TABLE 5.
Genomic subtypes of sequenced 1,248 L. monocytogenes isolates with locations and years detected
| CC or singleton, group total, and diversity index | ST | Serotype (serogroup)a | Lineage | No. of isolates | Yr(s) | No. of isolates in waterway/location |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | C | G | US | LS | T | X1 | X2 | X3 | ||||||
| CC | ||||||||||||||
| CC1 | ST1 | 4b (IVb) | I | 164 | 2011–2016 | 14 | 28 | 53 | 13 | 14 | 29 | 0 | 5 | 8 |
| ST308 | 4b (IVb) | I | 3 | 2012–2014 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
| ST2132 | 4b (IVb) | I | 1 | 2015 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | |
| CC2 | ST2 | 4b (IVb) | I | 18 | 2012–2016 | 2 | 5 | 0 | 0 | 2 | 9 | 0 | 0 | 0 |
| ST782 | 4b (IIb) | I | 7 | 2012, 2014–2016 | 0 | 2 | 3 | 1 | 0 | 1 | 0 | 0 | 0 | |
| ST1039 | 4b (IVb) | I | 1 | 2012 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| ST2125 | 4b (IVb) | I | 1 | 2014 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | |
| CC3 | ST3 | 1/2b (IIb) | I | 1 | 2014 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| ST1530 | 4b (IIb) | I | 1 | 2013 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | |
| CC4 | ST4 | 4b (IVb) | I | 10 | 2012–2016 | 0 | 4 | 0 | 2 | 2 | 2 | 0 | 0 | 0 |
| ST219 | 4b (IVb) | I | 3 | 2013 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| ST397 | 4b (IVb) | I | 3 | 2014–2015 | 0 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | |
| ST531 | 4b (IVb) | I | 4 | 2012, 2016 | 0 | 0 | 2 | 0 | 1 | 0 | 0 | 1 | 0 | |
| ST631 | 4b (IVb) | I | 15 | 2012–2013, 2015 | 0 | 9 | 0 | 1 | 1 | 4 | 0 | 0 | 0 | |
| ST1773 | 4b (IVb) | I | 3 | 2013–2014 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | |
| ST2128 | 4b (IVb) | I | 1 | 2016 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| CC5 | ST5 | 1/2b (IIb) | I | 16 | 2012–2016 | 0 | 4 | 0 | 0 | 3 | 9 | 0 | 0 | 0 |
| ST363 | 1/2b (IIb) | I | 10 | 2012–2016 | 0 | 3 | 0 | 2 | 0 | 0 | 0 | 5 | 0 | |
| ST784 | 4b (IVb-v1)b | I | 10 | 2012, 2014–2016 | 0 | 2 | 0 | 0 | 2 | 5 | 0 | 1 | 0 | |
| ST1526 | 1/2b (IIb) | I | 1 | 2014 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| CC6 | ST6 | 4b (IVb) | I | 63 | 2011–2016 | 12 | 13 | 10 | 1 | 3 | 15 | 0 | 0 | 9 |
| CC7 | ST7 | 1/2a (IIa) | II | 14 | 2013–2015 | 9 | 1 | 0 | 0 | 1 | 2 | 0 | 0 | 1 |
| CC8 | ST8 | 1/2a (IIa) | II | 1 | 2014 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| CC9 | ST9 | 1/2a [1], 1/2c [2] (IIc) | II | 3 | 2015–2016 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 |
| ST2134 | 1/2c (IIc) | II | 1 | 2014 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | |
| CC11 | ST11 | 1/2a (IIa) | II | 4 | 2014 | 0 | 1 | 0 | 0 | 0 | 3 | 0 | 0 | 0 |
| ST451 | 1/2a (IIa) | II | 2 | 2012, 2016 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | |
| CC26 | ST26 | 1/2a (IIa) | II | 1 | 2015 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| CC29 | ST29 | 1/2a (IIa) | II | 1 | 2014 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| CC37 | ST37 | 1/2a (IIa) | II | 2 | 2012 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| CC87 | ST87 | 1/2b (IIb) | I | 8 | 2013–2016 | 0 | 3 | 0 | 0 | 0 | 5 | 0 | 0 | 0 |
| CC88 | ST88 | 1/2b (IIb) | I | 2 | 2012, 2016 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 |
| ST296 | 1/2b (IIb) | I | 1 | 2015 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | |
| CC124 | ST124 | 1/2a (IIa) | II | 1 | 2012 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| CC155 | ST155 | 1/2a (IIa) | II | 2 | 2012, 2015 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| CC183 | ST382 | 4b (IVb-v1) | I | 225 | 2012–2016 | 16 | 70 | 12 | 29 | 21 | 53 | 0 | 12 | 12 |
| ST2126 | 4b (IVb-v1) | I | 8 | 2012, 2014–2016 | 0 | 8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| CC199 | ST199 | 1/2a (IIa) | II | 1 | 2014 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| CC217 | ST217 | 4b (IVb) | I | 28 | 2012–2016 | 3 | 3 | 9 | 4 | 6 | 3 | 0 | 0 | 0 |
| ST2127 | 4b (IVb) | I | 1 | 2014 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| CC224 | ST224 | 1/2b (IIb) | I | 6 | 2013–2016 | 0 | 4 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
| ST845 | 1/2b (IIb) | I | 1 | 2015 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
