Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi.
OBJECTIVE
This study aimed to define the molecular basis of co-trimoxazole resistance in Malawian pneumococci under the dual selective pressure of widespread co-trimoxazole and sulfadoxine/pyrimethamine use.


METHODS
We measured the trimethoprim and sulfamethoxazole MICs and analysed folA and folP nucleotide and translated amino acid sequences for 143 pneumococci isolated from carriage and invasive disease in Malawi (2002-08).


RESULTS
Pneumococci were highly resistant to both trimethoprim and sulfamethoxazole (96%, 137/143). Sulfamethoxazole-resistant isolates showed a 3 or 6 bp insertion in the sulphonamide-binding site of folP. The trimethoprim-resistant isolates fell into three genotypic groups based on dihydrofolate reductase (encoded by folA) mutations: Ile-100-Leu (10%), the Ile-100-Leu substitution together with a residue 92 substitution (56%) and those with a novel uncharacterized resistance genotype (34%). The nucleotide sequence divergence and dN/dS of folA and folP remained stable from 2004 onwards.


CONCLUSIONS
S. pneumoniae exhibit almost universal co-trimoxazole resistance in vitro and in silico that we believe is driven by extensive co-trimoxazole and sulfadoxine/pyrimethamine use. More than one-third of pneumococci employ a novel mechanism of co-trimoxazole resistance. Resistance has now reached a point of stabilizing evolution. The use of co-trimoxazole to prevent pneumococcal infection in HIV/AIDS patients in sub-Saharan Africa should be re-evaluated.
Malawi-Liverpool-Wellcome Clinical Research Programme, University of Malawi, College of Medicine, Blantyre, Malawi.
Jennifer E
JE
Cornick
Simon R
SR
Harris
Christopher M
CM
Parry
Michael J
MJ
Moore
Chikondi
C
Jassi
Arox
A
Kamng'ona
Benard
B
Kulohoma
Robert S
RS
Heyderman
Stephen D
SD
Bentley
Dean B
DB
Everett
D000595:Amino Acid Sequence; D005838:Genotype; D006801:Humans; D008295:Malawi / Q000453:epidemiology; D008826:Microbial Sensitivity Tests; D008969:Molecular Sequence Data; D011008:Pneumococcal Infections / Q000188:drug therapy / Q000453:epidemiology* / Q000235:genetics*; D015995:Prevalence; D013296:Streptococcus pneumoniae / Q000235:genetics* / Q000302:isolation & purification*; D015662:Trimethoprim, Sulfamethoxazole Drug Combination / Q000008:administration & dosage*
D015662:Trimethoprim, Sulfamethoxazole Drug Combination
pneumococcal disease; prophylaxis; sulfamethoxazole; trimethoprim