The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition

Amelieke J.H. Cremers1 (Amelieke.cremers@radboudumc.nl), Aldert L. Zomer1,2* (aldert.zomer@radboudumc.nl), Jenna F. Gritzfeld3 (J.Gritzfeld@liverpool.ac.uk), Gerben Ferwerda1 (gerben.ferwerda@radboudumc.nl), Sacha A.F.T. van Hijum2,4 (sacha.vanhijum@radboudumc.nl), Daniela M. Ferreira3 (D.Ferreira@liverpool.ac.uk), Joshua R. Shak5 (jshak@emory.edu), Keith P. Klugman5 (kklugman@emory.edu), Jos Boekhorst2,4 (Jos.Boekhorst@nizo.com), Harro M. Timmerman4 (Harro.Timmerman@nizo.com), Marien I. de Jonge1 (Marien.DeJonge@radboudumc.nl), Stephen B. Gordon3 (sbgordon@liverpool.ac.uk), Peter W.M. Hermans1# (Peter.Hermans@radboudumc.nl)

1 Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboudumc, 6500 HB Nijmegen, The Netherlands

2 Centre for Molecular and Biomolecular Informatics (CMBI) Bacterial Genomics, Radboudumc 6500 HB Nijmegen, The Netherlands

3 Department of Clinical Sciences, Liverpool School of Tropical Medicine, L3 5QA Liverpool, UK

4 NIZO food research B.V., 6710 BA Ede, The Netherlands

5 Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA

Equal contributions

# Current address: Crucell Johnson & Johnson, Leiden, The Netherlands

 

Abstract

Introduction: Several cohort studies have indicated associations between S. pneumoniae and other microbes in the nasopharynx. To study causal relationships between the nasopharyngeal microbiome and pneumococcal carriage, we employed an experimental human pneumococcal carriage model. Healthy adult volunteers were assessed for pneumococcal carriage by culture of nasal wash samples (NWS). Those without natural pneumococcal carriage received an intranasal pneumococcal inoculation with serotype 6B or 23F. The composition of the nasopharyngeal microbiome was longitudinally studied by 16S rDNA pyrosequencing on NWS collected before and after challenge.

Results: Among 40 selected volunteers 10 were natural carriers and 30 were experimentally challenged. At baseline, five distinct nasopharyngeal microbiome profiles were identified. The phylogenetic distance between microbiomes of natural pneumococcal carriers was particularly large compared to non-carriers. A more diverse microbiome prior to inoculation was associated with the establishment of pneumococcal carriage. Perturbation of microbiome diversity upon pneumococcal challenge was strain specific. Shifts in microbiome profile occurred after pneumococcal exposure, and those volunteers who acquired carriage more often diverted from their original profile. S. pneumoniae was little prominent in the microbiome of pneumococcal carriers.

Conclusion: Pneumococcal acquisition in healthy adults is more likely to occur in a diverse microbiome and appears to promote microbial heterogeneity.

Supplemental Table. Subject characteristics and all sff files split per file. Adapter sequence is tcag. Barcodes are listed. A combined sff file is available here

sample_alias

Subject code

sample_title

gender

age

Timepoint

pneumococcal challenge

Challenge strain serotype

Natural pneumococcal carrier

Samplecode

barcode

library_selection

library_strategy

instrument_model

spot_layout

file_name

link

V143A

V143

Nasopharyngeal wash subject V143 timepoint A

male

20

A

no

 

