UKMenCar4: carriage studies, high-resolution genomics, and disease control

Martin Maiden,UKMenCar4 Consortium

Meningococcal structure and characterisation

Jolley, K. A., Brehony, C. & Maiden, M. C. (2007). Molecular typing of meningococci: recommendations for target choice and nomenclature. FEMS Microbiol Rev 31, 89-96.

Component Phenotypic Genotypic

Capsule Serogroup cps region

OMPS Serotype,Subtype, etc.

porA, porB, fetA, etc.

Housekeeping genes

MLEE MLST

Ribosomes MALDITOF 16s rRNA,rMLST

Neisseria meningitidis B: P1.7,16: F3-3: ST-32 (cc32)

Meningococcal disease, England & Wales: the long view

1912 1916 1920 1924 1928 1932 1936 1940 1944 1948 1952 1956 1960 1964 1968 1972 1976 1980 1984 1988 1992 1996 2000 2004 2008 2012 -

5.00

10.00

15.00

20.00

25.00

30.00

35.00

Year

Incid

ence

rate

/100

,000

The Big Questions: (i) Why was there such high

disease incidence mid-1980s – mid-2000s?;

(ii) Why has it reduced?; and, (iii) What is likely to happen next?

Cerebrospinal Fever Meningococcal: infection meningitis & septicaemia

Data: courtesy Mary Ramsay Shamaz Ladhani, Public Health England

Meningococcal disease epidemics England & Wales 1984-2013

Data: Meningococcal Reference Unit, Public Health England

1982-1990StonehouseOutbreakGroup B

1993-1999Group C Outbreaks

2001 -Group BIncidencedeclines

Late 1999Group C Conjugate Meningococcal (MCC) Vaccinesintroduced

Meningitis Research Foundation Meningococcus Genome Library

• Charity funded.• Open access.• All available England

and Wales, Scotland (and Ireland, WT funded) meningococcal isolates.

• Assembled & annotated contiguous sequence data.

http://www.meningitis.org/current-projects/genome

Diversity of disease causing meningococciMRF-MGL isolates 2010-2012

Hill, D.M.C., Lucidarme, J., Gray S.J., Newbold , L.S., Ure, R., Brehony, C., Harrison, O.B., Bray, J.E., Jolley, K.A., Bratcher H.B.,, Parkhill, J., Tang, C.M., Borrow, R., and Maiden, M.C.J. Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study. Lancet Infectious diseases, DOI: http://dx.doi.org/10.1016/S1473-3099(15)00267-4.

• A total of 923 isolates from England, Wales and Northern Ireland.

• 899 from England and Wales:• Scanned at >2000 loci;• 2-313 alleles/locus;• 219 STs, 22 clonal

complexes;• 496 rSTs (ribosomal

sequence types);• Most isolates (78%)

belonged to 6 clonal complexes.

1975 ~ 1985 ~ 1995 ~ 1999 2000 2001 ~ 2005 2006 2007 2008 2009 2010 2011 20120

500

1000

1500

2000

2500

3000

41/44 269 11 32 8 213 23 167 174 22 Other UA NT

Epidemics are dominated by particular meningococci

Hill, D.M.C., Lucidarme, J., Gray S.J., Newbold , L.S., Ure, R., Brehony, C., Harrison, O.B., Bray, J.E., Jolley, K.A., Bratcher H.B.,, Parkhill, J., Tang, C.M., Borrow, R., and Maiden, M.C.J. Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study. Lancet Infectious diseases, DOI: http://dx.doi.org/10.1016/S1473-3099(15)00267-4.

Age association of meningococcal genotypes (MRF-MGL 2010-2012)

<1 1-4 5-9 10-14 15-19 20-24 25-29 30-39 40-49 50-69 >700%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

Minor clonal complexesNDST-174 complexST-461 complexST-162 complexST-22 complexST-23 complex/Cluster A3ST-213 complexST-60 complexST-41/44 complex/Lineage 3ST-269 complexST-32 complex/ET-5 complexST-11 complex/ET-37 complex

Age category

Prop

ortio

n of

case

s

Hill, D.M.C., Lucidarme, J., Gray S.J., Newbold , L.S., Ure, R., Brehony, C., Harrison, O.B., Bray, J.E., Jolley, K.A., Bratcher H.B.,, Parkhill, J., Tang, C.M., Borrow, R., and Maiden, M.C.J. Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study. Lancet Infectious diseases, DOI: http://dx.doi.org/10.1016/S1473-3099(15)00267-4.

