	A63881	Magnetic beads in solution for DNA library purification
DeNovix DS-11	DeNovix Inc.		UV-Vis spectophotometer to check the quality of the gDNA extracted
DNA LoBind Tubes	Eppendorf	0030108418	1.5 mL PCR tubes for DNA library pooling
DynaMag-2 Magnet	Invitrogen, Thermo Fisher Scientific	12321D	Magnetic microtube rack used during magnetic beads-based DNA purification
Gram-negative Multibac I.D.	Diagnostic reseach (Mexico)	PT-35	Commercial standard antibiotic disks for antimicrobial susceptibility testing
MiniSeq Mid Output Kit (300-cycles)	Illumina	FC-420-1004	Reagent cartdrige for paired-end sequencing (2x150)
MiniSeq System Instrument	Illumina	SY-420-1001	Benchtop sequencer used for Next-generation sequencing
MiniSpin centrifuge	Eppendorf	5452000816	Standard centrifuge for tubes
Nextera XT DNA Library Preparation Kit	Illumina	FC-131-1024	Reagents to perform DNA libraries for sequencing. Includes Box 1 and Box 2 reagents for 24 samples
Nextera XT Index Kit v2	Illumina	FC-131-2001, FC-131-2002, FC-131-2003, FC-131-2004	Index set A, B, C, D
PhiX Control v3	Illumina	FC-110-3001	DNA library control for sequencing
Precision waterbath	LabCare America	51221081	Water bath shaker used for bacterial culture
Qubit 1X dsDNA HS Assay Kit	Invitrogen, Thermo Fisher Scientific	Q33231	Reagents for fluorescence-based DNA quantification assay
Qubit 2.0 Fluorometer	Invitrogen, Thermo Fisher Scientific	Q32866	Fluorometer used for fluorescence assay
Qubit Assay tubes	Invitrogen, Thermo Fisher Scientific	Q32856	0.5 mL PCR tubes for fluorescence-based DNA quantification assay
SimpliAmp Thermal Cycler	Applied Biosystems, Thermo Fisher Scientific	A24811	Thermocycler used for DNA library amplification
Spectronic GENESYS 10 Vis	Thermo	335900	Spectophotometer used for bacterial suspension in antimicrobial susceptibility testing
ZymoBIOMICS DNA Miniprep Kit	Zymo Research Inc.	D4300	Kit for genomic DNA extraction (50 preps)