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Santibáñez N, Vega M, Pérez T, Enriquez R, Escalona CE, Oliver C, Romero A. In vitro effects of phytogenic feed additive on Piscirickettsia salmonis growth and biofilm formation. JOURNAL OF FISH DISEASES 2024; 47:e13913. [PMID: 38421380 DOI: 10.1111/jfd.13913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 03/02/2024]
Abstract
Piscirickettsiosis is the main cause of mortality in salmonids of commercial importance in Chile, which is caused by Piscirickettsia salmonis, a Gram-negative, γ-proteobacteria that can produce biofilm as one of its virulence factors. The Chilean salmon industry uses large amounts of antibiotics to control piscirickettsiosis outbreaks, which has raised concern about its environmental impact and the potential to induce antibiotic resistance. Thus, the use of phytogenic feed additives (PFA) with antibacterial activity emerges as an interesting alternative to antimicrobials. Our study describes the antimicrobial action of an Andrographis paniculate-extracted PFA on P. salmonis planktonic growth and biofilm formation. We observed complete inhibition of planktonic and biofilm growth with 500 and 400 μg/mL of PFA for P. salmonis LF-89 and EM-90-like strains, respectively. Furthermore, 500 μg/mL of PFA was bactericidal for both evaluated bacterial strains. Sub-inhibitory doses of PFA increase the transcript levels of stress (groEL), biofilm (pslD), and efflux pump (acrB) genes for both P. salmonis strains in planktonic and sessile conditions. In conclusion, our results demonstrate the antibacterial effect of PFA against P. salmonis in vitro, highlighting the potential of PFA as an alternative to control Piscirickettsiosis.
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Affiliation(s)
- Natacha Santibáñez
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Centro FONDAP, Concepción, Chile
| | - Matías Vega
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Centro FONDAP, Concepción, Chile
| | - Tatiana Pérez
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Centro FONDAP, Concepción, Chile
| | - Ricardo Enriquez
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Carla Estefanía Escalona
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Centro FONDAP, Concepción, Chile
| | - Cristian Oliver
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Alex Romero
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Centro FONDAP, Concepción, Chile
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2
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Schober I, Bunk B, Carril G, Freese HM, Ojeda N, Riedel T, Meier-Kolthoff JP, Göker M, Spröer C, Flores-Herrera PA, Nourdin-Galindo G, Gómez F, Cárdenas C, Vásquez-Ponce F, Labra A, Figueroa J, Olivares-Pacheco J, Nübel U, Sikorski J, Marshall SH, Overmann J. Ongoing diversification of the global fish pathogen Piscirickettsia salmonis through genetic isolation and transposition bursts. THE ISME JOURNAL 2023; 17:2247-2258. [PMID: 37853183 PMCID: PMC10689435 DOI: 10.1038/s41396-023-01531-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
The management of bacterial pathogens remains a key challenge of aquaculture. The marine gammaproteobacterium Piscirickettsia salmonis is the etiological agent of piscirickettsiosis and causes multi-systemic infections in different salmon species, resulting in considerable mortality and substantial commercial losses. Here, we elucidate its global diversity, evolution, and selection during human interventions. Our comprehensive analysis of 73 closed, high quality genome sequences covered strains from major outbreaks and was supplemented by an analysis of all P. salmonis 16S rRNA gene sequences and metagenomic reads available in public databases. Genome comparison showed that Piscirickettsia comprises at least three distinct, genetically isolated species of which two showed evidence for continuing speciation. However, at least twice the number of species exist in marine fish or seawater. A hallmark of Piscirickettsia diversification is the unprecedented amount and diversity of transposases which are particularly active in subgroups undergoing rapid speciation and are key to the acquisition of novel genes and to pseudogenization. Several group-specific genes are involved in surface antigen synthesis and may explain the differences in virulence between strains. However, the frequent failure of antibiotic treatment of piscirickettsiosis outbreaks cannot be explained by horizontal acquisition of resistance genes which so far occurred only very rarely. Besides revealing a dynamic diversification of an important pathogen, our study also provides the data for improving its surveillance, predicting the emergence of novel lineages, and adapting aquaculture management, and thereby contributes towards the sustainability of salmon farming.
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Affiliation(s)
- Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gabriela Carril
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Heike M Freese
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nicolás Ojeda
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Patricio A Flores-Herrera
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Guillermo Nourdin-Galindo
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Fernando Gómez
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Constanza Cárdenas
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Felipe Vásquez-Ponce
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Alvaro Labra
- Laboratorio de Patógenos Acuícolas, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jaime Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jorge Olivares-Pacheco
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Milenio para la Investigación Colaborativa en Resistencia Antimicrobiana (MICROB-R), Santiago, Chile
| | - Ulrich Nübel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany.
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.
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Carril G, Winther-Larsen HC, Løvoll M, Sørum H. Cohabitation of Piscirickettsia salmonis genogroups (LF-89 and EM-90): synergistic effect on growth dynamics. Front Cell Infect Microbiol 2023; 13:1253577. [PMID: 37953796 PMCID: PMC10634514 DOI: 10.3389/fcimb.2023.1253577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/25/2023] [Indexed: 11/14/2023] Open
Abstract
Piscirickettsia salmonis, the biological agent of Salmonid Rickettsial Septicemia (SRS), is a facultative intracellular bacterium that can be divided into two genogroups (LF-89 and EM-90) with different virulence levels and patterns. Studies have found co-infection of these genogroups in salmonid farms in Chile, but it is essential to assess whether this interaction within the host is related to virulence and changes in pathogen dynamics. In this study, we studied four isolates from EM-90 and one LF-89 isolate chosen based on their genomic differences. The aim was to evaluate how co-cultivation affects bacterial growth performance and virulence factor expression in Atlantic salmon (Salmo salar) in vitro and in vivo. In vitro results using FN2 medium, showed a similar growth curve between co-cultures of LF-89 and EM-90 compared to EM-90 monocultures. This was explained by the higher ratio of EM-90 to LF-89 in all co-cultures. When evaluating the expression of virulence factors, it was discovered that the luxR gene was expressed only in EM-90-like isolates and that there were significant differences between mono- and co-cultures for flaA and cheA, suggesting a response to cohabitation. Moreover, during in vivo co-cultures, transcriptomic analysis revealed an upregulation of transposases, flagellum-related genes (fliI and flgK), transporters, and permeases that could unveil novel virulence effectors used in the early infection process of P. salmonis. Thus, our work has shown that cohabitation of P. salmonis genogroups can modulate their behavior and virulence effector expression. These data can contribute to new strategies and approaches to improve the current health treatments against this salmonid pathogen.
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Affiliation(s)
- Gabriela Carril
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Hanne C. Winther-Larsen
- Department of Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
| | | | - Henning Sørum
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
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Oliver C, Céspedes C, Santibañez N, Ruiz P, Romero A. Subinhibitory concentrations of florfenicol increase the biofilm formation of Piscirickettsia salmonis. JOURNAL OF FISH DISEASES 2023; 46:591-596. [PMID: 36639965 DOI: 10.1111/jfd.13757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Public health is facing a new challenge due to the increased bacterial resistance to most of the conventional antibacterial agents. Inadequate use of antibiotics in the Chilean aquaculture industry leads to the generation of multidrug resistance bacteria. Many fish pathogenic bacteria produce biofilm upon various sources of stress such as antibiotics, which provides several survival advantages for the bacterial life in community and can constitute a reservoir of pathogens in the marine environment. Being florfenicol a broad-spectrum antibiotic commonly used to treat infections in aquaculture, the aim of this study was to assess whether this antibiotic modulates in vitro the biofilm formation in several isolates of Piscirickettsia salmonis. Standard antibiotic-micro broth 96-flat well plates were used to determinate the minimal inhibitory concentration of florfenicol in eight different P. salmonis isolates. In vitro findings, with P. salmonis growing in the presence and absence of the antibiotic, exhibited a statistically significantly increase (p < .05) in biofilm formation in all the bacterial isolates cultivated with sub-MIC (defined as the half of the minimal inhibitory concentration in the presence of antibiotic) of florfenicol compared with controls (antibiotic-free broth). In conclusion, sub-MIC of florfenicol induced an increased biofilm formation in all P. salmonis isolates tested.
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Affiliation(s)
- Cristian Oliver
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Facultad de Ciencias Veterinarias, Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
| | - Constanza Céspedes
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Facultad de Ciencias Veterinarias, Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
| | - Natacha Santibañez
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Facultad de Ciencias Veterinarias, Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
| | - Pamela Ruiz
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Talcahuano, Chile
| | - Alex Romero
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Facultad de Ciencias Veterinarias, Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
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5
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Karthik K, Anbazhagan S, Chitra MA, Sridhar R. Comparative phylogenomics of Trueperella pyogenes reveals host-based distinction of strains. Antonie Van Leeuwenhoek 2023; 116:343-351. [PMID: 36598708 DOI: 10.1007/s10482-022-01806-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023]
Abstract
Trueperella pyogenes, an opportunistic pathogen causes various ailments in different animals. Different strains from different animals have distinct characters phenotypically and genotypically. Hence understanding the strains in a particular geographical location helps in framing the preventive measures. Comparative genomics of all the available T. pyogenes genome in the NCBI was conducted to understand the relatedness among strains. Whole genome phylogeny showed host associated clustering of strains recovered from swine lungs. Core genome phylogeny also showed host associated clustering mimicking whole genome phylogeny results. MLST analysis showed that there was higher diversity among cattle strains. Multidimensional scaling revealed five swine clusters, two cattle and buffalo clusters. Pangenome analysis also showed that T. pyogenes had an open genome with 57.09% accessory genome. Host specific genes were identified by pangenome analysis, and (R)-citramalate synthase was specific for swine strains of Asian origin. Host specifc genes identified by pangenome analysis can be exploited for developing a molecular assay to specifically identify the strains. The study shows that MLST having higher discriminatory power can be used as an epidemiological tool for strain discrimination of T. pyogenes.