yes

V143A

ATCGTT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATCGTT]F*

V143A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V143A.sff

V183A

V183

Nasopharyngeal wash subject V183 timepoint A

female

24

A

yes

6B

no

V183A

AGAGGC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGAGGC]F*

V183A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V183A.sff

V183B

V183

Nasopharyngeal wash subject V183 timepoint B

female

24

B

yes

6B

no

V183B

AGAGTG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGAGTG]F*

V183B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V183B.sff

V183C

V183

Nasopharyngeal wash subject V183 timepoint C

female

24

C

yes

6B

no

V183C

AGATCG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGATCG]F*

V183C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V183C.sff

V183D

V183

Nasopharyngeal wash subject V183 timepoint D

female

24

D

yes

6B

no

V183D

AGATTA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGATTA]F*

V183D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V183D.sff

V198A

V198

Nasopharyngeal wash subject V198 timepoint A

female

23

A

yes

6B

no

V198A

ACAGTC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACAGTC]F*

V198A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V198A.sff

V198B

V198

Nasopharyngeal wash subject V198 timepoint B

female

23

B

yes

6B

no

V198B

ACATAC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACATAC]F*

V198B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V198B.sff

V198C

V198

Nasopharyngeal wash subject V198 timepoint C

female

23

C

yes

6B

no

V198C

ACATCA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACATCA]F*

V198C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V198C.sff

V198D

V198

Nasopharyngeal wash subject V198 timepoint D

female

23

D

yes

6B

no

V198D

ACCAAT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACCAAT]F*

V198D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V198D.sff

V211A

V211

Nasopharyngeal wash subject V211 timepoint A

male

22

A

yes

6B

no

V211A

AATGGT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AATGGT]F*

V211A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V211A.sff

V211B

V211

Nasopharyngeal wash subject V211 timepoint B

male

22

B

yes

6B

no

V211B

AATGTA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AATGTA]F*

V211B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V211B.sff

V211C

V211

Nasopharyngeal wash subject V211 timepoint C

male

22

C

yes

6B

no

V211C

ACAACC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACAACC]F*

V211C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V211C.sff

V211D

V211

Nasopharyngeal wash subject V211 timepoint D

male

22

D

yes

6B

no

V211D

ACAATG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACAATG]F*

V211D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V211D.sff

V226A

V226

Nasopharyngeal wash subject V226 timepoint A

male

20

A

yes

6B

no

V226A

ACTACG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACTACG]F*

V226A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V226A.sff

V226D

V226

Nasopharyngeal wash subject V226 timepoint D

male

20

D

yes

6B

no

V226D

ACTAGT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACTAGT]F*

V226D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V226D.sff

V229A

V229

Nasopharyngeal wash subject V229 timepoint A

female

28

A

yes

6B

no

V229A

AACACC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AACACC]F*

V229A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V229A.sff

V229B

V229

Nasopharyngeal wash subject V229 timepoint B

female

28

B

yes

6B

no

V229B

AACATG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AACATG]F*

V229B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V229B.sff

V229C

V229

Nasopharyngeal wash subject V229 timepoint C

female

28

C

yes

6B

no

V229C

AACCAC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AACCAC]F*

V229C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V229C.sff

V229D

V229

Nasopharyngeal wash subject V229 timepoint D

female

28

D

yes

6B

no

V229D

AACCGG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AACCGG]F*

V229D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V229D.sff

V233A

V233

Nasopharyngeal wash subject V233 timepoint A

male

58

A

yes

6B

no

V233A

AACCTT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AACCTT]F*

V233A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V233A.sff

V233B

V233

Nasopharyngeal wash subject V233 timepoint B

male

58

B

yes

6B

no

V233B

AACGCT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AACGCT]F*

V233B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V233B.sff

V233D

V233

Nasopharyngeal wash subject V233 timepoint D

male

58

D

yes

6B

no

V233D

AACTAA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AACTAA]F*

V233D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V233D.sff

V234A

V234

Nasopharyngeal wash subject V234 timepoint A

female

20

A

yes

6B

no

V234A

ACGCCG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACGCCG]F*

V234A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V234A.sff

V234B

V234

Nasopharyngeal wash subject V234 timepoint B

female

20

B

yes

6B

no

V234B

ACGCGC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACGCGC]F*

V234B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V234B.sff

V234C

V234

Nasopharyngeal wash subject V234 timepoint C

female

20

C

yes

6B

no

V234C

ACGGAC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACGGAC]F*

V234C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V234C.sff

V235A

V235

Nasopharyngeal wash subject V235 timepoint A

female

19

A

yes

6B

no

V235A

ACGTAA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACGTAA]F*

V235A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V235A.sff

V235B

V235

Nasopharyngeal wash subject V235 timepoint B

female

19

B

yes

6B

no

V235B

ACGTGG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACGTGG]F*

V235B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V235B.sff

V235C

V235

Nasopharyngeal wash subject V235 timepoint C

female

19

C

yes

6B

no

V235C

ACGTTC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACGTTC]F*

V235C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V235C.sff

V235D

V235

Nasopharyngeal wash subject V235 timepoint D

female

19

D

yes

6B

no

V235D

ACTAAC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACTAAC]F*

V235D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V235D.sff

V236A

V236

Nasopharyngeal wash subject V236 timepoint A

male

18

A

yes

6B

no

V236A

ACCGGA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACCGGA]F*

V236A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V236A.sff

V236B

V236

Nasopharyngeal wash subject V236 timepoint B

male

18

B

yes

6B

no

V236B

ACCTCC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACCTCC]F*

V236B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V236B.sff

V236C

V236

Nasopharyngeal wash subject V236 timepoint C

male

18

C

yes

6B

no

V236C

ACCTGT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACCTGT]F*

V236C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V236C.sff

V236D

V236

Nasopharyngeal wash subject V236 timepoint D

male

18

D

yes

6B

no

V236D

ACCTTG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACCTTG]F*

V236D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V236D.sff

V237A

V237

Nasopharyngeal wash subject V237 timepoint A

female

18

A

no

 

