Introduction
Shiga toxin-producing Escherichia coli (STEC) is a potentially
deadly foodborne pathogen that causes diarrhea, hemorrhagic colitis
(HC), and hemolytic uremic syndrome (HUS) in humans worldwide
(Smith, Fratamico, & Gunther, 2014).
Enterohemorrhagic E. coli (EHEC) is a subgroup of STEC
characterized by certain serogroups, which are often associated with
outbreaks and severe illnesses. In the US alone, EHEC outbreaks have
occurred nearly every year in the last 10 years
(CDC, 2017;
Fao/Who Stec Expert, 2019). The most
common EHEC serogroups are O157, O26, O121, O103, O111, and O145.
Although O157 is the predominant serogroup in STEC infections, recent
reports have demonstrated that non-O157 STECs are emerging as more
impactful pathogens associated with human infections and foodborne
illness outbreaks. In several countries including the US, non-O157
associated human infection cases have exceeded that caused by O157
isolates (CDC, 2017;
Valilis, Ramsey, Sidiq, & DuPont, 2018).
Thus far, over 200 non-O157 serotypes of STEC have been discovered and
linked to human diseases across the globe, among which the top six
serogroups are: O26, O45, O103, O111, O121, and O145
(Conrad, Stanford, McAllister, Thomas, &
Reuter, 2014). Certain serotypes that are usually associated with other
pathotypes have recently caused outbreaks such as O104:H4
(Johura et al., 2016;
Rasko et al., 2011).
STEC is defined by the production of one or more types of Shiga toxin,
which, upon entry into host cells, inhibit the protein synthesis of host
cells, eventually leading to cell death. Stx consists of two major
types, namely, Stx1 and Stx2, which are closely related and encoded bystx 1 and stx 2, respectively
(Melton-Celsa, 2014). Based on sequence
and biological differences, stx 1 is classified into three
subtypes (stx 1a, stx 1c, and stx 1d), and stx 2
into seven subtypes (stx 2a, stx 2b, stx 2c,stx 2d, stx 2e, stx 2f, and stx 2g)
(Scheutz et al., 2012). Certain subtypes
have been linked to human infections. For instance, STEC carryingstx 2a, stx 2c, or stx 2d is frequently associated
with patients with HUS (Fruth, Prager,
Tietze, Rabsch, & Flieger, 2015), whereas stx 2e is commonly
detected in diseased pigs (Tseng et al.,
2014). Aside from Shiga toxins, STEC strains utilize additional
virulence factors that allow them to attach, colonize, invade, and cause
damage. The locus of enterocyte effacement (LEE) pathogenicity island is
responsible for producing attaching and effacing (A/E) lesions on
intestinal epithelial cells. Specific contributing factors include
intimin encoded by the eae gene, secreted effector proteins
(Esp), an intimin receptor encoded by the tir gene, and others
present in the LEE island (Galli,
Miliwebsky, Irino, Leotta, & Rivas, 2010). However, LEE-negative STEC
strains have been shown to be culprits in some human HUS cases. These
could possess other genes responsible for attachment and colonization
such as STEC autoagglutinating adhesin (saa )
(Paton, Srimanote, Woodrow, & Paton,
2001). Key virulence genes also consist of ehxA , espP ,etpD , toxB , katP , subA , saa , andsab genes. The EHEC hemolysin encoded by ehxA is a
cytotoxin expressed during infection and is produced by a great majority
of EHEC serogroups, mostly frequently linked to HUS
(Bielaszewska, Aldick, Bauwens, & Karch,
2014; Schmidt, Kernbach, & Karch,
1996). The presence of ehxA along with stx 2 andeae represents a significant risk factor for severe clinical
manifestations, particularly HUS (Boerlin
et al., 1999).
As DNA sequencing cost decreases, whole-genome sequencing (WGS) has
become increasingly popular in characterizing clinical/environmental
bacterial isolates because the serotype, virulence genes, and
antimicrobial resistance profile can be well predicted from whole-genome
sequences. Additionally, DNA sequence data can provide much better
resolution for strain discrimination than any subtyping method used so
far for outbreak detection and bacteria tracking, rendering it the most
powerful tool in revealing phylogenetic relationships
(Bergholz, Moreno Switt, & Wiedmann,
2014; Dallman et al., 2015).
Importantly, WGS-based analysis tools have been developed and applied to
the characterization of STEC isolates
(Ferdous et al., 2016;
Gonzalez-Escalona & Kase, 2019;
Gonzalez-Escalona et al., 2016). With
sequencing coverages between 30 and 40, serotypes, virulence genes, and
antibiotic resistance genes/sites can be accurately predicted, thereby
providing a faster, cheaper, and better analytical method
(Lindsey, Pouseele, Chen, Strockbine, &
Carleton, 2016).
Cattle and sheep are ruminants that have been demonstrated to be
important reservoirs for non-O157 STEC strains. Foods such as uncooked
meat, unpasteurized milk, and vegetables contaminated by STEC strains
have been frequently associated with human HC and HUS cases
(CDC, 2017) and constitute a constant
threat to human health (Djordjevic et al.,
2004). Xinjiang Province is one of China’s largest provinces with vast
pasture land and is thus known for breeding and husbandry of cattle and
sheep. Large quantities of foods derived from cattle and sheep are
consumed by locals as well as transported to neighboring regions. Cattle
and/or sheep isolates from other parts of China were earlier studied
using traditional molecular and typing methods
(Bai et al., 2016;
Fan et al., 2019). Previously, we
isolated 56 STEC strains from cattle and sheep in Xinjiang, but the
molecular characteristics and phylogeny of these STEC isolates remain
untested. Thus, we here characterized this collection of STEC strains in
detail based on whole-genome sequencing (WGS) and assessed their
pathogenic potential.