Carbapenem-resistant Enterobacterales in patients with bacteraemia at tertiary academic hospitals in South Africa, 2019 - 2020: An update

Abstract


 
 
 
 Background. The emergence of carbapenem-resistant Enterobacterales (CRE) has become a serious and significant public health threat worldwide, owing to the limited antimicrobial therapy options, and the elevated mortality rates associated with these infections.Objectives. To present an update on the epidemiology of CRE bloodstream infections among hospitalised patients reported under the Group for Enteric, Respiratory and Meningeal Diseases Surveillance in South Africa (GERMS-SA) between January 2019 and December 2020. Methods. Patients of all ages with CRE bacteraemia were included and isolates, when available, were sent to the reference laboratory for confirmatory testing and molecular characterisation. Multivariable logistic regression analysis was performed to assess factors associated with in-hospital mortality.
 Results. We included 2 144 patients with CRE bacteraemia with a median age of 33 (interquartile range 1 - 51) years, of whom 1 145 (54.2%) were male. Klebsiella pneumoniae accounted for 79.8% of infections (n=863/1 082), of which 89.5% (n=611/683) were healthcare associated (HA). The most common carbapenemase genes were carbapenem-hydrolysing oxacillinase-48 (blaOXA-48-like) (76.8%; n=761/991), New Delhi metallo-β-lactamase (blaNDM) (21.1%; n=209/991) and Verona integron-encoded metallo-β-lactamase (blaVIM) (1.3%; n=13/991). None of the screened isolates with a colistin minimum inhibitory concentration >2 μg/mL harboured the mobilised colistin resistance (mcr)-1 to mcr-5 genes. The crude in-hospital mortality rate was 36.6% (n=377/1 029). Patients aged ≥60 years (v. 1.6 - 9 years) (adjusted odds ratio (aOR) 4.53; 95% confidence interval (CI) 2.21 - 9.28), those with comorbidities (diabetes, malignancy, renal and/or cardiovascular failure) (aOR 1.72; 95% CI 1.17 - 2.52), those with altered mental state (aOR 5.36; 95% CI 3.21 - 8.92) and those with previous antimicrobial use (aOR 1.88; 95% CI 1.27 - 2.77) had increased odds of in-hospital mortality.
 Conclusion. The epidemiology of CRE bloodstream infections remained similar compared with the previous surveillance report. Most infections were HA and caused by OXA-48-like carbapenemase-producing K. pneumoniae with no plasmid-mediated colistin resistance. Standard infection control measures should be strengthened.
 
 
 

Molecular Epidemiology of multidrug-resistantKlebsiella pneumoniae, Enterobacter cloacae,andEscherichia colioutbreak among neonates in Tembisa Hospital, South Africa

“…Similar findings with higher prevalence of bla OXA-181/48 and bla NDM carbapenemase genes in Gram-negative bacteria has been reported in South Africa, confirming this observation, and showing that these two carbapenemases are common in South African hospitals 16,23–27 . The phylogenomic analyses of the South African isolates confirm these observations and similar patterns (Table S4).…”

Genomic, Epigenomic, and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms inKlebsiella pneumoniaeandEnterobacterspecies

“…The emergence of colistin- and carbapenem-resistant K. pneumoniae is a major concern owing to limited treatment options. Epidemiological data in South Africa shows an increased prevalence of carbapenemase-positive Gram-negative bacteria and a low prevalence of mcr genes within the public health sector 4,14,25,26 . However, there are carbapenem- and colistin-resistant isolates without any known resistance mechanism.…”

“…Unfortunately, there is a high prevalence of colistin resistance in CRKP clinical isolates 13 . Although not common in South African clinical settings, mcr genes are responsible for majority of colistin resistance in Enterobacteriaceae, particularly in Escherichia coli 7,14,15 . The inactivation of mgrB , which inhibits the kinase activity of PhoPQ, is the most common colistin resistance mechanism in K. pneumoniae 16,17 .…”

Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization

“…The first carbapenemase enzymes detected in clinical isolates from South Africa were NDM and Klebsiella pneumoniae carbapenemase (KPC) in 2011 from the Gauteng province. 3 , 5 Subsequently, carbapenem-hydrolysing OXA-48, and its variant OXA-181, were detected in 2012. 6 More recently, a large clonal outbreak of OXA-181 in K. pneumoniae ST307 occurred across multiple provinces in the North-Eastern and North-Western regions of South Africa and a smaller outbreak of OXA-181-producing K. pneumoniae was reported from a public sector haematology/oncology unit in Cape Town.…”

“…The carbapenemases IMI, 9 VIM, 3 , 10 , 11 GES, 3 , 11 , 12 KPC 3 and IMP 10 , 11 have been infrequently documented in South Africa, with OXA-48 and its variants, followed by NDM, currently representing the greatest proportion of carbapenemases. Further, K. pneumoniae has been the most common CPE isolated in South Africa.…”