yes

V237A

ATCGAG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATCGAG]F*

V237A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V237A.sff

V239A

V239

Nasopharyngeal wash subject V239 timepoint A

female

18

A

yes

6B

no

V239A

AAGAGG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AAGAGG]F*

V239A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V239A.sff

V239B

V239

Nasopharyngeal wash subject V239 timepoint B

female

18

B

yes

6B

no

V239B

AAGATC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AAGATC]F*

V239B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V239B.sff

V239C

V239

Nasopharyngeal wash subject V239 timepoint C

female

18

C

yes

6B

no

V239C

AAGCGT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AAGCGT]F*

V239C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V239C.sff

V239D

V239

Nasopharyngeal wash subject V239 timepoint D

female

18

D

yes

6B

no

V239D

AAGGAG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AAGGAG]F*

V239D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V239D.sff

V240A

V240

Nasopharyngeal wash subject V240 timepoint A

female

20

A

yes

6B

no

V240A

AAGGCC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AAGGCC]F*

V240A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V240A.sff

V240B

V240

Nasopharyngeal wash subject V240 timepoint B

female

20

B

yes

6B

no

V240B

AAGGTT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AAGGTT]F*

V240B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V240B.sff

V240C

V240

Nasopharyngeal wash subject V240 timepoint C

female

20

C

yes

6B

no

V240C

AAGTAT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AAGTAT]F*

V240C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V240C.sff

V240D

V240

Nasopharyngeal wash subject V240 timepoint D

female

20

D

yes

6B

no

V240D

AAGTCG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AAGTCG]F*

V240D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V240D.sff

V245A

V245

Nasopharyngeal wash subject V245 timepoint A

female

24

A

yes

6B

no

V245A

ACCAGG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACCAGG]F*

V245A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V245A.sff

V245C

V245

Nasopharyngeal wash subject V245 timepoint C

female

24

C

yes

6B

no

V245C

ACCATA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACCATA]F*

V245C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V245C.sff

V245D

V245

Nasopharyngeal wash subject V245 timepoint D

female

24

D

yes

6B

no

V245D

ACCGCG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACCGCG]F*

V245D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V245D.sff

V247A

V247

Nasopharyngeal wash subject V247 timepoint A

female

20

A

yes

6B

no

V247A

ACGACT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACGACT]F*

V247A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V247A.sff

V247B

V247

Nasopharyngeal wash subject V247 timepoint B

female

20

B

yes

6B

no

V247B

ACGAGA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACGAGA]F*

V247B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V247B.sff

V247D

V247

Nasopharyngeal wash subject V247 timepoint D

female

20

D

yes

6B

no

V247D

ACGCAT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACGCAT]F*

V247D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V247D.sff

V249A

V249

Nasopharyngeal wash subject V249 timepoint A

female

22

A

yes

6B

no

V249A

ACACGA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACACGA]F*

V249A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V249A.sff

V249B

V249

Nasopharyngeal wash subject V249 timepoint B

female

22

B

yes

6B

no

V249B

ACACTT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACACTT]F*

