Open Access

Isolation, Identification, Antimicrobial Resistance, Genotyping, and Whole-Genome Sequencing Analysis of Salmonella Enteritidis Isolated from a Food-Poisoning Incident

Zhuru Hou
Zhuru Hou
, 
Benjin Xu
Benjin Xu
, 
Ling Liu
Ling Liu
, 
Rongrong Yan
Rongrong Yan
 and 
Jinjing Zhang
Jinjing Zhang
   | Mar 04, 2024
Polish Journal of Microbiology's Cover Image
About this article
Previous Article
Next Article
Cite
Article Category: ORIGINAL PAPER
Published Online: Mar 04, 2024
Page range: 69 - 89
Received: Sep 17, 2023
Accepted: Jan 21, 2024
DOI: https://doi.org/10.33073/pjm-2024-008
Keywords
© 2024 Zhuru Hou et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Fig. 1.

Clinical symptoms and treatment of patient 21A.
Clinical symptoms and treatment of patient 21A.

Fig. 2.

The clinical symptoms and treatment of patient 21A.
The clinical symptoms and treatment of patient 21A.

Fig. 3.

Circular representations of the genome and plasmid.
Circular representations of the genome and plasmid.

Fig. 4.

Resistance genes annotated with 21A based on CARD database.
Resistance genes annotated with 21A based on CARD database.

Fig. 5.

A, B, C, D, E, F. Functional annotations of 21A resistance genes and virulence genes based on database searches.
A, B, C, D, E, F. Functional annotations of 21A resistance genes and virulence genes based on database searches.

Fig. 6.

Minimum spanning tree based on MLST.
Minimum spanning tree based on MLST.

Fig. 7.

Phylogenetic tree based on SNPs and the distribution of resistance genes.
Phylogenetic tree based on SNPs and the distribution of resistance genes.

Fig. 8.

A, B, C. Core and pan genome analysis.
A, B, C. Core and pan genome analysis.

Fig. 9.

SNP distributions in the chromosome gene cluster of strain 21A.
SNP distributions in the chromosome gene cluster of strain 21A.

Matching scores of mass spectrometry identification results.

Grade (quality) Matching mode Score NCBI identifier
1 (++) Salmonella sp. (enterica st Hadar)Sa05 506 VAB 2.030 149385
2 (++) Salmonella sp. (enterica st Anatum)11 LAL 2.023 58712
3 (+) Salmonella sp. (choleraesuis)08 LAL 1.998 591
4 (+) Salmonella sp. (enterica st Dublin)Sa05 188 VAB 1.972 98360
5 (+) Salmonella sp. (enterica st Enterica)DSM 17058T HAM 1.915 59201
6 (+) Salmonella sp. (typhimurium)12 LAL 1.894 602
7 (+) Salmonella sp. (enteritidis)25089078 (PX)MLD 1.885 592
8 (+) Citrobacter koseri 9553-1 CHB 1.783 545
9 (+) Citrobacter koseri Mu15167-1 CHB 1.753 545
10 (+) Salmonella sp. (enterica st Stanley)15 LAL 1.752 192953

VFDB database predicted the virulence factors of strain 21A.

Type Genes
TTSS SPI-1 avrA, hilCD, iacP, iagB, invABCEFGHIJ, orgABC, prgHIJK, sicAP, sipABCD, sitABCD, sopABDEE2, spaOPQRS, sprB, sptP, steA
SPI-2 pipBB2, sifAB, sopD2, ssaCDEGHIJKLMNOPQRTUV, sscAB, sseBCDEFGIJKL, sspH2, ssrAB, steC
SPI-3 mgtBC, misL
SPI-4 siiE
T3SS ABB77417, hopAN1, hrpH, mlr6326, RSp0731, spvABCDR
Flagella and chemotaxis Flagella fleQ, fleR
Polar flagella fleR/flrC, nueA, flrA, flmH
Lateral flagella lafK
Peritrichous flagella cheABDRWYZ, flgABCDEFGHIJKLMN, flhABCDE, fliABDEFGHIJKLMNOPQRSTYZ, fljB, flk, motAB, tar/cheM
Fimbriae Fimbrial subunit bcfADEF, lpfE, pefA, pegA, safD, stbA, steADEF, stfAEFG, sthDE, stiA
Fimbrial chaperone bcfBC, fimC, lpfB, safB, sefB, stbBE, stdC, steC, stiB
Type IV pili vfr, rpoN, pilRTW
Other related genes algU, bcfC, fimADFHIWYZ, lpfAD, pefB, pegC, safC, sefCR, stbCD, stdAB, steB, stfC, sthA, stiCH
Lipopolysaccharide (LPS) LOS galU, gmhA, htrB, kdsA, lpxABCDHK, msbA, opsX, orfM, rfaDEF, wbaP, wecA
O-antigen ddhACD, prt, wbcC
Other related genes acpXL, bplF, fabZ, gtrAB, hisH2, kdtB, orfH, pagP, waaGP
Adhesins bcfH, csgABCDEFG, lpfC, pagN, pefCD, stdD, stfD, sthBC, upaGH
Capsule cap8J, cpsF, galF, gmd, gnd, kpsF, manB, oppF, rmlAB, uppS, wbfBD, wcaHI, wcbN, wzb
Efflux pump adeFG, ccmB, fbpC, fepC, hitC, mtrE, phuU, sugC
Others hlyA, entABCDEFS, rck, sodB, sodCI, acrB, allABCDRS, bfmR, btpA, cesT, clpEP, fes, icl, mip, pvcC, ratB, ricA, sinH, cofT, virB, mig-5

Basic genomic component information of strain 21A.

Type Number Total length (bp) GC content (%)
Genome 4663 4,118,712 53.34
Number Total length (bp) In genome (%)
ncRNA tRNA 21 1,647 0.0347
5S rRNA 8 920 0.0193
16S rRNA 7 10,702 0.2253
23S rRNA 7 20,453 0.4306
sRNA 68 7,926 0.1669
Tandem Repeat TRF 73 9,851 0.2074
Minisatellite DNA 50 3,611 0.076
Microsatellite DNA 5 190 0.004
CRISPR 2 1,155 0.0243
Prophage 9 217,435 4.5787

Resistant antimicrobial phenotype for strain 21A.

Type of antibiotics Drug MIC Resistance
β-lactam Ampicillin ≥ 32 μg/ml R
Piperacillin ≥ 128 μg/ml R
Ampicillin/sulbactam ≥ 32 μg/ml R
Piperacillin/sulbactam ≤ 4 μg/ml S
Cefoperazone 25 mm S
Cefatriaxone ≤ 1 μg/ml S
Ceftazidime ≤ 1 μg/ml S
Cefepime ≤ 1 μg/ml S
Aztreonam ≤ 1 μg/ml S
Carbopenem Imipenem ≤ 1 μg/ml S
Meropenem ≤ 1 μg/ml S
Sulfonamide Compound sulfamethoxazole ≤ 20 μg/ml S
Nitrofuran Furadantin ≥ 128 μg/ml I
Quinolone Levofloxacin ≥ 8 μg/ml R
Ciprofloxacin ≥ 4 μg/ml R
eISSN:
2544-4646
Language:
English
Publication timeframe:
4 times per year
Journal Subjects:
Life Sciences, Microbiology and Virology
Journal RSS Feed