Use of MALDI-TOF Mass Spectrometry for the Fast Identification of Gram-Positive Fish Pathogens

Characterization of Lactococcus garvieae and Streptococcus agalactiae in cultured red tilapia Oreochromis sp. in Thailand

OBJECTIVE

Acute mortality with clinical symptoms of streptococcal-like infections was observed in red tilapia Oreochromis sp. cultured in floating cages in Prachin Buri Province, Thailand, during May 2023. Herein, we identified an emerging pathogen, Lactococcus garvieae, as the etiological agent.

METHODS

After bacterial isolation from the brain and kidney of diseased fish, identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and the VITEK 2 system. Sequencing of the 16S ribosomal RNA (rRNA) gene and phylogenetic analysis were applied to confirm bacterial species. Antimicrobial susceptibility testing was conducted. Histopathological findings in the brain, kidney, spleen, liver, and heart were evaluated.

RESULT

From 20 fish samples, L. garvieae (n = 18 isolates) and Streptococcus agalactiae (n = 2 isolates) were identified. A phylogenetic tree of the 16S rRNA gene revealed that Thai isolates of either L. garvieae or S. agalactiae clustered with reference piscine isolates from intercontinental locations. Our isolates showed resistance against quinolones while being susceptible to other antimicrobials. Histopathological changes demonstrated severe septicemic conditions, with more invasive lesions-especially in the heart and liver-being apparent in L. garvieae-infected fish compared to S. agalactiae-infected fish.

CONCLUSION

This study represents the first reported outbreak of L. garvieae with a concurrent S. agalactiae infection in farmed red tilapia in Thailand.

Mixed Eimeria and Cryptosporidium infection and its effects on pathology and clinical outcomes in juvenile Asian seabass (Lates calcarifer) cultured in Thailand

Coccidiosis is an important disease in juvenile fish because of severe intestinal injury during infection. We first reported the mixed infection of intestinal coccidia and its association with health status and pathological findings in juvenile Asian seabass (Lates calcarifer) cultured in Thailand. Two groups of Asian seabass, 60-day fish and 90-day fish, were sampled to investigate prevalence and coccidian infection intensity using morphological characterization and PCR. Phylogenetic analysis of 18S rRNA gene amplified from the intestines revealed Eimeria sp. and Cryptosporidium sp. infection. The prevalence of Eimeria sp. and Cryptosporidium sp. in sampled fish was 100%. Clinical outcomes assessed, using health assessment index (HAI) scoring and semi-quantitative grading of intestinal lesions and inflammation, demonstrated that all fish developed variety of pathology and clinical illness; however, infection intensity in 60-day fish was significantly higher (p < .05) than 90-day fish. The HAI score of 60-day fish was poorer than 90-day fish, which correlated to a high infection intensity (r = .397), analysed by Pearson correlation coefficient. Overproduction of intestinal oxidants contributing to mucosal injury was examined by nitrotyrosine expression. The high production of reactive nitrogen species indicated severe inflammatory response, and intestinal injuries occurred mainly in the 60-day fish.

Comparison of MALDI-TOF mass spectrometry and 16S rDNA sequencing for identification of environmental bacteria: a case study of cave mussel-associated culturable microorganisms

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used as a rapid and cost-effective method for pathogen identification in clinical settings. In comparison, its performance in other microbiological fields, such as environmental microbiology, is still being tested, although isolates of environmental microbes are essential for in-depth in vivo studies of their biology, including biotechnological applications. We investigated the applicability of MALDI-TOF MS for the identification of bacterial isolates from a highly oligotrophic environment - Dinaric Karst caves, which likely harbor specific microorganisms. We cultured bacteria from the shell surface of the endemic mussel Congeria jalzici, one of the three known cave mussels in the world that lives in the Dinaric karst underground. The bacterial isolates were obtained by swabbing the shell surface of mussels living in microhabitats with different amounts of water: 10 air-exposed mussels, 10 submerged mussels, and 10 mussels in the hygropetric zone. A collection of 87 pure culture isolates was obtained, mostly belonging to the phylum Bacillota (72%), followed by Pseudomonadota (16%), Actinomycetota (11%), and Bacteroidota (1%). We compared the results of MALDI-TOF MS identification (Bruker databases DB-5989 and version 11, v11) with the results of 16S rDNA-based phylogenetic analysis, a standard procedure for bacterial identification. Identification to the genus level based on 16S rDNA was possible for all isolates and clearly outperformed the results from MALDI-TOF MS, although the updated MALDI-TOF MS database v11 gave better results than the DB-5989 version (85% versus 62%). However, identification to the species-level by 16S rDNA sequencing was achieved for only 17% of isolates, compared with 14% and 40% for the MALDI-TOF MS databases DB-5989 and v11 database, respectively. In conclusion, our results suggest that continued enrichment of MALDI-TOF MS libraries will result with this method soon becoming a rapid, accurate, and efficient tool for assessing the diversity of culturable bacteria from different environmental niches.

