Maternal pneumococcal nasopharyngeal carriage and risk factors for neonatal carriage after the introduction of pneumococcal conjugate vaccines in The Gambia

Accepted Manuscript Maternal pneumococcal nasopharyngeal carriage and risk factors for neonatal carriage following the introduction of Pneumococcal Conjugate Vaccines in The Gambia Effua Usuf, Abdoulie Bojang, Bully Camara, Isatou Jagne, Claire Oluwalana, Christian Bottomley, Umberto D’Alessandro, Anna Roca PII:

S1198-743X(17)30402-0

DOI:

10.1016/j.cmi.2017.07.018

Reference:

CMI 1017

To appear in:

Clinical Microbiology and Infection

Received Date: 20 March 2017 Revised Date:

15 July 2017

Accepted Date: 19 July 2017

Please cite this article as: Usuf E, Bojang A, Camara B, Jagne I, Oluwalana C, Bottomley C, D’Alessandro U, Roca A, Maternal pneumococcal nasopharyngeal carriage and risk factors for neonatal carriage following the introduction of Pneumococcal Conjugate Vaccines in The Gambia, Clinical Microbiology and Infection (2017), doi: 10.1016/j.cmi.2017.07.018. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

ACCEPTED MANUSCRIPT Title: Maternal pneumococcal nasopharyngeal carriage and risk factors for neonatal carriage following the introduction of Pneumococcal Conjugate Vaccines in The Gambia

Running title: Maternal and neonatal pneumococcal nasopharyngeal carriage

Bottomley 2, Umberto D’Alessandro 1,2,3 , Anna Roca 1,4

Affiliations 1

Medical Research Council Unit The Gambia

2

RI PT

Authors: Effua Usuf 1,2*, Abdoulie Bojang1, Bully Camara1, Isatou Jagne1, Claire Oluwalana1, Christian

United Kingdom

SC

Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London,

Institute of Tropical Medicine, Antwerp, Belgium

4

Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine,

M AN U

3

London, United Kingdom

*Corresponding author

MRC Unit The Gambia P O Box 273 Banjul

[email protected]

EP

The Gambia

TE D

Effua Usuf

AC C

+ 220 4495442 ext 5014

ACCEPTED MANUSCRIPT 1

Title: Maternal pneumococcal nasopharyngeal carriage and risk factors for neonatal carriage

2

following the introduction of Pneumococcal Conjugate Vaccines in The Gambia

3 Abstract

5

Objectives

6

Pneumococcal nasopharyngeal carriage occurs early in life. However, the role of vertical

7

transmission is not well understood. The aims of the study are to describe carriage among mothers

8

and their newborns, and assess for risk factors for neonatal carriage.

SC

9

RI PT

4

Methods

11

In a nested retrospective cohort study, we analysed data from the control arm of a randomized

12

control trial conducted in The Gambia two to three years after PCV13 introduction. Nasopharyngeal

13

swabs were collected from 374 women and their newborns on the day of delivery, and 3, 6, 14 and

14

28 days later. Pneumococci were isolated and serotyped using conventional microbiological

15

methods.

16

TE D

M AN U

10

Results

18

Carriage increased from 0.3% (1/373) at birth to 37.2% (139/374) at day 28 (p<0.001) among

19

neonates and from 17.1% (64/374) to 24.3% (91/374) [p=0.015] among women. In both groups,

20

PCV13 VT serotypes accounted for approximately one third of the pneumococcal isolates, with

21

serotype 19A being the most common VT. Maternal carriage [adjusted OR=2.82 (95% CI 1.77-4.80)],

22

living with other children in the household [adjusted OR=4.06 (95% CI 1.90-8.86)] and dry season

23

[OR=1.98 (95% CI 1.15-3.43)] were risk factors for neonatal carriage. Over half (62.6%) of the

24

neonatal carriage was attributable to living with other children in the same household.

AC C

EP

17

25 26

Conclusions

ACCEPTED MANUSCRIPT 27

Three years after the introduction of PCV in The Gambia, newborns are still rapidly colonised with

28

pneumococcus, including PCV13 VT. Current strategies for pneumococcal control in Africa do not

29

protect this age group beyond the herd effect.

30

RI PT

31 Introduction

33

Streptococcus pneumoniae is a leading cause of morbidity and mortality in children under 2 years of

34

age (1, 2). Generally, invasive pneumococcal disease (IPD) peaks in the second year of life in

35

developed countries and in the first year of life in sub-Saharan Africa [SSA] (3, 4). Nevertheless, a

36

substantial burden of neonatal IPD has been reported across different regions worldwide although

37

data are lacking in the least developed countries (5-10). In a recent systematic review, the global

38

pooled neonatal IPD was estimated at 36/100 000 live births [95% CI: 20.0–64.7/100 000] (5). From

39

one study in the Gambia it was estimated as 369.5/100,000 (95% CI: 119.2–1138.5/100,000) (3, 5).

M AN U

SC

32

TE D

40

Pneumococcal conjugate vaccines (PCVs) are effective against IPD and nasopharyngeal carriage of

42

vaccine serotypes (VT). The latter is important because carriage is a preliminary step towards disease

43

and a measure of community transmission. The introduction of PCV has been shown to reduce

44

acquisition of VT nasopharyngeal carriage among both vaccinated (11) and unvaccinated individuals

45

(12). However it has also been shown to increase non vaccine type (NVT) carriage such that the

46

overall carriage prevalence remains similar (11).

