Investigations of Carbapenem-resistant Klebsiella species and associated clinical considerations

The use of many antibiotics to treat infections has become limited in the last decade. Enterobacteriaceae, especially Klebsiella spp., have acquired resistance to quinolones, aminoglycosides, cephalosporins and carbapenems. Resistance to β-lactams is mediated via extended-spectrum β-lactamases, AmpC type β-lactamases and carbapenemases combined with porin loss. Carbapenems are the antibiotics of last resort.
The emergence of carbapenemase-producing organisms (CPOs) has led to Public Health England introducing a national toolkit to limit their spread. As part of this requirement, the
Charing Cross microbiology laboratory of the Imperial College Healthcare NHS Trust revised its screening programme for the detection of CPOs. This improved the detection and isolation of CPOs, and highlighted Klebsiella spp. were more of a problem with respect to multidrug resistance than previously thought.

Thirty-nine carbapenem-resistant Klebsiella strains were characterised. Phenotypic tests identified the strains as Klebsiella pneumoniae (n = 36) and Klebsiella oxytoca (n = 3). Detailed whole-genome sequence (WGS) analyses showed the K.oxytoca were Klebsiella michiganensis and one of the K. pneumoniae strains to be Klebsiella variicola subsp. variicola.

The K. michiganensis strains were all of sequence type 138. They were predicted to encode the β-lactamases blaGES-5, blaSHV-66, blaTEM-1, blaOXA and blaCTX-M-15, and the 12-
gene operon of the kleboxymycin biosynthetic gene cluster. This gene cluster encodes for tilimycin and tilivalline, enterotoxins previously thought only to be carried by K. oxytoca strains.

Incorporation of antimicrobial resistance and virulence gene data showed hypervirulent, multidrug-resistant K. pneumoniae strains encoding both aerobactin and rmpA (the regulator of mucoid phenotype) or colibactin are present in West London
Hospitals. These are a cause for concern, as they have the potential to cause outbreaks that are untreatable.

WGS analyses yield more accurate and comprehensive data compared with phenotypic testing, enabling exact identification of clinically important strains, detailed outbreak investigations and molecular characterisation of antibiotic resistance and virulence genes in clinical settings.

Thirty-two bacteriophages were isolated from sewage water and found to infect one or more of the clinical Klebsiella isolates. Some phages with broad host ranges (i.e. they infected K. pneumoniae, K. michiganensis, K. variicola and K. grimontii strains) were identified, which may have use in clinical therapeutics against multidrug-resistant infections. These bacteriophages remain to be characterised in detail.