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Affiliation(s)
- Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India.
- Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Udumalpet, Tamil Nadu, 642126, India.
| | - Subbaiyan Anbazhagan
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, 500078, India
| | - Murugesan Ananda Chitra
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
| | - Ramaswamy Sridhar
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
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Rozas-Serri M, Peña A, Gardner I, Peñaloza E, Maldonado L, Muñoz A, Mardones FO, Rodríguez C, Ildefonso R, Senn C, Aranis F. Co-Infection by Lf-89-like and Em-90-like Genogroups of Pis-Cirickettsia Salmonis in Farmed Atlantic Salmon in Chile: Implications for Surveillance and Control of Piscirickettsiosis. Pathogens 2023; 12:pathogens12030450. [PMID: 36986371 PMCID: PMC10053882 DOI: 10.3390/pathogens12030450] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Piscirickettsiosis (SRS), caused by Piscirickettsia salmonis, is the main infectious disease that affects farmed Atlantic salmon in Chile. Currently, the official surveillance and control plan for SRS in Chile is based only on the detection of P. salmonis, but neither of its genogroups (LF-89-like and EM-90-like) are included. Surveillance at the genogroup level is essential not only for defining and evaluating the vaccination strategy against SRS, but it is also of utmost importance for early diagnosis, clinical prognosis in the field, treatment, and control of the disease. The objectives of this study were to characterize the spatio-temporal distribution of P. salmonis genogroups using genogroup-specific real-time probe-based polymerase chain reaction (qPCR) to discriminate between LF-89-like and EM-90-like within and between seawater farms, individual fish, and tissues/organs during early infection in Atlantic salmon under field conditions. The spatio-temporal distribution of LF-89-like and EM-90-like was shown to be highly variable within and between seawater farms. P. salmonis infection was also proven to be caused by both genogroups at farm, fish, and tissue levels. Our study demonstrated for the first time a complex co-infection by P. salmonis LF-89-like and EM-90-like in Atlantic salmon. Liver nodules (moderate and severe) were strongly associated with EM-90-like infection, but this phenotype was not detected by infection with LF-89-like or co-infection of both genogroups. The detection rate of P. salmonis LF-89-like increased significantly between 2017 and 2021 and was the most prevalent genogroup in Chilean salmon aquaculture during this period. Lastly, a novel strategy to identify P. salmonis genogroups based on novel genogroup-specific qPCR for LF-89-like and EM-90-like genogroups is suggested.
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Affiliation(s)
| | - Andrea Peña
- Pathovet Labs SpA, Puerto Montt 5480000, Chile
| | - Ian Gardner
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | | | | | - Ariel Muñoz
- Pathovet Labs SpA, Puerto Montt 5480000, Chile
| | - Fernando O. Mardones
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 3542000, Chile
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7
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Levipan HA, Irgang R, Opazo LF, Araya-León H, Avendaño-Herrera R. Collective behavior and virulence arsenal of the fish pathogen Piscirickettsia salmonis in the biofilm realm. Front Cell Infect Microbiol 2022; 12:1067514. [PMID: 36544910 PMCID: PMC9760808 DOI: 10.3389/fcimb.2022.1067514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Piscirickettsiosis is a fish disease caused by the Gram-negative bacterium Piscirickettsia salmonis. This disease has a high socio-economic impact on the Chilean salmonid aquaculture industry. The bacterium has a cryptic character in the environment and their main reservoirs are yet unknown. Bacterial biofilms represent a ubiquitous mechanism of cell persistence in diverse natural environments and a risk factor for the pathogenesis of several infectious diseases, but their microbiological significance for waterborne veterinary diseases, including piscirickettsiosis, have seldom been evaluated. This study analyzed the in vitro biofilm behavior of P. salmonis LF-89T (genogroup LF-89) and CA5 (genogroup EM-90) using a multi-method approach and elucidated the potential arsenal of virulence of the P. salmonis LF-89T type strain in its biofilm state. P. salmonis exhibited a quick kinetics of biofilm formation that followed a multi-step and highly strain-dependent process. There were no major differences in enzymatic profiles or significant differences in cytotoxicity (as tested on the Chinook salmon embryo cell line) between biofilm-derived bacteria and planktonic equivalents. The potential arsenal of virulence of P. salmonis LF-89T in biofilms, as determined by whole-transcriptome sequencing and differential gene expression analysis, consisted of genes involved in cell adhesion, polysaccharide biosynthesis, transcriptional regulation, and gene mobility, among others. Importantly, the global gene expression profiles of P. salmonis LF-89T were not enriched with virulence-related genes upregulated in biofilm development stages at 24 and 48 h. An enrichment in virulence-related genes exclusively expressed in biofilms was also undetected. These results indicate that early and mature biofilm development stages of P. salmonis LF-89T were transcriptionally no more virulent than their planktonic counterparts, which was supported by cytotoxic trials, which, in turn, revealed that both modes of growth induced important and very similar levels of cytotoxicity on the salmon cell line. Our results suggest that the aforementioned biofilm development stages do not represent hot spots of virulence compared with planktonic counterparts. This study provides the first transcriptomic catalogue to select specific genes that could be useful to prevent or control the (in vitro and/or in vivo) adherence and/or biofilm formation by P. salmonis and gain further insights into piscirickettsiosis pathogenesis.
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Affiliation(s)
- Héctor A. Levipan
- Laboratorio de Ecopatología y Nanobiomateriales, Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile,Centro de Espectroscopía Atómica y Molecular (ATMOS-C), Universidad de Playa Ancha, Valparaíso, Chile,*Correspondence: Héctor A. Levipan, ; ; Ruben Avendaño-Herrera, ;
| | - Rute Irgang
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile,Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - L. Felipe Opazo
- Institute of Ecology and Biodiversity (IEB), Santiago, Chile,Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Henry Araya-León
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile,Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile,Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile,Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile,*Correspondence: Héctor A. Levipan, ; ; Ruben Avendaño-Herrera, ;
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8
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Valenzuela-Aviles P, Torrealba D, Figueroa C, Mercado L, Dixon B, Conejeros P, Gallardo-Matus J. Why vaccines fail against Piscirickettsiosis in farmed salmon and trout and how to avoid it: A review. Front Immunol 2022; 13:1019404. [PMID: 36466828 PMCID: PMC9714679 DOI: 10.3389/fimmu.2022.1019404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/24/2022] [Indexed: 09/28/2023] Open
Abstract
Piscirickettsiosis is the most severe, persistent, and damaging disease that has affected the Chilean salmon industry since its origins in the 1980s. As a preventive strategy for this disease, different vaccines have been developed and used over the last 30 years. However, vaccinated salmon and trout frequently die in the sea cages and the use of antibiotics is still high demonstrating the low efficiency of the available vaccines. The reasons why the vaccines fail so often are still debated, but it could involve different extrinsic and intrinsic factors. Among the extrinsic factors, mainly associated with chronic stress, we can distinguish: 1) biotic including coinfection with sea lice, sealions attacks or harmful algal blooms; 2) abiotic including low oxygen or high temperature; and 3) farm-management factors including overcrowding or chemical delousing treatments. Among the intrinsic factors, we can distinguish: 1) fish-related factors including host's genetic variability (species, population and individual), sex or age; 2) pathogen-related factors including their variability and ability to evade host immune responses; and 3) vaccine-related factors including low immunogenicity and poor matches with the circulating pathogen strain. Based on the available evidence, in order to improve the development and the efficacy of vaccines against P. salmonis we recommend: a) Do not perform efficacy evaluations by intraperitoneal injection of pathogens because they generate an artificial protective immune response, instead cohabitation or immersion challenges must be used; b) Evaluate the diversity of pathogen strains in the field and ensure a good antigenic match with the vaccines; c) Investigate whether host genetic diversity could be improved, e.g. through selection, in favor of better and longer responses to vaccination; d) To reduce the stressful effects at the cage level, controlling the co-infection of pathogens and avoiding fish overcrowding. To date, we do not know the immunological mechanisms by which the vaccines against P. salmonis may or may not generate protection. More studies are required to identify what type of response, cellular or molecular, is required to develop effective vaccines.
