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Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39162444
mra00110-24
10.1128/mra.00110-24
mra.00110-24
Genome Sequences
environmental-microbiologyEnvironmental MicrobiologyDraft genome sequences of Klebsiella spp. isolated from produce and agricultural water in South Korea
https://orcid.org/0000-0001-5300-2091
Oh Kwang-Kyo 1 Funding acquisition Investigation Project administration Resources ohkwang@korea.kr

https://orcid.org/0000-0002-3639-6663
Cho Gyu-Sung 2 Data curation Formal analysis Software Writing – original draft
Franz Charles M. A. P. 2 Conceptualization Supervision Writing – review and editing
1 Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration , Wanju, South Korea
2 Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße , Kiel, Germany
Editor Maresca Julia A. SUNY College of Environmental Science and Forestry , Syracuse, New York, USA

Address correspondence to Kwang-Kyo Oh, ohkwang@korea.kr
The authors declare a conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00110-2405 2 2024
28 6 2024
Copyright © 2024 Oh et al.
2024
Oh et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

ABSTRACT

This report outlines the draft genome sequences of six Klebsiella spp. strains from South Korea’s agricultural produce and environments. Genome sizes ranged from 5.25 to 6.21 Mbp with 55.64% to 57.55% GC content. Each strain contained multiple plasmid sequences identified by PlasmidFinder, indicating significant antimicrobial resistance.

KEYWORDS

Klebsiella spp.
antibiotic resistance
agricultural environment
Rural Development Administration (RDA) PJ016306 Oh Kwang-Kyo cover-dateSeptember 2024
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pmcANNOUNCEMENT

The genus Klebsiella belongs to the Gammaproteobacteria class of bacteria, of which species have been isolated from water, soil, environments, animals, and humans (1, 2). The Klebsiella (K.) spp. are well-known opportunistic pathogens that may cause infections, and these strains are also an important source of antibiotic resistance genes (3).

In this study, we report the genome sequences of six Klebsiella spp. samples collected from chili, Chinese cabbage, cultivation soil, and agricultural water across three provinces (Chungnam, Gyeongbuk, and Jeonnam) in South Korea. The samples were stored in sterile plastic bags, transported on ice, and processed within 4 to 6 hours. Each 25-g sample was enriched in 225 mL of nutrient broth at 37°C for 24 hours, then streaked onto MacConkey agar, and incubated at the same temperature for another 24 hours, yielding six pink, mucoid colonies. All isolates were grown in LB broth for 20 hours at 37°C under normoxic condition. Total genomic DNA was extracted using the peqGOLD Bacterial DNA extraction kit (VWR, Darmstadt, Germany) following the manufacturer’s instruction. DNA libraries were prepared using the TruSeq Nano DNA library preparation kit, and 2 × 150 bp paired-end sequencing was performed using the NextSeq 500 platform according to the manufacturers’ instructions (Illumina, Munich, Germany). The paired-end raw sequence data were trimmed using Trimmomatic (v. 0.39; parameters: Phred 33, sliding window; 4:15, leading; 3, and minlen; 36) (4), and de novo assembly was subsequently performed using SPAdes (v. 3.15.0; parameters: --isolate) (5). After genome assembly, contig sequences shorter than 500 bp or contaminated with the spiked PhiX genome sequence were removed using the BBDuk pipeline (BBDuk Guide - DOE Joint Genome Institute) with default parameters. The quality of the post-processed contigs was assessed using QUAST (v. 5.2.0) (6). All contigs were annotated using the NCBI Prokaryotic Genome Annotation Pipeline version (v. 6.6). For unequivocal identification of the isolates, draft genome sequences of six strains were compared to the closely related Klebsiella type strains, i.e., K. pneumoniae ATCC 13883T and K. michiganensis DSM 25444T using OrthoANI supported by USEARCH (7) and genome-to-genome distance calculator (formula 2) (8), with default parameters. Acquired antibiotic resistance genes, plasmid replicon type, and multilocus sequencing typing (MLST) were identified using the Staramr pipeline (v. 0.10.0) (9) with ResFinder (database 31.05.2023), PlasmidFinder (database 17.03.2023), and MLST (v.2.11), respectively. The genomic features of six Klebsiella spp. are shown in Table 1. The number of contigs ranged from 55 to 135, and the N50 values were between 94,183 and 189,448 for CN_Kp107 and CN_Kp115, respectively. Total genome length varied from 5.24 Mbp to 6.21 Mbp. All isolates carried more than four antibiotic resistance genes and contained at least one sequence related to plasmid replication (Table 1). The draft genome sequences of Klebsiella strains, isolated from agricultural water and produce, suggested the necessity for epidemiological surveillance and continuous monitoring of antibiotic-resistant bacteria in the agricultural field, particularly from a “One Health” perspective.

TABLE 1 Summary of whole-genome sequencing results of six Kleblsiella spp. strains.