Association between bacterial pathogenicity, endometrial histological changes and clinical prognosis in canine pyometra

Despite the high frequency and clinical relevance of canine pyometra, its pathogenesis remains poorly understood. In this study, the clinical data, histopathological alterations, and microbiological findings of 39 dogs with pyometra were analyzed to assess possible associations. The mean age of the affected animals was 9.6 ± 3.8 years; 76.3 % (29/38) had open cervix pyometra, 88 % (22/25) had tachypnea, 71 % (27/38) had anorexia, and 60.5 % (23/38) had leukocytosis. Histopathological analysis revealed that 66.5 % (26/39) of the uteri had a high degree of inflammation (score 4). Third-degree hyperplasia of the endometrial epithelium (72 %, 28/39) and intralesional or intrauterine bacteria (66.5 %, 26/39) were identified in most animals. Bacterial isolates were obtained from 82 % (32/39) of the uterine contents and five bacterial species were identified. Escherichia coli, classified in phylogroup B2, is associated with virulent adhesion genes (fimH, focG, and papC), and serum resistance (traT) was the most common isolate. There was an association between the detection of papC in E. coli isolates and higher necrosis scores. Additionally, the necrosis score was positively associated with the length of hospitalization, with each point increase in the necrosis score leading to two more days of hospitalization. These results suggest that papC-positive E. coli play an important role in the severity of pyometra in dogs. The present study revealed the possibility of using this virulence gene to better understand the prognosis of the disease in an affected animal.

Profile of lactic acid bacteria (MALDI-TOF-MS) and physico-chemical and microbiological characteristics of the raw milk and fresh artisanal cheese from Serra Geral, Minas Gerais, Brazil

Artisanal cheese from Serra Geral, Minas Gerais, Brazil, stands out for its cultural asset and socio-economic relevance. However, standards of identity and quality and the peculiar terroir associated with the edaphoclimatic conditions have not been established. Therefore, the production flow diagram and the physico-chemical and microbiological quality of the raw milk, pingo (natural starter culture), production benches, water and fresh cheese were investigated for the first time. In addition, lactic acid bacteria (LAB) from cheese and its production environment were identified by MALDI-TOF. For that, 12 cheese making facilities were selected. The raw milk and pingo showed adequate physico-chemical characteristics for cheesemaking; however, high microbial counts were found. In the water, total and thermotolerant coliforms were also identified. The fresh cheeses were classified as 'high moisture and fat' and 'soft mass'. Most physico-chemical parameters were satisfactory; however, there were high counts of total coliforms, Staphylococcus spp. and coagulase-positive staphylococci. There were high counts of LAB in the raw milk, pingo, bench surface and fresh cheese. A total of 84 microbial biotypes from MRS agar were isolated. Lactococcus lactis was the predominant LAB, followed by Lactococcus garvieae. Leuconostoc mesenteroides (benches), Leuconostoc pseudomesenteroides (fresh cheese), and Enterococcus faecium (pingo) were identified sporadically. These results indicate the risks to public health associated with the consumption of the fresh cheese, and measures to improve its safety are needed.

Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms

Long-term sequelae of coronavirus disease (COVID)-19 are frequent and of major concern. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection affects the host gut microbiota, which is linked to disease severity in patients with COVID-19. Here, we report that the gut microbiota of post-COVID subjects had a remarkable predominance of Enterobacteriaceae strains with an antibiotic-resistant phenotype compared to healthy controls. Additionally, short-chain fatty acid (SCFA) levels were reduced in feces. Fecal transplantation from post-COVID subjects to germ-free mice led to lung inflammation and worse outcomes during pulmonary infection by multidrug-resistant Klebsiella pneumoniae. transplanted mice also exhibited poor cognitive performance. Overall, we show prolonged impacts of SARS-CoV-2 infection on the gut microbiota that persist after subjects have cleared the virus. Together, these data demonstrate that the gut microbiota can directly contribute to post-COVID sequelae, suggesting that it may be a potential therapeutic target.

Isolation, screening, and identification of chitinase-producing bacterial strains from riverbank soils at Ambo, Western Ethiopia

Chitinases are hydrolytic enzymes that dissolve the glycosidic linkages in chitin. Chitin is a cell wall component of fungi and fund in exoskeleten of worms and arthropods. Chitinase has been applied in agriculture, as a biopesticide for the control of plant fungal infections, in medicine, and in waste management. This research aimed to isolate, screen, and identification of chitinase-producing bacteria from riverbank soils. Twenty nine chitinolytic bacteria were isolated from the river bank soil samples, from which 9 of them had strong chitinolytic properties. Chitinase production was determined by zones of hydrolysis produced after 96 h of incubation at 37 °C. The different bacterial isolates were characterized morphologically, microscopically, and biochemically and finally eight strain were identified at species level by Matrix Assisted Laser Desorption Ionization - Time of Flight Mass Spectrometry (MALDI-TOF MS). From the eight, bacterial isolates investigated in this study Stenotrophomonas maltophilia showed the highest chitinase enzyme activity (625 μg/mL) followed by Pseudomonas putida with the enzyme activity of (553 μg/mL) and the least enzyme activity was recorded for Lilliottia amnigena (80 μg/mL). An incubation temperature of 45 °C, neutral pH and an incubation period of 96 h are found to be the optimum condition for the chitinase enzyme production from Stenotrophomonas maltophilia. The results of this study indicated the possibility of the production of chitinase from the chitinolytic bacterial isolates, which was highly useful for a variety of applications, including biocontrol of harmful insects and pathogenic fungi as well as in the biochemical, pharmaceutical, and medical sectors.