<1 1 2 3 4-6 7-910-12

13-15

16-18

19-21

22-24

25-27

28-30

31-33

34-36

37-39

40-43

44-46

47-49

50-52

53-55

56-58

59-61

62-64

65-67

68-70

71-73

74-76

77-79

80-82

83-85

86-88

89-91

92-94

95-97 >9

7 NK0

5

10

15

20

25

2010/112011/12

Patient Age (Years)

Prop

ortio

n of

IMD

Case

s Epi

dem

iolo

gica

l Yea

r (%

)

<1 1-3 4-6 7-9 10-110123456789

Patient Age (Months)Pr

opor

tion

of C

ases

Epi

dem

iolo

gica

l Ye

ar (%

)

Age distribution of isolates in meningococcal genome library

Meningococcal carriage by age

Christensen, H., May, M., Bowen, L., Hickman, M. & Trotter, C. L. (2010). Meningococcal carriage by age: a systematic review and meta-analysis. The Lancet Infectious Diseases 10, 853-861.

100 years of disease and carriage studies

Glover, J. A. (1918). "Spacing out" in the Prevention of Military Epidemics of Cerebro-Spinal Fever. Br Med J 2, 509-512.

Glover, J. A. (1918). Observations on the Meningococcus Carrier-Rate in relation to density of population in Sleeping Quarters. J Hyg (Lond) 17, 367-379.

Glover, J. A. (1918). The Cerebro-Spinal Fever Epidemic of 1917 at X Depot. J Hyg (Lond) 17, 350-365.

Meningococcal disease England & Wales

Data: Meningococcal Reference Unit, Public Health England

Late 1999Group C Conjugate Meningococcal (MCC) Vaccinesintroduced

UK Meningococcal carriage study: UKMenCar1-3, 1999-2001

Ibarz-Pavon, A. B., et al. (2011). Changes in serogroup and genotype prevalence among carried meningococci in the United Kingdom during vaccine implementation. J Infect Dis 204, 1046-1053.Maiden, M. C., et al. (2008). Impact of Meningococcal Serogroup C Conjugate Vaccines on Carriage and Herd Immunity. J Infect Dis 197, 737-743.Maiden, M. C., Stuart, J. M. & Group, U. M. C. (2002). Carriage of serogroup C meningococci 1 year after meningococcal C conjugate polysaccharide vaccination. Lancet 359, 1829-1831.

Glasgow

Stockport

Nottingham Oxford

London

Plymouth

Wales

MRU/SMPRL Phenotype

16,700 X 3

Sequence type siaD/cnl

Questionnaire Risk factors for carriage

2,500 X 3

UKMenCar 1-3: 8,000 carried meningococci, a diverse population

1999 2000 20010

2

4

6

8

10

12

14

16ST-11 complex ST-865 complex ST-8 complexST-254 complex ST-212 complex ST-162 complex ST-92 complex ST-18 complex ST-178 complex ST-1136 complex ST-750 complex ST-41/44 complex ST-167 complex ST-32 complexST-60 complex ST-282 complex ST-364 complex ST-35 complex ST-22 complex ST-198 complex ST-103 complex ST-23 complexST-53 complex ST-1157 complex ST-269 complex ST-1117 complex ST-213 complex ST-461 complex ST-174 complex ST-106 complex ST-116 complex ST-334 complex ST-37 complex ST-376 complex

Year

Prop

ortio

n of

men

ingo

cocc

i (%

)

Ibarz-Pavon, A. B., Maclennan, J., Andrews, N. J., Urwin, R., Gray, S. J., Clarke, S. C., Walker, A. M., Evans, M. R., Kroll, J. S., Neal, K. R., Ala'aldeen, D. A., Crook, D. W., Cann, K., Harrison, S., Cunningham, R., Baxter, D., Kaczmarski, E., Cameron, J. C. & Stuart, J. M., & Maiden, M. C. (In press). Changes in serogroup and genotype prevalence among carried meningococci in the United Kingdom during vaccine implementation. J Infect Dis.

