Detection and identification of aquatic mycobacteria in formalin-fixed, paraffin-embedded fish tissues

Review of methods for detection and characterization of non-tuberculous mycobacteria in aquatic organisms

Mycobacteriosis is an emerging and often lethal disease of aquatic organisms caused by several non-tuberculous mycobacteria (NTM) species. Early diagnosis of mycobacteriosis in aquaculture and aquatic settings is critical; however, clinical diagnoses and laboratory detection are challenging, and the available literature is scarce. In an attempt to fill the gap, here we review the most relevant approaches to detect and characterize mycobacteria in clinical specimens of aquatic organisms. Emphasis is given to recent advances in molecular methods used to differentiate NTM species spanning from targeted gene sequencing to next-generation sequencing. Further, given that there are major gaps in our understanding of the prevalence of the different NTM species, partially because of their distinct requirements for in vitro growth, we also reviewed the most relevant NTM species reported to cause disease in aquatic organisms and their specific in vitro growth conditions. We also highlight that traditional bacterial culture continues to be relevant for NTM identification, particularly in non-automated laboratories. However, for NTM species discrimination, a high level of accuracy can be achieved with MALDI-TOF MS and molecular approaches, especially targeted gene sequencing applied from clinical specimens or from pure NTM isolates.

Mycobacteriosis in Farmed Sea Bream (Sparus aurata) Caused By Mycobacterium frederiksbergense in Turkey

Over the past decades, different mycobacteriosis agents have become important fish pathogens. The present study describes a different mycobacteriosis in farmed sea bream (Sparus aurata) caused by Mycobacterium frederiksbergense in Turkey. Affected 15 fish, weighing 15 to 20 g, showed lethargy, stunted growth, pale skin, dorsal fin necrosis, and a significant level of mortality (40 %) in fish stocks. Internally, no multifocal white-colored granulomas in the visceral organs were observed. Inoculation of the visceral organs onto Löwenstein-Jensen medium and Tryptic Soy Agar (1.5% NaCl) slants produced only fast-growing (2-3 weeks), orange to yellow-colored, photochromogenic acid-fast colonies. Ziehl-Nielsen positive bacterial isolates were identified using a commercially available line probe assay (Genotype Mycobacterium CM/AS assay) and with 16S rRNA gene sequencing analysis based on 16S rRNA gene sequencing, fifteen isolates were identified as Mycobacterium frederiksbergense. Histopathologically, epithelioid cell granulomas were not observed in any vicseral organs but acid-fast bacteria were detected in the liver, kidney, spleen, and heart tissue. This study shows that asystemic mycobacteriosis is observed in sea bream with high mortality.

First case report of human infection with Mycobacterium stomatepiae

Introduction

We describe the first detailed case report of human infection with Mycobacterium stomatepiae. Infection with non-tuberculous mycobacteria (NTM) related to M. stomatepiae is well described, despite the lack of previous confirmed reports of M. stomatepiae-related human disease. Localised cervical lymphadenitis is the most common NTM disease in children, with species closely related to M. stomatepiae, such as Mycobacterium triplex and Mycobacterium florentinum, having been shown to be rare causative agents.

Case presentation

A 19-month-old girl presented with persistent unilateral neck lumps which developed following a facial laceration. Both lumps were fluctuant with overlying erythema and no fistulae present. Incision and drainage with curettage was performed. The operative sample of purulent fluid revealed pleomorphic bacilli on Ziehl–Neelsen staining. The isolate cultured was referred for further genotypic identification via 16S rRNA gene sequencing, identifying the organism as M. stomatepiae.

Conclusion

We describe the first detailed case report of human infection with M. stomatepiae. This organism can now be added to the growing list of NTM that are opportunistic human pathogens, though it is likely to remain a very rare causative agent of this clinical syndrome. Early diagnosis relies on clinical suspicion by the treating doctor, flagging potential cases to the microbiology laboratory and hence allowing correct specimen set-up. Laboratory diagnosis requires incubation of cultures at lower temperatures, and definitive identification is best performed by sequencing methods, including 16S rRNA gene sequencing. The description of novel species of NTM causing human disease is likely to increase with further advancements in diagnostic methods.

Relative prevalence of Mycobacterium marinum in fish collected from aquaria and natural freshwaters in central Europe

A survey was carried out on occurrence of Mycobacterium marinum in fish kept in aquaria and those living in their natural environment. Species-specific qPCR targeting the erp and IS2404 genes together with the conventional culture method were used. The analysis of 72 ornamental fish (n = 216 samples: gills, muscle and intestine) collected from aquaria revealed the presence of M. marinum in 30 individuals (41.7%) of whom 17 (23.6%) were later culture positive. Culture-independent detection revealed the presence of M. marinum in 16 of 83 environmental samples (19.3%) collected in aquaria. The presence of viable M. marinum cells was later confirmed in 5 samples (6.0%). No qPCR or culture positivity was observed when 123 groundwater fish and their corresponding environmental samples (n = 142) were analysed.

