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In the summer months of 2015 Chinook salmon,Oncorhynchus tshawytscha(Walbaum), were submitted to the New Zealand Ministry for Primary Industries (MPI) for disease investigation. Gross examination of 10 moribund fish revealed multiple areas of ulceration over all areas of the body including fins and mouth in eight of the 10 fish. Pale livers (n = 4), mottled appearance of the kidney (n = 5) and reddening of the distal intestines (n = 5) were also observed. As these fish presented with skin lesions,Piscirickettsia salmoniswas included as a differential diagnosis. Testing for this agent was conducted and a rickettsia-like organism (RLO) was detected by histopathology in seven fish and by molecular methods in three fish. Nucleic acid sequencing revealed that this organism had highest similarity to a piscirickettsia-like organism with a 19 base pair (bp) deletion in the internal transcribed spacer (ITS) region of the rDNA operon when compared to the reference strainP. salmonis, LF-89 (ATCC VR-1361). The variation was similar to that of the Tasmanian RLO detected in Atlantic salmon,Salmo salarL (GenBank accession number AY578985). Based on these sequence variations, a tentative identification of New Zealand rickettsia-like organism (NZ-RLO) was suggested. NZ-RLO is not considered to be the primary cause of the mortalities in these fish, with the primary cause still under investigation. This is the first report of a RLO in New Zealand farmed salmon. [ABSTRACT FROM PUBLISHER]

A real-time PCR assay using a molecular beacon was developed and validated to detect the vapA (surface array protein) gene in the fish pathogen, Aeromonas salmonicida. The assay had 100% analytical specificity and analytical sensitivities of 5 ± 0 fg ( DNA), 2.2 × 104 ± 1 × 104 CFU g−1 (without enrichment) and 40 ± 10 CFU g−1 (with enrichment) in kidney tissue. The assay was highly repeatable and proved to be robust following equivalency testing using a different real-time PCR platform. Following analytical validation, diagnostic specificity was determined using New Zealand farmed Chinook salmon, Oncorhynchus tshawytscha ( Walbaum), ( n = 750) and pink shubunkin, Carassius auratus ( L.) ( n = 157). The real-time PCR was run in parallel with culture and all fish tested were found to be negative by both methods for A. salmonicida, resulting in 100% diagnostic specificity (95% confidence interval). The molecular beacon real-time PCR system is specific, sensitive and a reproducible method for the detection of A. salmonicida. It can be used for diagnostic testing, health certification and active surveillance programmes. [ABSTRACT FROM AUTHOR]

Yersiniosis (enteric red mouth disease) is a contagious bacterial disease caused by Yersinia ruckeri, which primarily affects salmonids. A real-time PCR assay using a molecular beacon has been developed and validated to improve the detection of the causative biotypes of Y. ruckeri. The assay, which targets the glnA (glutamine synthetase) gene, proved to have 100% analytical specificity and analytical sensitivities of 5 fg and 3 × 103 CFU g−1 for DNA and seeded kidney tissue, respectively. The assay was highly repeatable with low % CV for intra- and inter-run experiments, and the optimized parameters transferred easily between different real-time PCR platforms. Following analytical validation, diagnostic specificity was determined using New Zealand farmed Chinook salmon ( n = 750) from 10 farms during 2007/08. The real-time PCR was run in parallel with the bacterial culture detection method, and all fish tested were found to be negative by both methods for Y. ruckeri, resulting in 100% diagnostic specificity (95% confidence interval). The molecular beacon real-time PCR system is specific, sensitive, reproducible and a rapid method for the detection of Y. ruckeri and has the potential to be used for routine diagnostic testing, health certification and active surveillance programmes. [ABSTRACT FROM AUTHOR]

Two sampling approaches for the growth of common or dominant bacteria from bivalve haemolymph were compared: (1) samples processed in the field immediately after collection (field samples), and (2) samples processed in the laboratory at least 24 h after collection (laboratory samples). The sampling approaches were compared on 210 marine bivalve molluscs Paphies subtriangulata and P. australis from two shallow intertidal sites in North Island New Zealand. The approaches were evaluated for the amount of bacterial growth, type of growth, and diversity of growth. Differences in amount and type of growth between the two sampling approaches were observed. Samples processed in the field from P. subtriangulata had significantly more bacterial growth, and a higher diversity of bacteria, including more common or dominant bacterial species. Laboratory samples had a higher proportion of samples with no growth, however common or dominant bacteria were still isolated from these samples. For P. australis, field samples more often had no bacterial growth and laboratory samples had a significantly higher number of common or dominant growth present. Field samples did however contain a higher diversity of bacteria. By conducting bacteriology on bivalves in either the field or the laboratory only, there may be limitations to determining the significance of a bacterial agent isolated. Sampling of both field and laboratory samples should be carried out where possible to optimise detection of important bacteria., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

Farmed New Zealand Chinook salmon Oncorhynchus tshawytscha Walbaum have been found to be infected by rickettsia-like organisms (NZ-RLO). While these Gram-negative intra-cellular bacteria are closely related to Piscirickettsia salmonis, a significant pathogen for farmed salmon globally, the pathogenicity of NZ-RLO is unknown. The aim of the present study was to determine if one strain, NZ-RLO2, causes disease in Chinook salmon. Post-smolt salmon were inoculated with NZ-RLO2 by intraperitoneal injection at high, medium and low doses and observed for 30 d. All fish in the high and medium dosed groups died by the end of the study and 63% of the low dose group died within 30 d of inoculation. Necropsy revealed the fish inoculated with NZ-RLO2 had internal multifocal haemorrhages. The most consistent histological finding in fish inoculated with NZ-RLO2 was neutrophilic and necrotizing pancreatitis and steatitis with intra-cytoplasmic organisms often visible within areas of inflammation. Other histological lesions included multifocal hepatic necrosis, haematopoietic cell necrosis and splenic and renal lymphoid depletion. The presence of NZ-RLO2 within the inoculated fish was confirmed by replication in cell culture and qPCR. The results suggest NZ-RLO2 can cause disease in Chinook salmon and therefore could be a significant pathogen in farmed Chinook salmon.

