TABLE 2.
Core-genome multilocus sequence type groups containing more than two isolates
| cgMLST typea | No. (%) of isolates in CTb | Region(s)c | Yrs | Pulstotyped | No. of allele differences (maximum and minumum)e |
||
|---|---|---|---|---|---|---|---|
| cgMLST | wgMLST | SNP | |||||
| L1-SL2-ST2-CT5919 | 3f (0.7) | B, D, K | 2000, 2004, 2005 | Asc0030:Apa0025 | 0–2 | 7–10 | 9–10 |
| L1-SL1-ST1-CT2373 | 3 (0.7) | D, K, S | 2007, 2010 | Asc0058:Apa0005 | 0–2 | 0–2 | 0–2 |
| L1-SL224-ST224-CT3426 | 7 (1.6) | A, B, C, D, E, F, M | 2012, 2013, 2014, 2015, 2016 | Asc0060:Apa0124a, Asc0021:Apa0023, Asc0119:Apa0104, NT | 0–2 | 0–4 | 0–5 |
| L2-SL155-ST155-CT4612 | 8 (1.7) | E, F, G, L, K, M, N, S | 2000, 2003, 2004, 2006, 2007, 2013 | Asc0037:Apa0044 | 0–4 | 0–12 | 0–16 |
| L1-SL315-ST194-CT5908 | 5 (1.1) | S | 2008, 2009 | Asc00018:Apa006 | 0–6 | 1–8 | 1–10 |
| L2-SL8-ST120-CT786f | 23 (5.1) | A, B, C, D, F, K, L, M, O, Q, R, S | 1999, 2000, 2001, 2003, 2004, 2006, 2004, 2010, 2011, 2016, 2017, 2018 | Asc0011:Apa0002, Asc0069:Apa0002, Asc0002:Apa0002, Asc0028:Apa0002, Asc0023:Apa0002 | 0–9 | 0–14 | 0–15 |
| L1-SL1-ST1-CT4553 | 4 (0.9) | D, T | 2008, 2010, 2012, 2015 | Asc0045:Apa0013 | 1–4 | 5–12 | 5–7 |
| L1-SL1-ST1-CT4576 | 8 (1.7) | C, D, K, Q | 2003, 2005, 2009, 2011, 2014, 2016 | Asc0003:Apa0063, Asc0003:Apa0063a | 1–7 | 2–15 | 2–19 |
| L1-SL2-ST2-CT5935 | 5 (1.1) | B, C, G, K, Q, S | 1999, 2000, 2002, 2004, 2005, 2009 | Asc0023:Apa0065, Asc0023:Apa0071, Asc0063:Apa0012 | 1–7 | 7–15 | 8–15 |
| L1-SL4-ST4-CT5890 | 5 (1.1) | A, B | 2000, 2006, 2007 | Asc0021a:Apa0023 | 1–8 | 3–20 | 2–21 |
| L1-SL315-ST194-CT4541 | 6 (1.3) | B, C, D, E | 2001, 2002, 2003, 2006, 2012, 2016 | Asc0072:Apa0028 | 2–7 | 2–15 | 2–15 |
| L1-SL4-ST4-CT187 | 24 (5.3) | A, B, C, D, E, J, K, L, M, N, O, P, Q, S, NS | 1999, 2000, 2002, 2003, 2005, 2006 | Asc00021:Apa0023, Asc0021a:Apa0023, Asc0037:Apa0044, NT | 2–9 | 3–17 | 3–22 |
| L2-SL321-ST321-CT691 | 6 (1.3) | C, D, F, G, K, O | 2005, 2008, 2010, 2011, 2018, | Asc0128:Apa0001, Asc0031:Apa0001, Asc0001:Apa0001, Asc0074:Apa0001 | 3–7 | 8–17 | 8–16 |
| L2-SL155-ST155-CT852 | 6 (1.3) | B, D, K, F | 2006, 2009, 2012, 2017 | Asc0037:Apa0044, NT | 3–10 | 4–29 | 6–80 |
| L2-SL18-ST18-CT2990 | 3 (0.7) | A, S | 2003, 2014, 2018 | Asc0047:Apa0117, NT | 4–7 | 12–18 | 13–23 |
| L1-SL1-ST1-CT4574 | 10 (2.2) | B, C, D, L, M, Q | 2008, 2009, 2013, 2014, 2015, 2018 | Asc0088:Apa0126, Asc0081:Apa0063, Asc0068:Apa0064, NT | 4–7 | 9–11 | 6–20 |
| L2-SL9-ST9-CT4539 | 3 (0.7) | L, S | 2014, 2016, 2018 | Asc0046:Apa0058, NT | 5 | 11–15 | 11–14 |
| L1-SL1-ST1-CT4562 | 3 (0.7) | B, E, Q | 1999, 2004, 2011 | Asc0010:Apa0008 | 5 | 9–12 | 13–17 |
| L1-SL1-ST1-CT2810 | 4 (0.9) | B, C, L, N | 1999, 2003, 2005, 2015, | Asc0083:Apa0013, Asc0067:Apa0021, NT | 5–7 | 11–27 | 11–103 |
| L2-SL7-ST7-CT3420 | 3 (0.7) | E | 2005, 2012, 2015 | Asc0043:Apa0026, Asc0043a:Apa0026 | 5–7 | 13–19 | 16–24 |
| L1-SL324-ST324-CT4618 | 5 (1.1) | C, D, E | 2008, 2011, 2012 2015 | Asc0161:Apa0019, Asc0161a, Apa0119, Asc0161:Apa0132 | 6–11 | 12–21 | 12–27 |
| L2-SL20-ST424-CT2456 | 3 (0.7) | E, F | 2012, 2016, 2018 | Asc0094:Apa0104, Asc0119:Apa0104, NT | 9–11 | 27–36 | ND |
| L2-SL14-ST14-CT956 | 10 (2.2) | B, C, E, F, N, Q, R, | 2002, 2005, 2007, 2010, 2011, 2014, 2015, 2017, 2018, | Asc0059:Apa0046a, Asc0005:Apa0046a, Asc0038:Apa0046 | 10–12 | 11–38 | ND |
The lineage (L)-sublineage (SL)-multilocus sequence type (ST)-core genome multilocus sequence types (CTs) were inferred from WGS data and defined by using international nomenclature (13).
Percentage of isolates within the cgMLST type from total number of isolates in study (n = 453).
Regions within New Zealand that have been anonymized. NS, no region stated for the case.
Pulsotype assigned as a part of the PulseNet Aotearoa/New Zealand database; NT, not tested.
Minimum and maximum allele differences observed for isolates within a cgMLST type using cgMLST and whole-genome MLST; single-nucleotide polymorphism (SNP) analysis was performed for cgMLST groups that had fewer than 7 core genome MLSTs.
Single case from CT5919 included in an outbreak that also involved three cases identified within L2-SL8-ST120-CT786.