ANTIMICROBIAL SUSCEPTIBILITY OF STAPHYLOCOCCUS SPP. ISOLATED FROM FELIDS AND CANIDS IN BELO HORIZONTE ZOO, BRAZIL

The epidemiology of Staphylococcus spp. has become a major concern among humans and animals due to increasing antimicrobial resistance and frequent reports of infection. Despite the importance of animals as reservoirs for staphylococci, little is known about the epidemiology of Staphylococcus spp. in most nondomestic species, including canids and felids. This study evaluated the frequency, distribution, and patterns of antimicrobial resistance of staphylococcal species isolated from captive felids and canids from Belo Horizonte Zoo, Brazil. Rectal, oral, and nasal swabs from apparently healthy maned wolves (Chrysocyon brachyurus, n= 7), a lion (Panthera leo, n = 1), jaguars (Panthera onca, n = 3), and one swab of a cougar (Puma concolor) with an ear infection were streaked onto mannitol salt agar. Colonies identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry, polymerase chain reaction for the Staphylococcus intermedius group (SIG), and 16S rRNA gene sequencing. Isolates were subjected to antimicrobial susceptibility tests and Staphylococcus pseudintermedius strains were subjected to multilocus sequence typing. Staphylococcus species were isolated from 24 of the 34 samples (70.6%). Among the isolated strains, S. pseudintermedius and Staphylococcus felis were the most frequent species (41.7 and 25%, respectively). Five novel sequence types were identified among the S. pseudintermedius isolates. Resistance to tetracycline (7/24, 29.2%) or penicillin (6/23, 26.1%) was significantly higher than the other antimicrobial agents tested (P < 0.05). One isolate, Staphylococcus nepalensis, was positive for mecA and resistant to five antimicrobials, and was thus classified as multidrug-resistant. The present work suggests that maned wolves are natural hosts of SIG and also reports the isolation of S. felis in sick and healthy, captive, nondomestic carnivores. The isolated staphylococci were susceptible to most classes of antimicrobials tested. However, the multidrug-resistance capability of an S. nepalensis strain reinforces the hypothesis that felids and canids act as reservoirs of pathogens with antimicrobial resistance.

Risk Factors, Genetic Diversity, and Antimicrobial Resistance of Staphylococcus spp. Isolates in Dogs Admitted to an Intensive Care Unit of a Veterinary Hospital

Intensive Care Units (ICU) usually provide an excellent environment for the selection of pathogens associated with hospital-acquired infections (HAI), leading to increased mortality and hospitalization costs. Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a major cause of HAI in dogs worldwide, but the risk factors and dynamics of colonization by MRSP are largely unknown. This study aimed to evaluate the risk factors associated with the acquisition of MRSP in dogs admitted to an ICU, and to report the antimicrobial resistance profiles and genetic relatedness of MRSP isolates. Sterile swabs from the nostril, axilla, and rectum were collected daily during the hospitalization of 54 dogs. Samples were subjected to Mannitol Salt Agar, and colonies were identified by MALDI-ToF, polymerase chain reaction (PCR), and sequencing of the rpoB gene. Antimicrobial susceptibility testing and PCR detection of mecA were performed. Staphylococcus spp. was isolated from 94% of the dogs, and the most frequently isolated species was S. pseudintermedius (88.2%). Carriage of multidrug resistant (MDR) staphylococci was observed in 64.4% of the dogs, and approximately 39% had methicillin-resistant Staphylococcus sp. (MRS), of which 21.6% had MRSP and 1.9% had methicillin-resistant S. aureus (MRSA). The acquisition of MRSP during ICU hospitalization was associated with sex (female), age (>7 years), and dogs that had previously been treated with antimicrobials. Animals colonized by MRSP resistant to ≥9 antimicrobial classes had longer hospital stays than those colonized by other MRS strains. Among the 13 MRSP isolates that were subjected to whole-genome sequencing, ten were classified as ST71. A single nucleotide polymorphism (SNP) analysis revealed three clones, including one that was detected in infected dogs outside the ICU. This study indicates novel risk factors associated with colonization by MRSP. The detection of the same MRSP clone causing HAI outside the ICU reinforces the need for improved infection prevention and control practices at veterinary hospitals in general and at the ICU in particular.

Hydrothermal pre-treatment followed by anaerobic digestion for the removal of tylosin and antibiotic resistance agents from poultry litter

Hydrothermal pretreatment (HPT) followed by anaerobic digestion (AD) is an alternative for harvesting energy and removing organic contaminants from sewage sludge and animal manure. This study investigated the use, in an energetically sustainable way, of HPT and AD, alone or combined, to produce methane and remove tylosin and antimicrobial resistance genes (ARG) from poultry litter (PL). The results showed that HPT at 80 °C (HPT80), followed by single-stage AD (AD-1S), led to the production of 517.9 ± 4.7 NL CH₄ kg VS^-1, resulting in 0.11 kWh kg PL^-1 of electrical energy and 0.75 MJ kg PL^-1 of thermal energy, thus supplying 33.6% of the energy spent on burning firewood at a typical farm. In this best-case scenario, the use of HPT alone reduced tylosin concentration from PL by 23.6%, while the process involving HPT followed by AD-1S led to the removal of 91.6% of such antibiotic. The combined process (HPT80 + AD-1S), in addition to contributing to reduce the absolute and relative abundances of ARG ermB (2.13 logs), intI1 (0.39 logs), sul1 (0.63 logs), and tetA (0.74 logs), led to a significant removal in the relative abundance of tylosin-resistant bacteria present in the poultry litter.

