Draft Genome Sequences of 19 Clinical stx-Harboring Escherichia coli O80:H2 Strains

Shiga toxin-producing Escherichia coli (STEC) O80:H2 is an uncommon hybrid pathotype that has emerged in Switzerland and France. Here, we report the draft genome sequences of 19 stx-harboring Escherichia coli O80:H2 strains isolated between 2003 and 2019 from patients in Switzerland.

ABSTRACT

Shiga toxin-producing Escherichia coli (STEC) O80:H2 is an uncommon hybrid pathotype that has emerged in Switzerland and France. Here, we report the draft genome sequences of 19 stx-harboring Escherichia coli O80:H2 strains isolated between 2003 and 2019 from patients in Switzerland.

ANNOUNCEMENT

Shiga toxin (Stx)-producing Escherichia coli (STEC) strains are important foodborne pathogens and responsible for gastrointestinal illnesses which may involve nonbloody or bloody diarrhea, hemorrhagic colitis (HC), and hemolytic uremic syndrome (HUS) (1). STEC O80:H2 has recently emerged in France and Switzerland and is associated with severe cases of HUS, as well as HUS associated with bacteremia (2–5). These 19 stx-harboring E. coli O80:H2 strains were isolated by the National Center for Enteropathogenic Bacteria and Listeria (NENT) at the Swiss Reference Laboratory for STEC between 2003 and 2019 from stool samples (cultivation on MacConkey agar at 37°C for 24 h) of different patients in Switzerland. The presence of stx genes was initially determined by real-time PCR (LightCycler R 2.0 instrument; Roche Diagnostics Corporation, Indianapolis, IN, USA) using the method provided by the European Union (EU) Reference Laboratory.

The strains were grown on sheep blood agar at 37°C overnight prior to genomic DNA isolation using the DNA blood and tissue kit (Qiagen, Hombrechtikon, Switzerland). The DNA was prepared using a Nextera DNA Flex sample preparation kit (Illumina, San Diego, CA, USA), which produces transposome-based libraries that were sequenced on an Illumina MiniSeq sequencer. Up to 16 sequencing libraries were analyzed on one lane, and demultiplexing was performed using the GenerateFASTQ option in the MiniSeq local run manager v2.4.1.

The sequencing outputs were between 660,155 and 1,578,245 paired-end reads of 150 bp, resulting in a genome coverage of 37× to 89×. The Illumina read files passed the standard quality checks using the software package FastQC v0.11.7 (Babraham Bioinformatics, Cambridge, UK) and were assembled using the SPAdes v3.13.1-based software Shovill v1.0.4 (6, 7), using default settings. The assembly was filtered, retaining contigs of >500 bp, and annotated using the NCBI Prokaryotic Genome Annotation Pipeline (8). Multilocus sequence typing (MLST) was performed using the tool MLST v2.11 (https://github.com/tseemann/mlst) and the PubMLST database (https://pubmlst.org/) (9). Virulence factors were identified with VirulenceFinder v2.0 using the E. coli database (10). Stx types were determined by an in silico PCR using the perl script in_silico_pcr (https://github.com/egonozer/in_silico_pcr) with the option “-m, allow one mismatch” and the primers described in the EU Reference Laboratory for E. coli manual for stx gene detection (11). All software and databases were updated in October 2020, and default parameters were used for all in silico analyses.

The draft genome sequences of the 19 STEC strains consist of 5,140,014 to 5,604,512 bp divided over 204 to 361 contigs with an N₅₀ length between 71,463 and 121,369 bp (Table 1). The GC content of the genomes is between 49.5 and 49.7 mol%. The genomes harbor 5,206 to 5,770 genes (Table 1), as predicted by the NCBI Prokaryotic Genome Annotation Pipeline. All strains belonged to the MLST sequence type 301, carried stx_2a or stx_2d, the rare eae variant eae-ξ (xi), and several virulence genes typically associated with pS88 linked to extraintestinal pathogenic E. coli (ExPEC) (12). These genome sequences of clinical strains will improve the data set of the so-far limited number of sequenced STEC O80:H2 strains.

TABLE 1.

Characteristics of the sequences of the 19 stx-harboring Escherichia coli O80:H2 strains

Strain	Yr of isolation	No. of readsa	Coverage (×)	Length (bp)	No. of contigs	N50 (bp)	L50	No. of genes	stx subtype	GenBank accession no.
1384-03	2003	1,130,346	63	5,374,262	244	90,858	17	5,432	stx2a	JAEAMT000000000
1970-08	2008	953,415	53	5,365,261	271	90,740	17	5,474	stx2a	JAEANL000000000
P17-291	2017	827,772	45	5,472,126	306	78,353	20	5,607	stx2d	JAEANK000000000
S18-168	2018	660,155	39	5,140,014	274	83,959	19	5,206	stx2d	JAEANJ000000000
S18-215	2018	669,907	37	5,500,247	284	95,494	17	5,633	stx2a	JAEANI000000000
S18-73	2018	974,815	54	5,423,481	361	88,087	19	5,598	stx2d	JAEANH000000000
S18-9-1	2018	715,345	39	5,462,066	240	121,369	15	5,585	stx2d	JAEANG000000000
S19-101-1	2019	1,402,728	78	5,419,919	314	78,353	20	5,568	stx2d	JAEANF000000000
S19-18-1	2019	1,021,583	55	5,604,512	328	71,463	23	5,770	stx2a	JAEANE000000000
S19-2-2	2019	1,578,245	86	5,503,883	301	91,161	20	5,617	stx2a	JAEAND000000000
S19-30-1	2019	673,226	38	5,321,563	287	82,429	20	5,430	stx2d	JAEANC000000000
S19-615-1	2019	1,006,838	55	5,489,739	342	91,272	19	5,649	stx2d	JAEANB000000000
S19-64-1	2019	739,020	40	5,505,413	284	95,454	19	5,611	stx2a	JAEANA000000000
S19-677-1	2019	911,398	50	5,444,745	342	95,454	18	5,583	stx2a	JAEAMZ000000000
S19-710-1	2019	837,499	45	5,576,432	318	79,701	22	5,706	stx2d	JAEAMY000000000
2017-299-1	2017	991,420	56	5,329,337	310	73,469	19	5,460	stx2d	JAEAMX000000000
2017-353-1	2017	791,789	43	5,531,847	361	78,109	20	5,701	stx2d	JAEAMW000000000
2018-226	2018	922,198	50	5,508,417	290	94,354	20	5,647	stx2a	JAEAMV000000000
2018-439	2018	1,211,877	70	5,183,983	272	75,540	21	5,265	stx2d	JAEAMU000000000

^aRefers to the number of reads in one set of the paired-end 150-bp reads.

Data availability.

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. JAEAMT000000000 to JAEANL000000000. The versions described in this paper are version no. SAMN16883199 to SAMN16883217. The raw sequencing reads have been deposited in the SRA under the BioProject accession no. PRJNA680568.