Identification and Characterization of Antibiotic-Resistant, Gram-Negative Bacteria Isolated from Korean Fresh Produce and Agricultural Environment
Abstract
1. Introduction
2. Materials and Methods
2.1. Sampling
2.2. Microbiological Analyses
2.3. Preliminary Phenotypic Testing
2.4. Genotypic Characterization by RAPD-PCR Fingerprinting
2.5. Antibiotic Susceptibility Test
2.6. 16S rRNA Gene Sequencing and Identification
2.7. Whole Genome Sequencing
3. Results
3.1. Preliminary Physiological Tests
3.2. RAPD-PCR Fingerprinting
3.3. Strain Identification
3.4. Antibiotic Resistance Profiles
3.5. Whole Genome Sequencing
V98_8 | V88_4 | V104_6 | V104_10 | V89_4 | V89_7 | V106_11 | V108_6 | V87_3 | |
No. of contigs | 113 | 48 | 58 | 66 | 30 | 34 | 37 | 58 | 35 |
N50 | 115,019 | 382,325 | 138,943 | 195,255 | 250,587 | 215,337 | 320,651 | 163,040 | 211,224 |
GC content (mol%) | 59.99 | 60.55 | 61.77 | 62.3 | 38.64 | 43.03 | 53.33 | 53.37 | 55.70 |
Total length (bp) | 6,514,074 | 6,264,170 | 4,687,376 | 5,620,582 | 4,009,586 | 3,276,090 | 4,899,709 | 4,944,362 | 4,706,154 |
Genome coverage | x 25 | x 103 | x 46 | x 32 | x 147 | x 68 | x 41 | x 63 | x 104 |
No. of CDSs | 6043 | 5725 | 4326 | 5239 | 3771 | 3116 | 4956 | 5032 | 4443 |
No. of tRNAs | 49 | 53 | 62 | 56 | 45 | 65 | 57 | 40 | 47 |
No. of rRNAs | 3 | 5 | 6 | 5 | 3 | 3 | 5 | 5 | 4 |
Acquired resistance gene(s) | n.d. | n.d. | n.d. | n.d. | blaOXA-304, blaADC-25 | n.d. | OqxB | OqxB | fosA, blaMIR-6 |
Plasmid sequence(s) | n.d. | n.d. | n.d. | n.d. | n.d. | n.d. | n.d. | n.d. | n.d. |
Antibiotic resistance | n.d. | C, AMP, FOX, CTX | n.d. | AMP, FOX, CTX | C, AMP, FOX, CTX | AMP, MEM, CTX | n.d. | AMP | AMP, FOX |
OrthoANI identification (% similarity of top-hit) | Pseudomonas umsongensis DSM 16611T (96.75%) | Pseudomonas glycinae MS586T (96.48%) | Pseudomonas fulva DSM 17717T (99.48%) | Pseudomonas monteilii DSM 14164T (98.0%) | Acineotbacter oleivorans JCM 16667T (96.91%) | Acinetobacter soli KCTC 22184T (98.53%) | Pantoea ananatis LMG 2665T (99.07%) | Pantoea ananatis LMG 2665T (99.16%) | Enterobacter cancerogenus ATCC 33241T (98.55%) |
in silico DDH identification (% similarity of top-hit) | Pseudomonas umsongensis DSM 16611T (71.9%) | Pseudomonas glycinae MS586T (71.1%) | Pseudomonas fulva DSM 17717T (96.1%) | Pseudomonas monteilii DSM 14164T (83.4%) | Acineotbacter oleivorans JCM 16667T (72.9%) | Acinetobacter soli KCTC 22184T (88.2%) | Pantoea ananatis LMG 2665T (92.5%) | Pantoea ananatis LMG 2665T (93.2%) | Enterobacter cancerogenus ATCC 33241T (87.4%) |
Accession no. | JASCAE000000000 | JASCAF000000000 | JASCAG000000000 | JASCAH000000000 | JASCAI000000000 | JASCAJ000000000 | JASCAK000000000 | JASCAL000000000 | JASCAM000000000 |
V87_3 | V89_11 | V114_1 | V89_13 | V90_4 | V115_8 | V90_14 | |||
No. of contigs | 35 | 58 | 21 | 46 | 79 | 52 | 49 | ||
N50 | 211,224 | 201,295 | 2,533,332 | 173,726 | 134,120 | 194,518 | 197,099 | ||
GC content (mol%) | 55.70 | 54.60 | 59.89 | 55.84 | 56.41 | 58.21 | 61.53 | ||
Total length (bp) | 4,706,154 | 4,700,025 | 4,932,611 | 4,846,069 | 5,149,412 | 5,253,824 | 4,749,641 | ||
Genome coverage | x 104 | x 115 | x 41 | x 85 | x 103 | x 40 | x 127 | ||
No. of CDSs | 4443 | 4509 | 4720 | 4561 | 4976 | 5084 | 4422 | ||
No. of tRNAs | 47 | 36 | 76 | 48 | 52 | 65 | 56 | ||