Health Monitoring for Laboratory Salamanders

Laboratory animal health monitoring programs are necessary to protect animal health and welfare, the validity of experimental data, and human health against zoonotic infections. Health monitoring programs should be designed based on a risk assessment and knowledge about the biology and transmission of salamander pathogens. Both traditional and molecular diagnostic platforms are available for salamanders, and they provide complementary information. A comprehensive approach to health monitoring leverages the advantages of multiple platforms to provide a more complete picture of colony health and pathogen status. This chapter presents key considerations in the design and implementation of a colony health monitoring program for laboratory salamanders, including protocols for necropsy and sample collection.

First report and whole-genome sequencing of Pseudochrobactrum saccharolyticum in Latin America

The Brucellaceae family comprises microorganisms similar both phenotypically and genotypically, making it difficult to identify the etiological agent of these infections. This study reports the first isolation, identification, and characterization of Pseudochrobactrum saccharolyticum (strain 115) from Latin America. Strain 115 was isolated in 2007 from a bovine in Brazil and was initially classified as Brucella spp. by classical microbiological tests and bcsp31 PCR. The antimicrobial susceptibility of strain 115 was tested against drugs used to treat human brucellosis by minimal inhibitory concentration test. Subsequently, the whole genome of the strain was sequenced, assembled, and characterized. Phylogenetic trees built from 16S rRNA and recA gene sequences enabled the classification of strain 115 as Pseudochrobactrum spp. Phylogenomic analysis using Single Nucleotide Polymorphisms and Average Nucleotide Identity allowed the classification of the strain as P. saccharolyticum. Additionally, a Tetra Correlation Search identified one related genome from the same species, which was compared with strain 115 by analyzing genomic islands. This is the first identification and whole-genome sequence of P. saccharolyticum in Latin America and highlights a challenge in the diagnosis of bovine brucellosis, which could be solved by including the sequencing of 16S rRNA and recA genes in routine diagnostics.

Assessment of a plasmid conjugation procedure to monitor horizontal transfer of an extended-spectrum β-lactamase resistance gene under food chain scenarios

Plasmids are relevant reservoirs of antimicrobial resistance genes (ARGs) which confer adaptive advantages to their host and can be horizontally transferred. The aims of this study were to develop a conjugation procedure to monitor the horizontal transfer of a 193 kb plasmid containing the extended-spectrum β-lactamase production gene bla _CTX-M-14 between two Escherichia coli strains under a range of food chain-related scenarios, including temperature (20-37 °C), pH (5.0-9.0) or the presence of some biocidal agents (benzalkonium chloride, sodium hypochlorite or peracetic acid). The average conjugation rate in LB broth after 18 h at 37 °C was 2.09e-04 and similar rates were observed in a food matrix (cow's milk). The conjugation was reduced at temperatures below 37 °C, at alkaline pH (especially at pH 9.0) or in the presence of benzalkonium chloride. Peracetic acid and sodium hypochlorite slightly increased conjugation rates, which reached 5.59e-04 and 6.77e-03, respectively. The conjugation procedure described can be used to identify risk scenarios leading to an enhanced ARGs transmission via plasmid conjugation, as well as to identify novel intervention strategies impairing plasmid conjugation and tackling antimicrobial resistance.

Comparative polyphasic characterization of Weissella strains isolated from beaked whale and rainbow trout (Oncorhynchus mykiss): confirmation of Weissella ceti sp. nov. and description of the novel Weissella tructae sp. nov. isolated from farmed rainbow trout

The weissellosis agent bacterium (WS08T = CBMAI 2730) was isolated from diseased rainbow trout (Oncorhynchus mykiss) in Brazil. The whole genome sequence of this strain was compared with the Mexican W-1 strain, also isolated from diseased rainbow trout, and with the Weissella ceti type strain CECT 7719 T (= 1119-1A-09 T = CCUG 59653 T), recovered from the beaked whale. Digital DNA-DNA hybridization pairwise analyses scored 98.7% between the Mexican W-1 and Brazilian WS08T but just 24.4% for both fish isolates compared to the W. ceti type strain CECT 7719 T. The 16S rRNA gene sequence comparisons with isolates of W. ceti, available at GenBank, were conducted. All rainbow trout-pathogenic isolates grouped close (97% bootstrap confirmation), but when this group was compared to the W. ceti type strain CECT 7719 T the similarity varied from 78.9 to 79.1%. Phenotypic assays were also conducted, and the W. ceti type strain diverged from WS08T and W-1 in the hydrolysis of aesculin, D-mannose, and potassium gluconate and in the hydrolysis of hippurate. Moreover, WS08T and W-1 showed weak growth at 5 °C whereas no growth was observed for W. ceti CECT 7719 T. The major fatty acids (> 10% total fatty acids) presented by WS08T and W-1 were summed feature 8 (C18:1 ω7c/C18:1 ω6c), summed feature 3 (C16:1 ω6c/C16:1ω7c), and C16:0. The results of phylogenetic and phenotypic analyses clearly differentiated the W. ceti CECT 7719 T type strain from the assessed pathogenic strains obtained from rainbow trout. Therefore, Weissella strains isolated from rainbow trout, here represented by strain WS08T (= CBMAI 2730), should be known as members of a novel species for which the name Weissella tructae sp. nov. is proposed.

