One Health Genomic Study of Human and Animal Klebsiella pneumoniae Isolated at Diagnostic Laboratories on a Small Caribbean Island.

Patrick Butaye,Andrea Williams,Luca Guardabassi,Marc Stegger,Iona Halliday-Simmonds,Peter Damborg,Arshnee Moodley

doi:10.3390/antibiotics11010042

Abstract

Klebsiella pneumoniae causes a variety of infections in both humans and animals. In this study, we characterised the genomes of human and animal isolates from two diagnostic laboratories on St. Kitts, a small Caribbean island inhabited by a large population of vervet monkeys. In view of the increased chances of direct or indirect contact with humans and other animal species, we used the One Health approach to assess transmission of K. pneumoniae across host species by sequencing 82 presumptive K. pneumoniae clinical isolates from humans (n = 51), vervets (n = 21), horses (n = 5), dogs (n = 4) and a cat (n = 1). Whole genome sequencing (WGS) was carried out using Illumina technology. De novo assembly was performed in CLC Genomics Workbench v.11.0. Single nucleotide polymorphisms were detected using NASP followed by phylogenetic analysis using IQ-TREE. Virulence and antimicrobial resistance gene contents were analysed using the Kleborate and CGE pipelines. WGS-based analysis showed that 72 isolates were K. pneumoniae sensu stricto and five K. quasipneumoniae and five K. variicola. K. pneumoniae isolates belonged to 35 sequence types (ST), three of which were occasionally shared between humans and animals: ST23, ST37 and ST307. The ST23 strains from vervets formed a separate cluster amongst publicly available sequenced ST23 strains, indicating the presence of a specific vervet sublineage. Animal strains harbored fewer resistance genes and displayed distinct virulence traits that appeared to be host-specific in vervet isolates. Our results show that K. pneumoniae infections on this Caribbean island are usually caused by host-specific lineages.

Highlights

Klebsiella pneumoniae is an important nosocomial pathogen that often displays multidrug resistance, including resistance to last choice antimicrobials such as carbapenems
Among the 82 isolates identified as K. pneumoniae by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), 72 were K. pneumoniae sensu stricto (50 human, 17 vervet, three equine, one canine and one feline), five Klebsiella quasipneumoniae subspecies quasipneumoniae and four Klebsiella variicola subspecies variicola based on Whole Genome Sequence (WGS) analysis
Multilocus sequence typing (MLST) of the 72 K. pneumoniae sensu stricto isolates led to identification of 35 sequence types (ST), 27 of which were detected amongst human isolates

Summary

Introduction

Klebsiella pneumoniae is an important nosocomial pathogen that often displays multidrug resistance, including resistance to last choice antimicrobials such as carbapenems. While there are many publications describing the epidemiology, pathogenicity and antimicrobial resistance of this pathogen in humans [1], little information is available on clinical isolates from animals [2,3,4,5]. The types of infections seen in these animal species, except for mastitis in cattle, are similar to those observed in humans, mainly urinary tract infections (UTI) and septicemia [9]. Carbapenem resistance has been documented in clinical isolates from companion animals and, in some cases, from livestock [14]. Recent studies suggest that K. pneumoniae might be transmitted between dogs and owners within the same household [17], and that human and canine strains causing UTI are genetically related [9,17,18,19]

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Conclusion