AC C

47

EP

41

48

Since 2009, three formulations of PCV targeting pneumococcal serotypes most commonly associated

49

with IPD worldwide have been introduced into routine vaccination in SSA. First PCV7, then PCV10

50

and PCV13. Although two randomized trials in Kenya and Papua New Guinea showed that PCVs are

51

immunogenic and well tolerated when given at birth (13, 14), WHO recommends vaccination with

52

PCVs from 6 weeks of age (15). This means newborns until 6 weeks of age are only protected 2

ACCEPTED MANUSCRIPT 53

through indirect effects [i.e. maternal antibodies and herd effect] (16-18). New strategies are

54

required to reduce early infection and to minimize its long-term effects such as growth impairments

55

and neurological sequelae (19-21).

56 Risk factors for pneumococcal nasopharyngeal carriage are well known for African children (22-25)

58

but not for newborns. This study describes the prevalence of pneumococcal carriage among women

59

and their newborns in The Gambia and assesses risk factors for neonatal carriage after the

60

implementation of PCV through the Expanded Program on Immunisation.

SC

RI PT

57

61 Materials and Methods

63

Study site. The study was conducted at the Jammeh Foundation for Peace, a public health facility in

64

Western Gambia. PCV7 was introduced in The Gambia in August 2009 and replaced by PCV13 in May

65

2011. Coverage of two or more doses of PCV13 before 12 months of age was 94% among rural

66

Gambian children born in the second half of 2013 (26).

TE D

67

M AN U

62

Study design. This was a retrospective nested cohort study. The study cohort was mother-newborn

69

pairs included in the placebo arm of a phase-III, double-blind, placebo-controlled, randomized trial in

70

which women in labour were randomized to receive a single dose of 2g of oral azithromycin or

71

placebo (292.7mg Pregelatinized starch, 881.8mg Dibassic Calcium Phospate and 11.5mg

72

Magnesium stearate coated with 18mg Opadry). Study women, 18-45 years of age were recruited

73

between April 2013 and April 2014 when attending prenatal clinic.

AC C

74

EP

68

75

Nasopharyngeal swabs (NPS) were collected from mothers and their newborns during the 28 days of

76

active follow-up. An NPS was collected from women in labour and from newborns within six hours of

77

birth. Additional maternal and newborn NPS were collected at days 3, 6, 14 and 28 during household

3

ACCEPTED MANUSCRIPT 78

visits conducted by study nurses and field workers. Sample collection was discontinued if

79

participants received antibiotics as part of standard care.

80 Epidemiological data including demographic and other risk factor data were collected by trained

82

field staff using questionnaires.

RI PT

81

83

Sample collection. All NPS were collected in accordance with the WHO protocol for detecting S.

85

pneumoniae in the upper respiratory tract (27) and as described previously (28).

SC

84

86

Bacterial Isolation. Stored NPS were plated on appropriate agar for selective isolation of S.

88

pneumoniae and S. aureus (28). All pneumococcal isolates were serotyped using latex agglutination

89

test [Statens Serum Institute, Denmark](29).

90

M AN U

87

Data management and statistical analysis

92

All data were double entered into Openclinica and analysed using Stata 14. The analysis was

93

restricted to mothers and newborns in the placebo arm of the trial that were not missing day 28

94

carriage data.

EP

95

TE D

91

The prevalence of PCV13 VT carriage (i.e. carriage of serotype 1, 3, 4, 5, 6A, 6B 7F, 9V, 14, 18C, 19A,

97

19F or 23F) and NVT carriage was calculated for 0, 3, 6 and 14 days after birth where the latter

98

included non-typeable isolates. We estimated the proportion of concordant pairs defined as the

99

proportion of mother-newborn carrier pairs where both mother and newborn carried the same

100

serotype, either concurrently or at different times, during the neonatal period. The association

101

between maternal carriage—defined as carriage at any time during the neonatal period—and

102

neonatal carriage at day 28 was investigated using logistic regression. The following potential

AC C

96

4

ACCEPTED MANUSCRIPT 103

confounders were selected a priori for inclusion in the model (30): birth weight, other children in the

104

household, mother’s age, mother’s education and season.

105 The association between other children living in the household and neonatal carriage at day 28 was

107

also investigated. The potential confounders listed above were included in this second model, except

108

“other children in the household” since this variable was already included as the exposure of

109

interest. The model did not include maternal carriage as this may be on the causal pathway.

RI PT

106

SC

110

A similar analysis was conducted for the association between maternal carriage at day 14 and

112

acquisition of carriage in the newborn between day 6 and day 14—i.e., carriage of any serotype at

113

day 14 among non-carriers at day 6, and for the association between neonatal carriage at day 14 and

114

acquisition of carriage in the mother over the same period.

M AN U

111

115

The percentage of neonatal carriage attributable to each risk factor—i.e. maternal carriage and living

117

with other children, the population attributable fraction (PAF)—was calculated using the “punaf”

118

command in Stata (31).

EP

119

TE D

116

Ethical approval

121

The trial was approved by the joint MRCG-Gambia Government Ethics Committee (ClinicalTrials.gov

122

Identifier -NCT01800942).

