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we studied s. pneumoniae isolated from the blood or csf of children 2 months16 years of age , admitted to queen elizabeth central hospital ( qech ) , the main referral hospital for southern malawi , during april 2004october 2006 .
blood cultures were performed for all children admitted with signs of pneumonia or meningitis , and csf cultures were performed for all children with signs suggestive of meningitis during the collection period .
qech admits 25,000 children and 17,000 adults annually and serves a population of 1 million .
it is a government - funded teaching and referral hospital with 1,250 beds , although the total number of patients can exceed 2,000 .
participants were recruited to studies of the host and bacterial factors determining outcome in invasive pneumococcal infection ( 3 ) .
the college of medicine research committee , malawi , and the liverpool school of tropical medicine local research ethics committee granted ethics approval for this study .
s. pneumoniae isolates were identified by colony morphology and -hemolysis and then confirmed by gram staining and determination of optochin susceptibility ( oxoid , basingstoke , uk ) .
isolates were stored at 80c after primary isolation in bead and broth cryopreservers ( pro - lab diagnostics , richmond hill , on , canada ) .
mics were determined by the etest ( ab biodisk , solna , sweden ) according to the manufacturer s recommendation .
s. pneumoniae atcc 49619 was used as a quality control strain and gave values within an acceptable range .
antimicrobial drug susceptibility breakpoints were defined according to clinical and laboratory standards institute criteria ( 13 ) .
statistical analysis was performed by using stata 10 ( statacorp , college station , tx , usa ) . when calculating serotype coverage , we assumed serotype 6a / b cross - protection for pcv7 and the 10-valent pneumococcal vaccine ( pcv10 ) .
a total of 180 isolates were collected from children admitted to qech during the study period : 37 ( 21% ) from csf and 143 ( 79% ) from blood .
four isolates did not remain viable during storage ; 176 isolates were available for serotyping and mic determination .
median age of patients was 2.5 years ( range 2 months14 years ; interquartile range 8 months7 years ) .
of the isolates studied , 100 ( 57% ) were from hiv - positive children , and 71 ( 40% ) were from hiv - negative children .
the case - fatality rate was 25% for hiv - positive children and 21% for hiv - negative children ( p = 0.68 ) .
serotypes 1 and 6a/6b predominated , accounting for 23% and 18% of isolates , respectively ( table 1 ) .
of the 176 isolates , 69 ( 39% ) , 116 ( 66% ) , and 154 ( 88% ) had a serotype included in pcv7 , pcv10 , and pcv13 , respectively . *
serotypes in 7-valent pneumococcal conjugate vaccine : 4 , 6b , 9v , 14 , 18c , 19f , 23f .
clinical and laboratory standards institute breakpoints for penicillin and ceftriaxone varied for meningitis or nonmeningitis infections ( table 2 ) . using the meningitis breakpoints
, we found 158 ( 90% ) isolates were susceptible to penicillin , and 18 ( 10% ) were resistant to penicillin .
of the 150 children with meningitis , isolates from 16 ( 10.7% ) patients were resistant by meningitis breakpoints .
chloramphenicol - resistant pneumococci were isolated from 28 ( 39% ) of the 71 hiv - negative children and 18 ( 18% ) of the 100 hiv - positive children ( p = 0.0027 ) .
the 2 groups did not differ significantly in levels of resistance to the other antimicrobial agents .
* mic50 , 50% mic ; mic90 , 90% mic ; gm , geometric mean ; s , susceptible ; i , intermediate ; r , resistant ;  , no intermediate resistance values for these antimicrobial drugs , according to clinical and laboratory standards institute definitions .
our study describes recent pneumococcal serotyping and antimicrobial drug susceptibility data for children in malawi .
serotype distributions suggest that pcv7 would provide poor potential coverage for these children ; pcv7 includes only 39% of serotypes identified .
this information is supported by a previous study that found that pcv7 would cover 41% of invasive pneumococcal isolates from children ( 14 ) .
serotypes 1 and 5 , long regarded as essential in vaccines for use in sub - saharan africa , accounted for 23% and 1% of all isolates in this study , respectively .
our data suggest that use of the 13-valent vaccine , which includes serotypes 1 and 5 and is due to be introduced into malawi in late 2011 , will substantially increase vaccine coverage .
the nontypeable isolates included in the study may have been typeable by an alternative method .
however , the serotyping method used includes all serotypes in pcv7 , pcv10 , and pcv13 .
our study is not a formal epidemiologic study because it did not comprise a true random selection of isolates ; however , qech is the only public hospital in this area and most children admitted to the hospital live within the local community .
furthermore , we studied all consecutive cases during the study period , both severe and nonsevere .
the sample of pneumococcal disease in children studied is therefore likely to be representative of the incidence of disease in this area .
the high proportion of blood cultures studied implies that pneumonia was the primary clinical diagnosis , however , most had meningitis .
penicillin is the first - line treatment for pneumonia and presumed sepsis at qech , and ceftriaxone is the first - line treatment for suspected meningitis .
the susceptibility of all isolates to ceftriaxone confirms its suitability as a second - line treatment .
levels of resistance are comparable to those in other studies in sub - saharan africa but less than in many other areas in the world ( 7 ) , possibly because antimicrobial drug use in malawi is lower than that of other countries .
of 176 invasive streptococcus pneumoniae isolates from children in malawi , common serotypes were 1 ( 23% ) , 6a / b ( 18% ) , 14 ( 6% ) , and 23f ( 6% ) . 
 coverage with the 7-valent pneumococcal conjugate vaccine ( pcv ) was 39% ; pcv10 and pcv13 increased coverage to 66% and 88% , respectively . 
 we found chloramphenicol resistance in 27% of isolates and penicillin nonsusceptibility in 10% 
 ( by using meningitis breakpoints ) ; all were ceftriaxone susceptible .