UKMenCar1-3: major disease associated lineages

1999 2000 20010

2

4

6

8

10

12

14

16

ST-11 complex ST-8 complex ST-41/44 complex

ST-32 complex ST-269 complex

Year

Prop

ortio

n of

men

ingo

cocc

i (%

) Clonal complex

1998/9n

1998/9%

2000/1n

2000/1%

ST-11 complex

553 32.8 264 20.5

ST-41/44 complex

423 25.1 373 28.9

ST-269 complex

253 15.0 275 21.3

ST-32 complex

99 5.9 79 6.1

ST-8 complex

84 5.0 15 1.2

a) Carried meningococcal clonal complexes b) Clonal complexes isolated from disease

Maiden, M. C., Ibarz-Pavon, A. B., Urwin, R., Gray, S. J., Andrews, N. J., Clarke, S. C., Walker, A. M., Evans, M. R., Kroll, J. S., Neal, K. R., Ala'aldeen, D. A., Crook, D. W., Cann, K., Harrison, S., Cunningham, R., Baxter, D., Kaczmarski, E., Maclennan, J., Cameron, J. C. & Stuart, J. M. (2008). Impact of Meningococcal Serogroup C Conjugate Vaccines on Carriage and Herd Immunity. J Infect Dis 197, 737-743.

UKMenCar 1-3: Carriage of ST-11 genogroup C isolates

1999 2000 20010

0.05

0.1

0.15

0.2

0.25

0.3

0.35

NGC

Year

% C

arria

ge

Maiden, M. C., et al. (2008). Impact of Meningococcal Serogroup C Conjugate Vaccines on Carriage and Herd Immunity. J Infect Dis 197, 737-743.

Clonal complex, disease, and serogroup England and Wales, 1999

Clonal complex Disease association OR B C W-135 Y

ST-8 14.7 [6.8 - 31.9] 11 69 0 0

ST-11 28.7 [20.1 - 41.1] 7 525 1 0

ST-22 0.23 [0.17 - 0.32] 5 0 42 1

ST-23 0.14 [0.07 - 0.28] 0 1 0 9

ST-32 2.1 [1.5 - 3.0] 80 1 0 0

ST-35 0.29 [0.16 - 0.53] 13 0 0 0

ST-41/44 1.8 [1.5 - 2.1] 390 7 0 0

ST-213 0.4 [0.28 - 0.57] 39 1 0 0

ST-269 4.4 [3.4 - 5.8] 214 7 0 0

Unassigned 0.28 [0.24 - 0.34] 140 32 2 9

Data: Ure R., Gray S., McCarthy N.D., Pavon A.B., and Maiden, M.C. Unpublished.

Risk factors for carriage

Smoking Kissing

Y Y

Y N

N Y

N N

MacLennan, J., Kafatos, G., Neal, K., Andrews, N., Cameron, J. C., Roberts, R., Evans, M. R., Cann, K., Baxter, D. N., Maiden, M. C. & Stuart, J. M. (2006). Social behavior and meningococcal carriage in British teenagers. Emerg Infect Dis 12, 950-957.

The long-term impact of herd immunity

Trotter, C. L. & Maiden, M. C. (2009). Meningococcal vaccines and herd immunity: lessons learned from serogroup C conjugate vaccination programs. Expert Review Vaccines 8, 851-861.

Meningococcal disease England & Wales

Data: Meningococcal Reference Unit, Public Health England

1982-1990StonehouseOutbreakGroup B

1993-1999Group C Outbreaks

2001 -Group BIncidenceDeclines

Late 1999Group C Conjugate Meningococcal (MCC) Vaccineintroduced

UKMenCar4: Initial aims1) Compare the genotypes of

meningococcal disease and carriage isolates in high and low incidence settings (UK 1999 and UK 2014).

2) Investigate the risk factors for meningococcal carriage and in particular the effect of changes in social behaviour with respect to smoking, kissing, and socialising.

Incidence Carriage Disease

High (1999) ✔ ✔

Low (2014) ✔ ✔

UK Meningococcal carriage study, UKMenCar4: 2014-5

Glasgow

Stockport Manchester

Oxford

London

Plymouth

Cardiff

Maidstone Bristol

WiganPreston

• Multi-centre cross-sectional survey of meningococcal carriage

• 18,000 UK teenagers• Compared to UKmenCAR1-3:

– Similar study sites;– Same age group;– Sampling in schools/colleges;– Similar time of year (but

extended from autumn to spring);

– Similar microbiological methods;

– Same key risk factors.

