Bar plots showing percent distribution of pneumococcal carriage per month and per season among healthy, 0 to 2 year old children in Niamey, Niger.

<p>Bar plots showing percent distribution of pneumococcal carriage per month and per season among healthy, 0 to 2 year old children in Niamey, Niger.</p

Serotype Distribution and Antimicrobial Sensitivity Profile of <i>Streptococcus pneumoniae</i> Carried in Healthy Toddlers before PCV13 Introduction in Niamey, Niger

<div><p>Background</p><p>To mitigate the burden of pneumococcal infections in Niger, a 13-valent pneumococcal vaccine, PCV13, was introduced for routine child vaccination in July 2014. In order to provide pre-vaccine baseline data and allow appreciation of changes on carriage due to vaccination, we analyzed retrospectively pneumococcal isolates obtained from healthy, 0 to 2 year old children prior to the vaccine introduction.</p><p>Methods</p><p>From June 5, 2007, to May 26, 2008, 1200 nasopharyngeal swabs were collected from healthy 0 to 2 year old children and analyzed by standard microbiological methods. Serotyping was done by SM-PCR and the data were analyzed with R version 2.15.0 (2012-03-30).</p><p>Results</p><p><i>Streptococcus pneumoniae</i> was detected in 654/1200 children (54.5%) among whom 339 (51.8%) were males. The ages of the study subjects varied from few days to 26 months (mean = 7.1, median = 6, 95% CI [6.8–7.4]). Out of 654 frozen isolates, 377 (54.8%) were able to be re-grown and analyzed. In total, 32 different serogroups/serotypes were detected of which, the most prevalent were 6/(6A/6B/6C/6D) (15.6%), 23F (10.6%), 19F (9.3%), 14 (9%), 19A (5.6%), 23B (4.0%), 25F/38 (3.7%), 18/(18A/18B/18C/18F) (2.9%) and PCR non-typeable (16.4%). Eleven serogroups/serotypes accounting for 57.3% (216/377) were of PCV13 types. Of the 211/377 (56%) isolates tested for drug sensitivity, 23/211 (10.9%), 24/211 (11.4%), 9/211(4.3%) and 148/210 (70.5%) were respectively resistance to oxacillin, chloramphenicol, erythromycin and tetracycline. Thirteen of the oxacillin resistant isolates were additionally multidrug-resistant. No resistance was however detected to gentamycin_{<b>500μg</b>} and to fluoroquinolones (ø Norfloxacin_<b>5μg</b> <7mm). Age > 3 months and presence in family of more than one sibling aged < 6 years were significant risk factors for carriage.</p><p>Conclusion</p><p>A global rate of 54.5% pneumococcal carriage was detected in this study. The introduced PCV13 vaccine should cover 57.3% (216/377) of circulating serogroups/serotypes, among which were those resistant to antibiotics. Age > 3 months and presence in family of children aged < 6 years were significant factors for pneumococcal carriage. The present data should help understanding post vaccine introduction changes in pneumococcal carriage and infections for better action.</p></div

Number and percent distribution of pneumococcal carriage serogroups/serotypes isolated from healthy 0 to 2 year old children before PCV13 start in Niamey, Niger.

<p>Number and percent distribution of pneumococcal carriage serogroups/serotypes isolated from healthy 0 to 2 year old children before PCV13 start in Niamey, Niger.</p

Bar plots showing percent distribution of pneumococcal carriage per month and per season among healthy, 0 to 2 year old children in Niamey, Niger.

<p>Bar plots showing percent distribution of pneumococcal carriage per month and per season among healthy, 0 to 2 year old children in Niamey, Niger.</p

Percent distribution (Bar charts) and cumulative (curve) of pneumococcal carriage serotypes isolated from healthy, 0 to 2 year old children before PCV13 introduction in Niamey Niger.

<p>Legend: Dark bars represent serogroups/serotypes covered by PCV13 vaccine; gray bars represent non PCV13 vaccine serogroups/serotypes; curve represents cumulative percentage of serogroups/serotypes distribution.</p

Antibiotic sensitivity profile of pneumococcal carriage isolates detected from healthy, 0 to 2 year old children before PCV13 start in Niamey, Niger.

<p>Legend: OXA: oxacillin, GENTA: gentamycin, KANA: kanamycin, STREPT: streptomycin, CHL: chloramphenicol, ERY: erythromycin, TET: tetracycline, CLIN: clindamycin, PRIST: pristinamycin, LEVO: levofloxacin, NORF: norfloxacin, VAN: vancomycin.</p

Additional file 11: of Understanding pneumococcal serotype 1 biology through population genomic analysis

Distribution of genes associated with virulence and colonisation in the ST217 in serotype 1 isolates. Presence of the genes was screened in all the isolates using BLAST as described in the methods section. (PDF 1702 kb

Additional file 13: of Understanding pneumococcal serotype 1 biology through population genomic analysis

Distribution of the accessory genes and antibiotic resistance conferring elements in the ST217 isolates. a) Maximum likelihood phylogeny of the isolates rooted using isolates from ST615 as an outgroup (not shown). b) Number of shared accessory open reading frames (ORFs) or genes between pairs of isolates in the phylogeny on the left side and at the top. c) Colour strips showing the continent and country of origin of the isolates and their SCs. d) A heatmap showing the number of shared accessory genes between each pair of isolates in the phylogeny (panel [a] and [e]). (PDF 4076 kb