Agnès B Jousset1,2,3,4, Rémy A Bonnin1,3,4, Julie Takissian1, Delphine Girlich1,4, Liliana Mihaila2, Nicolas Cabanel4, Laurent Dortet1,2,3,4, Philippe Glaser4,5, Thierry Naas1,2,3,4. 1. EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', University Paris-Saclay, LabEx Lermit, Faculty of Medicine, Le Kremlin-Bicêtre, France. 2. Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France. 3. Associated French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France. 4. Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-Assistance Publique/Hôpitaux de Paris-University Paris-Saclay, Paris, France. 5. CNRS UMR3525, Paris, France.
Abstract
BACKGROUND: KPC-producing Klebsiella pneumoniae of clonal group 258 are prominent in healthcare settings in many regions of the world. The blaKPC gene is mostly carried by a multireplicon IncFIIk-IncFI plasmid suspected to be highly compatible and stable in this genetic background. Here, we analysed the genetic diversity of an ST512 K. pneumoniae population in a single patient. METHODS: Twelve K. pneumoniae isolates (n = 5 from urine samples and n = 7 from rectal swabs) were recovered from one patient over a 2 month period. Antimicrobial susceptibility testing, plasmid extraction and WGS were performed on all isolates. The first K. pneumoniae isolate, D1, was used as a reference for phylogenetic analysis. RESULTS: Antimicrobial susceptibility testing, plasmid analysis and WGS revealed concomitant carriage of carbapenem-resistant and carbapenem-susceptible K. pneumoniae isolates of ST512, with the absence of the entire blaKPC-carrying plasmid in the susceptible population. Furthermore, 14 other genetic events occurred within the genome, including 3 chromosomal deletions (of 71 kb, 33 kb and 11 bp), 2 different insertions of ISKpn26 and 9 SNPs. Interestingly, most of the events occurred in the same chromosomal region that has been deleted independently several times, probably after homologous recombination involving 259 bp repeated sequences. CONCLUSIONS: Our study revealed (to the best of our knowledge) the first case of in vivo blaKPC-carrying plasmid curing and a wide within-patient genetic diversity of a single K. pneumoniae ST512 clone over a short period of carriage. This within-patient diversity must be taken into account when characterizing transmission chains using WGS during nosocomial outbreaks.
BACKGROUND: KPC-producing Klebsiella pneumoniae of clonal group 258 are prominent in healthcare settings in many regions of the world. The blaKPC gene is mostly carried by a multireplicon IncFIIk-IncFI plasmid suspected to be highly compatible and stable in this genetic background. Here, we analysed the genetic diversity of an ST512 K. pneumoniae population in a single patient. METHODS: Twelve K. pneumoniae isolates (n = 5 from urine samples and n = 7 from rectal swabs) were recovered from one patient over a 2 month period. Antimicrobial susceptibility testing, plasmid extraction and WGS were performed on all isolates. The first K. pneumoniae isolate, D1, was used as a reference for phylogenetic analysis. RESULTS: Antimicrobial susceptibility testing, plasmid analysis and WGS revealed concomitant carriage of carbapenem-resistant and carbapenem-susceptible K. pneumoniae isolates of ST512, with the absence of the entire blaKPC-carrying plasmid in the susceptible population. Furthermore, 14 other genetic events occurred within the genome, including 3 chromosomal deletions (of 71 kb, 33 kb and 11 bp), 2 different insertions of ISKpn26 and 9 SNPs. Interestingly, most of the events occurred in the same chromosomal region that has been deleted independently several times, probably after homologous recombination involving 259 bp repeated sequences. CONCLUSIONS: Our study revealed (to the best of our knowledge) the first case of in vivo blaKPC-carrying plasmid curing and a wide within-patient genetic diversity of a single K. pneumoniae ST512 clone over a short period of carriage. This within-patient diversity must be taken into account when characterizing transmission chains using WGS during nosocomial outbreaks.
Authors: Neil A R Gow; Carolyn Johnson; Judith Berman; Alix T Coste; Christina A Cuomo; David S Perlin; Tihana Bicanic; Thomas S Harrison; Nathan Wiederhold; Mike Bromley; Tom Chiller; Keegan Edgar Journal: Nat Commun Date: 2022-09-12 Impact factor: 17.694
Authors: Letícia B Migliorini; Romário O de Sales; Paula C M Koga; Andre M Doi; Anja Poehlein; Alexandra R Toniolo; Fernando G Menezes; Marines D V Martino; Ana C Gales; Holger Brüggemann; Patricia Severino Journal: Pathogens Date: 2021-03-12