Draft genomes of two Enterobacter hormaechei strains isolated from catheterized urine samples from females experiencing overactive bladder symptoms

TL;DR

This paper reports the draft genomes of two Enterobacter hormaechei strains from urine samples of women with overactive bladder symptoms.

Contribution

The study provides new draft genome sequences of E. hormaechei linked to overactive bladder in females.

Findings

Two E. hormaechei strains were isolated from catheterized urine samples of women with overactive bladder symptoms.

Draft genome sequences were generated to explore the potential role of E. hormaechei in urinary tract health.

Abstract

In this study, we present the draft genome of two Enterobacter hormaechei strains isolated from catheterized urine specimens from females with overactive bladder (OAB) symptoms. Through the sequencing of these E. hormaechei strains, we aim to better understand its presence and putative role in OAB in the female urinary tract.

Tables

TABLE 1. Genome assembly statistics for E. hormaechei UMB2909 and UMB4920

Strain	UMB2909	UMB4920
No. of raw reads	2,665,950	1,801,394
Assembly length (bp)	4,888,222	4,888,358
G + C (%)	55.48	55.48
No. of contigs	37	38
Contigs N50 (bp)	396,383	396,383
Coverage (x)	73.73	49.35
Completeness (%)	99.51	99.51
Contamination (%)	1.19	1.19

Full text

ANNOUNCEMENT

Enterobacter hormaechei, a member of the Enterobacter cloacae complex (ECC), is a prominent pathogen frequently identified in clinical settings due to its prevalence in diverse sample types (1). Associated with a broad spectrum of nosocomial infectious diseases such as bacteremia, biliary tract infections, and urinary tract infections (UTIs), E. hormaechei poses a significant risk in clinical management as it exhibits a concerning level of resistance to numerous antibiotics (1, 2). In this study, we present the genome sequencing of two E. hormaechei strains, isolated from catheterized urine samples from two different females with overactive bladder (OAB) symptoms (3). Although E. hormaechei is the most frequent species related to Enterobacter-associated UTI (4), an association between this species and OAB has not yet been suggested.

Urine samples were collected as part of a prior institutional review board-approved study (LU207152) (3). Using the enhanced quantitative urine culture (EQUC) method (5), each strain was isolated, and the species identification was made via MALDI-TOF, as previously described (6). Each isolate was then stored in the Loyola Urinary Education and Research Collaborative (LUEREC) collection at −80°C. From the collection, we obtained Columbia Colistin Naladixic Acid (CNA) plates with the strains. Individual colonies were selected and streaked onto nutrient broth (NB) agar plates and incubated in 5% CO_2_ at 35°C for 24 hours. A single colony was selected and grown in NB medium in 5% CO_2_ at 35°C for 24 hours. DNA extraction was carried out using the Qiagen DNeasy Blood and Tissue Kit according to the manufacturer’s instructions for Gram-positive bacteria. DNA was quantified using a Qubit fluorometer. Library preparation and sequencing were performed by SeqCoast Genomics (Portsmouth, NH). Libraries were constructed using the Illumina DNA Prep tagmentation kit and unique dual indexes following the manufacturer’s protocol. Using a 300-cycle flow cell kit, sequencing was carried out on the Illumina NextSeq2000 platform (2 × 150 bp). Using the assembly service (“auto” parameter) through the website BV-BRC v3.35.5 (7), reads were trimmed by trim_galore v0.6.5dev (https://github.com/FelixKrueger/TrimGalore) and assembled with Unicycler v0.4.8 (8). Assemblies were polished in two rounds using pilon v1.23 (9). The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v6.7 (10) upon submission. Genome coverage, completeness, and contamination were calculated by BV-BRC and NCBI upon submission. Antibiotic resistance genes were identified using ResFinder v4.5.0 (11, 12), specifying the “Other” species option. Unless otherwise stated, default parameters were used for all software tools.

Information about the genome assemblies for E. hormaechei UMB2909 and UMB4920 can be found in Table 1. Both strains’ genomes were examined for antibiotic resistance genes, identifying blaACT, associated with beta-lactam resistance, and fosA, associated with fosfomycin resistance. The two strains had identical copies of these genes having 99.48% and 97.18% sequence identity to the resistance genes in the ResFinder database, respectively. In a prior study in 2001, E. hormaechei was identified as the member of ECC that was most susceptible to fosfomycin (13); future studies on this resistance among current strains in circulation must be carried out to assess if this resistance has increased over time or if simply the two strains examined here are outliers.