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Affiliation(s)
- Paula Valenzuela-Aviles
- Laboratorio de Genética y Genómica Aplicada, Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Débora Torrealba
- Laboratorio de Genética y Genómica Aplicada, Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Carolina Figueroa
- Laboratorio de Genética y Genómica Aplicada, Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Luis Mercado
- Grupo de Marcadores Inmunológicos en Organismos Acuáticos, Pontificia Universidad Católica de Valparaíso, Instituto de Biología, Valparaíso, Chile
| | - Brian Dixon
- Department of Biology, Faculty of Science, University of Waterloo, Waterloo, Canada
| | - Pablo Conejeros
- Centro de Investigación y Gestión de Recursos Naturales (CIGREN), Facultad de Ciencias, Instituto de Biología, Universidad de Valparaíso, Valparaíso, Chile
| | - José Gallardo-Matus
- Laboratorio de Genética y Genómica Aplicada, Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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9
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Isla A, Sánchez P, Ruiz P, Albornoz R, Pontigo JP, Rauch MC, Hawes C, Vargas-Chacoff L, Yáñez AJ. Effect of low-dose Piscirickettsia salmonis infection on haematological-biochemical blood parameters in Atlantic salmon (Salmo salar). JOURNAL OF FISH BIOLOGY 2022; 101:1021-1032. [PMID: 35838309 DOI: 10.1111/jfb.15167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Piscirickettsia salmonis is the etiological agent of Piscirickettsiosis, a severe disease that affects Atlantic salmon (Salmo salar) farmed in Chile and many other areas (Norway, Scotland, Ireland, Canada and the USA). This study investigated the effects of low-dose P. salmonis infection (1 × 102 CFU/ml) on Atlantic salmon. In this study, we challenged fish with an isolated representative of the EM-90 genogroup via intraperitoneal injection for 42 days. Infected fish displayed decreased haematocrit and haemoglobin levels at day 13 post-infection, indicating erythropenia, haemolysis and haemodilution. Conversely, their white blood cell counts increased on days 13 and 21 post-infection. Additionally, their iron levels decreased from day 2 post-infection, indicating iron deficiency and an inability to retrieve stored iron before infection. Their magnesium levels also decreased at day 28 post-infection, possibly due to osmoregulatory problems. Also, we observed an increase in lactate dehydrogenase activity on days 5, 21, and 28 post-infection, suggesting early symptoms of hepatotoxicity. Later analyses determined a decrease in plasma glucose levels from day 2 post-infection. This may be attributed to the hypoxic conditions caused by P. salmonis, leading to an excess utilization of stored carbohydrates. Our results suggest that the blood parameters we studied are useful for monitoring the physiological status of Atlantic salmon infected with P. salmonis.
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Affiliation(s)
- Adolfo Isla
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Patricio Sánchez
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pamela Ruiz
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Romina Albornoz
- Interdisciplinary Center for Aquaculture Research, Concepción, Chile
| | - Juan P Pontigo
- Laboratorio de Biotecnología Aplicada, Facultad de Ciencas de la Naturaleza, Escuela de Medicina Veterinaria, Universidad San Sebastián, Puerto Montt, Chile
| | - María Cecilia Rauch
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | | | - Luis Vargas-Chacoff
- Centro Fondap de Investigación de Altas Latitudes, Universidad Austral de Chile, Valdivia, Chile
| | - Alejandro J Yáñez
- Interdisciplinary Center for Aquaculture Research, Concepción, Chile
- Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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10
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Saldarriaga-Córdoba M, Avendaño-Herrera R. Comparative pan-genomic analysis of 51 Renibacterium salmoninarum indicates heterogeneity in the principal virulence factor, the 57 kDa protein. JOURNAL OF FISH DISEASES 2022; 45:1173-1188. [PMID: 35604683 DOI: 10.1111/jfd.13653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Renibacterium salmoninarum, a Gram-positive intracellular pathogen, is the causative agent of bacterial kidney disease (BKD), the impacts of which are high mortalities and economic losses for the salmon industry. This study provides novel analyses for the whole-genome sequences of 50 R. salmoninarum isolates and the reference strain ATCC 33209 using a pan-genomic approach to elucidate phylogenomic relationships and identify unique and shared genes associated with pathogenicity and infection mechanisms. Genome size varied from 3,061,638 to 3,155,332 bp; gene count from 3452 to 3580; and predicted coding sequences from 3402 to 3527. Comparative analyses revealed an open, but approaching closed, pan-genome. The pan-genome analysis recovered 4064 genes, with a core genome containing 3306 genes. Phylogenetic analysis of R. salmoninarum showed high genomic homogeneity, apart from one isolate obtained from Salmo trutta in Norway. All genomes presented the 57-kDa protein (p57). Strain ATCC 33209 and the Chilean isolates H-2 and DJ2R presented two copies of the msa gene, while the remaining isolates had one copy. The pan-genome analysis further identified differences in the number of copies and length of the signalling peptide for p57, the principal virulence factor reported for this bacterium. This heterogeneity could be associated with the secretion levels of p57, potentially influencing virulence. Additionally identified were numerous common genes related to iron uptake, the stress response and regulation, and cell signalling-all of which constitute the pathogenic repertoire of R. salmoninarum. This investigation provides information that is applicable in future studies for identifying therapeutic targets and/or for designing new strategies (e.g., vaccines) to prevent BKD infections in salmon farming.
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Affiliation(s)
- Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Santiago, Chile
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Centro de Investigaciones Marina Quintay (CIMARQ), Universidad Andés Bello, Quintay, Chile
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11
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Commercial Vaccines Do Not Confer Protection against Two Genogroups of Piscirickettsia salmonis, LF-89 and EM-90, in Atlantic Salmon. BIOLOGY 2022; 11:biology11070993. [PMID: 36101374 PMCID: PMC9312220 DOI: 10.3390/biology11070993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Vaccination represents one of the most relevant strategies to prevent and control infectious diseases in aquaculture. However, vaccines have failed to control and prevent Piscirickettsia salmonis, a bacterium that causes large economic losses to the industry. Therefore, we evaluated the performance of two commercial vaccines in Atlantic salmon through a cohabitation challenge (healthy fish were challenged by cohabitation with infected fish) of the two most prevalent and ubiquitous Piscirickettsia genetic variants in Chile. We found no evidence that vaccines confer protection against the LF-89 or EM-90 genogroups in Atlantic salmon. Abstract In Atlantic salmon, vaccines have failed to control and prevent Piscirickettsiosis, for reasons that remain elusive. In this study, we report the efficacy of two commercial vaccines developed with the Piscirickettsia salmonis isolates AL100005 and AL 20542 against another two genogroups which are considered highly and ubiquitously prevalent in Chile: LF-89 and EM-90. Two cohabitation trials were performed to mimic field conditions and vaccine performance: (1) post-smolt fish were challenged with a single infection of LF-89, (2) adults were coinfected with EM-90, and a low level coinfection of sea lice. In the first trial, the vaccine delayed smolt mortalities by two days; however, unvaccinated and vaccinated fish did not show significant differences in survival (unvaccinated: 60.3%, vaccinated: 56.7%; p = 0.28). In the second trial, mortality started three days later for vaccinated fish than unvaccinated fish. However, unvaccinated and vaccinated fish did not show significant differences in survival (unvaccinated: 64.6%, vaccinated: 60.2%, p = 0.58). Thus, we found no evidence that the evaluated vaccines confer effective protection against the genogroups LF-89 and EM-90 of P. salmonis with estimated relative survival proportions (RPSs) of −9% and −12%, respectively. More studies are necessary to evaluate whether pathogen heterogeneity is a key determinant of the lack of vaccine efficacy against P. salmonis.
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12
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Fuentes DE, Acuña LG, Calderón IL. Stress response and virulence factors in bacterial pathogens relevant for Chilean aquaculture: current status and outlook of our knowledge. Biol Res 2022; 55:21. [PMID: 35642071 PMCID: PMC9153119 DOI: 10.1186/s40659-022-00391-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
The study of the stress responses in bacteria has given us a wealth of information regarding the mechanisms employed by these bacteria in aggressive or even non-optimal living conditions. This information has been applied by several researchers to identify molecular targets related to pathogeny, virulence, and survival, among others, and to design new prophylactic or therapeutic strategies against them. In this study, our knowledge of these mechanisms has been summarized with emphasis on some aquatic pathogenic bacteria of relevance to the health and productive aspects of Chilean salmon farming (Piscirickettsia salmonis, Tenacibaculum spp., Renibacterium salmoninarum, and Yersinia ruckeri). This study will aid further investigations aimed at shedding more light on possible lines of action for these pathogens in the coming years.
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Affiliation(s)
- Derie E Fuentes
- Aquaculture and Marine Ecosystems, Center For Systems Biotechnology, Fraunhofer Chile Research, Santiago, Chile. .,Environmental Sustainability, Center for Systems Biotechnology (CSB-UNAB), Universidad Andres Bello, Facultad de Ciencias de la Vida, Santiago, Chile.
| | - Lillian G Acuña
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Interdisciplinary Center for Aquaculture Research, Universidad Andres Bello, Viña del Mar, Santiago, Chile
| | - Iván L Calderón
- Laboratorio de RNAs Bacterianos, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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13
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Mesa V, Monot M, Ferraris L, Popoff M, Mazuet C, Barbut F, Delannoy J, Dupuy B, Butel MJ, Aires J. Core-, pan- and accessory genome analyses of Clostridium neonatale: insights into genetic diversity. Microb Genom 2022; 8. [PMID: 35550024 PMCID: PMC9465065 DOI: 10.1099/mgen.0.000813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Clostridium neonatale is a potential opportunistic pathogen recovered from faecal samples in cases of necrotizing enterocolitis (NEC), a gastrointestinal disease affecting preterm neonates. Although the C. neonatale species description and name validation were published in 2018, comparative genomics are lacking. In the present study, we provide the closed genome assembly of the C. neonatale ATCC BAA-265T (=250.09) reference strain with a manually curated functional annotation of the coding sequences. Pan-, core- and accessory genome analyses were performed using the complete 250.09 genome (4.7 Mb), three new assemblies (4.6–5.6 Mb), and five publicly available draft genome assemblies (4.6–4.7 Mb). The C. neonatale pan-genome contains 6840 genes, while the core-genome has 3387 genes. Pan-genome analysis revealed an ‘open’ state and genomic diversity. The strain-specific gene families ranged from five to 742 genes. Multiple mobile genetic elements were predicted, including a total of 201 genomic islands, 13 insertion sequence families, one CRISPR-Cas type I-B system and 15 predicted intact prophage signatures. Primary virulence classes including offensive, defensive, regulation of virulence-associated genes and non-specific virulence factors were identified. The presence of a tet(W/N/W) gene encoding a tetracycline resistance ribosomal protection protein and a 23S rRNA methyltransferase ermQ gene were identified in two different strains. Together, our results revealed a genetic diversity and plasticity of C. neonatale genomes and provide a comprehensive view of this species genomic features, paving the way for the characterization of its biological capabilities.