123

AC C

120

124

Results

125

Characteristics of the mothers and their newborns

126

There were 417 mother-newborn pairs in the placebo arm of the trial and 374 (89.7%) were included

127

in the analysis. As there were four sets of twins, only 370 women were sampled. The median age of

128

the mothers was 26 years (IQR 22-30). Approximately half of the women had less than one year of 5

ACCEPTED MANUSCRIPT 129

any schooling 184/359 (51.2%) Forty-seven percent (173/367), of newborns were females, the

130

median birth weight was 3.1kg (IQR 2.9-3.4) and 22/373 (5.9%) were low birth weight (< 2.5kg). All

131

the newborns were breastfed and only seven were not exclusively breastfed.

132 Maternal and newborn pneumococcal nasopharyngeal carriage

134

Among the mothers, carriage increased from 17.1% to 24.3% (p=0.015) between days 0 and 28 and

135

among newborns it increased from 0.3% to 37.2% (p< 0.001) [Figure 1]. PCV13 VT represented

136

approximately one third (28.2%) of all pneumococci isolates; 27.1% (99/366) for mothers and 29.9%

137

(70/234) for newborns [Figure 2]. Serotype 19A was the most common serotype among newborns

138

and the second most common among mothers. Non-typeable pneumococci were also common,

139

among mothers 36/366 (9.8%) and among newborns 14/234 (6.0%). Only five mothers and seven

140

newborns carried multiple serotypes during the study period.

M AN U

SC

RI PT

133

141

In 76 (20.3%) of the mother-newborn pairs, the mother was a carrier but the newborn was not and

143

in 56 pairs (15.0%) the newborn was a carrier but the mother was not. Among the 97 (25.9%) pairs

144

where both the mother and newborn were carriers, 47(48.5%; 95%CI 38.2-58.9%) were concordant

145

(i.e. carried the same serotype). Of these 31.9% (15/47) pairs were concordant with VT; 19F was the

146

most common 8.5% (4/47). There were four concordant cases among those who do not have other

147

children in the household; serotype/group 9N, 19F, 21 and 47 [Figure 2].

EP

AC C

148

TE D

142

149

Risk factors for pneumococcal nasopharyngeal carriage in newborns

150

In the univariable analysis, the prevalence of carriage at day 28 was higher in newborns born during

151

the dry season (OR=1.84 95%CI 1.13-2.99), those whose mothers were carriers (OR=2.63 95%CI 1.71-

152

4.05), those living with other children (OR= 4.62 95%CI 2.28-9.36) and those with normal birth

153

weight (OR= 4.00 95% CI 1.16-13.79) [Table 1].

154 6

ACCEPTED MANUSCRIPT Maternal carriage remained a risk factor for neonatal carriage after adjusting for birth weight, other

156

children in household, mother’s age, mother’s education, and season [adjusted OR=2.69 (95% CI

157

1.68-4.30) p<0.001). Living with other children in the household after adjusting for birth weight,

158

mother’s age, mother’s education, and season was also a risk factor for neonatal carriage at day 28

159

(adjusted OR=3.40 95% CI 1.55-7.50, p=0.002). The fraction of neonatal carriage at day 28 attributed

160

to maternal carriage was 10.6% (95% CI; 2.5%-18.0%) and the fraction attributable to living with

161

other children in the household was 62.6% (95% CI; 35.4%- 78.4%).

SC

162

RI PT

155

Mothers who were not carriers at day 6 had a higher carriage at day 14 if their baby was a carrier at

164

day 14, although this was not statistically significant [adjusted OR 1.54 (95% CI 0.75-3.18) p=0.326].

165

Newborns who were non carriers at day 6 had a higher risk of being a carrier at day 14 if their

166

mother was a carrier at day 14 [adjusted OR1.88 (95% CI 1.01-3.48) p=0.045].

M AN U

163

167 Discussion

169

The prevalence of pneumococcal nasopharyngeal carriage among Gambian women and their

170

newborns during the four weeks following delivery was high. Although the study was conducted two

171

to three years after routine PCV13 introduction (and four to five years after PCV7 introduction), one

172

third of the serotypes identified were PCV13 VT. Both maternal carriage and living with other

173

children in the household were risk factors for neonatal carriage, with the latter accounting for

174

almost two -thirds of neonatal carriage.

EP

AC C

175

TE D

168

176

The prevalence of neonatal colonization (37.2%) was lower than in two previous studies conducted

177

before PCV introduction in The Gambia. In both these studies the prevalence was more than 50% by

178

the age of four weeks (17, 32). One difference between these previous studies and ours is that the

179

former were conducted in rural areas where most deliveries occurred at home, while the latter was

180

conducted in a peri-urban health facility. 7

ACCEPTED MANUSCRIPT 181 A striking finding in our study was the sharp increase in carriage in both mothers and newborns

183

between day 6 and 14 (carriage in newborns continued to increase up to day 28). In The Gambia,

184

newborns are given their name at day 7 after birth in a naming ceremony, and this is usually

185

preceded by cooking and movement of people around the compound. This may increase

186

pneumococcal transmission during this period as people visit the mother and newborn. In line with

187

our results, a previous longitudinal study in rural Gambia showed that maternal carriage doubled

188

within the first two months after delivery and remained high until the end of 1 year when follow up

189

ended (33).

