Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources
Abstract
:1. Introduction
2. Materials and Methods
2.1. Whole Genome Sequencing and Data Assembly
2.2. Core Genome Multilocus Sequence Typing (cgMLST)
2.3. Detection and Assessment of Antimicrobial Resistance, Stress Survival, and Pathogenicity Genes
2.4. Whole Genome SNP and Pangenome Analyses
2.5. Growth in the Presence of Quaternary Ammonium Compound (QAC) Sanitizer
3. Results
3.1. General Genome Characteristics
3.2. SNP Analyses
3.3. Highly Related CC37 Cluster in Facility 1
3.4. Accessory Genome Analysis
3.5. Phenotypic Analyses and Presence of Genetic Elements Assocaited with QAC Tolerance
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Isolate ID | Lineage a | ST | CC | cgMLST | Fac.# | bcrABC | SSI-1 b | cadA Type | LIPI1 c | LIPI3 | LIPI4 | inlAd | AMR Profile e |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
WRLP360 | 2 | 7 | 7 | CT9483 | 4 | - | + | - | + | - | - | + | CLI |
WRLP434 | 2 | 7 | 7 | CT9484 | 1 | - | - | - | + | - | - | + | CLI |
WRLP472 | 2 | 37 | 37 | CT9492 | 1 | - | - | - | + | - | - | + | PEN |
WRLP477 | 2 | 37 | 37 | CT9492 | 1 | - | - | - | + | - | - | + | PEN |
WRLP490 | 2 | 37 | 37 | CT9492 | 1 | - | - | - | + | - | - | + | CLI, PEN |
WRLP491 | 2 | 37 | 37 | CT9492 | 1 | - | - | - | + | - | - | + | CLI, PEN |
WRLP498 | 2 | 37 | 37 | CT9492 | 1 | - | - | - | + | - | - | + | |
WRLP508 | 2 | 37 | 37 | CT9492 | 1 | - | - | - | + | - | - | + | |
WRLP522 | 2 | 37 | 37 | CT9492 | 1 | - | - | - | + | - | - | + | |
WRLP525 | 2 | 37 | 37 | CT9492 | 1 | - | - | - | + | - | - | + | |
WRLP367 | 2 | 155 | 155 | CT9497 | 6 | - | +Δ | - | + | - | - | + | CLI |
WRLP370 | 2 | 155 | 155 | CT9497 | 6 | + | +Δ | - | + | - | - | + | CLI |
WRLP410 | 2 | 155 | 155 | CT9497 | 6 | + | +Δ | - | + | - | - | + | CIP, CLI |
WRLP417 | 2 | 1726 | 452 | CT9495 | 6 | - | - | - | + | - | - | + | CHL, CIP, NOV |
WRLP416 | 2 | 1726 | 452 | CT9495 | 6 | - | - | - | + | - | - | + | CHL, CIP, PEN |
WRLP354 | 1 | 2 | 2 | CT9485 | 2 | - | - | A1, A2 | + | - | - | + | CLI |
WRLP380 | 1 | 2 | 2 | CT9486 | 2 | - | - | A1, A2 | + | - | - | + | AMP, CIP, PEN |
WRLP386 | 1 | 2 | 2 | CT9487 | 2 | - | - | A1, A2 | + | - | - | + | CLI, PEN |
WRLP377 | 1 | 2 | 2 | CT9488 | 2 | - | - | A1, A2 | + | - | - | + | |
WRLP378 | 1 | 2 | 2 | CT9488 | 2 | - | - | A1, A2 | + | - | - | + | CLI |
WRLP382 | 1 | 2 | 2 | CT9488 | 2 | - | - | A1, A2 | + | - | - | + | CIP, CLI |
WRLP530 | 1 | 6 | 6 | CT9494 | 1 | - | - | A2 | + | + | - | Δ | CLI |
WRLP533 | 1 | 6 | 6 | CT9494 | 1 | - | - | A2 | + | + | - | Δ | CLI |
WRLP499 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | |
WRLP521 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI |
WRLP455 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI, PEN |
WRLP463 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI, PEN |
WRLP466 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI, PEN |
WRLP468 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI, PEN, NOV |
WRLP469 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI, PEN, NOV |
