Draft genomes of Klebsiella aerogenes, Klebsiella huaxiensis, and Klebsiella michiganensis isolates from the urinary tract

ABSTRACT Several Klebsiella spp. can be the cause of urinary tract infections. Here we present the draft genome assemblies for four urinary isolates of three Klebsiella spp.: Klebsiella aerogenes UMB7541, Klebsiella michiganensis UMB11142 and UMB11423, and Klebsiella huaxiensis UMB11391 to further explore the genetic diversity of Klebsiella in the urinary tract.

oxytoca complex (KOC).KOC species are common causes of urinary tract infections (UTIs), particularly among pregnant females [see review (1)].K. michiganensis has been isolated from urine samples of both males and females with hospital-acquired UTIs (2).K. huaxiensis was first described from a urine sample of the cause of a patient's UTI (3).Klebsiella aerogenes (previously Enterobacter aerogenes) also has been associated with UTIs (4).Prior research found that K. aerogenes and KOC species exhibit a higher incidence of antibiotic resistance than E. coli strains associated with UTIs (4,5).Here we present the genomes of one strain of K. aerogenes, two strains of K. michiganensis, and one strain of K. huaxiensis, all isolated from catheterized urine samples.While the K. aerogenes strain was from a female diagnosed with recurrent UTI, the KOC strains were from three males, none of which presented with UTI symptoms at the time of collection.
Urine samples were collected as part of prior institutional review board (IRB)approved studies [Klebsiella aerogenes: IRB 170077AW (University of California San Diego) (6,7), Klebsiella michiganensis and Klebsiella huaxiensis: IRBs LU212677 and LU217801 (Loyola University Chicago)].Each urine sample was processed using the expanded quantitative urine culture method (8).Microbial identification was determined using a matrix-assisted laser desorption ionization-time of flight mass spectrometer (Bruker Daltonics, Billerica, MA) as previously described (9).The isolates were stored at −80°C in the Loyola Urinary Education and Research Collaborative (LUEREC) collection.Samples were obtained from this collection and streaked on tryptone soy agar plates and incubated at 35°C in 5% CO 2 for 24 hours.A single colony was selected and grown in liquid tryptone soy medium under the same culture conditions.The DNeasy Blood and Tissue Kit (Qiagen) was used to extract DNA following the manufacturer's protocol for Gram-positive organisms.DNA was sent to SeqCoast Genomics (Portsmouth, NH).There libraries were constructed with the DNA Prep tagmentation kit (Illumnia) and sequenced with the Illumina NextSeq2000 platform (2 × 150 bp reads).Assembly was performed using the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) web platform v.3.35.5 (10) with the "auto" parameter.There, the raw reads were trimmed using Trim Galore v.0.6.5 (https://github.com/FelixKrueger/TrimGalore)and assembled using Unicycler v.0.4.8 (11) followed by polishing with Pilon v.1.23(12).Genome coverage was computed by BV-BRC.Genome annotations were produced using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline v.6.7 (13).Completeness and contamination were computed by CheckM v.1.2.2 ( 14) upon submission to the NCBI.Antibiotic resistance genes were identified using ResFinder v.4.5.0 (15,16), specifying the Klebsiella species option.Default parameters were used for all software tools unless indicated otherwise.
Genome assembly statistics are provided in Table 1.All four strains are predicted to be resistant to cephalosporins.Table 1 lists the other antibiotic resistance genes identified.As this analysis shows, the three strains that are members of the KOC are predicted to be multi-drug resistant.Details about the patient's antibiotic use prior to collection may provide insight into the predicted resistances observed.

ACKNOWLEDGMENTS
We acknowledge the study participants who consented to donate urine samples, the clinical members of LUEREC who recruited those participants and collected their urine samples, and members of the Wolfe lab who processed the samples.• aadA16: 99.64%.
a Percentage indicates the sequence identity to the ResFinder database sequence record.

TABLE 1
Genome statistics and strain details