Genomic Characterization of Listeria monocytogenes Isolates Associated with Clinical Listeriosis and the Food Production Environment in Ireland
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Isolates
2.2. Pulsed Field Gel Electrophoresis
2.3. Genome Sequencing and Annotation
2.4. Multilocus Sequence Typing and Clonal Complex
2.5. Single Nucleotide Polymorphisms Analysis
2.6. Public Data Sources
2.7. Pan- and Core-Genomic Profiling of Protein-Coding Genes
3. Results and Discussion
3.1. Serotypes and Clonal Complexes of Clinical Isolates
3.2. Relationship between Sequence Type and PFGE Profiles
3.3. Single-Nucleotide Polymorphism Analysis of Isolates
3.4. Pan- and Core-Genome Analysis
3.5. Listeria Pathogenicity Islands
3.6. Internalins
3.7. Stress Survival Islet (SSI-1)
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Isolate | Genbank Accession Number | ST 1 | CC 2 | Lineage | Serotype | Year of Isolation | Sample Type | Pulsotype |
---|---|---|---|---|---|---|---|---|
MQ130026 | MUZG00000000 | ST-1 | CC1 | I | 4b | 2013 | Blood | P2 * |
L970 | PJJD00000000 | ST-1 | CC1 | I | 4b | 2013 | Food production ** | P2 * |
MQ130029 | MVED00000000 | ST-1 | CC1 | I | 4b | 2013 | CSF 3 | P2 * |
MQ130032 | MVEE00000000 | ST-1 | CC1 | I | 4b | 2013 | Blood | P2 * |
MQ130042 | MVEG00000000 | ST-1 | CC1 | I | 4b | 2013 | Pleural Swab | P1 * |
MQ140025 | MVEK00000000 | ST-1 | CC1 | I | 4b | 2014 | Ear Swab | P68 |
MQ140031 | MVEN00000000 | ST-1 | CC1 | I | 4b | 2014 | Blood | P2 * |
MQ140033 | MVEP00000000 | ST-1 | CC1 | I | 4b | 2014 | Blood | P1 * |
L2113 | PJJE00000000 | ST-1 | CC1 | I | 4b | 2015 | Food production | P2 * |
MQ150012 | MVEY00000000 | ST-6 | CC6 | I | 4b | 2015 | Blood | P13 * |
MQ150005 | MVEU00000000 | ST-6 | CC6 | I | 4b | 2015 | Blood | P13 * |
MQ130058 | MVEH00000000 | ST-6 | CC6 | I | 4b | 2013 | Blood | P13 * |
MQ140030 | MVEM00000000 | ST-4 | CC4 | I | 4b | 2014 | CSF 3 | NC 4 |
MQ150004 | MVET00000000 | ST-54 | CC54 | I | 4b | 2015 | Placental Swab | P6 * |
MQ130033 | MVEF00000000 | ST-54 | CC54 | I | 4b | 2013 | Blood | P12 |
L2259 | PJJF00000000 | ST-54 | CC54 | I | 4b | 2015 | Food production | P6 * |
MQ150013 | MVEZ00000000 | ST-2 | CC2 | I | 4b | 2015 | Blood | P16 * |
MQ130037 | MVFA00000000 | ST-18 | CC18 | II | 1/2a | 2013 | Blood | P32 * |
MQ150011 | MVEX00000000 | ST-20 | CC20 | II | 1/2a | 2015 | Nasal Swab | NC |
MQ150001 | MVES00000000 | ST-37 | CC37 | II | 1/2a | 2015 | Blood | P32 * |
MQ140029 | MVEL00000000 | ST-7 | CC7 | II | 1/2a | 2014 | Blood | P31 * |
L1445 | PJJG00000000 | ST-7 | CC7 | II | 1/2a | 2014 | Food production | P31 * |
L1976 | PJJI00000000 | ST-8 | CC8 | II | 1/2c | 2015 | Food production | P48 * |
MQ140034 | MVEQ00000000 | ST-121 | CC121 | II | 1/2a | 2014 | Blood—Mother/Infant | P59 * |
L2256 | PJJH00000000 | ST-121 | CC121 | II | 1/2c | 2015 | Food production | P59 * |
MQ140035 | MVER00000000 | ST-121 | CC121 | II | 1/2a | 2014 | Ear Swab—Mother/Infant | P59 * |
MQ140032 | MVEO00000000 | ST-425 | CC90 | II | 1/2a | 2014 | Blood | NC |
MQ140012 | MVEJ00000000 | ST-101 | CC101 | II | 1/2a | 2014 | Blood—Mother/Infant | P30 |
MQ140011 | MVEI00000000 | ST-101 | CC101 | II | 1/2a | 2014 | Placental Surface Swab—Mother/Infant | P30 |
MQ150008 | MVEW00000000 | ST-431 | CC101 | II | 1/2a | 2015 | Blood | P30 |
MQ150007 | MVEV00000000 | ST-431 | CC101 | II | 1/2a | 2015 | CSF 3 | P30 |
Sequence Type | Isolates | Reference Genome | Minimum SNPs | Maximum SNPs |
---|---|---|---|---|
ST1 | L970, L2113, MQ130026, MQ130029, MQ130032 *, MQ130042, MQ140025, MQ140031, MQ140033 | F2365 | 43 | 261 |
F2365, L2113, MQ130026, MQ130029, MQ130032 *, MQ130042, MQ140025, MQ140031, MQ140033 | L970 | 42 | 256 | |
