Objectives
Chloramphenicol is a broad-spectrum antimicrobial widely available in sub-Saharan Africa. With susceptibility re-emerging among Enterobacteriaceae in Blantyre, Malawi, we designed and evaluated a new high-resolution melt (HRM) RT-PCR assay, ChloS-HRM, to identify chloramphenicol-susceptible infections in a hospital setting.
Methods
Seventy-two previously whole-genome sequenced isolates of
Escherichia coli
and
Klebsiella pneumoniae
from the Queen Elizabeth Central Hospital, Malawi, were subjected to determination of chloramphenicol MICs. Primers were designed to detect 18 chloramphenicol resistance genes that produce seven distinct peaks correlating with different gene groups (
catA1, catA2, catA3, catB2, catB
group 3,
cmlA
and
floR
) following HRM analysis. ChloS-HRM results were compared with MIC and WGS results.
Results
ChloS-HRM correctly identified 15 of 17 phenotypically susceptible isolates and 54 of 55 resistant isolates, giving an accuracy of 88% in identifying susceptibility and 98% in identifying resistance. WGS identified 16 of 17 susceptible and 54 of 55 resistant isolates, giving an accuracy of 94% in identifying susceptibility and 98% in identifying resistance. The single false-susceptible result had no detectable gene by ChloS-HRM or WGS. Compared with WGS, ChloS-HRM had 100% sensitivity and specificity for
catA
(
catA1–3
),
cmlA
and
floR
, and 96% specificity for
catB
; sensitivity could not be estimated due to the lack of
catB
in the clinical sample collection. The overall agreement between MIC and HRM was 96% and between MIC and WGS it was 97%.
Conclusions
ChloS-HRM could support antimicrobial stewardship in enabling de-escalation from third-generation cephalosporins by identifying chloramphenicol-susceptible infections. This would be valuable in areas with chloramphenicol-susceptible MDR and XDR Enterobacteriaceae.