Exploring the MALDI Biotyper for the Identification of Corynebacterium pseudotuberculosis biovar Ovis and Equi

Biochemical, serological, and molecular methods have been developed for the laboratory diagnosis of diseases caused by C. pseudotuberculosis (CP), but the identification of the pathogen and biovars differentiation may be time-consuming, expensive, and confusing compared with other bacteria. This study aimed to evaluate MALDI Biotyper and Overall Genome Relatedness Index (OGRI) analysis to optimize the identification and differentiation of biovars of C. pseudotuberculosis. Out of 230 strains isolated from several hosts and countries, 202 (87.8%) were precisely classified using MALDI Biotyper and the BioNumerics platform. The classification accuracies for the Ovis and Equi biovars were 80 (88.75%) and 82 (92.68%), respectively. When analyzing a sampling of these strains by Average Nucleotide Identity based on BLAST and TETRA analyses using genomic sequence data, it was possible to differentiate 100% of the strains in Equi and Ovis. Our data show that MALDI Biotyper and OGRI analysis help identify C. pseudotuberculosis at the species and biovar levels.

First report of infectious spleen and kidney necrosis virus in Nile tilapia in Brazil

In June 2020, an atypical fatal outbreak in a Brazilian Nile tilapia farm was investigated. Twenty-three animals were collected and different tissues were used for bacterial isolation, histopathological and electron microscopic examination and viral detection using molecular methods. A large number of megalocytes were observed in the histopathological analysis of several tissues. Icosahedral virions, with a diameter of approximately 160 nm, were visualized inside the megalocytes through transmission electron microscopy of the spleen tissue. The virions were confirmed to be infectious spleen and kidney necrosis virus (ISKNV) through PCR and sequencing analyses of the fish samples. Phylogenetic analysis indicated that the virus belongs to the Clade 1 of ISKNV. This viral pathogen is associated with high mortality in the early stages of cultured Nile tilapia in the United States, Thailand and Ghana; however, until now, there have been no reports from ISKNV affecting cultured fish in Brazil. Additionally, in 14 out of 23 sampled fish, Streptococcus agalactiae, Edwardsiella tarda or Aeromonas hydrophila infections were also detected. This is the first report of fatal ISKNV infections in the Brazilian Nile tilapia fish farms and represents a new challenge to the aquaculture sector in the country.

ETosis in tambaqui Colossoma macropomum: A programmed cell death pathway and approach of leukocytes immune response

Tambaqui Colossoma macropomum is the most cultivated native fish in South America and Aeromonas hydrophila is one of the main bacteria infecting tropical fish. Despite the economic importance of this round fish, to date, there has been a paucity of investigations into haematological changes in tambaqui. In this study, detailed blood analyses (0 h, 6 h, 24 h, 7 d and 14 d) following intraperitoneal challenge with A. hydrophila were performed. After analysing the results, there was a suspicion of a novel cell death mechanism via extracellular traps (ETosis) in tambaqui. The search for ETosis was based on differential interference contrast (DIC) microscopy and scanning electron microscopy (SEM) assays through application of an adapted protocol applying co-incubation of leukocytes with A. hydrophila. The cells were investigated at: 0 h (control), 4 h and 7 h after incubation. The complete haemogram profile showed an uncommon severe leukopenia in early phases of infection (6 h, p < 0.001 and ≤ 0.05), due to significant decreases in the three main leukocytes: lymphocytes (6 h, p ≤ 0.001), monocytes (6 h, p ≤ 0.05) and neutrophils (6 h and 24 h, p ≤ 0.01 and p ≤ 0.05). Leucocytosis and lymphocytosis (p ≤ 0.01) were ascertained only 7 days post-infection. Through DIC and SEM, we discovered that leukocyte suicide exposed the nuclear contents between 4 and 7 h after stimuli with bacteria. The leukogram profile associated with DIC and SEM analyses suggested that tambaqui leukocytes underwent a programmed death (ETosis) in order to expose chromatin and granule proteins as a trap to bind and then kill bacteria; thus, preventing A. hydrophila from spreading and resulting in leukopenia during the early phase of bacterial infection. In this paper, we presume that ETosis is one of the last resources for tambaqui to contain the infection, and after this leukocyte strategy, a high number of phagocytic cells are produced and released into the peripheral circulation.

