Table 1.
Genomic characteristics of the different STs, including SCCmec and spa-type, presence of PVL, genome length, N50 (shortest sequence length at 50% of the genome), and number of contigs, coding DNA sequences (CDS), and genes
| ST | CC | # isolates (MRSA) | Predominant SCCmec type (# isolates) | Predominant spa-type (# isolates) | # PVL+ | Avg. genome length (bp) | Avg. # contigs | Avg. N50 | Avg. # CDS | Avg. # genes |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1 | 12 (12) | IV (11) | t127 (3) | 0 | 2,814,074.3 | 29.4 | 326,193.0 | 2601.3 | 2666.8 |
| 772 | 2 (2) | V (2) | t657 (2) | 2 | 2,768,135.0 | 46.0 | 208,282.5 | 2538.0 | 2605.0 | |
| 5 | 5 | 14 (13) | IV (10) | t002 (5) | 8 | 2,785,946.1 | 39.4 | 250,660.3 | 2580.1 | 2640.5 |
| 228 | 16 (16) | I (16) | t001 (5) | 0 | 2,837,918.4 | 81.9 | 87,688.4 | 2639.8 | 2700.7 | |
| 228 | 6 | 1 (1) | IV (1) | t5238 (1) | 0 | 2,796,820.0 | 40.0 | 150,271.0 | 2584.0 | 2648.0 |
| 7 | 7 | 3 (0) | n.a. | t1743 (1) | 0 | 2,747,478.7 | 66.0 | 147,717.0 | 2521.3 | 2588.0 |
| 8 | 8 | 11 (6) | IV (6) | t008 (6) | 5 | 2,821,267.1 | 52.7 | 259,331.5 | 2625.2 | 2681.8 |
| 293 | 2 (2) | V (1) | t037 (1) | 0 | 2,900,431.5 | 90.5 | 90,036.5 | 2697.5 | 2762.0 | |
| 241 | 1 (1) | n.d. | t030 (1) | 0 | 2,884,707.0 | 87.0 | 105,325.0 | 2707.0 | 2768.0 | |
| 247 | 1 (1) | I (1) | t197 (1) | 0 | 2,776,359.0 | 76.0 | 74,230.0 | 2567.0 | 2630.0 | |
| 10 | 10 | 1 (0) | n.a. | n.a. | 0 | 2,799,287.0 | 110.0 | 52,819.0 | 2634.0 | 2698.0 |
| 1162 | 2 (0) | n.a. | n.a. | 0 | 2,867,105.0 | 58.0 | 184,821.5 | 2702.0 | 2767.0 | |
| 15 | 15 | 5 (2) | IV (1); I (1) | t084 (1); t853 (1) | 1 | 2,719,481.8 | 45.6 | 226,394.0 | 2496.2 | 2556.6 |
| 22 | 22 | 15 (14) | IV (13) | t852 (1); t1977 (7); t223 (1); t005 (1) | 3 | 2,793,443.3 | 56.0 | 124,918.3 | 2599.5 | 2662.4 |
| 1327 | 1 (1) | IV (1) | n.a. | 0 | 2,758,892.0 | 42.0 | 167,290.0 | 2547.0 | 2612.0 | |
| 25 | 25 | 2 (0) | n.a. | t258 (1); t2242 (1) | 0 | 2,758,786.5 | 16.5 | 697,459.0 | 2554.5 | 2617.5 |
| 30 | 30 | 7 (3) | IV (3) | t019 (2) | 5 | 2,792,108.9 | 58.1 | 139,913.6 | 2603.3 | 2666.1 |
| 34 | 2 (0) | n.a. | t3905 (1) | 0 | 2,821,562.0 | 57.5 | 140,057.0 | 2665.5 | 2730.5 | |
| 45 | 45 | 8 (2) | IV (2) | t015 (2) | 0 | 2,762,203.4 | 34.4 | 390,455.1 | 2591.5 | 2654.6 |
| 59 | 59 | 3 (3) | IV (1) | t216 (1); t437 (1) | 1 | 2,799,567.0 | 53.0 | 130,817.3 | 2595.7 | 2662.0 |
| 88 | 88 | 1 (1) | IV (1) | t4701 (1) | 0 | 2,791,324.0 | 36.0 | 206,283.0 | 2575.0 | 2642.0 |
| 96 | 96 | 1 (0) | n.a. | n.a. | 1 | 2,783,146.0 | 39.0 | 141,877.0 | 2591.0 | 2652.0 |
| 97 | 97 | 2 (2) | IV (2) | t359 (1) | 0 | 2,756,222.0 | 27.0 | 401,302.0 | 2570.0 | 2635.5 |
| 121 | 121 | 12 (0) | n.a. | t3274 (1); t314 (1); t2530 (1) | 9 | 2,814,764.5 | 48.0 | 146,041.3 | 2631.3 | 2694.3 |
| 152 | 152 | 3 (2) | V (2) | t355 (1) | 2 | 2,753,826.7 | 31.0 | 267,208.7 | 2551.0 | 2608.0 |
| 395 | 395 | 1 (0) | n.a. | n.a. | 0 | 2,759,659.0 | 22.0 | 574,657.0 | 2574.0 | 2640.0 |
| 398 | 398 | 2 (1) | V (1) | t011 (1) | 0 | 27,540,120.0 | 57.5 | 20,645,930 | 2524.0 | 2589.5 |
| 942 | 942 | 1 (0) | n.a. | n.a. | 0 | 2,813,978.0 | 82.0 | 61,174.0 | 2654.0 | 2718.0 |
| – | n.a. | 3 (1) | IV (1) | n.a. | 0 | 2,739,763.7 | 46.0 | 157,754.0 | 2535.0 | 2599.3 |
The combination of the four methods (MLST, SCCmec-, and spa-typing, and PVL presence) yielded 80 different lineages. Three isolates were not assigned to any specific ST and are reported in the last row of the table