A PCR protocol was optimised and validated for the detection of viable Tenacibaculum maritimum cells in salmon skin tissue. Viability conventional (vPCR) and quantitative PCR (v-qPCR) assays both had a limit of detection of 10 3  CFU mL -1 viable cells. The v-qPCR assay showed a linear quantification over 4 log units. Conventional vPCR showed complete signal suppression when only dead cells were present at concentrations lower than 10 6  CFU mL -1 . While the v-qPCR did not result in complete suppression when only dead cells were present, a method was developed to determine if viable cells were present based on the % Δ in cycle threshold (Ct) value. The procedure was validated for high-throughput processing and an enrichment protocol was validated to reliably detect low concentrations of viable cells both with and without a high background of dead cells. Performing this protocol on naturally infected tissues showed that vPCR and v-qPCR reduced the potential for false positives compared to using conventional PCR and qPCR. The optimised protocol developed for this study provides an efficient, reliable and robust alternative for the detection of viable T. maritimum in skin tissue., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Case History: An investigation was conducted to identify the cause of mortalities in freshwater reared Chinook salmon (Oncorhynchus tshawytscha). Mortalities occurred in juvenile salmon, at a salmon rearing facility in the South Island of New Zealand. The affected fish were from a pen inside the facility with no surrounding pens or other year classes affected., Clinical Findings: Clinically affected fish presented with skin lesions. The majority of skin lesions were unruptured, boil-like, raised circular masses up to 4 cm in diameter, particularly on the dorsolateral aspects and the flank. A number of fish presented with large ulcers resulting from rupturing of the raised lesions described above. This clinical presentation showed similarities to that of furunculosis caused by typical Aeromonas salmonicida, a bacterium exotic to New Zealand., Laboratory Findings: Samples were taken from two representative fish in the field for histopathology, bacterial culture and molecular testing. Histopathological findings included granulomatous lesions in the kidney, liver, spleen and muscle. When stained with Fite-Faraco modified acid fast stain filamentous branching rods were identified within these granulomas. Following bacterial culture of kidney swabs pure growth of small white matt adherent colonies was observed. This isolate was identified as a Nocardia species by biochemical testing and nucleotide sequencing of the partial 16S rRNA gene. All samples were negative for A. salmonicida based on bacterial culture and PCR testing., Diagnosis: Nocardiosis caused by a Nocardia species., Clinical Relevance: Nocardiosis in these fish was caused by a previously undescribed Nocardia species that differs from the species known to be pathogenic to fish: N. asteroides, N. salmonicida and N. seriole. This bacterium is likely to be a new or unnamed environmental species of Nocardia that has the potential to cause disease in Chinook salmon under certain conditions. The clinical presentation of this Nocardia species manifested as raised, boil-like skin lesions which has similarities to the presentation of furunculosis caused by the bacterium typical A. salmonicida, a species exotic to New Zealand.

Yersinia ruckeri is a salmonid pathogen with widespread distribution in cool-temperate waters including Australia and New Zealand, two isolated environments with recently developed salmonid farming industries. Phylogenetic comparison of 58 isolates from Australia, New Zealand, USA, Chile, Finland and China based on non-recombinant core genome SNPs revealed multiple deep-branching lineages, with a most recent common ancestor estimated at 18 500 years BP (12 355-24 757 95% HPD) and evidence of Australasian endemism. Evolution within the Tasmanian Atlantic salmon serotype O1b lineage has been slow, with 63 SNPs describing the variance over 27 years. Isolates from the prevailing lineage are poorly/non-motile compared to a lineage pre-vaccination, introduced in 1997, which is highly motile but has not been isolated since from epizootics. A non-motile phenotype has arisen independently in Tasmania compared to Europe and USA through a frameshift in fliI , encoding the ATPase of the flagella cluster. We report for the first time lipopolysaccharide O-antigen serotype O2 isolates in Tasmania. This phenotype results from deletion of the O-antigen cluster and consequent loss of high-molecular-weight O-antigen. This phenomenon has occurred independently on three occasions on three continents (Australasia, North America and Asia) as O2 isolates from the USA, China and Tasmania share the O-antigen deletion but occupy distant lineages. Despite the European and North American origins of the Australasian salmonid stocks, the lineages of Y. ruckeri in Australia and New Zealand are distinct from those of the northern hemisphere, suggesting they are pre-existing ancient strains that have emerged and evolved with the introduction of susceptible hosts following European colonization.

During the 2010-11 summer outbreak of ostreid herpesvirus 1 (OsHV-1) in New Zealand, an opportunistic longitudinal field study was conducted. OsHV-1 PCR-negative oyster spat (Crassostrea gigas) were relocated to an OsHV-1 PCR-positive area of the North Island of New Zealand that was experiencing juvenile oyster mortalities. Over a period of 13 d, spat were monitored for mortality, sampled for histopathology, and tested for the presence of OsHV-1 using real time PCR and Vibrio culture. Histopathology showed some evidence of tissue pathology; however, no consistent progressive pathology was apparent. Field mortalities were evident from Day 6 on. After 5 and 7 d of exposure, 83 and 100% of spat, respectively, tested positive for the virus by real time PCR. Vibrio species recovered during the longitudinal study included V. splendidus and V. aestuarianus. This study offers insight into the rapidity of onset and virulence of the virus in naïve oyster spat in New Zealand waters.