	KB_Kp057	CN_Kp090	CN_Kp094	CN_Kp107	CN_Kp115	JN_Kp126	
No. of contigs	69	55	58	135	59	105	
N50	140319	172849	185818	94183	189448	114984	
GC content (mol %)	57.40	57.55	57.35	57.45	57.23	55.64	
Total length (bp)	5454083	5241811	5363655	5340572	5399707	6210983	
Genome coverage	X47	X73	X55	X50	X50	X43	
No. of raw reads	907689	1368998	1060902	933891	932446	929866	
No. of CDSs	5348	5136	5278	5264	5322	6131	
No. of tRNAs	46	44	49	46	46	54	
No. of rRNAs	7	8	7	5	7	6	
Acquired resistance gene(s)	aadA2, blaSHV-27, dfrA12, mph(A), oqxA, oqxB, sul1,
and sul2	blaSHV-81,
dfrA1, fosA6, oqxA,
oqxB, qnrS1,
sul1, and
tet(A)	aph(3'')-Ib, aph(6)-Id, blaLAP-2, blaSHV-27, fosA6, oqxA, oqxB, qnrS1, sul2, and tet(A)	aph(3'')-Ib, aph(6)-Id , blaTEM-1B, dfrA14 , fosA6, oqxA , oqxB, qnrS1 , sul2,
and tet(D)	blaSHV-100, oqxA, oqxB, and tet(A)	aph(3'')-Ib, aph(3')-Ia, aph(6)-Id, blaOXY-1–4, dfrA21, sul1, and tet(B)	
Plasmid replicon type
(s)	IncFIB(K) and IncFII(K)	IncFIA(pBK30683)	IncFIB(K)	IncFIB(K)(pCAV1099-114), IncN,
and IncR	IncFIB(K)	IncFIA(HI1)	
MLST	Klebsiella pneumoniae 280	Klebsiella pneumoniae 37	Klebsiella pneumoniae 661	Klebsiella pneumoniae 1306	Klebsiella pneumoniae 101	Klebsiella oxytoca 170	
DDH	K. pneumoniae ATCC
13883T (93.5%)	K. pneumoniae ATCC
13883T (93.2%)	K. pneumoniae ATCC
13883T (93.3%)	K. pneumoniae ATCC
13883T (93.4%)	K. pneumoniae ATCC
13883T (93.2%)	K. michiganensis DSM
25444T (91.0%)	
Average nucleotide identity (%)	K. pneumoniae ATCC 13,883T(98.97%)	K. pneumoniae ATCC 13,883T(99.0%)	K. pneumoniae ATCC 13,883T(98.98%)	K. pneumoniae ATCC 13,883T(99.19%)	K. pneumoniae ATCC 13883T (98.91%)	K. michiganensis DSM 25444T (98.96%)	
Isolation source	Chilli	Agricultural water	Soil	Agricultural water	Soil	Chinese cabbage	
SRA accession no.	SRX23442547	SRX23442548	SRX23442549	SRX23442550	SRX23442551	SRX23442552	

ACKNOWLEDGMENTS

This work was supported by the Rural Development Administration (RDA) Cooperative Research Program (Project No. PJ016306), Republic of Korea.

DATA AVAILABILITY

The whole-genome sequences were deposited in the DDBJ/ENA/GenBank under the accession no. PRJNA1039570. The SRA accessions are available at SRX23442547, SRX23442548, SRX23442549, SRX23442550, SRX23442551, and SRX23442552.
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REFERENCES

1 Solomon SA, Bharadwaj AR, Singh NK, Wood JM, Debieu M, O’Hara NB, Mason CE, Venkateswaran K. 2020. Draft genome sequences of Klebsiella species isolated from the international space station. Microbiol Resour Announc 9 :e00923-20. doi:10.1128/MRA.00923-20 33060271
2 Brisse S, Verhoef J. 2001. Phylogenetic diversity of Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates revealed by randomly amplified polymorphic DNA, gyrA and parC genes sequencing and automated ribotyping. Int J Syst Evol Microbiol 51 :915–924. doi:10.1099/00207713-51-3-915 11411715
3 Wyres KL, Holt KE. 2018. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr Opin Microbiol 45 :131–139. doi:10.1016/j.mib.2018.04.004 29723841
4 Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 :2114–2120. doi:10.1093/bioinformatics/btu170 24695404
5 Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19 :455–477. doi:10.1089/cmb.2012.0021 22506599
6 Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29 :1072–1075. doi:10.1093/bioinformatics/btt086 23422339
7 Yoon SH, Ha SM, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110 :1281–1286. doi:10.1007/s10482-017-0844-4 28204908
8 Auch AF, von Jan M, Klenk H-P, Göker M. 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2 :117–134. doi:10.4056/sigs.531120 21304684
9 Bharat A, Petkau A, Avery BP, Chen JC, Folster JP, Carson CA, Kearney A, Nadon C, Mabon P, Thiessen J, Alexander DC, Allen V, El Bailey S, Bekal S, German GJ, Haldane D, Hoang L, Chui L, Minion J, Zahariadis G, Domselaar GV, Reid-Smith RJ, Mulvey MR. 2022. Correlation between phenotypic and in silico detection of antimicrobial resistance in Salmonella enterica in Canada using staramr. Microorganisms 10 :292. doi:10.3390/microorganisms10020292 35208747
