One Health Genomic Study of Human and Animal <i>Klebsiella pneumoniae</i> Isolated at Diagnostic Laboratories on a Small Caribbean Island
<i>Klebsiella pneumoniae</i> 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 v...
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| Format: | Article |
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MDPI AG
2021-12-01
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| Series: | Antibiotics |
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| Online Access: | https://www.mdpi.com/2079-6382/11/1/42 |
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| author | Patrick Butaye Marc Stegger Arshnee Moodley Peter Damborg Andrea Williams Iona Halliday-Simmonds Luca Guardabassi |
| author_facet | Patrick Butaye Marc Stegger Arshnee Moodley Peter Damborg Andrea Williams Iona Halliday-Simmonds Luca Guardabassi |
| author_sort | Patrick Butaye |
| collection | DOAJ |
| description | <i>Klebsiella pneumoniae</i> 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 <i>K. pneumoniae</i> across host species by sequencing 82 presumptive <i>K. pneumoniae</i> 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 <i>K. pneumoniae</i> sensu stricto and five <i>K. quasipneumoniae</i> and five <i>K. variicola</i>. <i>K. pneumoniae</i> 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 <i>K. pneumoniae</i> infections on this Caribbean island are usually caused by host-specific lineages. |
| first_indexed | 2024-03-10T03:02:41Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2079-6382 |
| language | English |
| last_indexed | 2024-03-10T03:02:41Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Antibiotics |
| spelling | doaj.art-60f91e25bbb7471093038c714bdbf5a82023-11-23T12:43:36ZengMDPI AGAntibiotics2079-63822021-12-011114210.3390/antibiotics11010042One Health Genomic Study of Human and Animal <i>Klebsiella pneumoniae</i> Isolated at Diagnostic Laboratories on a Small Caribbean IslandPatrick Butaye0Marc Stegger1Arshnee Moodley2Peter Damborg3Andrea Williams4Iona Halliday-Simmonds5Luca Guardabassi6Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and NevisDepartment of Bacteria, Parasites, and Fungi, Statens Serum Institute, 2300 Copenhagen, DenmarkDepartment of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Frederiksberg, DenmarkDepartment of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Frederiksberg, DenmarkJoseph N France General Hospital, St Kitts, Brumaire, Saint Kitts and NevisDepartment of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and NevisDepartment of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Frederiksberg, Denmark<i>Klebsiella pneumoniae</i> 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 <i>K. pneumoniae</i> across host species by sequencing 82 presumptive <i>K. pneumoniae</i> 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 <i>K. pneumoniae</i> sensu stricto and five <i>K. quasipneumoniae</i> and five <i>K. variicola</i>. <i>K. pneumoniae</i> 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 <i>K. pneumoniae</i> infections on this Caribbean island are usually caused by host-specific lineages.https://www.mdpi.com/2079-6382/11/1/42<i>Klebsiella pneumoniae</i>One Healthvervetanimalwhole genome sequencing |
| spellingShingle | Patrick Butaye Marc Stegger Arshnee Moodley Peter Damborg Andrea Williams Iona Halliday-Simmonds Luca Guardabassi One Health Genomic Study of Human and Animal <i>Klebsiella pneumoniae</i> Isolated at Diagnostic Laboratories on a Small Caribbean Island Antibiotics <i>Klebsiella pneumoniae</i> One Health vervet animal whole genome sequencing |
| title | One Health Genomic Study of Human and Animal <i>Klebsiella pneumoniae</i> Isolated at Diagnostic Laboratories on a Small Caribbean Island |
| title_full | One Health Genomic Study of Human and Animal <i>Klebsiella pneumoniae</i> Isolated at Diagnostic Laboratories on a Small Caribbean Island |
| title_fullStr | One Health Genomic Study of Human and Animal <i>Klebsiella pneumoniae</i> Isolated at Diagnostic Laboratories on a Small Caribbean Island |
| title_full_unstemmed | One Health Genomic Study of Human and Animal <i>Klebsiella pneumoniae</i> Isolated at Diagnostic Laboratories on a Small Caribbean Island |
| title_short | One Health Genomic Study of Human and Animal <i>Klebsiella pneumoniae</i> Isolated at Diagnostic Laboratories on a Small Caribbean Island |
| title_sort | one health genomic study of human and animal i klebsiella pneumoniae i isolated at diagnostic laboratories on a small caribbean island |
| topic | <i>Klebsiella pneumoniae</i> One Health vervet animal whole genome sequencing |
| url | https://www.mdpi.com/2079-6382/11/1/42 |
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