ABSTRACT
Carbapenem-resistant
Klebsiella pneumoniae
strains are formidable hospital pathogens that pose a serious threat to patients around the globe due to a rising incidence in health care facilities, high mortality rates associated with infection, and potential to spread antibiotic resistance to other bacterial species, such as
Escherichia coli
. Over 6 months in 2011, 17 patients at the National Institutes of Health (NIH) Clinical Center became colonized with a highly virulent, transmissible carbapenem-resistant strain of
K. pneumoniae
. Our real-time genomic sequencing tracked patient-to-patient routes of transmission and informed epidemiologists’ actions to monitor and control this outbreak. Two of these patients remained colonized with carbapenemase-producing organisms for at least 2 to 4 years, providing the opportunity to undertake a focused genomic study of long-term colonization with antibiotic-resistant bacteria. Whole-genome sequencing studies shed light on the underlying complex microbial colonization, including mixed or evolving bacterial populations and gain or loss of plasmids. Isolates from NIH patient 15 showed complex plasmid rearrangements, leaving the chromosome and the
bla
KPC
-carrying plasmid intact but rearranging the two other plasmids of this outbreak strain. NIH patient 16 has shown continuous colonization with
bla
KPC
-positive organisms across multiple time points spanning 2011 to 2015. Genomic studies defined a complex pattern of succession and plasmid transmission across two different
K. pneumoniae
sequence types and an
E. coli
isolate. These findings demonstrate the utility of genomic methods for understanding strain succession, genome plasticity, and long-term carriage of antibiotic-resistant organisms.
IMPORTANCE
In 2011, the NIH Clinical Center had a nosocomial outbreak involving 19 patients who became colonized or infected with
bla
KPC
-positive
Klebsiella pneumoniae
. Patients who have intestinal colonization with
bla
KPC
-positive
K. pneumoniae
are at risk for developing infections that are difficult or nearly impossible to treat with existing antibiotic options. Two of those patients remained colonized with
bla
KPC
-positive
Klebsiella pneumoniae
for over a year, leading to the initiation of a detailed genomic analysis exploring mixed colonization, plasmid recombination, and plasmid diversification. Whole-genome sequence analysis identified a variety of changes, both subtle and large, in the
bla
KPC
-positive organisms. Long-term colonization of patients with
bla
KPC
-positive
Klebsiella pneumoniae
creates new opportunities for horizontal gene transfer of plasmids encoding antibiotic resistance genes and poses complications for the delivery of health care.
Antibiotics in Food Chain: The Consequences for Antibiotic Resistance