SC

RI PT

182

M AN U

190

In our study, a third of the isolates were PCV13 VT, a lower proportion than that observed in a pre-

192

PCV study conducted in rural Gambia where 50% of isolates were PCV13 VT. Serotype 19A, included

193

in PCV13 but not in PCV7, was one of the most common VT serotypes, representing approximately

194

9% of pneumococcal carriage. By comparison, in the United States, serotype 19A significantly

195

decreased after PCV13 introduction although it still contributed up to 5% of the total S. pneumoniae

196

carriage 5 years later (34). In South Africa, prevalence of serotype 19A in children was 2.7% two

197

years after the introduction of PCV13 (35).

EP

198

TE D

191

The prevalence of PCV13 VT among mothers in our study was 8.8% and among newborns 11.8%.

200

These estimates are consistent with the predictions of a mathematical model of carriage in The

201

Gambia, which predicted that PCV13 VT carriage would decline to 7% three years post PCV13 (36).

202

Although it appears that VT have decreased, Gambian newborn babies are still unprotected against

203

VT during a period when they are at high risk of infection since the first dose in the EPI schedule is

204

given at 8 weeks of age in the national EPI.

AC C

199

205

8

ACCEPTED MANUSCRIPT 206

Between 6-10% of isolates were non-typeables similar to earlier studies conducted following PCV

207

(18, 37), but different from the pre-vaccine estimates in the Gambia which were about 2% (38). An

208

increase in non-typeables following PCV has been related to serotypeable isolates that do not

209

express their capsule (18).

RI PT

210 Serotype concordance for mother-newborn carrier pairs was close to 50%. In Malawi, a lower

212

concordance (9.1%) between mothers and their newborns was reported, but these infants were

213

older(<3 months of age) and therefore more likely to acquire carriage from sources other than the

214

mother (39). The high concordance appears to be at odds with the low proportion of neonatal

215

carriage attributable to maternal carriage (PAF), observed both in our study (10.6%), and in a

216

previous study in rural Gambia, 9.5% (33). This discrepancy may suggest that other children in the

217

household may be transmitting to both mothers and newborns. Compared with the proportion of

218

neonatal carriage attributable to maternal carriage, the proportion attributable to living with other

219

children was considerably higher (62.6%). This was both because the odds ratio was higher and

220

because carriage was more common in children than in mothers.

TE D

M AN U

SC

211

221

Although the association between other children living in the household and neonatal carriage was

223

strong and has been observed in Asia and other parts of Africa (35, 40-42), we cannot rule out that it

224

is due to differences in socio-economic status between households with small and large number of

225

children.

AC C

226

EP

222

227

Other factors associated with neonatal carriage were low birth weight and dry season. The

228

decreased carriage risk with low birth weight was a surprising finding though it has already been

229

reported in Indian and Dutch babies (19, 43) and may be due to behavioral factors as these children

230

are perhaps less exposed to other family members. The association with season was previously

231

shown among older children in rural Gambia and, therefore, we would expect the same pattern with 9

ACCEPTED MANUSCRIPT 232

neonates. Such association may reflect greater social mixing during the dry season when villagers

233

spend less time on their farms (44).

234 Our analysis has a number of limitations. First, the rates of carriage may have been underestimated

236

since the women and their newborns received relatively more medical attention than the general

237

local population during the study period. In addition, only healthy mothers and newborns were

238

recruited into the study. Second, the analysis was restricted to mother-newborn pairs with both

239

swabbed at day 28. Third, the risk factors tested were not exhaustive. In particular, we did not assess

240

for the presence of upper respiratory tract infections, which has been shown to increase the risk of

241

carriage (45) and we were unable to explore the role of breastfeeding since the newborns were all

242

breastfed. The effect of maternal carriage on newborn carriage may have been diluted as about half

243

of the mother-newborns pairs were discordant. Fourth we did not use molecular techniques (46),

244

and so may have missed low-density carriers and cases of multiple carriage.

M AN U

SC

RI PT

235

TE D

245

Conclusions Gambian newborns are rapidly colonized by pneumococcus during the first month of

247

life and current strategies for pneumococcal control in Africa do not protect this age group beyond

248

the herd effect. More than 2 years after PCV13 introduction (4 years after PCV7 introduction), PCV13

249

VT are still transmitted in the community, representing one third of strains isolated from neonatal

250

and maternal nasopharyngeal carriage. Living with other children was the major risk factor for

251

neonatal carriage.

AC C

252

EP

246

253

Legend: Figure 1

254

Missing swabs on day 0, 3, 6, and 14 respectively: Newborns 1, 5, 5 and 3 & Mothers 0, 3, 2 and 3. All

255

had swabs on D 28.

256

VT vaccine type, NVT non vaccine type

257

Legend Figure 2 10

ACCEPTED MANUSCRIPT 258

Red bars, vaccine type serotypes, blue bars non vaccine type

259 Acknowledgments

261

We are grateful to the mothers and their newborns who participated in the original trial. Special

262

thanks to the study team who conducted the original study particularly the nurses led by Edrissa

263

Sabally, the Field staff led by Pity Nasso, the Head of Data management, Bai Lamin Dondeh, the data

264

entry manager, Mainuna Sowe and the Project Support Officer , Isatou Foon. We also appreciate the

265

collaboration with the Jammeh Foundation for Peace Hospital.

SC

RI PT

260

266 Author contributions

268

EU and AR designed the study. EU analysed the data and wrote the first draft. BC and CO did the

269

field work AB and IJ supervised the laboratory work. All other authors reviewed and approved the

270

manuscript.