F2365, L970, MQ130026, MQ130029, MQ130032 *, MQ130042, MQ140025, MQ140031, MQ140033 | L2113 | 42 | 254 | |
F2365, L970, MQ130029, MQ130032 *, MQ130042 | MQ130026 | 44 | 190 | |
F2365, L2113, MQ140031, MQ140033 * | MQ140025 | 66 | 259 | |
ST6 | H7858, MQ130058, MQ150012 * | MQ150005 | 199 | 373 |
ST54 | LM07-01337, MQ130033, MQ150004 * | L2259 | 65 | 115 |
ST7 | J2692, L1846, L2676, MQ140029 * | L1445 | 1 | 409 |
ST121 | 4423, 6179, L2256, La111, Lm1880, N53-1, MQ140035 * | MQ140034 | 3 | 461 |
ST101 | 2012-L5240, 2012-L5323, Lm1840, MQ140012, MQ150007, MQ150008 * | MQ140011 | 1 | 145 |
2012-L5240, 2012-L5323, Lm1840, MQ150008 * | MQ150007 | 2 | 146 |
Isolate | ST 1 | CC 2 | LIPI1 | LIPI3 | LIPI4 | InlA | SSI-1 |
---|---|---|---|---|---|---|---|
MQ130026 | ST-1 | CC1 | + 3 | + | − 4 | + 5 | − |
L970 | ST-1 | CC1 | + | + | − | + | − |
MQ130029 | ST-1 | CC1 | + | + | − | + | − |
MQ130032 | ST-1 | CC1 | + | + | − | + | − |
MQ130042 | ST-1 | CC1 | + | + | − | + | − |
MQ140025 | ST-1 | CC1 | + | + | − | + | − |
MQ140031 | ST-1 | CC1 | + | + | − | + | − |
MQ140033 | ST-1 | CC1 | + | + | − | + | − |
L2113 | ST-1 | CC1 | + | + | − | + | − |
MQ150012 | ST-6 | CC6 | + | + | − | + | − |
MQ150005 | ST-6 | CC6 | + | + | − | + | − |
MQ130058 | ST-6 | CC6 | + | + | − | + | − |
MQ140030 | ST-4 | CC4 | + | + | + | + | − |
MQ150004 | ST-54 | CC54 | + | + | − | + | − |
MQ130033 | ST-54 | CC54 | + | + | − | + | − |
L2259 | ST-54 | CC54 | + | + | − | + | − |
MQ150013 | ST-2 | CC2 | + | − | − | + | − |
MQ130037 | ST-18 | CC18 | + | − | − | + | + |
MQ150011 | ST-20 | CC20 | + | − | − | + | − |
MQ150001 | ST-37 | CC37 | + | − | − | + | − |
MQ140029 | ST-7 | CC7 | + | − | − | + | + |
L1445 | ST-7 | CC7 | + | − | − | + | + |
L1976 | ST-8 | CC8 | + | − | − | + | + |
MQ140034 | ST-121 | CC121 | + | − | − | + | − |
L2256 | ST-121 | CC121 | + | − | − | − | − |
MQ140035 | ST-121 | CC121 | + | − | − | + | − |
MQ140032 | ST-425 | CC90 | + | − | − | + | − |
MQ140012 | ST-101 | CC101 | + | − | − | + | − |
MQ140011 | ST-101 | CC101 | + | − | − | + | − |
MQ150008 | ST-431 | CC101 | + | − | − | + | − |
MQ150007 | ST-431 | CC101 | + | − | − | + | − |
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Hilliard, A.; Leong, D.; O’Callaghan, A.; Culligan, E.P.; Morgan, C.A.; DeLappe, N.; Hill, C.; Jordan, K.; Cormican, M.; Gahan, C.G.M. Genomic Characterization of Listeria monocytogenes Isolates Associated with Clinical Listeriosis and the Food Production Environment in Ireland. Genes 2018, 9, 171. https://doi.org/10.3390/genes9030171
Hilliard A, Leong D, O’Callaghan A, Culligan EP, Morgan CA, DeLappe N, Hill C, Jordan K, Cormican M, Gahan CGM. Genomic Characterization of Listeria monocytogenes Isolates Associated with Clinical Listeriosis and the Food Production Environment in Ireland. Genes. 2018; 9(3):171. https://doi.org/10.3390/genes9030171
Chicago/Turabian StyleHilliard, Amber, Dara Leong, Amy O’Callaghan, Eamonn P. Culligan, Ciara A. Morgan, Niall DeLappe, Colin Hill, Kieran Jordan, Martin Cormican, and Cormac G.M. Gahan. 2018. "Genomic Characterization of Listeria monocytogenes Isolates Associated with Clinical Listeriosis and the Food Production Environment in Ireland" Genes 9, no. 3: 171. https://doi.org/10.3390/genes9030171
APA StyleHilliard, A., Leong, D., O’Callaghan, A., Culligan, E. P., Morgan, C. A., DeLappe, N., Hill, C., Jordan, K., Cormican, M., & Gahan, C. G. M. (2018). Genomic Characterization of Listeria monocytogenes Isolates Associated with Clinical Listeriosis and the Food Production Environment in Ireland. Genes, 9(3), 171. https://doi.org/10.3390/genes9030171