WRLP486 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI, PEN |
WRLP494 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI, PEN |
WRLP496 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | |
WRLP502 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | |
WRLP512 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | |
WRLP517 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI |
WRLP519 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI |
WRLP520 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI, PEN |
WRLP527 | 1 | 219 | 4 | CT9489 | 1 | - | - | A2 | +Δ | + | + | + | CLI |
WRLP394 | 1 | 219 | 4 | CT9490 | 1 | - | - | A2 | +Δ | + | + | + | CLI |
WRLP483 | 1 | 219 | 4 | CT9491 | 1 | - | - | A2 | +Δ | + | + | + | PEN, NOV |
WRLP422 | 1 | 388 | 388 | CT9493 | 1 | - | - | A2 | + | - | + | + | CLI |
WRLP440 | 1 | 388 | 388 | CT9493 | 1 | - | - | A2 | + | - | + | + | CLI |
WRLP443 | 1 | 388 | 388 | CT9493 | 1 | - | - | A2 | + | - | + | + | AMP, CLI |
WRLP446 | 1 | 388 | 388 | CT9493 | 1 | - | - | A2 | + | - | + | + | CLI |
WRLP459 | 1 | 688 | 688 | CT9498 | 1 | - | A2 | + | + | + | + | CLI, NOV | |
WRLP408 | 1 | 2165 | 345 | CT9496 | 3 | - | - | A1, A2 | +Δ | - | - | + | CIP, CLI, NOV |
WRLP409 | 1 | 2165 | 345 | CT9496 | 3 | - | - | A1, A2 | +Δ | - | - | + | CIP, CLI |
Isolate Grouping (Lineage/Serogroup; Sequence Type; Strain ID) | No. Unique Genes a |
---|---|
Lineage I/Serogroup 4b, 4d, 4e | 11 |
ST7 | 20 |
WRLP360 | 62 |
WRLP434 | 16 |
ST37 | 49 |
WRLP472 | 118 |
WRLP477 | 143 |
WRLP490 | 108 |
WRLP491 | 141 |
WRLP498 | 96 |
WRLP508 | 94 |
WRLP522 | 139 |
WRLP525 | 210 |
ST155 | 39 |
WRLP367 | 103 |
WRLP370 | 239 |
WRLP410 | 536 |
ST1726 | 47 |
WRLP416 | 406 |
WRLP417 | 46 |
Lineage II/Serogroup 1/2a or 3a | 104 |
ST2 | 36 |
WRLP354 | 12 |
WRLP377 | 1 |
WRLP378 | 7 |
WRLP380 | 1 |
WRLP382 | 4 |
WRLP386 | 13 |
ST6 | 21 |
WRLP530 | 509 |
WRLP533 | 308 |
ST219 | 3 |
WRLP394 | 22 |
WRLP455 | 41 |
WRLP463 | 72 |
WRLP466 | 26 |
WRLP468 | 30 |
WRLP469 | 26 |
WRLP483 | 110 |
WRLP486 | 75 |
WRLP494 | 101 |
WRLP496 | 70 |
WRLP499 | 64 |
WRLP502 | 1 |
WRLP512 | 52 |
WRLP517 | 67 |
WRLP519 | 83 |
WRLP520 | 56 |
WRLP521 | 46 |
WRLP527 | 51 |
ST388 | 9 |
WRLP422 | 212 |
WRLP440 | 129 |
WRLP443 | 173 |
WRLP446 | 683 |
ST688 | 19 |
WRLP459 | nd b |
ST2165 | 103 |
WRLP408 | 157 |
WRLP409 | 530 |
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Bland, R.N.; Johnson, J.D.; Waite-Cusic, J.G.; Weisberg, A.J.; Riutta, E.R.; Chang, J.H.; Kovacevic, J. Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources. Foods 2021, 10, 2454. https://doi.org/10.3390/foods10102454
Bland RN, Johnson JD, Waite-Cusic JG, Weisberg AJ, Riutta ER, Chang JH, Kovacevic J. Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources. Foods. 2021; 10(10):2454. https://doi.org/10.3390/foods10102454
Chicago/Turabian StyleBland, Rebecca N., Jared D. Johnson, Joy G. Waite-Cusic, Alexandra J. Weisberg, Elizabeth R. Riutta, Jeff H. Chang, and Jovana Kovacevic. 2021. "Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources" Foods 10, no. 10: 2454. https://doi.org/10.3390/foods10102454