Sampling

Tributyrin Test * Positive reaction: yellow/yellow orange * Negative reaction: red

Results: Moraxella catarrhalis (+) Neisseria spp. (-)

Microbiology testing

Genome sequencing of Neisseria meningitidis isolates

|||||||||||OX40001 |||||||||||

OX40001

|||||||||||OX40001

Sequence read processing

Visualization

Analysis of study data

These are just some of the types of analyses possible …

Cluster 1

Cluster 2

Cluster 3

Genome analysis of disease and carriage isolates from Chad

Reference genome: 2070 genes from ST5 WUE2594 [Schoen, C. et al., 2011]

Genome comparator output: 1542 genes identical in all genomes (1347

share same allele as ref/196 have a different allele);

66 genes missing in all 23 genomes; 221 incomplete genes were excluded; 242 variable genes.

Diallo K, Trotter C, Borrow R, Stuart JM, Greenwood BM, Maiden MCJ, & MenAfriCar consortium. Unpublished.

UKMenCar4 totals by centreCentre Recruitment

targetFinal total

Glasgow 2600 2632

Bristol 2600 1814

London 2600 1933

Oxford 2600 2141

Stockport 2600 2438

Cardiff 2600 3130

Plymouth 1500 2252

Maidstone 1000 1022

Preston 1000 1016

Central Manchester & Wigan

1000 3497

Total 20,100 21,874

UKMenCar4: Meningococcal carriage rates

1999-2000 2000-2001 2001-2002 2014-2015Carriage of Neisseria meningitidis * Putative

meningococciStockport 25.4 % 24.9 % 24.4 % 11.7 %Cardiff 14.4 % 17.6 % 16.7 % 8.6 %Glasgow 11.7 % 16.2 % 17.5 % 7.1 %Oxford 25.2 % 22.6 % 20.3 % 9.3 %Plymouth 8.2 % 15.4 % 19.9 % 5.9 %Bristol N/A N/A N/A 8.4 %North Thames 9.1 % 12.5 % 14.4 % N/ABangor 20.9 % 19.2 % 22.9 % N/ANottingham 19.9 % 19.8 % 16.0 % N/A

Shisha smokingSmoking ban 2006/7

Changes since UKMencar1-3: smoking

Meningococcal disease England & Wales

Data: Meningococcal Reference Unit, Public Health England

1982-1990StonehouseOutbreakGroup B

1993-1999Group C Outbreaks

2001 -Group BIncidencedeclines

Late 1999Group C Conjugate Meningococcal (MCC) Vaccineintroduced

WhatNext?

MRF Genome Library Era:England and Wales 2010-2015

07/2010-06/2011

07/2011-06/2012

07/2012-06/2013

07/2013-06/2014

07/2014-06/2015

0

50

100

150

200

250

300

350

400

450

BCWY

http://www.meningitis.org/current-projects/genome

Lineage 11 (cc11) Group W: UK epidemiology

Current UK

UK Hajj

UK1996 (n=3)1997 (n=2)1998 (n=2)

UK1975 (n=6)1987 (n=1)1989 (n=1)1990 (n=1)

UK1996 (n=2)1998 (n=1)

Argentina 2008-2012

Brazil 2008-2011

Current South Africa

Lucidarme, J., Hill, D. M., Bratcher, H. B., Gray, S. J., du Plessis, M., Tsang, R. S., Vazquez, J. A., Taha, M. K., Ceyhan, M., Efron, A. M., Gorla, M. C., Findlow, J., Jolley, K. A., Maiden, M. C. & Borrow, R. (2015). Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage. J Infect In the press.

2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012

0

10

20

30

40

50

60

70

80

90

N. meningitidis cases per year among inpatients in Bamako, Mali (2002-2012)

Group A meningococcal cases

Group W135 meningococcal cases

Year

Num

ber o

f Cas

es

Nm W England and Wales

2015 vaccine introductions

UKMenCar5: Evaluation of changes in the UK national meningococcal immunisation programme

UKMenCar4 provides the pre-vaccination baseline for circulating meningococci and will allow full evaluation of the impact of ACWY vaccine on meningococcal populations.

2014 2015 2016 2017 2018

UKMenCar4 ACWY vaccination UKMenCar5 with catch up

UKMenCar4 Team