Patterns of the innate immune response in tambaqui Colossoma macropomum: Modulation of gene expression in haemorrhagic septicaemia caused by Aeromonas hydrophila

The production of tambaqui Colossoma macropomum has recently reached a milestone, being considered the main native species produced in South American continental waters. Despite the importance of this fish, its immunity is not well understood. In this study we established some patterns of innate immunity for the species via two experiments. Both studies evaluated the fish in the absence (intraperitoneal saline) or presence (intraperitoneal, 3 x 10⁷ CFU/mL of Aeromonas hydrophila at 0.1 mL/10 g of living weight) of infection at 5 points over time-course of 14 days (0 h, 6 h, 24 h, 7 d, 14 d). In the first experiment, the partial gene sequences and gene expression of IL-1β, IRAK-1, C3, C4, lysozyme, IL-10, HSP70 and β-actin were determined in the main secondary lymphoid organs of fish: the spleen and head kidney. The second study was performed to analyse the alternative complement pathway ACH₅₀ in serum to support the elucidation of C3 gene expression. Results of the gene expression assays showed a tendency towards up-regulation of immune genes in infected fish in early phases of infection (mostly around 6 h and 24 h) and in the chronic phase (7 d and 14 d), with the exception of HSP70 which showed a down-regulation in infected fish. Our results also suggested that lysozyme was evolved in both pro- and anti-inflammatory activities. For genes of the complement system, it was demonstrated that C4 regulation followed the tendency of pro-inflammatory genes. However, the C3 gene was, surprisingly, not expressed in most fish and this corroborated with the results of the complement system activity in serum that also did not show activity in most fish. The possible reasons for the regulation of gene expression and association with fish disease are addressed in this paper.

Motile Aeromonas septicemia in tambaqui Colossoma macropomum: Pathogenicity, lethality and new insights for control and disinfection in aquaculture

Tambaqui Colossoma macropomum is the most produced native fish in South America. Besides the lack of knowledge regarding bacteria-stricken diseases, the unappropriated using of off-label therapies are common. In this study, Aeromonas hydrophila pathogenicity for tambaqui was first established by Koch's Postulate. Lethal doses (LD) were settled for investigation of clinical signs and mortality. The antimicrobial activities were investigated by disk-diffusion test against 11 antibiotics and by broth microdilution methods against 3 antibiotics, 7 disinfectants and 11 herbal medicines. LD experiment showed up to 80% of fish mortality, skin darkness, ulcers, hemorrhage, lethargy and hypo/anorexia in all groups, with exception of control. The LD₁₀,₅₀,₉₀ and ₉₉ were established in 4.1 × 10⁷, 8.8 × 10⁷, 1.9 × 10⁸ e 3.6 × 10⁸ CFU/mL, respectively. Ceftriaxone, florfenicol, oxytetracycline and thiamphenicol were considered promising against A. hydrophila. All herbal medicines were classified as bactericides, but clove Eugenia caryophyllata and cinnamon Cinnamomum zeylanicum displayed strongest activities. Among disinfectants, malachite green was the only that did not present acceptable values, discouraging its use. In conclusion, Koch's postulate was fulfilled and tambaqui entered to the vast list of A. hydrophila hosts and promising results of chemical substances were provided, contributing to motile Aeromonas septicemia (MAS) control.

Recent methods and biosensors for foodborne pathogen detection in fish: progress and future prospects to sustainable aquaculture systems

The aquaculture industry has advanced toward sustainable recirculating systems, in where parameters of food quality are strictly monitored. Despite that, as in the case of conventional aquaculture practices, the recirculating systems also suffer threats from Aeromonas spp., Vibrio spp., Streptococcus spp., among other foodborne pathogens infecting farmed fish. The aquaculture pathogens are routinely detected by conventional PCR methods or antibody-based tests, with the detection protocols confined to laboratory use. Emerging assay technologies and biosensors recently reported in the literature open new opportunities to the development of sensitive, specific, and portable analytical devices to use in the field. Techniques of DNA/RNA analysis, immunoassays and other nanomolecular technologies have been facing important advances in response time, sensitivity, and enhanced power of discrimination among and within species. Moreover, the recent developments of electrochemical and optical signal transduction have facilitated the incorporation of the innovative assays to practical miniaturized devices. In this work, it is provided a critical review over foodborne pathogen detection by existing and promising methods and biosensors applied to fish samples and extended to other food matrices. While isothermal DNA/RNA amplification methods can be highlighted among the assay methods for their promising analytical performance and suitability for point-of-care testing, the electrochemical transduction provides a way to achieve cost-effective biosensors amenable to use in the aquaculture field. The adoption of new methods and biosensors would constitute a step forward in securing sustainable aquaculture systems.

Atypical Multibacterial Granulomatous Myositis in a Horse: First Report in Italy

Infectious causes of myositis are reported relatively uncommonly in horses. Among them, bacterial causes include Streptococcus equi subsp. zooepidemicus, Actinobacillus equuli, Fusobacterium spp. Staphylococcus spp, and Corynebacterium pseudotuberculosis. Infection can be spread to muscles via haematogenous or extension from skin lesions. Parasitic myositis has also been documented. In this report, a 12 year-old Italian Quarter Horse mare presented with diffuse subcutaneous nodules and masses ranging from 2 × 3 to 5 × 20 cm in size, and adherent to subcutis and muscles that were first macroscopically and cytologically diagnosed as pyogranulomas. Subsequently, histological, molecular, bacteriological, and biochemical investigations were performed. All the data obtained allowed to diagnose a severe and diffuse multibacterial granulomatous myositis caused by Corynebacterium pseudotuberculosis and Corynebacterium amycolatum. Following the therapy and an initial disappearance of most of the lesions together with a general improvement of the mare, the clinical condition deteriorated, and new nodules appeared. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and PCR techniques revealed the presence of bacteria as Glutamicibacter creatinolyticus and Dietzia spp. To the authors’ knowledge, this case report represents the first description of multibacterial granulomatous myositis due to Corynebacterium pseudotuberculosis, Corynebacterium amycolatum, Glutamicibacter creatinolyticus, and Dietzia spp. in a horse reared in Italy.