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Affiliation(s)
- Victoria Mesa
- Université de Paris, UMR-S1139, F-75006, Paris, France
| | - Marc Monot
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques, Institut Pasteur, F-75015, Paris, France.,Institut Pasteur, Université de Paris, UMR-CNRS 2001, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
| | | | - Michel Popoff
- Institut Pasteur, Université de Paris, Centre National de Référence des Bactéries anaérobies et Botulisme, F-75015, Paris, France
| | - Christelle Mazuet
- Institut Pasteur, Université de Paris, Centre National de Référence des Bactéries anaérobies et Botulisme, F-75015, Paris, France
| | - Frederic Barbut
- Université de Paris, UMR-S1139, F-75006, Paris, France.,Assistance Publique-Hôpitaux de Paris, Hôpital saint Antoine, Infection Control Unit, F-75012, Paris, France
| | | | - Bruno Dupuy
- Institut Pasteur, Université de Paris, UMR-CNRS 2001, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
| | | | - Julio Aires
- Université de Paris, UMR-S1139, F-75006, Paris, France
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14
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Rozas-Serri M. Why Does Piscirickettsia salmonis Break the Immunological Paradigm in Farmed Salmon? Biological Context to Understand the Relative Control of Piscirickettsiosis. Front Immunol 2022; 13:856896. [PMID: 35386699 PMCID: PMC8979166 DOI: 10.3389/fimmu.2022.856896] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/22/2022] [Indexed: 11/28/2022] Open
Abstract
Piscirickettsiosis (SRS) has been the most important infectious disease in Chilean salmon farming since the 1980s. It was one of the first to be described, and to date, it continues to be the main infectious cause of mortality. How can we better understand the epidemiological situation of SRS? The catch-all answer is that the Chilean salmon farming industry must fight year after year against a multifactorial disease, and apparently only the environment in Chile seems to favor the presence and persistence of Piscirickettsia salmonis. This is a fastidious, facultative intracellular bacterium that replicates in the host’s own immune cells and antigen-presenting cells and evades the adaptive cell-mediated immune response, which is why the existing vaccines are not effective in controlling it. Therefore, the Chilean salmon farming industry uses a lot of antibiotics—to control SRS—because otherwise, fish health and welfare would be significantly impaired, and a significantly higher volume of biomass would be lost per year. How can the ever-present risk of negative consequences of antibiotic use in salmon farming be balanced with the productive and economic viability of an animal production industry, as well as with the care of the aquatic environment and public health and with the sustainability of the industry? The answer that is easy, but no less true, is that we must know the enemy and how it interacts with its host. Much knowledge has been generated using this line of inquiry, however it remains insufficient. Considering the state-of-the-art summarized in this review, it can be stated that, from the point of view of fish immunology and vaccinology, we are quite far from reaching an effective and long-term solution for the control of SRS. For this reason, the aim of this critical review is to comprehensively discuss the current knowledge on the interaction between the bacteria and the host to promote the generation of more and better measures for the prevention and control of SRS.
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15
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Yuan PB, Zhan Y, Zhu JH, Ling JH, Chen EZ, Liu WT, Wang LJ, Zhong YX, Chen DQ. Pan-Genome Analysis of Laribacter hongkongensis: Virulence Gene Profiles, Carbohydrate-Active Enzyme Prediction, and Antimicrobial Resistance Characterization. Front Microbiol 2022; 13:862776. [PMID: 35432229 PMCID: PMC9008761 DOI: 10.3389/fmicb.2022.862776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
Laribacter hongkongensis is a new emerging foodborne pathogen that causes community-acquired gastroenteritis and traveler’s diarrhea. However, the genetic features of L. hongkongensis have not yet been properly understood. A total of 45 aquatic animal-associated L. hongkongensis strains isolated from intestinal specimens of frogs and grass carps were subjected to whole-genome sequencing (WGS), along with the genome data of 4 reported human clinical strains, the analysis of virulence genes, carbohydrate-active enzymes, and antimicrobial resistance (AMR) determinants were carried out for comprehensively understanding of this new foodborne pathogen. Human clinical strains were genetically more related to some strains from frogs inferred from phylogenetic trees. The distribution of virulence genes and carbohydrate-active enzymes exhibited different patterns among strains of different sources, reflecting their adaption to different host environments and indicating different potentials to infect humans. Thirty-two AMR genes were detected, susceptibility to 18 clinical used antibiotics including aminoglycoside, chloramphenicol, trimethoprim, and sulfa was checked to evaluate the availability of clinical medicines. Resistance to Rifampicin, Cefazolin, ceftazidime, Ampicillin, and ceftriaxone is prevalent in most strains, resistance to tetracycline, trimethoprim-sulfamethoxazole, ciprofloxacin, and levofloxacin are aggregated in nearly half of frog-derived strains, suggesting that drug resistance of frog-derived strains is more serious, and clinical treatment for L. hongkongensis infection should be more cautious.
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16
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Xue X, Caballero-Solares A, Hall JR, Umasuthan N, Kumar S, Jakob E, Skugor S, Hawes C, Santander J, Taylor RG, Rise ML. Transcriptome Profiling of Atlantic Salmon ( Salmo salar) Parr With Higher and Lower Pathogen Loads Following Piscirickettsia salmonis Infection. Front Immunol 2022; 12:789465. [PMID: 35035387 PMCID: PMC8758579 DOI: 10.3389/fimmu.2021.789465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/03/2021] [Indexed: 12/29/2022] Open
Abstract
Salmonid rickettsial septicemia (SRS), caused by Piscirickettsia salmonis, is one of the most devastating diseases of salmonids. However, the transcriptomic responses of Atlantic salmon (Salmon salar) in freshwater to an EM-90-like isolate have not been explored. Here, we infected Atlantic salmon parr with an EM-90-like isolate and conducted time-course qPCR analyses of pathogen load and four biomarkers (campb, hampa, il8a, tlr5a) of innate immunity on the head kidney samples. Transcript expression of three of these genes (except hampa), as well as pathogen level, peaked at 21 days post-injection (DPI). Multivariate analyses of infected individuals at 21 DPI revealed two infection phenotypes [lower (L-SRS) and higher (H-SRS) infection level]. Five fish from each group (Control, L-SRS, and H-SRS) were selected for transcriptome profiling using a 44K salmonid microarray platform. We identified 1,636 and 3,076 differentially expressed probes (DEPs) in the L-SRS and H-SRS groups compared with the control group, respectively (FDR = 1%). Gene ontology term enrichment analyses of SRS-responsive genes revealed the activation of a large number of innate (e.g. “phagocytosis”, “defense response to bacterium”, “inflammatory response”) and adaptive (e.g. “regulation of T cell activation”, “antigen processing and presentation of exogenous antigen”) immune processes, while a small number of general physiological processes (e.g. “apoptotic process”, development and metabolism relevant) was enriched. Transcriptome results were confirmed by qPCR analyses of 42 microarray-identified transcripts. Furthermore, the comparison of individuals with differing levels of infection (H-SRS vs. L-SRS) generated insights into the biological processes possibly involved in disease resistance or susceptibility. This study demonstrated a low mortality (~30%) EM-90-like infection model and broadened the current understanding of molecular pathways underlying P. salmonis-triggered responses of Atlantic salmon, identifying biomarkers that may assist to diagnose and combat this pathogen.
