ALPPACA - A tooL for Prokaryotic Phylogeny And
Clustering Analysis

Kaspersen, Håkon; Fiskebeck, Eve Zeyl

doi:10.21105/joss.04677

Cited by 6 publications

(5 citation statements)

References 12 publications

(12 reference statements)

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“…The alppaca pipeline [21] version 0.4.1 (DOI: 10.5281/zenodo.4452122) was used to generate a core-gene phylogeny. Briefly, all draft assemblies were annotated using Prokka [22] version 1.14.5.…”

Section: Pangenome and Phylogenetic Analysismentioning

confidence: 99%

Highly conserved composite transposon harbouring aerobactin iuc3 in Klebsiella pneumoniae from pigs

et al. 2023

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Klebsiella pneumoniae is an important opportunistic pathogen associated with severe invasive disease in humans. Hypervirulent K. pneumoniae , which are K. pneumoniae with several acquired virulence determinants such as the siderophore aerobactin and others, are more prominent in countries in South and South-East Asia compared to European countries. This Klebsiella pathotype is capable of causing liver abscesses in immunocompetent persons in the community. K. pneumoniae has not been extensively studied in non-human niches. In the present study, K. pneumoniae isolated from caecal samples (n=299) from healthy fattening pigs in Norway were characterized with regard to population structure and virulence determinants. These data were compared to data from a previous study on K. pneumoniae from healthy pigs in Thailand. Lastly, an in-depth plasmid study on K. pneumoniae with aerobactin was performed. Culturing and whole-genome sequencing was applied to detect, confirm and characterize K. pneumoniae isolates. Phylogenetic analysis described the evolutionary relationship and diversity of the isolates, while virulence determinants and sequence types were detected with Kleborate. Long-read sequencing was applied to obtain the complete sequence of virulence plasmids harbouring aerobactin. A total of 48.8 % of the investigated Norwegian pig caecal samples (n=299) were positive for K. pneumoniae . Acquired virulence determinants were detected in 72.6 % of the isolates, the most prominent being aerobactin (69.2 %), all of which were iuc3. In contrast, only 4.6 % of the isolates from Thailand harboured aerobactin. The aerobactin operon was located on potentially conjugative IncFIBK/FIIK plasmids of varying sizes in isolates from both countries. A putative, highly conserved composite transposon with a mean length of 16.2 kb flanked by truncated IS3-family IS407-group insertion sequences was detected on these plasmids, harbouring the aerobactin operon as well as several genes that may confer increased fitness in mammalian hosts. This putative composite transposon was also detected in plasmids harboured by K. pneumoniae from several countries and sources, such as human clinical samples. The high occurrence of K. pneumoniae harbouring aerobactin in Norwegian pigs, taken together with international data, suggest that pigs are a reservoir for K. pneumoniae with iuc3. Truncation of the flanking ISKpn78-element suggest that the putative composite transposon has been permanently integrated into the plasmid, and that it is no longer mobilizable.

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Section: Pangenome and Phylogenetic Analysismentioning

confidence: 99%

Highly conserved composite transposon harbouring aerobactin iuc3 in Klebsiella pneumoniae from pigs

et al. 2023

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“…Both datasets were run through Kleborate (Lam et al, 2021) version 2.2.0 to detect STs, virulence-, and antimicrobial resistance (AMR) determinants. ALPPACA (Kaspersen and Fiskebeck, 2022) version 2.0.3 was used to run a core gene phylogenetic analysis, which included all isolates from the 2018 and 2020 datasets. Briefly, all assemblies were annotated with Prokka (Seemann, 2014) version 1 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 2 https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ 1.14.5, followed by a pangenome analysis with Panaroo (Tonkin-Hill et al, 2020) version 1.2.9.…”