M AN U

267

TE D

271 Funding

273

The original trial was jointly funded by the UK MRC and the UK Department for International

274

Development (DFID) under the MRC/DFID Concordat agreement (reference number MR/J010391/1)

275

and is also part of the EDCTP2 programme supported by the European Union. This ancillary study

276

was part of EU’s funded work under a West Africa Fellowship a joint initiative MRC/LSHTM. EU (first

277

and corresponding author) is funded under a West Africa Fellowship a joint MRC/LSHTM initiative.

AC C

278

EP

272

279

Conflict of Interest

280

EU does consultancy for GSK Malaria RTSS team. All other authors declare no conflict of interest.

281 282

References

11

ACCEPTED MANUSCRIPT

EP

TE D

M AN U

SC

RI PT

1. O'Brien KL, Wolfson LJ, Watt JP, Henkle E, Deloria-Knoll M, McCall N, et al. Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates. Lancet. 2009 Sep 12;374(9693):893-902. PubMed PMID: 19748398. Epub 2009/09/15. eng. 2. Walker CL, Rudan I, Liu L, Nair H, Theodoratou E, Bhutta ZA, et al. Global burden of childhood pneumonia and diarrhoea. Lancet. 2013 Apr 20;381(9875):1405-16. PubMed PMID: 23582727. 3. O'Dempsey TM, TF Lloyd-Evans,N Baldeh,I Laurence,BE Secka O, Greenwood,BM. Pneumococcal disease among children in a rural area of West Africa. Pediatric Infectious disease. 1996;15:431-7. 4. Zangwill KM, Vadheim CM, Vannier AM, Hemenway LS, Greenberg DP, Ward JI. Epidemiology of invasive pneumococcal disease in southern California: implications for the design and conduct of a pneumococcal conjugate vaccine efficacy trial. The Journal of infectious diseases. 1996 Oct;174(4):752-9. PubMed PMID: 8843213. 5. Billings ME, Deloria-Knoll M, O'Brien KL. Global Burden of Neonatal Invasive Pneumococcal Disease: A Systematic Review and Meta-analysis. The Pediatric infectious disease journal. 2016 Feb;35(2):172-9. PubMed PMID: 26517330. 6. Mulholland EK, Ogunlesi OO, Adegbola RA, Weber M, Sam BE, Palmer A, et al. Etiology of serious infections in young Gambian infants. Pediatr Infect Dis J. 1999 Oct;18(10 Suppl):S35-41. PubMed PMID: 10530572. Epub 1999/10/26. eng. 7. Muhe L, Tilahun M, Lulseged S, Kebede S, Enaro D, Ringertz S, et al. Etiology of pneumonia, sepsis and meningitis in infants younger than three months of age in Ethiopia. 1999 Oct. 8. Berkley JA, Lowe BS, Mwangi I, Williams T, Bauni E, Mwarumba S, et al. Bacteremia among children admitted to a rural hospital in Kenya. The New England journal of medicine. 2005 Jan 6;352(1):39-47. PubMed PMID: 15635111. 9. Campbell JD, Kotloff KL, Sow SO, Tapia M, Keita MM, Keita T, et al. Invasive pneumococcal infections among hospitalized children in Bamako, Mali. The Pediatric infectious disease journal. 2004 Jul;23(7):642-9. PubMed PMID: 15247603. 10. Sigauque B, Roca A, Mandomando I, Morais L, Quinto L, Sacarlal J, et al. Communityacquired bacteremia among children admitted to a rural hospital in Mozambique. The Pediatric infectious disease journal. 2009 Feb;28(2):108-13. PubMed PMID: 19131902. 11. Davis SM, Deloria-Knoll M, Kassa HT, O'Brien KL. Impact of pneumococcal conjugate vaccines on nasopharyngeal carriage and invasive disease among unvaccinated people: Review of evidence on indirect effects. Vaccine. 2013 May 16. PubMed PMID: 23684824. 12. O'Brien KL, Millar EV, Zell ER, Bronsdon M, Weatherholtz R, Reid R, et al. Effect of pneumococcal conjugate vaccine on nasopharyngeal colonization among immunized and unimmunized children in a community-randomized trial. J Infect Dis. 2007 Oct 15;196(8):1211-20. PubMed PMID: 17955440. Epub 2007/10/24. eng. 13. Scott JA, Ojal J, Ashton L, Muhoro A, Burbidge P, Goldblatt D. Pneumococcal conjugate vaccine given shortly after birth stimulates effective antibody concentrations and primes immunological memory for sustained infant protection. Clin Infect Dis. 2011 Oct;53(7):663-70. PubMed PMID: 21865175. Pubmed Central PMCID: 3166350. Epub 2011/08/26. eng. 14. Pomat WS, van den Biggelaar AH, Phuanukoonnon S, Francis J, Jacoby P, Siba PM, et al. Safety and immunogenicity of neonatal pneumococcal conjugate vaccination in Papua New Guinean children: a randomised controlled trial. PloS one. 2013;8(2):e56698. PubMed PMID: 23451070. Pubmed Central PMCID: 3579820. 15. Publication WHO. Pneumococcal vaccines WHO position paper - 2012 - recommendations. Vaccine. 2012 Jul 6;30(32):4717-8. PubMed PMID: 22621828. 16. Poehling KA, Talbot TR, Griffin MR, Craig AS, Whitney CG, Zell E, et al. Invasive pneumococcal disease among infants before and after introduction of pneumococcal conjugate vaccine. JAMA. 2006 Apr 12;295(14):1668-74. PubMed PMID: 16609088. Epub 2006/04/13. eng.

