Antimicrobial susceptibility and genomic profiling of from bloodstream infections at a tertiary referral hospital in Lusaka, Zambia, 2018-2019.

OBJECTIVES

This study investigated antimicrobial susceptibility and genomic profiling of isolated from bloodstream infections at a tertiary referral hospital in Lusaka, Zambia, 2018-2019.

METHOD

This was a prospective hospital-based study involving routine blood culture samples submitted to the microbiology laboratory at the University Teaching Hospital. Identification of and determination of antimicrobial susceptibility profiles was achieved through conventional and automated methods. Whole-genome sequencing (WGS) was conducted, and the sequence data outputs were processed for species identification, serotype determination, multilocus sequence typing (MLST) profile determination, identification of antimicrobial resistance determinants, and phylogeny.

RESULTS

Seventy-six were isolated and 64 isolates underwent WGS. Typhi (72%) was the most prevalent serotype. Notable was the occurrence of invasive non-typhoidal Typhimurium ST313 (3%), resistance to cephalosporins (4%) and ciprofloxacin (5%), multidrug resistance (46%), and reduced susceptibility to ciprofloxacin (30%) and imipenem (3%). Phylogenetic cluster analysis showed multiple serovars with a wide range of genetic diversity.

CONCLUSION

The genetic diversity of Typhi, high prevalence of multidrug resistance, and the emergence of ciprofloxacin and cephalosporin resistance warrants improved hygiene and water and sanitation provision, continued surveillance to apprise antibiograms and inform policy, and the introduction of the typhoid conjugate vaccine.