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Affiliation(s)
- Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Jennifer R Hall
- Aquatic Research Cluster, CREAIT Network, Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Eva Jakob
- Cargill Innovation Centre - Colaco, Colaco, Chile
| | - Stanko Skugor
- Cargill Aqua Nutrition, Cargill, Sea Lice Research Center (SLRC), Sandnes, Norway
| | | | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Lab, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Richard G Taylor
- Cargill Animal Nutrition and Health, Elk River, MN, United States
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
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17
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Lin S, Sun B, Shi X, Xu Y, Gu Y, Gu X, Ma X, Wan T, Xu J, Su J, Lou Y, Zheng M. Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains. Front Microbiol 2021; 12:770191. [PMID: 34867904 PMCID: PMC8634615 DOI: 10.3389/fmicb.2021.770191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Coagulase-negative Staphylococcus (CoNS) is the most common pathogen causing traumatic endophthalmitis. Among which, Staphylococcus epidermidis is the most common species that colonizes human skin, eye surfaces, and nasal cavity. It is also the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of S. epidermidis, the genome of ocular trauma-sourced S. epidermidis strain and a comprehensive understanding of its pathogenicity are still lacking. Our study sequenced, analyzed, and reported the whole genomes of 11 ocular trauma-sourced samples of S. epidermidis that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract, and blood. Combined with pan-genome, phylogenetic, and comparative genomic analyses, our study showed that S. epidermidis, regardless of niche source, exhibits two founder lineages with different pathogenicity. Moreover, we identified several potential biomarkers associated with the virulence of S. epidermidis, including essD, uhpt, sdrF, sdrG, fbe, and icaABCDR. EssD and uhpt have high homology with esaD and hpt in Staphylococcus aureus, showing that the genomes of S. epidermidis and S. aureus may have communicated during evolution. SdrF, sdrG, fbe, and icaABCDR are related to biofilm formation. Compared to S. epidermidis from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study provided additional data resources for studies on S. epidermidis and improved our understanding of the evolution and pathogenicity among strains of different sources.
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Affiliation(s)
- Shudan Lin
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Bianjin Sun
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Xinrui Shi
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Yi Xu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Yunfeng Gu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Xiaobin Gu
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueli Ma
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Tian Wan
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jie Xu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jianzhong Su
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Yongliang Lou
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Meiqin Zheng
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
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18
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Epi-Gene: An R-Package for Easy Pan-Genome Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5585586. [PMID: 34595238 PMCID: PMC8478537 DOI: 10.1155/2021/5585586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/28/2021] [Indexed: 11/18/2022]
Abstract
The main aim of this study was to develop a set of functions that can analyze the genomic data with less time consumption and memory. Epi-gene is presented as a solution to large sequence file handling and computational time problems. It uses less time and less programming skills in order to work with a large number of genomes. In the current study, some features of the Epi-gene R-package were described and illustrated by using a dataset of the 14 Aeromonas hydrophila genomes. The joining, relabeling, and conversion functions were also included in this package to handle the FASTA formatted sequences. To calculate the subsets of core genes, accessory genes, and unique genes, various Epi-gene functions have been used. Heat maps and phylogenetic genome trees were also constructed. This whole procedure was completed in less than 30 minutes. This package can only work on Windows operating systems. Different functions from other packages such as dplyr and ggtree were also used that were available in R computing environment.
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19
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Pan-Genome Portrait of Bacillus mycoides Provides Insights into the Species Ecology and Evolution. Microbiol Spectr 2021; 9:e0031121. [PMID: 34287030 PMCID: PMC8552610 DOI: 10.1128/spectrum.00311-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacillus mycoides is poorly known despite its frequent occurrence in a wide variety of environments. To provide direct insight into its ecology and evolutionary history, a comparative investigation of the species pan-genome and the functional gene categorization of 35 isolates obtained from soil samples from northeastern Poland was performed. The pan-genome of these isolates is composed of 20,175 genes and is characterized by a strong predominance of adaptive genes (∼83%), a significant amount of plasmid genes (∼37%), and a great contribution of prophages and insertion sequences. The pan-genome structure and phylodynamic studies had suggested a wide genomic diversity among the isolates, but no correlation between lineages and the bacillus origin was found. Nevertheless, the two B. mycoides populations, one from Białowieża National Park, the last European natural primeval forest with soil classified as organic, and the second from mineral soil samples taken in a farm in Jasienówka, a place with strong anthropogenic pressure, differ significantly in the frequency of genes encoding proteins enabling bacillus adaptation to specific stress conditions and production of a set of compounds, thus facilitating their colonization of various ecological niches. Furthermore, differences in the prevalence of essential stress sigma factors might be an important trail of this process. Due to these numerous adaptive genes, B. mycoides is able to quickly adapt to changing environmental conditions. IMPORTANCE This research allows deeper understanding of the genetic organization of natural bacterial populations, specifically, Bacillus mycoides, a psychrotrophic member of the Bacillus cereus group that is widely distributed worldwide, especially in areas with continental cold climates. These thorough analyses made it possible to describe, for the first time, the B. mycoides pan-genome, phylogenetic relationship within this species, and the mechanisms behind the species ecology and evolutionary history. Our study indicates a set of functional properties and adaptive genes, in particular, those encoding sigma factors, associated with B. mycoides acclimatization to specific ecological niches and changing environmental conditions.
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20
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Zúñiga A, Solis C, Cartes C, Nourdin G, Yañez A, Romero A, Haussmann D, Figueroa J. Transcriptional analysis of metabolic and virulence genes associated with biofilm formation in Piscirickettsia salmonis strains. FEMS Microbiol Lett 2021; 367:5948097. [PMID: 33128546 DOI: 10.1093/femsle/fnaa180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Piscirickettsia salmonis is a facultative intracellular bacterium that generates piscirickettsiosis affecting salmonids in Chile. The bacterium has the adaptability to survive in the marine environment under multiple stressful conditions. In this sense, this work focused on the analysis of a gene battery associated with biofilm formation under different culture conditions and on the adaptability of this biofilm to different media. The results indicated that the strains LF-89, IBM-034 and IBM-040 were strong biofilm producers, evidencing adaptability to the media by increasing the amount of biofilm through successive growths. Transcript levels of six genes described in various bacteria and P. salmonis, considered to have metabolic functions, and playing a relevant role in biofilm formation, were analyzed to evaluate bacterial functionality in the biofilm. The genes mazE-mazF, implicated in biofilm and stress, were markedly overexpressed in the biofilm condition in the three strains. For its part, gene gltA, an indicator of metabolic activity and related to virulence inhibition in Salmonella typhimurium, also seems to restrain the pathogenesis process in P. salmonis by inhibiting the expression of the virulence-associated genes liso and tcf. Finally, the expression of the glnA gene suggests the use of glutamine as an essential element for the growth of the biofilm.
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Affiliation(s)
- A Zúñiga
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - C Solis
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - C Cartes
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile.,FONDAP Centre: Interdisciplinary Centre for Aquaculture Research (INCAR), O'Higgins 1695, Concepción, Chile
| | - G Nourdin
- FONDAP Centre: Interdisciplinary Centre for Aquaculture Research (INCAR), O'Higgins 1695, Concepción, Chile
| | - A Yañez
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile.,FONDAP Centre: Interdisciplinary Centre for Aquaculture Research (INCAR), O'Higgins 1695, Concepción, Chile
| | - A Romero
- FONDAP Centre: Interdisciplinary Centre for Aquaculture Research (INCAR), O'Higgins 1695, Concepción, Chile.,Institute of Animal Pathology, Faculty of Veterinary Sciences, Universidad Austral de Chile. Valdivia, Chile
| | - D Haussmann
- Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Valdivia, Chile
| | - J Figueroa
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile.,FONDAP Centre: Interdisciplinary Centre for Aquaculture Research (INCAR), O'Higgins 1695, Concepción, Chile
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21
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Isla A, Martinez-Hernandez JE, Levipan HA, Haussmann D, Figueroa J, Rauch MC, Maracaja-Coutinho V, Yañez A. Development of a Multiplex PCR Assay for Genotyping the Fish Pathogen Piscirickettsia salmonis Through Comparative Genomics. Front Microbiol 2021; 12:673216. [PMID: 34177855 PMCID: PMC8226252 DOI: 10.3389/fmicb.2021.673216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/17/2021] [Indexed: 11/20/2022] Open
Abstract
Piscirickettsia salmonis is a bacterial pathogen that severely impact the aquaculture in several countries as Canada, Scotland, Ireland, Norway, and Chile. It provokes Piscirickettsiosis outbreaks in the marine phase of salmonid farming, resulting in economic losses. The monophyletic genogroup LF-89 and a divergent genogroup EM-90 are responsible for the most severe Piscirickettsiosis outbreaks in Chile. Therefore, the development of methods for quick genotyping of P. salmonis genogroups in field samples is vital for veterinary diagnoses and understanding the population structure of this pathogen. The present study reports the development of a multiplex PCR for genotyping LF-89 and EM-90 genogroups based on comparative genomics of 73 fully sequenced P. salmonis genomes. The results revealed 2,322 sequences shared between 35 LF-89 genomes, 2,280 sequences in the core-genome of 38 EM-90 genomes, and 331 and 534 accessory coding sequences each genogroup, respectively. A total of 1,801 clusters of coding sequences were shared among all tested genomes of P. salmonis (LF-89 and EM-90), with 253 and 291 unique sequences for LF-89 and EM-90 genogroups, respectively. The Multiplex-1 prototype was chosen for reliable genotyping because of differences in annealing temperatures and respective reaction efficiencies. This method also identified the pathogen in field samples infected with LF-89 or EM-90 strains, which is not possible with other methods currently available. Finally, the genome-based multiplex PCR protocol presented in this study is a rapid and affordable alternative to classical sequencing of PCR products and analyzing the length of restriction fragment polymorphisms.