Purinergic signaling and gene expression of purinoceptors in the head kidney of the silver catfish Rhamdia quelen experimentally infected by Flavobacterium columnare

The head kidney is a lymphoid immune organ that plays a key role in the immune and inflammatory responses of teleost fish. It is associated with immunoglobulin G production and differentiation of B cells. The presence of a multi-enzymatic complex found anchored in the plasma membrane makes the head kidney an important purinergic-dependent tissue. Purinergic signaling has been associated with these responses under pathological conditions via regulation of extracellular adenosine triphosphate (ATP), the main damage molecular associated pattern agent released during bacterial infections. The aim of this study was to determine whether purinergic signaling is a pathway associated with impairment of immune responses in silver catfish (Rhamdia quelen) experimentally infected by Flavobacterium columnare, as well as to evaluate the role of P2 purine receptors in this response. Triphosphate diphosphohydrolase (NTPDase) activity in the head kidney was significantly lower in silver catfish experimentally-infected F. columnare 72 h post-infection (hpi) than in the control group, while no significant difference was observed with respect NTPDase activity on adenosine diphosphate, as well as on 5'-nucleotidase and adenosine deaminase activities. Extracellular ATP levels were significantly higher in the head kidney of experimentally-infected fish than in the control group at 72 hpi. Finally, p2ry11 and p2rx3 purine receptor levels were significantly higher in experimentally-infected fish than in the control group at 72 hpi. We conclude that purinergic signaling in the head kidney of silver catfish infected by F. columnare creates a pro-inflammatory profile that may contribute to impairment of immune and inflammatory responses via reduction of ATP hydrolysis and its accumulation in the extracellular milieu, accompanied by upregulation of p2ry11 and p2rx3 purine receptors, leading to pro-inflammatory status.

Identification of bacterial pathogens in cultured fish with a custom peptide database constructed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)

Background

The majority of infectious diseases of cultured fish is caused by bacteria. Rapid identification of bacterial pathogens is necessary for immediate management. The present study developed a custom Main Spectra Profile (MSP) database and validate the method using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of fish bacterial pathogens. Streptococcus agalactiae, Streptococcus iniae, Aeromonas hydrophila, Aeromonas veronii, and Edwardsiella tarda obtained from diseased fish were used as representative bacterial pathogens in this study. Bacterial peptides were extracted to create a Main Spectra Profile (MSP), and the MSPs of each bacterial species was added into the MALDI Biotyper database. Fifteen additional isolates of each bacterial species were tested to validate the utilized technique.

Results

The MSPs of all field isolates were clearly distinguishable, and the MSPs of the same species were clustered together. The identification methodology was validated with 75 bacterial isolates. The reliability and specificity of the method were determined with MALDI Biotyper log score values and matching results with 16 s rDNA sequencing. The species identification using the public MALDI Biotyper library (Bruker MALDI Biotyper) showed unreliable results (log score < 2.000) with 42.67% matching result with the reference method. In contrast, accurate identification was obtained when using the custom-made database, giving log score > 2.115, and a 100% matching result.

Conclusion

This study demonstrates an effective identification of fish bacterial pathogens when a complete custom-made MSP database is applied. Further applications require a broad, well-established database to accommodate prudent identification of many fish bacterial pathogens by MALDI-TOF MS.

Virulence factors and antimicrobial resistance of Staphylococcus aureus isolated from the production process of Minas artisanal cheese from the region of Campo das Vertentes, Brazil