No. of rRNAs | 4 | 4 | 4 | 5 | 6 | 6 | 5 | ||
Acquired resistance gene(s) | fosA, blaMIR-6 | blaACT-12, OqxA, OqxB, fosA2 | aac(6′)-Ic, blaSST-1, OqxB, tet(41) | fosA2, OqxA, OqxB | n.d. | OqxA, OqxB, fosA, blaOKP-A-11 | ampH, blaMOX-4, cphA1 | ||
Plasmid sequence(s) | n.d. | n.d. | n.d. | n.d. | IncFII(Yp) | n.d. | n.d. | ||
Antibiotic resistance | AMP, FOX | AMP, FOX | AMP | n.d. | AMP | CIP, AMP, MEM, CTX | AMP | ||
OrthoANI identification (% similarity of top-hit) | Enterobacter cancerogenus ATCC 33241T (98.55%) | Enterobacter ludwigii DSM 16688T (98.88%) | Serratia marcescens ATCC 13880T (98.64%) | Lelliottia jeotgali PFL01T (91.19%), Lelliottia amnigena LMG2784T (85.24%), Lelliottia nimipressuralis CIP 104980T (84.15%) | Erwinia aphidicola JCM 21238T (99.02%) | Klebsiella quasipneumoniae subsp. quasipneumoniae 01A030T (99.19%) | Aeromonas hydrophila ATCC 7966T (96.91%) | ||
in silico DDH identification (% similarity of top-hit) | Enterobacter cancerogenus ATCC 33241T (87.4%) | Enterobacter ludwigii DSM 16688T (91.4%) | Serratia marcescens ATCC 13880T (89.1%) | Lelliottia jeotgali PFL01T (43.6%), Lelliottia nimipressuralis CCUG 25894T (27.8%), Lelliottia amnigena LMG2784T (29.1%) | Erwinia aphidicola JCM 21238T (91.9%) | Klebsiella quasipneumoniae subsp. quasipneumoniae 01A030T (93.9%) | Aeromonas hydrophila ATCC 7966T (73.3%) | ||
Accession no. | JASCAM000000000 | JASCAN000000000 | JASCAO000000000 | JASCAP000000000 | JASCAQ000000000 | JASCAR000000000 | JASCAS000000000 |
4. Discussion
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Fertilizer Source | Surrounding Soils | Lettuce Leaves |
---|---|---|
Non-treated soil | 20 | 44 |
Cow manure | 5 | 26 |
Pig manure | 3 | 25 |
Poultry manure | 3 | 18 |
Chemical fertilizer | 10 | 25 |
Chemical fertilizer + cow and poultry manure | 12 | 23 |
Chemical fertilizer + cow + poultry + pig manure | 13 | 21 |
Total number of isolates | 66 | 182 |
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Jeong, S.; Kim, I.; Kim, B.-E.; Jeong, M.-I.; Oh, K.-K.; Cho, G.-S.; Franz, C.M.A.P. Identification and Characterization of Antibiotic-Resistant, Gram-Negative Bacteria Isolated from Korean Fresh Produce and Agricultural Environment. Microorganisms 2023, 11, 1241. https://doi.org/10.3390/microorganisms11051241
Jeong S, Kim I, Kim B-E, Jeong M-I, Oh K-K, Cho G-S, Franz CMAP. Identification and Characterization of Antibiotic-Resistant, Gram-Negative Bacteria Isolated from Korean Fresh Produce and Agricultural Environment. Microorganisms. 2023; 11(5):1241. https://doi.org/10.3390/microorganisms11051241
Chicago/Turabian StyleJeong, Sunyoung, Ile Kim, Bo-Eun Kim, Myeong-In Jeong, Kwang-Kyo Oh, Gyu-Sung Cho, and Charles M. A. P. Franz. 2023. "Identification and Characterization of Antibiotic-Resistant, Gram-Negative Bacteria Isolated from Korean Fresh Produce and Agricultural Environment" Microorganisms 11, no. 5: 1241. https://doi.org/10.3390/microorganisms11051241
APA StyleJeong, S., Kim, I., Kim, B.-E., Jeong, M.-I., Oh, K.-K., Cho, G.-S., & Franz, C. M. A. P. (2023). Identification and Characterization of Antibiotic-Resistant, Gram-Negative Bacteria Isolated from Korean Fresh Produce and Agricultural Environment. Microorganisms, 11(5), 1241. https://doi.org/10.3390/microorganisms11051241