AC C

283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332

12

ACCEPTED MANUSCRIPT

EP

TE D

M AN U

SC

RI PT

17. Egere U, Townend J, Roca A, Akinsanya A, Bojang A, Nsekpong D, et al. Indirect effect of 7valent pneumococcal conjugate vaccine on pneumococcal carriage in newborns in rural Gambia: a randomised controlled trial. PLoS One. 2012;7(11):e49143. PubMed PMID: 23185303. Pubmed Central PMCID: 3504064. Epub 2012/11/28. eng. 18. Roca A, Bojang A, Bottomley C, Gladstone RA, Adetifa JU, Egere U, et al. Effect on nasopharyngeal pneumococcal carriage of replacing PCV7 with PCV13 in the Expanded Programme of Immunization in The Gambia. Vaccine. 2015 Dec 16;33(51):7144-51. PubMed PMID: 26592141. 19. Coles CL, Rahmathullah L, Kanungo R, Katz J, Sandiford D, Devi S, et al. Pneumococcal carriage at age 2 months is associated with growth deficits at age 6 months among infants in South India. The Journal of nutrition. 2012 Jun;142(6):1088-94. PubMed PMID: 22535764. Pubmed Central PMCID: 3349980. 20. Goetghebuer T, West TE, Wermenbol V, Cadbury AL, Milligan P, Lloyd-Evans N, et al. Outcome of meningitis caused by Streptococcus pneumoniae and Haemophilus influenzae type b in children in The Gambia. Trop Med Int Health. 2000 Mar;5(3):207-13. PubMed PMID: 10747284. Epub 2000/04/04. eng. 21. Edmond K, Dieye Y, Griffiths UK, Fleming J, Ba O, Diallo N, et al. Prospective Cohort Study of Disabling Sequelae and Quality of Life in Children With Bacterial Meningitis in Urban Senegal. Pediatr Infect Dis J. 2010 May 28. PubMed PMID: 20517172. Epub 2010/06/03. Eng. 22. Hill PC, Townend J, Antonio M, Akisanya B, Ebruke C, Lahai G, et al. Transmission of Streptococcus pneumoniae in rural Gambian villages: a longitudinal study. Clin Infect Dis. 2010 Jun 1;50(11):1468-76. PubMed PMID: 20420503. Epub 2010/04/28. eng. 23. Lloyd-Evans N, O'Dempsey TJD, Baldeh I, Secka O, Demba E, Todd JE, et al. Nasopharyngeal carriage of pneumococci in Gambian children and in their families. Pediatric Infectious Disease Journal. 1996;15(10):866-71. 24. Regev-Yochay G, Raz M, Dagan R, Porat N, Shainberg B, Pinco E, et al. Nasopharyngeal carriage of Streptococcus pneumoniae by adults and children in community and family settings. Clin Infect Dis. 2004 Mar 1;38(5):632-9. PubMed PMID: 14986245. Epub 2004/02/27. eng. 25. Cheung YB, Zaman SM, Nsekpong ED, Van Beneden CA, Adegbola RA, Greenwood B, et al. Nasopharyngeal Carriage of Streptococcus pneumoniae in Gambian Children who Participated in a 9valent Pneumococcal Conjugate Vaccine Trial and in Their Younger Siblings. Pediatr Infect Dis J. 2009 Jun 16. PubMed PMID: 19536041. Epub 2009/06/19. Eng. 26. Mackenzie GA, Hill PC, Jeffries DJ, Hossain I, Uchendu U, Ameh D, et al. Effect of the introduction of pneumococcal conjugate vaccination on invasive pneumococcal disease in The Gambia: a population-based surveillance study. The Lancet Infectious diseases. 2016 Jun;16(6):70311. PubMed PMID: 26897105. 27. O'Brien KL, Nohynek H. Report from a WHO Working Group: standard method for detecting upper respiratory carriage of Streptococcus pneumoniae. Pediatr Infect Dis J. 2003 Feb;22(2):e1-11. PubMed PMID: 12586987. Epub 2003/02/15. eng. 28. Roca A, Oluwalana C, Camara B, Bojang A, Burr S, Davis TM, et al. Prevention of bacterial infections in the newborn by pre-delivery administration of azithromycin: Study protocol of a randomized efficacy trial. BMC pregnancy and childbirth. 2015;15:302. PubMed PMID: 26585192. Pubmed Central PMCID: 4653934. 29. Austrian R. The quellung reaction, a neglected microbiologic technique. Mt Sinai J Med. 1976 Nov-Dec;43(6):699-709. PubMed PMID: 13297. Epub 1976/11/01. eng. 30. Greenland S. Invited commentary: variable selection versus shrinkage in the control of multiple confounders. American journal of epidemiology. 2008 Mar 01;167(5):523-9; discussion 301. PubMed PMID: 18227100. 31. Newson RB. Attributable and unattributable risks and fractions and other scenario comparisons. . The Stata Journal 2013;13(4):672-98. 32. Usuf E, Bojang A, Hill PC, Bottomley C, Greenwood B, Roca A. Nasopharyngeal colonization of Gambian infants by Staphylococcus aureus and Streptococcus pneumoniae before the

