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Microbiol Resour Announc
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Microbiology Resource Announcements
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39084684
mra01281-23
10.1128/mra.01281-23
mra.01281-23
Genome Sequences
bacteriologyBacteriologyGenomic characteristics of carbapenem-non-susceptible Cronobacter sakazakii isolated from an ICU patient at the Songkhla Hospital, Thailand
Lalakorn Siriporn 1
https://orcid.org/0000-0002-0063-7787
Singkhamanan Kamonnut 2
Chukamnerd Arnon 3
Chumtong Sanicha 2
Dechathai Thitaporn 2
Boonsan Jirasa 2
Kompramool Siriwan 2
Muangkaew Thanchanok 2
https://orcid.org/0000-0003-0170-079X
Yaikhan Thunchanok 2
Chintakovid Nutwadee 2
https://orcid.org/0000-0002-3116-2518
Chusri Sarunyou 3
https://orcid.org/0000-0002-9541-3224
Pomwised Rattanaruji 1
Wonglapsuwan Monwadee 1
https://orcid.org/0000-0001-7793-7561
Surachat Komwit 2 4 komwit.s@psu.ac.th

1 Division of Biological Science, Faculty of Medicine, Prince of Songkla University , Songkhla, Thailand
2 Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University , Songkhla, Thailand
3 Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University , Songkhla, Thailand
4 Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University , Songkhla, Thailand
Editor Bruno Vincent Michael University of Maryland School of Medicine , Baltimore, Maryland, USA

Address correspondence to Komwit Surachat, komwit.s@psu.ac.th
The authors declare no conflict of interest.

9 2024
31 7 2024
31 7 2024
13 9 e01281-2325 12 2023
16 7 2024
Copyright © 2024 Lalakorn et al.
2024
Lalakorn 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

Cronobacter sakazakii is a pathogen that causes severe diseases such as meningitis and necrotizing enterocolitis in infants, associated with the consumption of rehydrated powder infant formula. We report a whole-genome sequence of carbapenem-non-susceptible C. sakazakii isolated from the nasopharynx of the patient admitted to the ICU ward, Songkhla Hospital, Thailand.

KEYWORDS

carbapenem-non-susceptible Cronobacter sakazakii
whole-genome sequence
National Science, Research and Innovation Fund MED6601319S Surachat Komwit Prince of Songkla University (PSU) MED6601319S Surachat Komwit Postdoctoral Fellowship from Prince of Songkla University Chukamnerd Arnon Yaikhan Thunchanok Chintakovid Nutwadee cover-dateSeptember 2024
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pmcANNOUNCEMENT

Cronobacter, a gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive genus within the Enterobacteriaceae family, includes desiccation-resistant species found in products, particularly powder infant formula (1). This bacterium is associated with severe diseases, such as meningitis, septicemia, and necrotizing enterocolitis (2, 3). However, the Cronobacter genome has not been well characterized. We aimed to sequence the entire genome of carbapenem-non-susceptible C. sakazakii and reported its genomic features.

C. sakazakii SK012 was isolated by nasopharyngeal swab of a 77-year-old hypertension patient from ICU in the Songkhla Hospital, Thailand on 21 May 2019. The patient was treated with ceftriaxone, ciprofloxacin, gentamicin, piperacillin/tazobactam, meropenem, and ertapenem. Access to the clinical data was approved by the Human Research Ethics Committee of Prince of Songkla University. The isolate was cultured on MacConkey agar with 2 µg meropenem at 37°C overnight. MALDI-TOF MS was used for the identification of bacterial species. For DNA extraction, a single colony was inoculated into 3 mL Tryptic Soy Broth and incubated at 37°C overnight. Genomic DNA was extracted using the GF-1 Bacterial DNA Extraction Kit, following the manufacturer’s instructions. The DNA library was constructed using the MGIEasy Library Prep Kit V1.1 (MGI Tech). Then, sequencing was conducted on an MGISEQ-2000 platform (BGI, Beijing, China), generating paired-end reads of 150 bp in length. A total of 4,070,902 paired-end reads generated by the sequencer underwent quality verification using FastQC v0.11.9 (4). BacSeq v1.0 (5), which integrates SPAdes v3.15.4 (6), Prokka v1.12 (7), QUAST v4.0 (8), and BUSCO v5.2.2 (9), facilitated the assembly and annotation of the reads. In silico species identification employed BLASTN against the NCBI database (10), and PubMLST database identified the sequence type (ST) as ST1, belonging to clonal complex 1 (11). Antimicrobial resistance genes (ARGs) were detected using the CARD database, with a ≥80% identity match (12). Default parameters were employed for all software, unless specified otherwise.

WGS of C. sakazakii SK012 generated 4,515,439 bp, with N50 value of 470,914 bp, 37 contigs, and 56.69% GC content. Prokka reported the amounts of 92 tRNA, 7 rRNA, 1 tmRNA, and 15 CRISPR arrays. Importantly, the strain carried many ARGs conferring resistance to several antimicrobial classes such as fluoroquinolone, cephalosporin, tetracycline, carbapenem, and aminoglycoside (Table 1). These ARGs are commonly encoded for antibiotic efflux pumps, antibiotic target alteration, and/or antibiotic inactivation. For carbapenem non-susceptibility, this strain harbored marA encoding for efflux pump, which might be associated with multiple antibiotic-resistant phenotypes, especially carbapenem (13).