V249B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V249B.sff

V249C

V249

Nasopharyngeal wash subject V249 timepoint C

female

22

C

yes

6B

no

V249C

ACAGAG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACAGAG]F*

V249C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V249C.sff

V249D

V249

Nasopharyngeal wash subject V249 timepoint D

female

22

D

yes

6B

no

V249D

ACAGCT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACAGCT]F*

V249D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V249D.sff

V251A

V251

Nasopharyngeal wash subject V251 timepoint A

female

22

A

yes

6B

no

V251A

ACTCAA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACTCAA]F*

V251A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V251A.sff

V251C

V251

Nasopharyngeal wash subject V251 timepoint C

female

22

C

yes

6B

no

V251C

ACTCGG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACTCGG]F*

V251C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V251C.sff

V251D

V251

Nasopharyngeal wash subject V251 timepoint D

female

22

D

yes

6B

no

V251D

ACTCTC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ACTCTC]F*

V251D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V251D.sff

V253A

V253

Nasopharyngeal wash subject V253 timepoint A

female

24

A

yes

6B

no

V253A

AAGTGC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AAGTGC]F*

V253A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V253A.sff

V253B

V253

Nasopharyngeal wash subject V253 timepoint B

female

24

B

yes

6B

no

V253B

AATAAG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AATAAG]F*

V253B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V253B.sff

V253C

V253

Nasopharyngeal wash subject V253 timepoint C

female

24

C

yes

6B

no

V253C

AATAGA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AATAGA]F*

V253C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V253C.sff

V253D

V253

Nasopharyngeal wash subject V253 timepoint D

female

24

D

yes

6B

no

V253D

AATATT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AATATT]F*

V253D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V253D.sff

V255A

V255

Nasopharyngeal wash subject V255 timepoint A

female

30

A

no

 

yes

V255A

ATGATT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATGATT]F*

V255A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V255A.sff

V255B

V255

Nasopharyngeal wash subject V255 timepoint B

female

30

B

no

 

yes

V255B

ATGCAA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATGCAA]F*

V255B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V255B.sff

V255C

V255

Nasopharyngeal wash subject V255 timepoint C

female

30

C

no

 

yes

V255C

TTCTCC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[TTCTCC]F*

V255C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V255C.sff

V255D

V255

Nasopharyngeal wash subject V255 timepoint D

female

30

D

no

 

yes

V255D

ATGGAT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATGGAT]F*

V255D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V255D.sff

V257A

V257

Nasopharyngeal wash subject V257 timepoint A

female

19

A

yes

6B

no

V257A

AATCAT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AATCAT]F*

V257A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V257A.sff

V257B

V257

Nasopharyngeal wash subject V257 timepoint B

female

19

B

yes

6B

no

V257B

AATCCA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AATCCA]F*

V257B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V257B.sff

V257C

V257

Nasopharyngeal wash subject V257 timepoint C

female

19

C

yes

6B

no

V257C

AATCGC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AATCGC]F*

V257C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V257C.sff

V282A

V282

Nasopharyngeal wash subject V282 timepoint A

male

22

A

no

 