Analysis of sediments and plants from the system of five fishponds in the Czech Republic using culture and PCR methods

Nontuberculous mycobacteria (NTM) are ubiquitous organisms that have been isolated from a variety of environmental sources. Several NTM species are responsible for diseases in humans and/or animals known as mycobacterioses. The aim of this study was to determine the levels of NTM in the sediments and plants of five fish ponds in the Czech Republic using culture and quantitative real time PCR (qPCR). Additionally, we investigated if there was any link between environmental samples from the fish ponds and the fish occupying them. A total of 8 NTM (14.0%) were cultured from the aquatic environment. qPCR analysis showed that Mycobacterium avium hominissuis was most frequently present (54.4%), followed by Mycobacterium avium paratuberculosis (42.1%). The least frequently isolated NTM was Mycobacterium avium avium (5.3%). Thus, in this study we confirm the presence of mycobacteria in sediments and aquatic plants in fishponds, which are occupied by fish intended for human consumption. We successfully isolated NTM from the tissue of one fish and confirmed a possible transmission of mycobacteria from the aquatic environment to the fish. Consequently, the consumption of such fish represents a possible risk for consumers, particularly immunocompromised individuals.

Mycobacteriosis in zebrafish colonies

Mycobacteriosis, a chronic bacterial infection, has been associated with severe losses in some zebrafish facilities and low-level mortalities and unknown impacts in others. The occurrence of at least six different described species (Mycobacterium abscessus, M. chelonae, M. fortuitum, M. haemophilum, M. marinum, M. peregrinum) from zebrafish complicates diagnosis and control because each species is unique. As a generalization, mycobacteria are often considered opportunists, but M. haemophilum and M. marinum appear to be more virulent. Background genetics of zebrafish and environmental conditions influence the susceptibility of fish and progression of disease, emphasizing the importance of regular monitoring and good husbandry practices. A combined approach to diagnostics is ultimately the most informative, with histology as a first-level screen, polymerase chain reaction for rapid detection and species identification, and culture for strain differentiation. Occurrence of identical strains of Mycobacterium in both fish and biofilms in zebrafish systems suggests transmission can occur when fish feed on infected tissues or tank detritus containing mycobacteria. Within a facility, good husbandry practices and sentinel programs are essential for minimizing the impacts of mycobacteria. In addition, quarantine and screening of animals coming into a facility is important for eliminating the introduction of the more severe pathogens. Elimination of mycobacteria from an aquatic system is likely not feasible because these species readily establish biofilms on surfaces even in extremely low nutrient conditions. Risks associated with each commonly encountered species need to be identified and informed management plans developed. Basic research on the growth characteristics, disinfection, and pathogenesis of zebrafish mycobacteria is critical moving forward.

Comparison of fixatives and fixation time for PCR detection of Mycobacterium in zebrafish Danio rerio

Mycobacteriosis is a common disease of laboratory zebrafish Danio rerio. Different infection patterns occur in zebrafish depending on mycobacterial species. Mycobacterium marinum and M. haemophilum produce virulent infections associated with high mortality, whereas M. chelonae is more widespread and is not associated with high mortality. Identification of mycobacterial infections to the species level provides important information for making management decisions. Observation of acid-fast bacilli in histological sections or tissue imprints is the most common diagnostic method for mycobacteriosis in fish, but only allows for diagnosis to the genus level. Mycobacterial culture followed by molecular or biochemical identification is the traditional approach, but DNA of diagnostic value can also be retrieved from paraffin blocks. Here we investigated the type of fixative, time in fixative before processing, species of mycobacteria, and severity of infection as parameters to determine whether the hsp gene PCR assay (primer set HS5F/hsp667R) could detect and amplify mycobacterial DNA from paraffin-embedded zebrafish. Whole zebrafish were experimentally infected with either M. chelonae or M. marinum, and then preserved in 10% neutral buffered formalin or Dietrich's fixative for 3, 7, 21, and 45 d. Subsequently, fish were evaluated by hematoxylin and eosin and Fite's acid-fast stains to detect mycobacteria within granulomatous lesions. The PCR assay was quite effective and obtained PCR product from 75 and 88% of the M. chelonae- and M. marinum-infected fish, respectively. Fixative type, time in fixative, and mycobacterial species showed no statistical relationship with the efficacy of the PCR test.

