This study investigated pneumococcal carriage in a Nigerian population to determine carriage rates, prevalent serotypes, theoretical coverage of available pneumococcal conjugate vaccines and population biology of isolated pneumococci. Since recently acquired pneumococci in carriage are usually the primary source of serotypes that cause invasive disease, carriage of pneumococcus can provide information on prevalence of antimicrobial resistance and some insight into need for vaccines and potential impact of selected vaccine on IPD. 
Nigeria is one of the countries in the west sub-Saharan Africa region that currently plans to introduce one of the available PCVs. This may likely be PCV-13 if the example of other African countries (Mali, Rwanda, Gambia and Sierra Leone) is followed. If introduced, the likely benefit of this vaccine is currently unknown and baseline data to inform expected changes or trends in pneumococcal carriage and IPD are unavailable. We hope this study will address some of these knowledge gaps. To our knowledge, this is the first investigation into the risk factors and population structure of carried pneumococcal in Nigeria.
The prevalence of pneumococcal carriage varies within country and setting ranging from <10% in some developed countries like Italy and France 
to values >50% in indigenous children in developed countries and among populations in developing countries 
. We found high levels of pneumococcal carriage in Nigeria as described in similar settings 
. The higher prevalence of pneumococcal carriage in children especially young infants compared to adults is also consistent with reports in the literature 
. These findings are consistent with those from a smaller study of infants in South East, Nigeria 
The 42 pneumococci serotypes found in this study population provide the first detailed description of the repertoire of carried pneumococcal serotypes in Nigeria. The most common serotypes were 19F, 6A, 6B, 23F, 11 and 15B. Interestingly, these are among the most common serotypes reported in carriage studies in similar settings 
. Pneumococci serotypes carried by children <5 years are the major source of transmission to older children and adults within households and communities 
. Vaccination with PCVs directly reduces carriage thus reducing transmission and there is a herd effect or benefit to communities among the unvaccinated populations 
. Our findings here of high carriage rates especially in infants and children <2 years highlights the potential impact of PCVs on carriage and community transmission of pneumococcus if introduced in Nigeria.
Although data on serotypes implicated in IPD in Nigeria is limited, serotypes 19F, 4 and 5 were found in a recent report on surveillance of IPD 
and serotypes 1, 2, 3 and 5 were reported in children <12 years over 30 years ago 
. Since a third of isolates found in this carriage study belong to this group of serotypes previously reported to be associated with IPD in Nigeria, this implies IPD will be reduced significantly by introducing PCV-13 that contains these serotypes. However, we did not find any serotype 5 isolate and serotype 1 was only isolated in 2 subjects despite their frequent isolation in IPD 
. Since they are both are rarely seen or occur at very low frequencies in carriage, our findings are not surprising 
. Despite the low numbers of serotypes 1 and 5 found, 4 of the top 6 serotypes in this study are included in the list of the 7 serotypes most commonly found in IPD globally thus confirming the need to introduce PCV in this setting 
The serotype coverage for PCV-7 (44%) is limited in Nigeria and similar settings because of the few serotypes it contains. In particular, it does not contain serotypes 1 and 5 that have been implicated 25–30% of IPD found in low resource settings 
. Although some countries are switching from PCV-7 to PCV-10, PCV-10 did not provide any significant added coverage over PCV-7 in our study population based on the prevalent serotypes we found in carriage. In contrast, the coverage for the PCV-13 was 62% in our study population as a whole and 70% in those <5 years. Our finding of highest serotype coverage for all licensed PCVs in very young children who bear most of the morbidity and mortality associated with IPD is evidence for the potential benefit of introducing PCVs into the Nigerian immunization schedule for children. The evidence from our data confirms PCV-13 as the best option. Taken together, our findings here in carriage i.e. 70% coverage of serotypes in children <5 years and the available information on prevalent serotypes in IPD suggest introduction of PCV-13 will significantly reduce morbidity and mortality associated with pneumococcus in the short and long term. The communal benefits of PCVs even of limited serotype coverage to all age groups in similar settings has been well described 
Although replacement by non-vaccine serotypes in both carriage and disease occurs following prolonged routine use of PCVs 
, this has not diminished the gains associated with introduction of PCV. Rather, this highlights the need for introduction of routine surveillance to confirm continued utility of PCV-13 once widely deployed in Nigeria.
