we performed sequential cross - sectional assessments from a prospective cohort study of andean children in peru ( 3 ) . during 20092011 ,
children <3 years of age from the district of san marcos , cajamarca , peru , were assessed for aris during weekly household visits .
the population was rural and had low incomes and limited access to healthcare ( 3,4 ) .
institutional review boards of vanderbilt university ( nashville , tn , usa ) and the instituto de investigacion nutricional ( lima , peru ) approved the study .
an ari episode was defined as the length of time a child had cough or fever ( 5,6 ) . if a child was ill during a household visit , we assessed for pneumonia or lower respiratory tract infection using imci - who ( integrated management of childhood illness  world health organization ) criteria ( 5,7 ) . if the child had an ari during the preceding 7 days , we collected a nasal swab sample and tested it for respiratory viruses by reverse transcription pcr at vanderbilt university ( 6,811 ) .
nasopharyngeal swab samples were collected monthly without regard to ari and tested at emory university ( atlanta , ga , usa ) by using quantitative pcr for pneumococcal density determinations . for this study , we used samples collected in 2009 and 2011 , representing periods before and after routine pcv7 use ( 12 ) ( technical appendix ) .
nasopharyngeal samples were classified according to their collection time surrounding aris : peri - ari periods included pre - ari ( 814 or 17 days before an ari ) and post - ari ( 17 or 814 days after an ari ) .
we compared log - transformed pneumococcal nasopharyngeal densities of samples from ari , peri - ari , and non - ari periods by using multivariable quantile regression with robust ses and adjusting for relevant covariates .   in secondary analyses , we assessed the role of respiratory viruses on pneumococcal density in children with aris . because detection of nonrhinovirus respiratory viruses in nasal swabs was infrequent , we grouped samples into 4 distinct groups : rhinovirus only , rhinovirus and other viruses , other viruses only , and negative for any viruses .
we examined the role of pneumococcal acquisition on pneumococcal density using pneumococci - positive nasopharyngeal samples from children who had a sample collected within the preceding 60 days .
samples were categorized as 1 ) new colonization if the prior sample was negative , 2 ) serotype persistence if the prior sample was the same serotype , and 3 ) serotype replacement if the prior sample was a different serotype .
we assessed 3,579 nasopharyngeal samples from 833 children : 450 ( 12.6% ) were collected during aris , 956 ( 26.7% ) during peri - ari periods , and 2,173 ( 57.8% ) during non - ari periods .
the median duration for aris was 8 days ( interquartile range [ iqr ] 513 days ) . according to imci - who criteria ,
33 samples were associated with pneumonia or severe pneumonia ( 13 ) ( table ) .
overall , 36.7% of nasopharyngeal samples were from children who had received > 2 pcv7 doses and were considered vaccinated .
approximately 5.0% of samples were from children who had received aminopenicillins , cotrimoxazole , chloramphenicol , or furazolidone within the 7 days preceding sample collection .
quantitative pcr detected s. pneumoniae in 68.9% of nasopharyngeal samples ; 78.9% of ari and 65.3% of non - ari samples were positive ( p = 0.06 ) .
adjusted analyses showed that densities peaked during aris . in post hoc adjusted comparisons , densities were higher during the 17 days pre - ari ( p<0.0001 ) , ari ( p<0.0001 ) , 17 days post - ari ( p<0.0001 ) , and 814 days post - ari ( p = 0.007 ) than during the non - ari period ( figure 1 ) .
estimated median pneumococcal densities with 95% cis ( vertical bars ) by acute respiratory illness ( ari ) period .
estimates derived from a quantile regression model that accounted for sex , age , daycare attendance , electricity , water supply , housing materials , kitchen type , smokers at home , vaccination , antimicrobial drug use , season , and altitude of residence .
asterisk indicates significantly different from ari samples ; dagger indicates significantly different from non - ari samples .
of 450 ari nasopharyngeal samples , 435 ( 97% ) had corresponding nasal swab samples available for identification of respiratory viruses ; 299 ( 68.7% ) tested positive for at least 1 virus .
rhinovirus , which was detected in 44.6% ( 194/435 ) of samples , was the most common virus ( technical appendix ) .
