Fig. 1.
Clinical symptoms and treatment of patient 21A.
Fig. 2.
The clinical symptoms and treatment of patient 21A.
Table I
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 |
Fig. 3.
Circular representations of the genome and plasmid.
Table II
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 | |
Fig. 4.
Resistance genes annotated with 21A based on CARD database.
Table III
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 |
Table IV
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 | |
Fig. 5.
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.
Fig. 7.
Phylogenetic tree based on SNPs and the distribution of resistance genes.
Fig. 8.
A, B, C. Core and pan genome analysis.
Fig. 9.
SNP distributions in the chromosome gene cluster of strain 21A.