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Affiliation(s)
- Adolfo Isla
- Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepcion, Concepción, Chile.,Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Santiago, Chile
| | - J Eduardo Martinez-Hernandez
- Centro de Modelamiento Molecular, Biofísica y Bioinformática - CM2B2, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.,Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile.,Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Héctor A Levipan
- Laboratorio de Ecopatología y Nanobiomateriales, Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaiso, Chile
| | - Denise Haussmann
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Santiago, Chile
| | - Jaime Figueroa
- Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepcion, Concepción, Chile
| | - Maria Cecilia Rauch
- Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
| | - Vinicius Maracaja-Coutinho
- Centro de Modelamiento Molecular, Biofísica y Bioinformática - CM2B2, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.,Instituto Vandique, João Pessoa, Brazil.,Beagle Bioinformatics, Santiago, Chile
| | - Alejandro Yañez
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepcion, Concepción, Chile.,Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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22
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Long A, Goodall A, Jones SR. Development of a Piscirickettsia salmonis immersion challenge model to investigate the comparative susceptibility of three salmon species. JOURNAL OF FISH DISEASES 2021; 44:1-9. [PMID: 33067883 PMCID: PMC7756497 DOI: 10.1111/jfd.13261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 05/03/2023]
Abstract
Piscirickettsia salmonis, the aetiological agent of salmonid rickettsial septicaemia (SRS), is a global pathogen of wild and cultured marine salmonids. Here, we describe the development and application of a reproducible, standardized immersion challenge model to induce clinical SRS in juvenile pink (Oncorhynchus gorbuscha), Atlantic (Salmo salar) and sockeye salmon (O. nerka). Following a 1-hr immersion in 105 colony-forming units/ml, cumulative mortality in Atlantic salmon was 63.2% while mortality in sockeye salmon was 10%. Prevalence and levels of the bacterium in kidney prior to onset of mortality were lower in sockeye compared with Atlantic or pink salmon. The timing and magnitude of bacterial shedding were estimated from water samples collected during the exposure trials. Shedding was estimated to be 82-fold higher in Atlantic salmon as compared to sockeye salmon and peaked in the Atlantic salmon trial at 36 d post-immersion. These data suggest sockeye salmon are less susceptible to P. salmonis than Atlantic or pink salmon. Finally, skin lesions were observed on infected fish during all trials, often in the absence of detectable infection in kidney. As a result, we hypothesize that skin is the primary point of entry for P. salmonis during the immersion challenge.
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Affiliation(s)
- Amy Long
- Fisheries and Ocean CanadaNanaimoBCCanada
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23
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Santibañez N, Vega M, Pérez T, Yáñez A, González-Stegmaier R, Figueroa J, Enríquez R, Oliver C, Romero A. Biofilm Produced In Vitro by Piscirickettsia salmonis Generates Differential Cytotoxicity Levels and Expression Patterns of Immune Genes in the Atlantic Salmon Cell Line SHK-1. Microorganisms 2020; 8:E1609. [PMID: 33092013 PMCID: PMC7594049 DOI: 10.3390/microorganisms8101609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/10/2020] [Accepted: 09/19/2020] [Indexed: 11/17/2022] Open
Abstract
Piscirickettsia salmonis is the causative agent of Piscirickettsiosis, an infectious disease with a high economic impact on the Chilean salmonid aquaculture industry. This bacterium produces biofilm as a potential resistance and persistence strategy against stressful environmental stimuli. However, the in vitro culture conditions that modulate biofilm formation as well as the effect of sessile bacteria on virulence and immune gene expression in host cells have not been described for P. salmonis. Therefore, this study aimed to analyze the biofilm formation by P. salmonis isolates under several NaCl and iron concentrations and to evaluate the virulence of planktonic and sessile bacteria, together with the immune gene expression induced by these bacterial conditions in an Atlantic salmon macrophage cell line. Our results showed that NaCl and Fe significantly increased biofilm production in the LF-89 type strain and EM-90-like isolates. Additionally, the planktonic EM-90 isolate and sessile LF-89 generated the highest virulence levels, associated with differential expression of il-1β, il-8, nf-κb, and iκb-α genes in SHK-1 cells. These results suggest that there is no single virulence pattern or gene expression profile induced by the planktonic or sessile condition of P. salmonis, which are dependent on each strain and bacterial condition used.
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Affiliation(s)
- Natacha Santibañez
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; (N.S.); (M.V.); (T.P.); (R.G.-S.); (R.E.)
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070386, Chile; (A.Y.); (J.F.)
| | - Matías Vega
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; (N.S.); (M.V.); (T.P.); (R.G.-S.); (R.E.)
| | - Tatiana Pérez
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; (N.S.); (M.V.); (T.P.); (R.G.-S.); (R.E.)
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070386, Chile; (A.Y.); (J.F.)
| | - Alejandro Yáñez
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070386, Chile; (A.Y.); (J.F.)
- Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Roxana González-Stegmaier
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; (N.S.); (M.V.); (T.P.); (R.G.-S.); (R.E.)
| | - Jaime Figueroa
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070386, Chile; (A.Y.); (J.F.)
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Ricardo Enríquez
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; (N.S.); (M.V.); (T.P.); (R.G.-S.); (R.E.)
| | - Cristian Oliver
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; (N.S.); (M.V.); (T.P.); (R.G.-S.); (R.E.)
| | - Alex Romero
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; (N.S.); (M.V.); (T.P.); (R.G.-S.); (R.E.)
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070386, Chile; (A.Y.); (J.F.)
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24
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Kumar R, Bröms JE, Sjöstedt A. Exploring the Diversity Within the Genus Francisella - An Integrated Pan-Genome and Genome-Mining Approach. Front Microbiol 2020; 11:1928. [PMID: 32849479 PMCID: PMC7431613 DOI: 10.3389/fmicb.2020.01928] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/22/2020] [Indexed: 01/13/2023] Open
Abstract
Pan-genome analysis is a powerful method to explore genomic heterogeneity and diversity of bacterial species. Here we present a pan-genome analysis of the genus Francisella, comprising a dataset of 63 genomes and encompassing clinical as well as environmental isolates from distinct geographic locations. To determine the evolutionary relationship within the genus, we performed phylogenetic whole-genome studies utilizing the average nucleotide identity, average amino acid identity, core genes and non-recombinant loci markers. Based on the analyses, the phylogenetic trees obtained identified two distinct clades, A and B and a diverse cluster designated C. The sizes of the pan-, core-, cloud-, and shell-genomes of Francisella were estimated and compared to those of two other facultative intracellular pathogens, Legionella and Piscirickettsia. Francisella had the smallest core-genome, 692 genes, compared to 886 and 1,732 genes for Legionella and Piscirickettsia respectively, while the pan-genome of Legionella was more than twice the size of that of the other two genera. Also, the composition of the Francisella Type VI secretion system (T6SS) was analyzed. Distinct differences in the gene content of the T6SS were identified. In silico approaches performed to identify putative substrates of these systems revealed potential effectors targeting the cell wall, inner membrane, cellular nucleic acids as well as proteins, thus constituting attractive targets for site-directed mutagenesis. The comparative analysis performed here provides a comprehensive basis for the assessment of the phylogenomic relationship of members of the genus Francisella and for the identification of putative T6SS virulence traits.
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Affiliation(s)
- Rajender Kumar
- Department of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Jeanette E Bröms
- Department of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Anders Sjöstedt
- Department of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
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25
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Sun Z, Zhou D, Zhang X, Li Q, Lin H, Lu W, Liu H, Lu J, Lin X, Li K, Xu T, Bao Q, Zhang H. Determining the Genetic Characteristics of Resistance and Virulence of the "Epidermidis Cluster Group" Through Pan-Genome Analysis. Front Cell Infect Microbiol 2020; 10:274. [PMID: 32596166 PMCID: PMC7303328 DOI: 10.3389/fcimb.2020.00274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/07/2020] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus caprae, Staphylococcus capitis, and Staphylococcus epidermidis belong to the “Epidermidis Cluster Group” (ECG) and are generally opportunistic pathogens. In this work, whole genome sequencing, molecular cloning and pan-genome analysis were performed to investigate the genetic characteristics of the resistance, virulence and genome structures of 69 ECG strains, including a clinical isolate (S. caprae SY333) obtained in this work. Two resistance genes (blaZ and aadD2) encoded on the plasmids pSY333-41 and pSY333-45 of S. caprae SY333 were confirmed to be functional. The bla region in ECG exhibited three distinct structures, and these chromosome- and plasmid-encoded bla operons seemed to follow two different evolutionary paths. Pan-genome analysis revealed their pan-genomes tend to be “open.” For the virulence-related factors, the genes involved in primary attachment were observed almost exclusively in S. epidermidis, while the genes associated with intercellular aggregation were observed more frequently in S. caprae and S. capitis. The type VII secretion system was present in all strains of S. caprae and some of S. epidermidis but not in S. capitis. Moreover, the isd locus (iron regulated surface determinant) was first found to be encoded on the genomes of S. caprae and S. capitis. These findings suggested that the plasmid and chromosome encoded bla operons of ECG species underwent different evolution paths, as well as they differed in the abundance of virulence genes associated with adherence, invasion, secretion system and immune evasion. Identification of isd loci in S. caprae and S. capitis indicated their ability to acquire heme as nutrient iron during infection.