TABLE 1 ARGs identified in C. sakazakii SK012a

ARGs	SNPs	Antibiotics	
CRP		Macrolide, fluoroquinolone, penam	
CSA-1		Cephalosporin	
Mutation in EF-Tu	R234F	Elfamycin	
Mutation in GlpT	E448K	Phosphonic acid	
msbA		Nitroimidazole	
emrB		Fluoroquinolone	
H-NS		Macrolide, fluoroquinolone, cephalosporin, cephamycin, penam, tetracycline	
emrR		Fluoroquinolone	
marA		Fluoroquinolone, monobactam, carbapenem, cephalosporin, glycylcycline, cephamycin, penam, tetracycline, rifamycin, phenicol	
Mutation in MarR	S3N	Fluoroquinolone, cephalosporin, glycylcycline, penam, tetracycline, rifamycin, phenicol	
rsmA		Fluoroquinolone, diaminopyrimidine, phenicol	
acrA		Fluoroquinolone, cephalosporin, glycylcycline, penam, tetracycline, rifamycin, phenicol	
kpnF		Macrolide, aminoglycoside, cephalosporin, tetracycline, rifamycin	
kpnE		Macrolide, aminoglycoside, cephalosporin, tetracycline, rifamycin	
FosA8		Phosphonic acid	
Mutation in PBP3	D350N, S357N	Cephalosporin, cephamycin, penam	
adeF		Fluoroquinolone, tetracycline	
vanG		Glycopeptide	
a SNP, single-nucleotide polymorphism.

ACKNOWLEDGMENTS

This research was funded by the National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University, Thailand, grant number MED6601319S.

DATA AVAILABILITY

The genome sequence has been deposited in GenBank database under BioProject accession number PRJNA1049972, BioSample accession number SAMN38721045, SRA accession number SRR27308067, and genome accession number JAXOAS000000000.

ETHICS APPROVAL

This research was approved by the Human Research Ethics Committee (HREC) of Prince of Songkla University, reference number: 64–284-14–1.
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REFERENCES

1 Osaili T, Forsythe S. 2009. Desiccation resistance and persistence of Cronobacter species in infant formula. Int J Food Microbiol 136 :214–220. doi:10.1016/j.ijfoodmicro.2009.08.006 19720413
2 Tall BD, Chen Y, Yan Q, Gopinath GR, Grim CJ, Jarvis KG, Fanning S, Lampel KA. 2014. Cronobacter: an emergent pathogen causing meningitis to neonates through their feeds. Sci Prog 97 :154–172. doi:10.3184/003685014X13994743930498 25108996
3 Iversen C, Mullane N, McCardell B, Tall BD, Lehner A, Fanning S, Stephan R, Joosten H. 2008. Cronobacter gen. nov., a new genus to accommodate the biogroups of Enterobacter sakazakii, and proposal of Cronobacter sakazakii gen. nov., comb. nov., Cronobacter malonaticus sp. nov., Cronobacter turicensis sp. nov., Cronobacter muytjensii sp. nov., Cronobacter dublinensis sp. nov., Cronobacter genomospecies 1, and of three subspecies, Cronobacter dublinensis subsp. dublinensis subsp. nov., Cronobacter dublinensis subsp. lausannensis subsp. nov. and Cronobacter dublinensis subsp. lactaridi subsp. nov. Int J Syst Evol Microbiol 58 :1442–1447. doi:10.1099/ijs.0.65577-0 18523192
4 Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data 1 :1.
5 Chukamnerd A, Jeenkeawpiam K, Chusri S, Pomwised R, Singkhamanan K, Surachat K. 2023. BacSeq: a user-friendly automated pipeline for whole-genome sequence analysis of bacterial genomes. Microorganisms 11 :1769. doi:10.3390/microorganisms11071769 37512941
6 Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. 2020. Using SPAdes de novo assembler. Curr Protoc Bioinformatics 70 :e102. doi:10.1002/cpbi.102 32559359
7 Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30 :2068–2069. doi:10.1093/bioinformatics/btu153 24642063
8 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
9 Manni M, Berkeley MR, Seppey M, Zdobnov EM. 2021. BUSCO: assessing genomic data quality and beyond. Curr Protoc 1 :e323. doi:10.1002/cpz1.323 34936221
10 Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol 7 :203–214. doi:10.1089/10665270050081478 10890397
11 Jolley KA, Bray JE, Maiden MCJ. 2018. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 3 :124. doi:10.12688/wellcomeopenres.14826.1 30345391
12 Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen A-LV, Cheng AA, Liu S, et al. . 2020. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48 :D517–D525. doi:10.1093/nar/gkz935 31665441
13 Chetri S, Das BJ, Bhowmik D, Chanda DD, Chakravarty A, Bhattacharjee A. 2020. Transcriptional response of mar, sox and rob regulon against concentration gradient carbapenem stress within Escherichia coli isolated from hospital acquired infection. BMC Res Notes 13 :168. doi:10.1186/s13104-020-04999-2 32192538
