Genomics of Re-Emergent in Atlantic Salmon Outbreaks

Overview

Journal Microorganisms

Specialty Microbiology

Date 2024 Jan 23

PMID 38257891

Authors

Marcos Godoy

Marco Montes de Oca

Rudy Suarez

Alexis Martinez

Juan Pablo Pontigo

Diego Caro

Karina Kusch

Yoandy Coca

Harry Bohle

Sion Bayliss

Molly Kibenge

Frederick Kibenge

Affiliations

Soon will be listed here.

Abstract

Furunculosis, caused by , poses a significant threat to both salmonid and non-salmonid fish in diverse aquatic environments. This study explores the genomic intricacies of re-emergent outbreaks in Atlantic salmon (). Previous clinical cases have exhibited pathological characteristics, such as periorbital hemorrhages and gastrointestinal abnormalities. Genomic sequencing of three Chilean isolates (ASA04, ASA05, and CIBA_5017) and 25 previously described genomes determined the pan-genome, phylogenomics, insertion sequences, and restriction-modification systems. Unique gene families have contributed to an improved understanding of the psychrophilic and mesophilic clades, while phylogenomic analysis has been used to identify mesophilic and psychrophilic strains, thereby further differentiating between typical and atypical psychrophilic isolates. Diverse insertion sequences and restriction-modification patterns have highlighted genomic structural differences, and virulence factor predictions can emphasize exotoxin disparities, especially between psychrophilic and mesophilic strains. Thus, a novel plasmid was characterized which emphasized the role of plasmids in virulence and antibiotic resistance. The analysis of antibiotic resistance factors revealed resistance against various drug classes in Chilean strains. Overall, this study elucidates the genomic dynamics of re-emergent and provides novel insights into their virulence, antibiotic resistance, and population structure.

References

Vincent A, Trudel M, Freschi L, Nagar V, Gagne-Thivierge C, Levesque R . Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida. BMC Genomics. 2016; 17:44. PMC: 4709979. DOI: 10.1186/s12864-016-2381-3. View

Jain C, Rodriguez-R L, Phillippy A, Konstantinidis K, Aluru S . High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018; 9(1):5114. PMC: 6269478. DOI: 10.1038/s41467-018-07641-9. View

Grant J, Enns E, Marinier E, Mandal A, Herman E, Chen C . Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res. 2023; 51(W1):W484-W492. PMC: 10320063. DOI: 10.1093/nar/gkad326. View

Vincent A, Intertaglia L, Loyer V, Paquet V, Adouane E, Martin P . AsaGEI2d: a new variant of a genomic island identified in a group of Aeromonas salmonicida subsp. salmonicida isolated from France, which bears the pAsa7 plasmid. FEMS Microbiol Lett. 2021; 368(4). DOI: 10.1093/femsle/fnab021. View

McCarthy D . Fish furunculosis caused by Aeromonas salmonicida var. achromogenes. J Wildl Dis. 1975; 11(4):489-93. DOI: 10.7589/0090-3558-11.4.489. View

Ingerslev H, Ronneseth A, Pettersen E, Wergeland H . Differential expression of immune genes in Atlantic salmon (Salmo salar L.) challenged intraperitoneally or by cohabitation with IPNV. Scand J Immunol. 2009; 69(2):90-8. DOI: 10.1111/j.1365-3083.2008.02201.x. View

Godoy M, Gherardelli V, Heisinger A, Fernandez J, Olmos P, Ovalle L . First description of atypical furunculosis in freshwater farmed Atlantic salmon, Salmo salar L., in Chile. J Fish Dis. 2010; 33(5):441-9. DOI: 10.1111/j.1365-2761.2010.01142.x. View

Smith I . THE CLASSIFICATION OF 'BACTERIUM SALMONICIDA'. J Gen Microbiol. 1963; 33:263-74. DOI: 10.1099/00221287-33-2-263. View

Long M, Fan H, Gan Z, Jiang Z, Tang S, Xia H . Comparative genomic analysis provides insights into taxonomy and temperature adaption of Aeromonas salmonicida. J Fish Dis. 2023; 46(5):545-561. DOI: 10.1111/jfd.13767. View

10.

Kalyaanamoorthy S, Minh B, Wong T, von Haeseler A, Jermiin L . ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017; 14(6):587-589. PMC: 5453245. DOI: 10.1038/nmeth.4285. View

11.

Vasquez I, Hossain A, Gnanagobal H, Valderrama K, Campbell B, Ness M . Comparative Genomics of Typical and Atypical Complete Genomes Revealed New Insights into Pathogenesis Evolution. Microorganisms. 2022; 10(1). PMC: 8780938. DOI: 10.3390/microorganisms10010189. View

12.

Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M . ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2005; 34(Database issue):D32-6. PMC: 1347377. DOI: 10.1093/nar/gkj014. View

13.

Alcock B, Raphenya A, Lau T, Tsang K, Bouchard M, Edalatmand A . CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2019; 48(D1):D517-D525. PMC: 7145624. DOI: 10.1093/nar/gkz935. View

14.

Snow M, McKay P, McBeath A, Black J, Doig F, Kerr R . Development, application and validation of a Taqman real-time RT-PCR assay for the detection of infectious salmon anaemia virus (ISAV) in Atlantic salmon (Salmo salar). Dev Biol (Basel). 2006; 126:133-45. View

15.

Long M, Nielsen T, Leisner J, Hansen L, Shen Z, Zhang Q . Aeromonas salmonicida subsp. salmonicida strains isolated from Chinese freshwater fish contain a novel genomic island and possible regional-specific mobile genetic elements profiles. FEMS Microbiol Lett. 2016; 363(17). DOI: 10.1093/femsle/fnw190. View

16.

Chen S, Zhou Y, Chen Y, Gu J . fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34(17):i884-i890. PMC: 6129281. DOI: 10.1093/bioinformatics/bty560. View

17.

Keeling S, Brosnahan C, Johnston C, Wallis R, Gudkovs N, McDonald W . Development and validation of a real-time PCR assay for the detection of Aeromonas salmonicida. J Fish Dis. 2012; 36(5):495-503. DOI: 10.1111/jfd.12014. View

18.

Bayliss S, Thorpe H, Coyle N, Sheppard S, Feil E . PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria. Gigascience. 2019; 8(10). PMC: 6785682. DOI: 10.1093/gigascience/giz119. View

19.

Wick R, Judd L, Gorrie C, Holt K . Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017; 13(6):e1005595. PMC: 5481147. DOI: 10.1371/journal.pcbi.1005595. View

20.

Corvaglia A, Francois P, Hernandez D, Perron K, Linder P, Schrenzel J . A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains. Proc Natl Acad Sci U S A. 2010; 107(26):11954-8. PMC: 2900679. DOI: 10.1073/pnas.1000489107. View