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Affiliation(s)
- Zhewei Sun
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Danying Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Hailong Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Wei Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Hongmao Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
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26
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Aravena P, Pulgar R, Ortiz-Severín J, Maza F, Gaete A, Martínez S, Serón E, González M, Cambiazo V. PCR-RFLP Detection and Genogroup Identification of Piscirickettsia salmonis in Field Samples. Pathogens 2020; 9:pathogens9050358. [PMID: 32397152 PMCID: PMC7281544 DOI: 10.3390/pathogens9050358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 02/01/2023] Open
Abstract
Piscirickettsia salmons, the causative agent of piscirickettsiosis, is genetically divided into two genomic groups, named after the reference strains as LF-89-like or EM-90-like. Phenotypic differences have been detected between the P. salmonis genogroups, including antibiotic susceptibilities, host specificities and pathogenicity. In this study, we aimed to develop a rapid, sensitive and cost-effective assay for the differentiation of the P. salmonis genogroups. Using an in silico analysis of the P. salmonis 16S rDNA digestion patterns, we have designed a genogroup-specific assay based on PCR-restriction fragment length polymorphism (RFLP). An experimental validation was carried out by comparing the restriction patterns of 13 P. salmonis strains and 57 field samples obtained from the tissues of dead or moribund fish. When the bacterial composition of a set of field samples, for which we detected mixtures of bacterial DNA, was analyzed by a high-throughput sequencing of the 16S rRNA gene amplicons, a diversity of taxa could be identified, including pathogenic and commensal bacteria. Despite the presence of mixtures of bacterial DNA, the characteristic digestion pattern of the P. salmonis genogroups could be detected in the field samples without the need of a microbiological culture and bacterial isolation.
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Affiliation(s)
- Pamela Aravena
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
| | - Javiera Ortiz-Severín
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
| | - Felipe Maza
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Sebastián Martínez
- Laboratorio Especialidades Técnicas Marinas (ETECMA), Puerto Montt 5500001, Chile; (S.M.); (E.S.)
| | - Ervin Serón
- Laboratorio Especialidades Técnicas Marinas (ETECMA), Puerto Montt 5500001, Chile; (S.M.); (E.S.)
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile; (P.A.); (R.P.); (J.O.-S.); (F.M.); (A.G.); (M.G.)
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
- Correspondence:
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Kim S, Kim H, Kim Y, Kim M, Kwak H, Ryu S. Whole-Genome Sequencing-Based Characteristics in Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Retail Meats in Korea. Microorganisms 2020; 8:E508. [PMID: 32252466 PMCID: PMC7232390 DOI: 10.3390/microorganisms8040508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/23/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023] Open
Abstract
The spread of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) has posed a critical health risk to both humans and animals, because resistance to beta-lactam antibiotics makes treatment for commonly infectious diseases more complicated. In this study, we report the prevalence and genetic characteristics of ESBL-ECs isolated from retail meat samples in Korea. A total of 1205 E. coli strains were isolated from 3234 raw meat samples, purchased from nationwide retail stores between 2015 and 2018. Antimicrobial susceptibility testing was performed for all isolates by a broth microdilution method, and the ESBL phenotype was determined according to the Clinical and Laboratory Standards Institute (CLSI) confirmatory method. All ESBL-EC isolates (n = 29) were subjected to whole-genome sequencing (WGS). The antimicrobial resistance genes, plasmid incompatibility types, E. coli phylogroups, and phylogenetic relations were investigated based on the WGS data. The prevalence of ESBL-ECs in chicken was significantly higher than that in other meat samples. The results in this study demonstrate that clonally diverse ESBL-ECs with a multidrug resistance phenotype were distributed nationwide, although their prevalence from retail meat was 0.9%. The dissemination of ESBL-ECs from retail meat poses a potential risk to consumers and food-handlers, suggesting that the continuous surveillance of ESBL-ECs in retail meat should be conducted at the national level.
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Affiliation(s)
- Seokhwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Korea; (S.K.); (H.K.); (Y.K.); (M.K.)
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Hansol Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Korea; (S.K.); (H.K.); (Y.K.); (M.K.)
| | - Yonghoon Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Korea; (S.K.); (H.K.); (Y.K.); (M.K.)
| | - Migyeong Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Korea; (S.K.); (H.K.); (Y.K.); (M.K.)
| | - Hyosun Kwak
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Korea; (S.K.); (H.K.); (Y.K.); (M.K.)
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
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28
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Jones SRM, Long A, MacWilliams C, Polinski M, Garver K. Factors associated with severity of naturally occurring piscirickettsiosis in netpen- and tank-reared juvenile Atlantic salmon at a research aquarium in western Canada. JOURNAL OF FISH DISEASES 2020; 43:49-55. [PMID: 31709554 PMCID: PMC6972981 DOI: 10.1111/jfd.13102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 05/05/2023]
Abstract
The opportunistic examination of factors associated with an outbreak of piscirickettsiosis (SRS) is described in Atlantic salmon Salmo salar post-smolts held in an open netpen or in tanks supplied with raw sea water at a research aquarium in western Canada. During the outbreak, seawater temperature was significantly higher and salinity significantly lower in the netpen compared with the tanks. Mortality in the netpen began approximately 3 weeks prior to that in the tanks, and cumulative mortality in the netpen (34%) was significantly higher than in the tanks (12%). Piscirickettsia salmonis was confirmed by qPCR in tissues from moribund and dead fish and from colonies grown on enriched blood agar medium. Neither P. salmonis nor SRS were observed in salmon held concurrently in UV-irradiated sea water. The elevated mortality was curtailed by treatment with oxytetracycline. These observations further indicate warmer, less saline and periodically hypoxic seawater are risk factors for SRS. UV irradiation of sea water is shown to be a tool for SRS management in fish-holding facilities.
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Affiliation(s)
- Simon R. M. Jones
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Amy Long
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | | | - Mark Polinski
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Kyle Garver
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
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29
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Figueroa J, Castro D, Lagos F, Cartes C, Isla A, Yáñez AJ, Avendaño-Herrera R, Haussmann D. Analysis of single nucleotide polymorphisms (SNPs) associated with antibiotic resistance genes in Chilean Piscirickettsia salmonis strains. JOURNAL OF FISH DISEASES 2019; 42:1645-1655. [PMID: 31591746 DOI: 10.1111/jfd.13089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
The aetiological agent of Piscirickettsiosis is Piscirickettsia salmonis, a Gram-negative intracellular pathogen, and high doses of antibiotics have regularly been employed to treat this infection. Seven florfenicol and/or oxytetracycline resistance genes (tet pump, tetE, Tclor/flor, Tbcr, TfloR, ompF and mdtN) were identified in strains by in silico genome analyses. Later, the number of single nucleotide polymorphisms (SNPs) and its relationship with the resistance to these antibiotics were identified and analysed, using the original LF-89 strain as reference. Trials to determine and compare the minimum inhibitory concentration (MIC) of oxytetracycline and florfenicol in each strain, as well as to quantify the gPCR transcripts levels in the selected genes, were performed. Therefore, variations in the resistance to both antibiotics were observed, where the strain with fewer SNPs showed the highest susceptibility. Consistently, the in silico 3D analyses of proteins encoded by the selected genes revealed structural changes, evident in the sequences with the highest number of SNPs. These results showed that the bacterial resistance to oxytetracycline was mainly linked to the presence of SNPs in relevant sites, antibiotic resistance genes and an OmpF porin, leading to important changes in the protein structure.
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Affiliation(s)
- Jaime Figueroa
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
- FONDAP Centre, Interdisciplinary Centre for Aquaculture Research (INCAR), Concepción, Chile
| | - Diana Castro
- FONDAP Centre, Interdisciplinary Centre for Aquaculture Research (INCAR), Concepción, Chile
| | - Fernando Lagos
- FONDAP Centre, Interdisciplinary Centre for Aquaculture Research (INCAR), Concepción, Chile
| | - Carlos Cartes
- FONDAP Centre, Interdisciplinary Centre for Aquaculture Research (INCAR), Concepción, Chile
| | - Adolfo Isla
- FONDAP Centre, Interdisciplinary Centre for Aquaculture Research (INCAR), Concepción, Chile
| | - Alejandro J Yáñez
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
- FONDAP Centre, Interdisciplinary Centre for Aquaculture Research (INCAR), Concepción, Chile
| | - Rubén Avendaño-Herrera
- FONDAP Centre, Interdisciplinary Centre for Aquaculture Research (INCAR), Concepción, Chile
- Laboratory of Pathology of Aquatic Organisms and Aquaculture Biotechnology, Faculty of Life Sciences, Universidad Andrés Bello, Viña del Mar, Chile
| | - Denise Haussmann
- Department of Basic Sciences, Faculty of Sciences, Universidad Santo Tomás, Valdivia, Chile
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Piscirickettsia salmonis Cryptic Plasmids: Source of Mobile DNA and Virulence Factors. Pathogens 2019; 8:pathogens8040269. [PMID: 31795181 PMCID: PMC6963756 DOI: 10.3390/pathogens8040269] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/18/2019] [Accepted: 11/22/2019] [Indexed: 11/16/2022] Open
Abstract
Four large cryptic plasmids were identified in the salmon pathogen Piscirickettsia salmonis reference strain LF-89. These plasmids appeared highly novel, with less than 7% nucleotidic identity to the nr plasmid database. Plasmid copy number analysis revealed that they are harbored in chromosome equivalent ratios. In addition to plasmid-related genes (plasmidial autonomous replication, partitioning, maintenance, and mobilization genes), mobile genetic elements such as transposases, integrases, and prophage sequences were also identified in P. salmonis plasmids. However, bacterial lysis was not observed upon the induction of prophages. A total of twelve putative virulence factors (VFs) were identified, in addition to two global transcriptional regulators, the widely conserved CsrA protein and the regulator Crp/Fnr. Eleven of the putative VFs were overexpressed during infection in two salmon-derived cellular infection models, supporting their role as VFs. The ubiquity of these plasmids was also confirmed by sequence similarity in the genomes of other P. salmonis strains. The ontology of P. salmonis plasmids suggests a role in bacterial fitness and adaptation to the environment as they encode proteins related to mobilization, nutrient transport and utilization, and bacterial virulence. Further functional characterization of P. salmonis plasmids may improve our knowledge regarding virulence and mobile elements in this intracellular pathogen.
