Multiclonal spread of Klebsiella pneumoniae across hospitals in Khartoum, Sudan.

OBJECTIVES: Multidrug-resistant (MDR) Klebsiella pneumoniae is increasing worldwide with poorly characterised epidemiology in many parts of the world, particularly in Africa. This study aimed to investigate the molecular epidemiology of K. pneumoniae, to identify the diversity of sequence types (ST), and to detect carbapenem resistance genes in major regional hospitals in Khartoum, Sudan. METHODS: Klebsiella pneumoniae isolates (n = 117) were cultured from four hospitals in Khartoum, from April 2015 to October 2016. The isolates were characterised by sequencing of 16S-23S rDNA internal transcribed spacer (ITS) region. Molecular epidemiology was determined by multilocus sequence typing (MLST), and analysed by maximum likelihood phylogeny (PhyML). Antimicrobial susceptibility was determined by disk diffusion. Isolates phenotypically resistant to carbapenem were screened for carbapenemase genes: blaNDM, blaOXA48, blaIMP, blaVIM and blaGES by PCR. RESULTS: ITS sequencing confirmed the 117 isolates as K. pneumoniae. MLST revealed 52 different STs grouped in four distinct clusters by PhyML. All isolates were MDR, and carbapenemase-producing K. pneumoniae (CP-KP) isolates accounted for 44/117 (37.6%) mostly harbouring blaNDM (28/44) and blaOXA-48 (7/44), with several isolates harbouring multiple genes. CONCLUSION: MDR and CP-KP K. pneumoniae is widespread in Khartoum hospitals, with a diverse population of 52 STs clustering in four major lineages. There is an urgent need for systematic epidemiological studies of drug-resistant infections across all healthcare institutions in Sudan to inform local infection prevention and control strategies.

Molecular characterisation of an Acinetobacter baumannii outbreak.

BACKGROUND: Acinetobacter baumannii are problematic hospital pathogens, and the increased incidence of multi drug resistance has significantly limited treatment options. The global epidemiology is not fully characterised due to large data gaps from low- and middle-income countries. This study characterised the molecular epidemiology of an A. baumanniii outbreak in Egypt. METHODS: Fifty-four A. baumannii isolates were recovered from a 4-month-outbreak at Tanta University Hospitals (TUH). Associated clinical and demographic data, and the antibiograms were analysed, and Carbapenem resistant isolates were screened for acquired carbapenemase genes by PCR and sequencing. Epidemiological typing was performed by single-locus sequencing of bla OXA-51-like and Multi Locus Sequence Typing (MLST), and sequence types (STs) were analysed based on maximum-likelihood phylogeny (PhyML) to identify relatedness. FINDINGS: Immune suppression and ICU admission were the most common co-morbidity and risk factor. Carbapenem resistance accounted for 81%, and correlated with the presence of OXA-23, NDM-1 and -2, and VIM-1 and -2 carbapenemases. Nine different bla OXA-51-like genes were identified which corresponded to 22 different Sequence Types (STs), including 10 novel. International clone (IC2) was the predominant clone. PhyML analysis revealed the presence of 2 distinct clones with multiple sub-lineages. CONCLUSION: Given the short duration of the study, there was a rare heterogeneous population in the hospital. Carbapenem resistance is mediated by acquired carbapenemases in diverse lineages indicating the possibility of horizontal gene transfer. The diversity indicates the influx of multiple lineages of IC2 into TUH from unknown sources. Molecular epidemiological studies are essential for infection prevention and control measures.