yes

V282A

ATGGCG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATGGCG]F*

V282A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V282A.sff

V289A

V289

Nasopharyngeal wash subject V289 timepoint A

female

18

A

yes

23F

no

V289A

AGTTCC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGTTCC]F*

V289A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V289A.sff

V289B

V289

Nasopharyngeal wash subject V289 timepoint B

female

18

B

yes

23F

no

V289B

AGTTGT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGTTGT]F*

V289B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V289B.sff

V289C

V289

Nasopharyngeal wash subject V289 timepoint C

female

18

C

yes

23F

no

V289C

ATACAG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATACAG]F*

V289C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V289C.sff

V289D

V289

Nasopharyngeal wash subject V289 timepoint D

female

18

D

yes

23F

no

V289D

ATACGT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATACGT]F*

V289D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V289D.sff

V292A

V292

Nasopharyngeal wash subject V292 timepoint A

female

19

A

no

 

yes

V292A

ATGGTC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATGGTC]F*

V292A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V292A.sff

V294A

V294

Nasopharyngeal wash subject V294 timepoint A

male

19

A

no

 

yes

V294A

ATGTGT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATGTGT]F*

V294A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V294A.sff

V295A

V295

Nasopharyngeal wash subject V295 timepoint A

female

18

A

yes

23F

no

V295A

AGTCTT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGTCTT]F*

V295A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V295A.sff

V295B

V295

Nasopharyngeal wash subject V295 timepoint B

female

18

B

yes

23F

no

V295B

AGTGAA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGTGAA]F*

V295B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V295B.sff

V295C

V295

Nasopharyngeal wash subject V295 timepoint C

female

18

C

yes

23F

no

V295C

AGTGCG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGTGCG]F*

V295C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V295C.sff

V295D

V295

Nasopharyngeal wash subject V295 timepoint D

female

18

D

yes

23F

no

V295D

AGTGTC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGTGTC]F*

V295D.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V295D.sff

V298A

V298

Nasopharyngeal wash subject V298 timepoint A

male

20

A

yes

23F

no

V298A

ATACTA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATACTA]F*

V298A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V298A.sff

V298B

V298

Nasopharyngeal wash subject V298 timepoint B

male

20

B

yes

23F

no

V298B

ATAGAC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATAGAC]F*

V298B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V298B.sff

V298C

V298

Nasopharyngeal wash subject V298 timepoint C

male

20

C

yes

23F

no

V298C

ATAGCA

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATAGCA]F*

V298C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V298C.sff

V304A

V304

Nasopharyngeal wash subject V304 timepoint A

male

21

A

no

 

yes

V304A

ATGTTG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATGTTG]F*

V304A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V304A.sff

V306A

V306

Nasopharyngeal wash subject V306 timepoint A

male

21

A

no

 

yes

V306A

ATTAAT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATTAAT]F*

V306A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V306A.sff

V307B

V307

Nasopharyngeal wash subject V307 timepoint B

female

22

B

yes

6B

no

V307B

AGGAGC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGGAGC]F*

V307B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V307B.sff

V307C

V307

Nasopharyngeal wash subject V307 timepoint C

female

22

C

yes

6B

no

V307C

AGGATG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[AGGATG]F*

V307C.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V307C.sff

V308A

V308

Nasopharyngeal wash subject V308 timepoint A

female

21

A

no

 

yes

V308A

ATTAGG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATTAGG]F*

V308A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V308A.sff

V312A

V312

Nasopharyngeal wash subject V312 timepoint A

male

23

A

yes

23F

no

V312A

ATCACG

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATCACG]F*

V312A.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V312A.sff

V312B

V312

Nasopharyngeal wash subject V312 timepoint B

male

23

B

yes

23F

no

V312B

ATCAGC

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATCAGC]F*

V312B.sff

http://bamics2.cmbi.umcn.nl/supplementary/cremers_2014_ehpc/V312B.sff

V312C

V312

Nasopharyngeal wash subject V312 timepoint C

male

23

C

yes

23F

no

V312C

ATCCAT

PCR

AMPLICON

454 GS FLX Titanium

A[tcag]B[ATCCAT]F*

V312C.sff