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31
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Sánchez P, Oliver C, Hernández M, Cortés M, Cecilia Rauch M, Valenzuela K, Garduño RA, Avendaño-Herrera R, Yáñez AJ. In vitro genomic and proteomic evidence of a type IV pili-like structure in the fish pathogen Piscirickettsia salmonis. FEMS Microbiol Lett 2019; 365:5050058. [PMID: 29986002 DOI: 10.1093/femsle/fny169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/04/2018] [Indexed: 01/24/2023] Open
Abstract
Piscirickettsia salmonis is an intracellular γ-proteobacteria and the etiological agent of piscirickettsiosis, which causes massive economic losses in the Chilean salmon industry. The type IV pili (T4P) play an important role in adherence to host cell surfaces and bacterial pathogenicity. T4P contains a variable number of components, as predicted in P. salmonis genomes. However, no studies have determined if P. salmonis possesses T4P. The aims of this investigation were to identify T4P components in the P. salmonis type strain LF-89T, evaluate respective transcript expressions, and analyze the main putative T4P proteins using bioinformatics and proteomic approaches. Two main clusters of P. salmonis T4P genes were found. Expression of the pilA gene was upregulated at 4 h post-infection (hpi), while pilQ was upregulated 4 days post-infection. At 16 hpi, pilB and pilD were strongly upregulated. The PilA amino acid sequence analysis showed a conserved N-terminal domain and sequence motifs critical for T4P biosynthesis. MudPIT analysis revealed PilA in the P. salmonis LF-89T proteome, and TEM showed pili-like filamentous structures on the P. salmonis surface. These results strongly suggest the presence of a T4P-like structure in P. salmonis.
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Affiliation(s)
- Patricio Sánchez
- Department of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070007, Chile
| | - Cristian Oliver
- Department of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070007, Chile.,Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias Biológicas, Viña del Mar 8370146, Chile
| | - Mauricio Hernández
- Austral-OMICS, Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile
| | - Marcos Cortés
- Department of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070007, Chile
| | - María Cecilia Rauch
- Department of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile
| | - Karla Valenzuela
- Microbiology and Immunology Department, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Rafael A Garduño
- Microbiology and Immunology Department, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.,Canadian Food Inspection Agency, Dartmouth Laboratory, Dartmouth, Nova Scotia B3B 1Y9, Canada
| | - Rubén Avendaño-Herrera
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070007, Chile.,Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias Biológicas, Viña del Mar 8370146, Chile
| | - Alejandro J Yáñez
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4070007, Chile.,Faculty of Sciences, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile
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Isla A, Saldarriaga-Córdoba M, Fuentes DE, Albornoz R, Haussmann D, Mancilla-Schulz J, Martínez A, Figueroa J, Avendaño-Herrera R, Yáñez A. Multilocus sequence typing detects new Piscirickettsia salmonis hybrid genogroup in Chilean fish farms: Evidence for genetic diversity and population structure. JOURNAL OF FISH DISEASES 2019; 42:721-737. [PMID: 30851000 DOI: 10.1111/jfd.12976] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
Piscirickettsia salmonisis the causative bacterial pathogen of piscirickettsiosis, a salmonid disease that causes notable mortalities in the worldwide aquaculture industry. Published research describes the phenotypic traits, virulence factors, pathogenicity and antibiotic-resistance potential for various P. salmonisstrains. However, evolutionary and genetic information is scarce for P. salmonis. The present study used multilocus sequence typing (MLST) to gain insight into the population structure and evolution of P. salmonis. Forty-two Chilean P. salmonisisolates, as well as the type strain LF-89T , were recovered from diseased Salmo salar, Oncorhynchus kisutchand Oncorhynchus mykissfrom two Chilean Regions. MLST assessed the loci sequences of dnaK, efp, fumC, glyA, murG, rpoD and trpB. Bioinformatics analyses established the genetic diversity among P. salmonis isolates (H = 0.5810). A total of 23 sequence types (ST) were identified, 53.48% of which were represented by ST1, ST5 and ST2. Population structure analysis through polymorphism patterns showed few polymorphic sites (218 nucleotides from 4,010 bp), while dN/dS ratio analysis indicated purifying selection for dnaK, epf, fumC, murG, and rpoD but neutral selection for the trpB loci. The standardized index of association indicated strong linkage disequilibrium, suggesting clonal population structure. However, recombination events were detected in a group of seven isolates. Findings included genogroups homologous to the LF-89T and EM-90 strains, as well as a seven-isolate hybrid genogroup recovered from both assessed regions (three O. mykiss and four S. salar isolates). The presented MLST scheme has comparative potential, with promising applications in studying distinct P. salmonis isolates (e.g., from different hosts, farms, geographical areas) and in understanding the epidemiology of this pathogen.
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Affiliation(s)
- Adolfo Isla
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Derie E Fuentes
- Fraunhofer Chile Research Foundation, Center for Systems Biotechnology, Santiago, Chile
| | - Romina Albornoz
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
| | - Denise Haussmann
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Valdivia, Chile
| | | | | | - Jaime Figueroa
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Santiago, Chile
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Alejandro Yáñez
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
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Zoledowska S, Motyka-Pomagruk A, Sledz W, Mengoni A, Lojkowska E. High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes. BMC Genomics 2018; 19:751. [PMID: 30326842 PMCID: PMC6192338 DOI: 10.1186/s12864-018-5140-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 10/03/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops (e.g. potato) in a wide range of different environmental conditions, encountered in Europe, North America, Africa, and New Zealand. Severe disease symptoms result from the activity of P. parmentieri virulence factors, such as plant cell wall degrading enzymes. Interestingly, we observe significant phenotypic differences among P. parmentieri isolates regarding virulence factors production and the abilities to macerate plants. To establish the possible genomic basis of these differences, we sequenced 12 genomes of P. parmentieri strains (10 isolated in Poland, 2 in Belgium) with the combined use of Illumina and PacBio approaches. De novo genome assembly was performed with the use of SPAdes software, while annotation was conducted by NCBI Prokaryotic Genome Annotation Pipeline. RESULTS The pan-genome study was performed on 15 genomes (12 de novo assembled and three reference strains: P. parmentieri CFBP 8475T, P. parmentieri SCC3193, P. parmentieri WPP163). The pan-genome includes 3706 core genes, a high number of accessory (1468) genes, and numerous unique (1847) genes. We identified the presence of well-known genes encoding virulence factors in the core genome fraction, but some of them were located in the dispensable genome. A significant fraction of horizontally transferred genes, virulence-related gene duplications, as well as different CRISPR arrays were found, which can explain the observed phenotypic differences. Finally, we found also, for the first time, the presence of a plasmid in one of the tested P. parmentieri strains isolated in Poland. CONCLUSIONS We can hypothesize that a large number of the genes in the dispensable genome and significant genomic variation among P. parmentieri strains could be the basis of the potential wide host range and widespread diffusion of P. parmentieri. The obtained data on the structure and gene content of P. parmentieri strains enabled us to speculate on the importance of high genomic plasticity for P. parmentieri adaptation to different environments.
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Affiliation(s)
- S Zoledowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - A Motyka-Pomagruk
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - W Sledz
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - A Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - E Lojkowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
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Abstract
Piscirickettsia salmonis, a fastidious Gram-negative intracellular facultative bacterium, is the causative agent o Piscirickettsiosis. P. salmonis has broad host range with a nearly worldwide distribution, causing significant mortality. The molecular regulatory mechanisms of P. salmonis pathogenesis are relatively unknown, mainly due to its difficult in vitro culture and genomic differences between genogroups. Bacterial non-coding RNAs (ncRNAs) are important post-transcriptional regulators of bacterial physiology and virulence that are predominantly transcribed from intergenic regions (trans-acting) or antisense strand of open reading frames (cis-acting). The repertoire of ncRNAs present in the genome of P. salmonis and its possible role in bacterial physiology and pathogenesis are unknown. Here, we predicted and analyzed the core ncRNAs of P. salmonis base on structure and correlate this prediction to RNA sequencing data. We identified a total of 69 ncRNA classes related to tRNAs, rRNA, thermoregulators, antitoxins, ribozymes, riboswitches, miRNAs and antisense-RNAs. Among these ncRNAs, 29 classes of ncRNAs are shared between all P. salmonis genomes, constituting the core ncRNAs of P. salmonis. The ncRNA core of P. salmonis could serve to develop diagnostic tools and explore the role of ncRNA in fish pathogenesis.
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Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas. Front Microbiol 2018; 9:771. [PMID: 29765358 PMCID: PMC5938378 DOI: 10.3389/fmicb.2018.00771] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022] Open
Abstract
The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.
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Affiliation(s)
- Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luz E Ochoa-Sánchez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas, Zaragoza, Spain.,Fundación Agencia Aragonesa para la Investigacion y el Desarrollo (ARAID), Zaragoza, Spain
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