AC C

333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383

13

ACCEPTED MANUSCRIPT

EP

TE D

M AN U

SC

RI PT

introduction of pneumococcal conjugate vaccines. New microbes and new infections. 2016 Mar;10:13-8. PubMed PMID: 26909154. Pubmed Central PMCID: 4733216. 33. Darboe MK, Fulford AJ, Secka O, Prentice AM. The dynamics of nasopharyngeal streptococcus pneumoniae carriage among rural Gambian mother-infant pairs. BMC Infect Dis. 2010;10:195. PubMed PMID: 20602782. Pubmed Central PMCID: 2910019. Epub 2010/07/07. eng. 34. Kaur R, Casey JR, Pichichero ME. Emerging Streptococcus pneumoniae Strains Colonizing the Nasopharynx in Children After 13-valent Pneumococcal Conjugate Vaccination in Comparison to the 7-valent Era, 2006-2015. The Pediatric infectious disease journal. 2016 Aug;35(8):901-6. PubMed PMID: 27420806. Pubmed Central PMCID: 4948952. 35. Nzenze SA, von Gottberg A, Shiri T, van Niekerk N, de Gouveia L, Violari A, et al. Temporal Changes in Pneumococcal Colonization in HIV-infected and HIV-uninfected Mother-Child Pairs Following Transitioning From 7-valent to 13-valent Pneumococcal Conjugate Vaccine, Soweto, South Africa. The Journal of infectious diseases. 2015 Oct 01;212(7):1082-92. PubMed PMID: 25784729. 36. Bottomley C, Roca A, Hill PC, Greenwood B, Isham V. A mathematical model of serotype replacement in pneumococcal carriage following vaccination. Journal of the Royal Society, Interface / the Royal Society. 2013 Dec 6;10(89):20130786. PubMed PMID: 24132203. Pubmed Central PMCID: 3808555. 37. Roca A, Dione MM, Bojang A, Townend J, Egere U, Darboe O, et al. Nasopharyngeal carriage of pneumococci four years after community-wide vaccination with PCV-7 in The Gambia: long-term evaluation of a cluster randomized trial. PLoS One. 2013;8(9):e72198. PubMed PMID: 24086259. Pubmed Central PMCID: 3785494. 38. Usuf E, Badji H, Bojang A, Jarju S, Ikumapayi UN, Antonio M, et al. Pneumococcal carriage in rural Gambia prior to the introduction of pneumococcal conjugate vaccine: a population-based survey. Tropical medicine & international health : TM & IH. 2015 Jul;20(7):871-9. PubMed PMID: 25778937. 39. Heinsbroek E, Tafatatha T, Chisambo C, Phiri A, Mwiba O, Ngwira B, et al. Pneumococcal Acquisition Among Infants Exposed to HIV in Rural Malawi: A Longitudinal Household Study. American journal of epidemiology. 2016 Jan 1;183(1):70-8. PubMed PMID: 26628514. Pubmed Central PMCID: 4690474. 40. Turner P, Turner C, Jankhot A, Helen N, Lee SJ, Day NP, et al. A longitudinal study of Streptococcus pneumoniae carriage in a cohort of infants and their mothers on the ThailandMyanmar border. PloS one. 2012;7(5):e38271. PubMed PMID: 22693610. Pubmed Central PMCID: 3365031. 41. Tigoi CC, Gatakaa H, Karani A, Mugo D, Kungu S, Wanjiru E, et al. Rates of acquisition of pneumococcal colonization and transmission probabilities, by serotype, among newborn infants in Kilifi District, Kenya. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2012 Jul;55(2):180-8. PubMed PMID: 22523268. Pubmed Central PMCID: 3381638. 42. Nunes MC, Shiri T, van Niekerk N, Cutland CL, Groome MJ, Koen A, et al. Acquisition of Streptococcus pneumoniae in pneumococcal conjugate vaccine-naive South African children and their mothers. The Pediatric infectious disease journal. 2013 May;32(5):e192-205. PubMed PMID: 23340555. 43. Labout JAM. Bacterial carriage in infancy Risk factors and consequences, The Generation R study. Netherlands Eramus; 2010. 44. Bojang A, Jafali J, Egere UE, Hill PC, Antonio M, Jeffries D, et al. Seasonality of Pneumococcal Nasopharyngeal Carriage in Rural Gambia Determined within the Context of a Cluster Randomized Pneumococcal Vaccine Trial. PloS one. 2015;10(7):e0129649. PubMed PMID: 26132206. Pubmed Central PMCID: 4488590. 45. Mackenzie GA, Leach AJ, Carapetis JR, Fisher J, Morris PS. Epidemiology of nasopharyngeal carriage of respiratory bacterial pathogens in children and adults: cross-sectional surveys in a

AC C

384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433

14

ACCEPTED MANUSCRIPT

EP

TE D

M AN U

SC

RI PT

population with high rates of pneumococcal disease. BMC Infect Dis. 2010;10:304. PubMed PMID: 20969800. Pubmed Central PMCID: 2974682. Epub 2010/10/26. eng. 46. Turner P, Hinds J, Turner C, Jankhot A, Gould K, Bentley SD, et al. Improved detection of nasopharyngeal cocolonization by multiple pneumococcal serotypes by use of latex agglutination or molecular serotyping by microarray. J Clin Microbiol. 2011 May;49(5):1784-9. PubMed PMID: 21411589. Pubmed Central PMCID: 3122683. Epub 2011/03/18. eng.