the median log - transformed pneumococcal densities of 299 virus - positive samples and 136 virus - negative samples were not significantly different ( 4.73 vs 3.94 , respectively ; adjusted p = 0.06 ) . during ari , the median log - transformed pneumococcal densities varied among virus groups : virus - negative ( 3.94 , iqr 0.005.67 ; n = 136 ) , nonrhinovirus ( 4.49 , iqr 3.125.48 ; n = 105 ) , rhinovirus - only ( 4.91 , iqr 3.436.23 ; n = 147 ) , and rhinovirus detected with other viruses samples ( 5.03 , iqr 3.286.53 ; n = 47 ) . in multivariable analyses ,
the only significant difference was between rhinovirus - only and virus - negative samples ( p = 0.02 ) ( figure 2 ) .
pneumococcal densities of current acute respiratory illness samples subdivided by reverse transcription pcr detection of respiratory viruses .
each circle represents a single bacterial density measurement . the median for the samples of each subgroup
asterisk indicates significantly different from virus - negative samples . for the colonization patterns assessment , 2,479 ( 69.3% )
nasopharyngeal samples had another sample collected < 60 days before the current sample ; the median time between samples was 28 days .
the median log - transformed pneumococcal densities among samples that represented new colonizations ( 5.14 , iqr 3.566.24 ; n = 411 ) , serotype replacement ( 5.49 , iqr 4.536.44 ; n = 322 ) , and serotype persistence ( 5.79 , iqr 4.826.47 ; n = 489 ) were compared . in multivariable analysis , serotype - replacement ( p = 0.005 ) and serotype - persistence ( p = 0.0003 ) samples had higher density than new colonization samples .
the difference between serotype replacement and serotype persistence was not significant ( p = 0.2 ) .
our findings demonstrate a dynamic evolution of pneumococcal densities before , during , and after ari episodes among young children .
we observed a gradual increase in pneumococcal density leading up to an ari episode , peak density during symptomatic ari , and a decrease in density post - ari to levels similar to those in baseline non - ari periods .
our observations of higher densities during ari than non - ari episodes align with those in studies from vietnam and south africa ( 14,15 ) and complement those assessments by illustrating the dynamic evolution of pneumococcal densities and the role of virus co - infections and pneumococcal colonization patterns .
unlike other studies that focused on hospitalized children , our community - based study showed relatively modest variations in nasopharyngeal pneumococcal density .  
rhinovirus detection was associated with increased pneumococcal density during ari . although we observed an even higher median pneumococcal density in samples co -
infected with rhinovirus and other respiratory viruses , the number of observations was small and statistical power to demonstrate significant differences was limited .
compared with new colonization in our study , serotype persistence and replacement were associated with higher pneumococcal density . because many new colonizations might ultimately succumb to host mechanisms and fail to establish stable colonization ( 2 ) , the observed lower densities might reflect a decline of pneumococcal populations as clearance evolved . nevertheless , although statistically significant , the differences in density were relatively modest , and we can not establish the precise time of colonization or clearance in our samples .
ari identification depended on the presence of cough or fever , which are subjective but widely used for routine ari surveillance ( 57 ) . because our study used household - based rather than health facility 
based surveillance , severe disease was infrequent , precluding detailed assessments of disease severity . due to small numbers , we could not study serotype - specific pneumococcal densities .
in addition , because the study was conducted in rural communities of peru , caution is warranted when extrapolating our findings to other settings .
our findings demonstrated that , among young children , nasopharyngeal pneumococcal density started increasing before the onset of ari symptoms , peaked during symptomatic ari , and decreased after symptoms subsided .
rhinovirus co - infection , serotype persistence , and serotype replacement were associated with increased nasopharyngeal pneumococcal density .
nasopharyngeal pneumococcal density is dynamic surrounding ari episodes and likely driven by complex virus  bacteria  host interactions .
expanded description of methods and results for a study of the role of nasopharyngeal pneumococcal density in the evolution of acute respiratory illnesses in young children , peru , 20092011 .
 we examined nasopharyngeal pneumococcal colonization density patterns surrounding acute respiratory illnesses ( ari ) in young children in peru . 
 pneumococcal densities were dynamic , gradually increasing leading up to an ari , peaking during the ari , and decreasing after the ari . 
 rhinovirus co - infection was associated with higher pneumococcal densities . 
The Study
Conclusions
None