Section: Bioinformatic Analysis 221 Short Read Sequencingmentioning

confidence: 99%

Population dynamics and characteristics of Klebsiella pneumoniae from healthy poultry in Norway

et al. 2023

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Klebsiella pneumoniae is an important opportunistic pathogen widely studied in relation to human infection and colonization. However, there is a lack of knowledge regarding other niches that K. pneumoniae may inhabit. K. pneumoniae isolated from healthy broiler and turkey flocks in Norway in 2018 have previously been described with regard to population structure, sequence types (STs), and the presence of virulence- and antimicrobial resistance (AMR) genes. In the present study we aimed to evaluate the dynamics of the K. pneumoniae population in poultry over time, with regards to AMR and virulence, and with a special focus on persistence of STs. A total of 391 flocks sampled in 2020 were included in the present study, of which 271 were from broiler flocks and 120 from turkey flocks. Similar to findings from 2018, the occurrence of K. pneumoniae was significantly higher based on culturing in turkey flocks (62.5%) compared to broiler flocks (24.0%). Major STs in 2020 included ST5827 (n = 7), ST37 (n = 7), ST370 (n = 7), ST17 (n = 5), and ST4710 (n = 5). Several STs persisted over time in both host species, including ST35, ST37, ST590, and ST17. This persistence may be due to local re-circulation or reintroduction from parent flocks. Of these five major STs, only ST590 carried AMR genes, indicating that the persistence was not associated with the presence of AMR genes. An ST4710 strain with a hypervirulence-encoding plasmid (p4710; iro5, iuc5) was recovered from turkeys in 2018. The same strain was present in turkeys in 2020, but the plasmid had lost the salmochelin locus. This loss may be attributed to reductive evolution due to the presence of several siderophores within the same isolates. In this study we also characterized a clinical ST4710 isolate from a turkey with airsacculitis. The isolate was closely related to two intestinal ST4710 isolates from healthy turkeys in 2018. These three isolates were sampled within the same location and time frame in 2018, and all carried the full p4710 virulence plasmid. These findings highlight the transmission- and infectious potential of ST4710 in turkeys.

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“…Twelve M. viscosa genome assemblies available via the NCBI RefSeq repository (accession nos. GCF_000953735.1, GCF_900119925.1, GCF_900119985.1, GCF_900120015.1, GCF_900120025.1, GCF_900120035.1, GCF_900120065.1, GCF_900120075.1, GCF_900120105.1, GCF_900120115.1, GCF_900120145.1 and GCF_900120305.1) were downloaded and subjected to phylogenetic recreation using the in‐house pipeline ALPPACA v1.0.0 (Kaspersen & Fiskebeck, 2022). Briefly, this involved core genome alignment with ParSNP v1.6.1 (Treangen et al, 2014), recombination identification with Gubbins v3.1.3 (Croucher et al, 2015) and alignment masking with maskrc‐svg v0.5 (https://www.github.com/kwongj/maskrc-svg), all run on default settings.…”

Section: Methodsmentioning

confidence: 99%

MLVA genotyping of Moritella viscosa reveals serial emergence of novel, host‐specific clonal complexes in Norwegian salmon farming

Sørgaard

Patel

Nilsen

et al. 2023

Journal of Fish Diseases

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Moritella viscosa-associated winter ulcer affects intensively seafarmed Atlantic salmon (Salmo salar L.) during periods of low water temperature. The clinical presentation varies but often involves prolonged low-grade mortality, with affected fish displaying clearly demarcated lesions on lateral body surfaces, which may in severe cases cover large areas, penetrate deep into underlying muscle tissues and result in terminal septicaemia (Benediktsdóttir et al., 1998;Lunder et al., 1995). The disease is a particular problem in Norwegian aquaculture but also impacts the salmon farming industries of Scotland, Ireland, Iceland, the Faroe Isles and the eastern seaboard of the United States/Canada (Benediktsdóttir

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ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis

Cited by 6 publications

References 12 publications

Highly conserved composite transposon harbouring aerobactin iuc3 in Klebsiella pneumoniae from pigs

Highly conserved composite transposon harbouring aerobactin iuc3 in Klebsiella pneumoniae from pigs

Population dynamics and characteristics of Klebsiella pneumoniae from healthy poultry in Norway

MLVA genotyping of Moritella viscosa reveals serial emergence of novel, host‐specific clonal complexes in Norwegian salmon farming

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