A One Health Study of the Genetic Relatedness of Klebsiella pneumoniae and Their Mobile Elements in the East of England

Abstract

Background: Klebsiella pneumoniae is a human, animal, and environmental commensal and a leading cause of nosocomial infections, which are often caused by multiresistant strains. We evaluate putative sources of K. pneumoniae that are carried by and infect hospital patients.

Methods: We conducted a 6-month survey on 2 hematology wards at Addenbrooke's Hospital, Cambridge, United Kingdom, in 2015 to isolate K. pneumoniae from stool, blood, and the environment. We conducted cross-sectional surveys of K. pneumoniae from 29 livestock farms, 97 meat products, the hospital sewer, and 20 municipal wastewater treatment plants in the East of England between 2014 and 2015. Isolates were sequenced and their genomes compared.

Results: Klebsiella pneumoniae was isolated from stool of 17/149 (11%) patients and 18/922 swabs of their environment, together with 1 bloodstream infection during the study and 4 others over a 24-month period. Each patient carried 1 or more lineages that was unique to them, but 2 broad environmental contamination events and patient-environment transmission were identified. Klebsiella pneumoniae was isolated from cattle, poultry, hospital sewage, and 12/20 wastewater treatment plants. There was low genetic relatedness between isolates from patients/their hospital environment vs isolates from elsewhere. Identical genes encoding cephalosporin resistance were carried by isolates from humans/environment and elsewhere but were carried on different plasmids.

Conclusion: We identified no patient-to-patient transmission and no evidence for livestock as a source of K. pneumoniae infecting humans. However, our findings reaffirm the importance of the hospital environment as a source of K. pneumoniae associated with serious human infection.

Keywords: Klebsiella pneumonia; One Health; antimicrobial resistance; genomics; surveillance.

Figure 1.

Patient recruitment and phylogeny of healthcare-associated Klebsiella pneumoniae isolates. A, Patients recruited and samples collected from study participants. B, Maximum likelihood tree of isolates from patient stool, blood, and the hospital environment based on single-nucleotides polymorphisms in the core genome. Abbreviations: ESBL, extended-spectrum beta-lactamase; IQR, interquartile range; MLST, multilocus sequence type; SNP, single-nucleotide polymorphism

Figure 2.

Relatedness of Klebsiella pneumoniae isolated from different sources. A, Distribution of multilocus sequence types (STs) by source of isolation. B, Maximum-likelihood core genome phylogeny of K. pneumoniae from humans, the hospital environment, hospital sewage, livestock, and municipal wastewater from the East of England. The 3 clades are highlighted in orange (KpI), blue (KpII), and green (KpIII). The 2 right-hand columns (from left to right) show isolate source and those cases where STs were the same for both human and nonhuman isolates. Abbreviation: SNP, single-nucleotide polymorphism.

Figure 3.

Phylogeny of sequence type (ST) ST307 Klebsiella pneumoniae isolates and characterization of plasmids present in isolates from patients and their environment. A, Maximum likelihood tree of ST307 K. pneumoniae isolates from patient stool, blood, and the hospital environment based on single-nucleotide polymorphisms in the core genome after removal of recombination. B, Antimicrobial resistance genes and associated mobile elements in the pKPN3-307 Type B (GenBank KY271405.1) reference plasmid and in the human (GenBank MH745929) and environmental plasmids (GenBank MH745930). The shared 31 533-bp antimicrobial resistance region containing the bla_CTX-M-15 element is highlighted in gray. Arrows indicate the orientation of features, with the forward direction defined as the direction of transcription for genes, toward the main part of the attC site for cassettes, in integrons toward attI for 5’ flanking regions, away from the cassette array for 3’ flanking regions, relative to the direction of transcription of the transposase gene for insertion sequences and transposons (Tn) (ie, inverted repeat left to inverted repeat right) and to the direction of the reverse transcriptase for Group II introns. The missing end of a feature is shown by a zig-zag line. Abbreviation: SNP, single-nucleotide polymorphism.

Figure 4.

Sampling locations and phenotypic antimicrobial susceptibility across the Klebsiella pneumoniae phylogeny. A, Map of the East Anglia region of the United Kingdom, showing the locations of the farms (images indicate the animal species), wastewater treatment plants (water drops), and hospitals in the region (indicated by a white “H” in a blue square). The hospital where the clinical and environmental isolates were collected is shown with H surrounded by a square. Adapted from Gouliouris et al [29]. Copyright 2018 Gouliouris et al. Adapted with permission. B, Maximum likelihood core genome phylogeny of 249 K. pneumoniae from human stool, blood, livestock, municipal wastewater, and hospital sewage (left) and their phenotypic antimicrobial susceptibility (right). The first vertical column shows isolate source and the remainder, the susceptibility to 19 antimicrobial drugs. Abbreviation: SNP, single-nucleotide polymorphism.