Carbapenem-resistant Klebsiella pneumoniae ST11 index from a single strain enhances rapid parallel evolution during persistent infection
image: Medical history, variable drug susceptibility of Klebsiella pneumoniae, and phylogenetic, genetic, and phenotypic differences among the seven ST11 isolates
Credit: Jiuxin Qu, Shenzhen Third People's Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology
The research team led by Professor Qu investigated the intrahost evolution of carbapenem-resistant Klebsiella pneumoniae (CRKP) ST11 by collecting a series of K. pneumoniae strains isolated from a 69-year-old male patient who had been suffering from a challenging-to-treat pulmonary infection for two months. The strains were then subjected them to whole genome sequencing and analysis. They found that this patient was initially predominantly infected with ST101, followed by the emergence of hypervirulent (hv) and multidrug-resistant ST11. The ST101 (2 BALF isolates) and hv-CRKP ST11 (7 isolates, with 4 from sputum, 1 from blood, and 1 from BALF) both caused persistent infections in the respiratory tract, lasting for 77 and 58 days, respectively, and persisted until the patient's clinical improvement and subsequent discharge.
ST11 isolates were found to rapidly adjust their susceptibility to adapt and survive the antibiotic treatment. By contrast, ST101 exhibited little susceptibility changes. ST11 variants with resistance to all three carbapenems were identified on day 20 during meropenem treatment for Acinetobacter baumannii infection. Subsequently, Ceftazidime/avibactam (CAZ/AVI) resistant ST11 variant emerged on day 41 during CAZ/AVI treatment and persisted until near discharge (day 77). This resistance could be explained genetically by KPC-2 to KPC-33 mutation (D178Y) conferring resistance to CAZ/AVI. Meanwhile, ST11 became susceptible to carbapenems and exhibited decreased resistance to penicillin combination formulations simultaneously, even after a 267Asn (N) insertion in KPC-33 (denote KPC-250). The mutation from KPC-2 to KPC-33 has been frequently reported in K. pneumoniae, thus the researchers proposed that there may be a possible fixed pathway for KPC2 mutation under antibiotics stress.
In addition to the intrahost variation of antibiotics susceptibility, the virulence phenotype of ST11 isolates also diverged during infection. Two phenotypically and genetically diverged population, Pop I corresponding to Clade I and II, Pop II corresponding to clade III, could be identified each derived from the first isolate 161483. Phenotypically, all ST11 isolates showed no significant differences in growth rate. Pop II isolates were CAZ/AVI resistant and hypervirulent. While all three Pop I isolates exhibited low virulence. The researchers presume that the transition from Pop I to Pop II explains the clinical changes from carbapenem resistance to CAZ/AVI resistance, which is additionally associated with virulence regulation.
Subsequently, pangenome analysis was conducted to identify potential acquired genes related to virulence divergence. The accessory gene profiles among ST11 isolates showed rapid divergence corresponding to the differentiation between Pop I and II. Among the 5505-gene pangenome, 136 accessory genes were involved in rapid gene gain and loss during evolution. Three out of four Pop II isolates shared an acquired esiB-carrying genomic region. The blood isolate 161667 lost most genes of the ybt locus and retaining only the left ybtS and ybtX (both became duplicated) and the right ybtT and ybtU.
From an intra-host view, the researchers propose that, like viral quasispecies, drug resistant K. pneumoniae should also be considered as composite population of nonidentical genomes, each of which is under selection and adapts to survive. Combination antibiotics therapy, which may induce catastrophic mutations toward achieving a cure, should be investigated and considerate in bacterial infection treatment.
About Author:
Dr. Qu Jiuxin currently serves as the Deputy Director of the Department of Laboratory Medicine at Shenzhen Third People's Hospital. Dr. Qu holds multiple significant positions within prominent national and regional medical associations, including Committee Member of the 5th Committee of the Chinese Medical Doctor Association (CMDA) Laboratory Physician Branch, Standing Committee Member of the Clinical Laboratory Committee of the Chinese Anti-tuberculosis Association, and Vice Chairperson of the Shenzhen Medical Association Laboratory Medicine Committee (concurrently serving as Head of the Microbiology Group).
His primary research focuses on investigating the gene functions of pathogenic bacteria and developing rapid detection methods for pathogens. Dr. Qu has established a strong publication record, with multiple research articles published in leading international journals such as Clinical Infectious Diseases and Emerging Infectious Diseases.