Molecular detection of nontuberculous mycobacteria: advantages and limits of a broad-range sequencing approach

The isolation of nontuberculous mycobacteria (NTM) from clinical specimens has become very common in recent years. Such organisms are typically environmental and occasionally pathogenic for humans and animals. Standard diagnosis of mycobacterial infections relies on direct examination and culture. However, molecular tools are now available which allow quicker and more accurate diagnosis. Detection of NTM can be performed directly from clinical samples, although identification is mostly carried out after isolation. Sequencing of genomic targets (such as 16S rRNA, ITS, rpoB or hsp65) allows accurate and rapid identification, but has some technical limitations. A brief summary of the molecular methods available for NTM identification and a discussion of the problems associated with the use of sequencing analysis together with a description of available algorithms for NTM identification are the major objectives of this review.

Micobacteriose por Mycobacterium marinum em "linguado" Paralichthys orbignyanus e em "barber goby" Elacatinus figaro: diagnóstico histopatológico e imuno-histoquímico

As micobacterioses afetam várias espécies de peixes, tanto comerciais como ornamentais. É uma enfermidade sistêmica com formação de granulomas, conhecida como micobacteriose de peixes. O desenvolvimento da aquicultura tem aumentado o número de casos com essa enfermidade que muitas vezes é de difícil diagnóstico. Neste trabalho apresentamos dois casos de micobacterioses em Paralichthys orbignyanus e Elacatinus figaro provenientes do Laboratório de Piscicultura Estuarina e Marinha da Universidade Federal do Rio Grande (FURG). As micobactérias de peixes possuem menos ácidos graxos que as de mamíferos, por isso foi utilizado o protocolo de coloração de Fite-Faraco, uma vez que o protocolo de coloração clássico de Ziehl Neelsen pode resultar em falsos negativos. Para determinar o tipo de micobactéria foi utilizada a imuno-histoquímica com a qual se pode diagnosticar a presença de Mycobacterium marinum. A enfermidade pode ser transmitida para o homem e com esse trabalho ressalta-se a necessidade de fazer o diagnóstico correto e implantar medidas de proteção para as pessoas que estão em contato com os peixes infectados.

Diagnosis of mycobacterial infections in the exotic pet patient with emphasis on birds

The term “mycobacteriosis” encompasses a variety of infectious diseases of animals caused by bacteria of the genus Mycobacterium, which are chronic and debilitating diseases. More than 35 Mycobacterium spp can cause mycobacteriosis. The wide range of possible clinical signs and physical exam findings can make the antemortem diagnosis inconsistent and challenging. Proper sample collection and test modality in relation to the state of the disease process are essential. Clinicians can determine a presumptive diagnosis of mycobacteriosis, but the definitive etiologic diagnosis of mycobacteriosis relies on the correct identification of the mycobacteria through microbiological and molecular diagnostic methods.

Mycobacterial lesions in fish, amphibians, reptiles, rodents, lagomorphs, and ferrets with reference to animal models

Mycobacteriosis is a serious disease across many animal species. Approximately more than 120 species are currently recognized in the genus Mycobacterium. This article describes the zoonotic potential of mycobacteria and mycobacteriosis in fish, amphibians, rodents, rabbits, and ferrets. It considers clinical signs; histology; molecular methods of identification, such as polymerase chain reaction and DNA sequencing; routes of infection; and disease progression. Studying the disease in animals may aid in understanding the pathogenesis of mycobacterial infections in humans and identify better therapy and preventative options such as vaccines.

Mycobacterium marinum infections in humans and tracing of its possible environmental sources

The low frequency of nontuberculous mycobacterial infections, nonspecific symptoms for individual mycobacteria, and the lack of specific identification methods could alter correct diagnosis. This study presents a combined microbiology and molecular-based approach for Mycobacterium marinum detection in four aquarists with cutaneous mycobacterial infection. Simultaneously, ecology screening for M. marinum presence in the aquarists' fish tanks was performed. A total of 38 mycobacterial isolates originated from four human patients (n = 20), aquarium animals (n = 8), and an aquarium environment (n = 10). Isolate identification was carried out using 16S rRNA sequence analysis. A microbiology-based approach, followed by 16S rRNA sequence analysis, was successfully used for detection of M. marinum in all four patients. Animal and environmental samples were simultaneously examined, and a total of seven mycobacterial species were isolated: Mycobacterium chelonae , Mycobacterium fortuitum , Mycobacterium gordonae , Mycobacterium kansasii , Mycobacterium mantenii , Mycobacterium marinum , and Mycobacterium peregrinum . The presence of M. marinum was proven in the aquarium environments of two patients. Although M. marinum is described as being present in water, it was detected only in fish.