| CC288 | ST288 | 1/2b (IIb) | I | 8 | 2012–2013, 2015–2016 | 0 | 1 | 3 | 0 | 0 | 3 | 0 | 1 | 0 |
| CC321 | ST321 | 1/2a (IIa) | II | 6 | 2012–2014 | 0 | 0 | 1 | 0 | 0 | 5 | 0 | 0 | 0 |
| CC388 | ST388 | 4b (IVb) | I | 29 | 2012–2016 | 6 | 7 | 1 | 7 | 0 | 3 | 0 | 4 | 1 |
| ST824 | 4b (IVb) | I | 2 | 2015 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | |
| CC389 | ST389 | 4b (IVb) | I | 4 | 2012, 2014–2015 | 1 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 0 |
| CC392 | ST392 | 1/2b (IIb) | I | 4 | 2012, 2013, 2014, 2016 | 1 | 0 | 0 | 1 | 0 | 2 | 0 | 0 | 0 |
| CC412 | ST412 | 1/2a (IIa) | II | 12 | 2012–2015 | 1 | 1 | 0 | 5 | 3 | 2 | 0 | 0 | 0 |
| CC426 | ST426 | 1/2b (IIb) | I | 1 | 2012 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| CC429 | ST429 | 1/2b (IIb) | I | 2 | 2014, 2016 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 |
| ST2141 | 1/2b (IIb) | I | 1 | 2013 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | |
| CC506 | ST506 | 1/2b (IIb) | I | 2 | 2012, 2013 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| CC554 | ST554 | 4b (IVb-v1) | I | 11 | 2012–2016 | 1 | 2 | 0 | 1 | 1 | 5 | 0 | 1 | 0 |
| CC639 | ST639 | 4b (IVb) | I | 317 | 2011–2016 | 31 | 22 | 94 | 7 | 33 | 97 | 0 | 3 | 30 |
| ST2129 | 4b (IVb) | I | 4 | 2012, 2014, 2015, 2016 | 0 | 1 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | |
| ST2130 | 4b (IVb) | I | 10 | 2012–2013 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 7 | |
| ST2133 | 4b (IVb) | I | 1 | 2016 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | |
| CC663 | ST663 | 4b (IVb) | I | 83 | 2012–2016 | 10 | 4 | 32 | 3 | 4 | 12 | 0 | 6 | 12 |
| CC666 | ST666 | 4b (IVb) | I | 1 | 2012 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| CC688 | ST688 | 4b (IVb) | I | 8 | 2012–2015 | 0 | 6 | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
| CC736 | ST736 | 1/2b (IIb) | I | 4 | 2015 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| CC842 | ST1004 | 1/2a (?)c | II | 6 | 2013–2016 | 1 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 0 |
| ST2138 | 4b (?) | II | 1 | 2012 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | |
| ST2139 | 1/2a [29], 4b [6] (?) | II | 35 | 2011–2016 | 0 | 2 | 15 | 7 | 5 | 5 | 1 | 0 | 0 | |
| ST2140 | 1/2a (?) | II | 2 | 2013, 2016 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | |
| CC1000 | ST1000 | 1/2b (IIb) | I | 1 | 2015 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| CC1800 | ST2136 | 1/2a (IIa) | II | 1 | 2012 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| Singletons | ||||||||||||||
| ST2131 | ST2131 | 4b (IVb) | I | 1 | 2013 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| ST2135 | ST2135 | 4b (?) | II | 1 | 2012 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| ST2137 | ST2137 | 1/2a (?) | II | 4 | 2012–2013 | 0 | 0 | 0 | 2 | 1 | 0 | 1 | 0 | 0 |
| ST2142 | ST2142 | 4a/4c [17], 4 [4], ? [13], 1/2b [1] (?) | II | 35 | 2011–2016 | 1 | 0 | 32 | 0 | 1 | 1 | 0 | 0 | 0 |
| ST2143 | ST2143 | 1/2a (IIa) | II | 1 | 2016 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| ST2144 | ST2144 | 1/2a (IIa) | II | 1 | 2016 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Total no. of: | ||||||||||||||
| Sequenced isolates | 116 | 223 | 281 | 93 | 106 | 304 | 2 | 41 | 82 | |||||
| STs | 20 | 38 | 21 | 23 | 20 | 42 | 2 | 12 | 10 | |||||
| Clones | 19 | 26 | 16 | 20 | 16 | 29 | 2 | 11 | 9 | |||||
| Diversity index | ||||||||||||||
| Shannon’s | 2.35 | 2.70 | 2.11 | 2.46 | 2.26 | 2.62 | 0.18 | 2.12 | 1.82 | |||||
| Simpson’s | 0.87 | 0.87 | 0.82 | 0.86 | 0.84 | 0.85 | 1.00 | 0.85 | 0.80 | |||||
a
The serotype was determined by ELISA to assign the O antigen and serotype 4 strains. PCR was used to assign the H antigen for serotype 1/2 and 3 strains. Values in parentheses are the serogroup determined through cgMLST. Values in brackets are the number of isolates of that serotype. If there are no values in brackets, then all the isolates of the subtype displayed the shown serotype.
b
The 4b-v1 serotype cannot be determined by the ELISA serotyping method, so this grouping was assigned through the serogroup.
c
The serogroup and/or lineage was not clearly discernible.