Characterisation of colistin resistant Enterobacterales isolated from clinical specimens from public hospitals in Tshwane, Gauteng

Abstract

The rate of antimicrobial resistance (AMR) is constantly increasing due to the exposure to and overuse of antimicrobials, bacterial chromosomal mutations or acquisition of resistance genes. The lack of development of new antimicrobials has led to the recycling of old antimicrobials such as colistin. Colistin belongs to the antimicrobial class of polymyxins and targets the lipid A region of the lipopolysaccharide (LPS) in the cell wall of Gram-negative bacteria. However, a rise in colistin resistance in Gram-negative bacteria has been seen over the past few years. Colistin resistance can either be conferred intrinsically or by acquired mechanisms such as chromosomal mutations or mobile colistin resistance (mcr) genes. To date, ten mcr genes have been detected in clinical and environmental Enterobacterales isolates across the globe and have implications in public health due to their transmissibility, infection prevention and control policies and in the search for alternative treatment options. Information on the colistin resistance mechanisms circulating in public hospitals in Tshwane is limited. This study aimed to phenotypically and genotypically characterise colistin resistance in Enterobacterales isolated from clinical specimens from public hospitals in Tshwane, South Africa.

This study included 80 colistin resistant Enterobacterales isolates from various invasive and non-invasive clinical specimens from patients in public hospitals. The isolates were identified using the Vitek® MS Prime system (bioMérieux, France). Sensititre (Thermo Fisher Scientific, USA) was used to determine colistin minimum inhibitory concentrations (MICs) and was compared to the gold standard, colistin broth microdilution (BMD). Conventional polymerase chain reaction assays were used to detect mobile colistin resistance genes: mcr-1 to mcr-10. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC PCR) was utilised to determine the genetic relatedness between the colistin resistant isolates. Based on patient demographics, colistin susceptibility testing and genetic relatedness of the isolates, ten isolates were selected for whole genome sequencing (WGS).

A total of 46 Klebsiella pneumoniae (K. pneumoniae), 13 Escherichia coli (E. coli), 11 Salmonella enterica (S. enterica) and 10 Enterobacter cloacae (E. cloacae) isolates were identified. Patient demographics indicated isolates were obtained from 61.25% (49/80) female and 38.75% (31/80) male patients with a mean age of 42 years. The colistin MICs by Sensititre (Thermo Fisher Scientific, USA) ranged from 0.25 µg/mL to >128 µg/mL and had an essential agreement of 57% with colistin BMD. Of all the mcr genes screened for, none were detected in any of the isolates which suggested alternative resistance mechanisms as confirmed by WGS. The ERIC PCR results indicated high genetic diversity between colistin resistant K. pneumoniae isolates, colistin resistant E. coli isolates and colistin resistant E. cloacae complex isolates while the colistin resistant S. enterica isolates were genetically similar. The WGS results indicated that chromosomal mechanisms and efflux pumps conferred colistin resistance in the selected isolates.

The findings from the study provided insight into colistin resistant Enterobacterales isolates obtained from public hospitals in Tshwane, South Africa. A low prevalence of colistin resistance and mcr genes amongst Enterobacterales was detected and colistin resistance was conferred by chromosomal mechanisms and efflux pumps. Continued surveillance is crucial in infection prevention and control.