Genome Sequences of Five Multidrug-Resistant Escherichia coli Sequence Type 117 Isolates Recovered from Dairy Calves.

Escherichia coli sequence type 117 (ST117) strains have been recovered from poultry with colibacillosis, as well as from urinary tract infections and fatal septic infections in humans. To further investigate ST117 isolates recovered from nonpoultry food animals, we sequenced the genomes of five ST117 isolates from dairy calves in Pennsylvania.

GENOME ANNOUNCEMENT

Escherichia coli sequence type 117 (ST117) encompasses a group of multiserotype avian pathogenic E. coli (APEC) and extraintestinal pathogenic E. coli (ExPEC) strains of phylogenetic group D (1–5). Recent studies have indicated that poultry may be a reservoir of E. coli strains that frequently cause extraintestinal infections in humans (1–5). However, the literature suggests that these strains are infrequently isolated from dairy and beef cattle. During an ongoing study focused on the prevalence of antibiotic resistance in E. coli recovered from dairy calves, we isolated five ST117 strains with various levels of resistance. ST117 represented 4% of a subset of E. coli isolates selected for whole-genome sequencing. These data indicate that some lineages associated with human extraintestinal infections, particularly ST117, may be occasionally isolated from cattle and that their prevalence among nonavian food-producing animals has not been adequately evaluated. To further evaluate the genomic characteristics and the phylogeny of these strains, we sequenced the genomes of these five ST117 isolates.

The E. coli isolates were originally recovered from dairy calf feces enriched in buffered peptone water and subsequently streaked onto CHROMagar EC plates (Hardy Diagnostics, France). DNA was extracted from purified colonies grown in Luria-Bertani (LB) broth. To sequence the genomes of these isolates, libraries were constructed using the Nextera XT library prep kit (Illumina, La Jolla, CA), which were then sequenced using a high-output version 2.0 flow cell on a NextSeq 500 platform (Illumina). Raw reads were cleaned and trimmed using DeconSeq (6) and Trimmomatic (7) and assembled using SPAdes version 3.8.0 (8). After assembly, the genomes were analyzed in silico using the Center for Genomic Epidemiology Web server (http://www.genomicepidemiology.org/).

Two isolates were serotyped in silico as O119:H4 (ARS-CC9640 and ARS-CC9604), and three were individually serotyped as O161:H4 (ARS-CC9622), O114:H4 (ARS-CC9624), and O33:H4 (ARS-CC9591). Strains of each of these serotypes have been previously isolated from human-derived samples (http://enterobase.warwick.ac.uk/). Antibiotic resistance genes were variably distributed among the isolates. ARS-CC9591 contained the β-lactamase blaCTX-M-14, blaTEM-1B, and blaCMY-2 genes. ARS-CC9624 contained both a blaCMY-2 and a blaTEM-1C gene. ARS-CC9640 contained a blaCMY-2 gene. The sulfonamide resistance genes sul1 and sul2 or sul2-like were detected in two (ARS-CC9624 and ARS-CC9591) and four strains (ARS-CC9624, ARS-CC9640, ARS-CC9604, and ARS-CC9591), respectively. A floR-like and a catA1-like phenicol resistance gene were each detected in two separate strains (ARS-CC9604 and ARS-CC9591, respectively).

In a single-nucleotide polymorphism (SNP)-based neighbor-joining phylogenetic analysis of 295 E. coli ST117 genomes deposited in GenBank, the study isolates were scattered across the tree and nested within clades that contain poultry and human-derived isolates, indicating that cattle may be a reservoir of strains involved in human infections. However, this remains yet to be studied in-depth. Future research should investigate the role of cattle and other livestock as reservoirs of APEC and ExPEC strains.

Accession number(s).

The genome sequences of these five isolates of E. coli have been deposited in GenBank under the accession numbers listed in Table 1.

TABLE 1 

Accession numbers and metadata for the E. coli strains sequenced in this study

Isolate IDa	Source	Serotypeb	AMR profilec	AMR gene(s)b	Virulence profileb	GenBank accession no.
ARS-CC9624	Dairy calf	O114:H4	AMP, AUG, AXO, CEP, CTX (FOT), FIS, FOX, SXT, TET	aadA1, blaCMY-2, blaTEM-1C, dfrA1, sul1, sul2-like, tet(A), tet(B)	espP, ireA, iss, lpfA, mchB, mchC, mchF, pic, vat	NBVY00000000
ARS-CC9640	Dairy calf	O119:H4	AMP, AUG, AXO, CEP, CTX (FOT), FIS, FOX	aph(3′)-Ic-like, blaCMY-2, sul2	espP, ireA, iss, lpfA, vat	NBVX00000000
ARS-CC9604	Dairy calf	O119:H4	AMP, AUG, AXO, CEP, CHL, CTX (FOT), FIS, FOX, STR, TET, TIO	aph(3′)-Ic-like, blaCMY-2, floR-like, strA, strB, sul2, tet(A)-like, tet(B)	espP, gad, ireA, iroN, iss, lpfA, mchB, mchC, mchF, pic	NBVW00000000
ARS-CC9622	Dairy calf	O161:H4	TET	tet(B)	iroN, iss, lpfA, pic, vat	NBVV00000000
ARS-CC9591	Dairy calf	O33:H4	AMP, AUG, AXO, CEP, CHL, CTX (FOT), FIS, FOX, STR, SXT, TET, TIO	aadA1, aph(3′)-Ic-like, blaCMY-2, blaCTX-M-14, blaTEM-1B, catA1-like, dfrA1, strA, strB, sul1, sul2, tet(B)-like	espP, ireA, iss, lpfA, pic, vat	NBVT00000000

ID, identification.

Determined in silico using the Center for Genomic Epidemiology Web server (http://www.genomicepidemiology.org/).

Antibiotic susceptibility was determined using a Sensititre automated antimicrobial susceptibility system (Trek Diagnostic Systems, Westlake, OH) with specialty plates CVM3AGNF and ESB1F. AMP, ampicillin; AMR, antimicrobial resistance; AUG, augmentin; AXO, ceftriaxone; CEP, cefepime; CTX (FOT), cefotaxime; FIS, sulfisoxazole; FOX, cefoxitin; SXT, trimethoprim-sulfamethoxazole; TET, tetracycline; CHL, chloramphenicol; STR, streptomycin; TIO, ceftiofur.