AC C

434 435 436 437 438 439 440 441

15

ACCEPTED MANUSCRIPT Table 1 Risk factors for neonatal nasopharyngeal pneumococcal carriage at day 28 (N=374) Total (N)

OR*(95% CI)

P-value

Female Male

67(38.7) 72(37.1)

173 194

1 0.93(0.61-1.42)

0.750

<2.5 kg ≥2.5kg

3(13.6) 136(38.8)

22 351

1 4.00(1.16-13.79)

0.028

<37 wks ≥37 wks

85(38.8) 54(35.5)

219 152

1 0.87(0.56-1.33)

No Yes

87(36.0) 52(39.4)

242 132

1 1.15(0.75-1.79)

N Y

94(33.2) 45(49.5)

283 91

1 1.97(1.21-3.18)

Mother carrier day 14 & carrier day 28

N Y

117(35.1) 22(53.7)

333 41

1 2.13(1.11-4.11)

Mother carrier day 28 noncarrier day 14

N Y

118(36.2) 21(43.8)

326 48

Mother carrier at anytime during neonatal

N Y

54(26.9) 85(49.1)

201 173

Mother S. aureus carrier at day 28

N Y

99(36.0) 40(40.4)

Mothers age (years)

< 25 ≥ 25

72(34.0) 67(41.6)

Ethnicity

Mandinka Wollof Jola Fula Others

Mothers years of schooling

S. aureus Carriage at day 28 Maternal Mother carrier S. pneumoniae at day 28

0.006

0.023

1 1.37(0.74-2.53)

0.313

1 2.63(1.71-4.05)

<0.001

0.437

212 161

1 1.39(0.91-2.11)

0.131

54(32.7) 17(40.5) 22(42.3) 25(44.6) 21(35.6)

165 42 52 56 59

1 1.40(0.70-2.81) 1.51(0.80-2.86) 1.66(0.89-3.08) 1.13(0.61-2.12)

None or < 1 year ≥ 1 year

74(40.2) 59(33.7)

184 175

1 0.76(0.49-1.16)

0.203

Mother can read

N Y

99(40.4) 40(31.0)

245 129

1 0.66(0.42-1.04)

0.075

Mother can write

N Y

98(40.2) 41(31.5)

244 130

1 0.69(0.44-1.08)

0.101

Household Smoker in the house

N Y

126(36.7) 13(41.9)

343 31

1 1.24(0.59-2.62)

0.567

Mother Other

82(40.4) 53(32.9)

203 161

1 0.72(0.47-1.11)

0.143

EP

0.068

0.510

1 1.21(0.75-1.93)

AC C

1 3.461(0.91-13.11)

0.520

275 99

Who baths child

P-value

SC

Gestational age

M AN U

Birth weight

OR adj

RI PT

Carriage n (%)

TE D

Risk Factor Newborn Gender

0.469

1 2.82(1.77-4.80)

<0.001

ACCEPTED MANUSCRIPT N Y

10(13.9) 129(42.7)

72 302

1 4.62(2.28-9.36)

<0.001

Number of children at school

none ≥1

62(34.3) 76(39.8)

181 191

1 1.26(0.83-1.93)

0.270

Rainy Dry

30(27.5) 109(41.1)

109 265

1 1.84(1.13-2.99)

*crude odds ratio,

<0.001

0.014

1 1.98(1.15-3.43)

0.014

OR adj: adjusted odds ratio for birth weight, other children living in household, mother’s age, mother’s education, and season

EP

TE D

M AN U

SC

^ model did not include maternal carriage, thought to be on the casual pathway

AC C

Other factors Season

1 4.06(1.90-8.86)^

RI PT

Other children in household

ACCEPTED MANUSCRIPT Figure 1 Pneumococcal nasopharyngeal carriage in mothers and newborns 40 35

Mother Any serotype

25

Mother NVT

RI PT

20

Mother VT 15

Newborn Any serotype

10

Newborn NVT

5

Newborn VT

0 3

6 Day

AC C

EP

TE D

VT – vaccine type, NVT non vaccine type

14

28

M AN U

0

SC

Prevalence (%)

30

EP TE D

VT

NT 16F 11B 35B 21 20 24F 17F 34 13 15B 23A 15A 47 9N 23B 22A 40 35 9A 12F 31 19B 16A 11A 38 16 11 35F 28F 18B 10B 10A 48 39 19 9L 7B 33D 32A 28A 18A 17A 11F 46 45 24 8 7 6

Serotypes among mothers

10

9

7

5

4

3

2

NVT

Serotypes

RI PT

8

SC

6

M AN U

1

AC C

0

19A 19F 6A 3 14 5 23F 18C 4 6B 7F 1

Percentage

ACCEPTED MANUSCRIPT

Figure 2: Serotypes isolated from mothers and their babies during the neonatal period

2A

EP TE D

M AN U

VT

35B NT 21 10A 15A 15B 23B 16F 23A 13 24F 34 11B 19 20 38 7B 11 17F 19B 40 7C 16 11A 11D 15C 22A 39 8 11F 17A 18B 22F 42 45 46 47 48 9N

19A 19F 6A 14 18C 3 6B 5 23F 4

SC

RI PT

10 9 8 7 6 5 4 3 2 1 0

AC C

Percentage

ACCEPTED MANUSCRIPT

2B

Serotypes among newborns

NVT

Serotypes