MLST analysis shows not only a higher proportion of novel STs but also a highly diverse pneumococcal population structure in Nigeria which is consistent with other studies of carried pneumococcal population in similar settings like The Gambia and Ghana 
. As most MLST studies thus far have focused on pneumococcus isolated in the USA and Europe although most pneumococcal disease occurs in the developing world 
this result is not surprising; hence a considerable portion of the global diversity of pneumococcal is currently unexplored. Knowledge of prevailing STs, strains or serotypes to target in a vaccine is crucial in terms of future vaccine development in Africa because clonal groupings may differ substantially according to geographical regions and these varied clonal groupings may predominate at different periods. For example, the serotype 1-ST 217 identified in this study belongs to the ST217 clonal complex which predominates in Africa but rare in Europe or US. The ST 217 clonal complex is one of the most important lethal genotypes implicated in meningitis outbreaks in Ghana and Burkina Faso 
We also found evidence of capsular switching in three STs (280, 310 and 5543). After the introduction of the pneumococcal conjugate vaccine, particular strains with genetic advantage may change their capsules from vaccine serotypes to non-vaccine serotype through capsular switching 
. It is important to enhance surveillance of pneumococcal disease in Africa prior to routine use of pneumococcal conjugate vaccine to allow the detection of capsular switching and monitoring of the long-term effectiveness of the conjugate vaccine in use.
The high frequency of resistance to commonly used antibiotics is a source of worry especially as TS, to which 93% of isolates were resistant, is one the WHO recommended first line antibiotic for treatment for respiratory tract infections in most developing countries 
. In many developing countries with high burden of pneumococci in carriage and disease, high levels of resistance to TS and TC have also been reported 
. The pattern of resistance is not surprising considering these top the list of antibiotics purchased over the counter that are misused by caregivers in Nigeria and similar settings. However, it is unclear how in vitro resistance relates to clinical response to treatment with TS in pneumococcal disease 
. Finding almost a third of isolates resistant to penicillin G (though entirely of the intermediate category) is also a cause for concern. This is in contrast to observations from The Gambia 
and Kenya 
where penicillin resistant pneumococci are not prevalent. This is probably associated with indiscriminate antibiotic use and poor regulatory oversight of drug supply including unlimited access to prescription antibiotics, which Nigeria has in common with other settings of penicillin resistance. Most of the antimicrobial resistant isolates were of vaccine-type (96%) and invasive serotypes suggesting use of PCVs will lower the prevalence of resistant pneumococci. All the isolates were fully susceptible to erythromycin but the emerging resistance to chloramphenicol especially with the observed resistance to first-line antimicrobials calls for intervention.
Age <5 years 
, concurrent acute respiratory tract infection 
, household smoke or cooking fuel 
, recent use of antibiotics 
, and overcrowding 
are some of the risk factors that have been associated with pneumococcal carriage. The only significant individual risk factor for carriage found in this study was age and this association remained significant after adjusting for clustering of data. This is consistent with data from both developing and developed world settings 
. That such risk factors as socioeconomic class and breast-feeding were not associated with carriage may reflect the lack of socioeconomic diversity in the study population. In addition, breastfeeding for prolonged periods is a cultural norm in this part of the world.
The absence of community age-distribution data during determination of sample size did not affect our results. The study did not have sufficient power for serotype specific sub analysis despite achieving the target sample size. Our risk factor analyses did not include day care or school attendance so the contribution if any of this exposure to pneumococcal carriage among children in this population is still unknown. However, this risk factor was not associated with carriage in other studies conducted in settings like ours 
. That people are in crowded environments in these settings regardless of whether they are at a day care, in school or at home is the likely explanation for this finding.
In conclusion, carriage of pneumococcus is very high in this Nigerian community indicating a high burden of pneumococcal disease. Young age is a major risk factor for carriage. Results
from this study provide much needed data on the profile of prevalent pneumococcal serotypes and antimicrobial susceptibility patterns in a well-defined Nigerian population. Further research is required to quantify the burden of IPD, the serotypes involved, associated risk factors and outcomes especially as not all serotypes implicated in IPD are found in carriage. However, data from this study provides a starting point and baseline for future comparisons.
The consequence of findings from this study, and essential to the introduction of routine immunization against pneumococcus is the need for an extensive regional/nationwide surveillance of pneumococcal carriage, IPD and antimicrobial resistance that are crucial for vaccination impact assessment. The global vaccine preventable invasive bacterial disease (VP-IBD's) 3-tiered approach to sentinel surveillance should be the model implemented in Nigeria alongside introduction of PCV-13. This should start with tier-1 i.e. surveillance for suspected meningitis in children under five years across the country with rapid expansion to tier-2 level surveillance that includes cases of suspected pneumonia and septicaemia. Revisions to local antibiotic policy and prescription practice are required in light of the significant resistance seen to commonly used antibiotics.