Staphylococcus aureus is one of the main pathogens found in cheeses produced with raw milk, including Minas artisanal cheese from Brazil. However, information about S. aureus isolated from artisanal cheeses and its sources of production in small-scale dairies is very limited. We aimed to characterize the virulence factors of S. aureus isolated from raw milk, endogenous starter culture, Minas artisanal cheese, and cheese handlers from the region of Campo das Vertentes, Minas Gerais, Brazil. We identified the staphylococcal isolates by MALDI-TOF mass spectrometry. We evaluated biofilm production on Congo red agar and polystyrene plates. We used PCR to detect icaA, icaB, icaC, sea, seb, sec, sed, see, tsst-1, agr, and mecA. We evaluated the expression of staphylococcal toxin genes in PCR-positive staphylococcal isolates using quantitative reverse-transcription PCR, and we evaluated the production of these toxins and their hemolytic activity in vitro. We also evaluated the antimicrobial resistance profile of the staphylococcal isolates. For statistical analysis, we used cluster analysis, χ² tests, and correspondence tests. We analyzed 76 staphylococcal isolates. According to PCR, 18.42, 18.42, 2.63, and 77.63% were positive for sea, tsst-1, sec, and agr, respectively. We found low expression of staphylococcal toxin genes according to quantitative reverse-transcription PCR, and only 2 staphylococcal isolates produced toxic shock syndrome toxins. A total of 43 staphylococcal isolates (56.58%) had hemolytic activity; 53 were biofilm-forming on Congo red agar (69.73%), and 62 on polystyrene plates (81.58%). None of the staphylococcal isolates expressed the mecA gene, and none presented a multi-drug resistance pattern. The highest resistance was observed for penicillin G (67.11%) in 51 isolates and for tetracycline (27.63%) in 21 isolates. The staphylococcal isolates we evaluated had toxigenic potential, with a higher prevalence of sea and tsst-1. Biofilm production was the main virulence factor of the studied bacteria. Six clusters were formed whose distribution frequencies differed for hemolytic activity, biofilm formation (qualitative and quantitative analyses), and resistance to penicillin, tetracycline, and erythromycin. These findings emphasize the need for effective measures to prevent staphylococcal food poisoning by limiting S. aureus growth and enterotoxin formation throughout the food production chain and the final product.

Identification and characterization of methicillin-resistant Staphylococcus spp. isolated from surfaces near patients in an intensive care unit of a hospital in southeastern Brazil

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Streptococcus agalactiae Sequence Type 283 in Farmed Fish, Brazil

In 2016 and 2017, we characterized outbreaks caused by Streptococcus agalactiae serotype III sequence type (ST) 283 in Nile tilapia farms in Brazil. Whole-genome multilocus sequence typing clustered the fish isolates together with the zoonotic ST283 and other STs related to cases in humans, frogs, dogs, cattle, and dolphins.

Rapid MALDI-TOF MS identification of commercial truffles

Truffles are edible mushrooms with similar morphological characteristics, that make it difficult to distinguish between highly prized truffles (such as the Périgord black T. melanosporum) and inexpensive truffles (such as the Asian Black T. indicum). These biological and economic features have led to several misidentifications and/or fraudulent profit in the truffle markets. In this paper, we investigate Matrix-assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) biotyping to identify 34 commercial fresh truffles from Europe and Asia. The MALDI-TOF MS clustering rapidly distinguished seven Tuber species identified by ITS phylogenetic analysis. The tasty T. melanosporum was clearly differentiated from the Chinese and less expensive truffles. These cheaper mushrooms were marketed as T. indicum but corresponded to a mix of three species. In total, the method confirmed misidentifications in 26% of commercial specimens. Several unknown blind-coded truffles were rapidly identified, with scores >= 2, using the Bruker Biotyper algorithm against MS databases. This study demonstrates that MALDI-TOF MS is a reliable, rapid and cheaper new tool compared with molecular methods for the identification of truffle species and could be used to control frauds in the truffle markets. It could also be useful for the certification of truffle-inoculated seedlings and/or diversity in forest ecosystems.

Proteomic fingerprinting for the fast and accurate identification of species in the Polyporoid and Hymenochaetoid fungi clades

Basidiomycotan fungi play significant roles in the biogeochemical cycle of carbon as wood decomposers and are used in the food industry for mushroom production and in biotechnology for the production of diverse bioactive compounds and bioremediation. The correct identification of basidiomycotan isolates is crucial for understanding their biology and being able to expand their applications. Currently, the identification of these organisms is performed by analyzing morphological and genomic characteristics, primarily those based on DNA biomarkers. Despite their efficiency, such methods require considerable expertise and are both time-consuming and error-prone (multistep workflow). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged in the last decade as an accurate, fast, and powerful alternative for the identification of microorganisms. MALDI-TOF MS has been widely applied for the identification and taxonomical characterization of both bacteria and ascomycotan fungi from clinical origins. However, species of Basidiomycota have been poorly evaluated using this method. In the present study, we assessed the performance of MALDI-TOF MS using basidiomycotan isolates of two distinct taxonomical families: Polyporaceae and Hymenochaetaceae. Using a simple protocol, which eliminates the protein extraction step, we obtained high-quality mass spectra data and demonstrated that this method is efficient for the discrimination of isolates at the species level. SIGNIFICANCE: In this study, the MALDI-TOF mass spectrometry was employed to test its accuracy on the recognition of fungal species with high biotechnological and environmental interest. Using a simple and fast protocol, we obtained high-quality mass-spectra (protein fingerprinting) and proved that MALDI-TOF MS is sufficiently robust to the identification at species level and to evaluate the relationships among the isolates of the polyporoid and hymenochaetoid clades (Basidiomycota).

Identification and typing of Vagococcus salmoninarum using genomic and proteomic techniques

This study reports on the characterization of Vagococcus salmoninarum using phenotypic, serological, antigenic, genetic and proteomic methods. All strains of V. salmoninarum were resistant to most of the antimicrobials tested, and only 10% of strains were sensitive to florfenicol. Serological analysis demonstrated a high antigenic homogeneity within the species. No cross-reaction was detected with other fish pathogenic species causing streptococcosis (Lactococcus garvieae, Streptococcus parauberis, Streptococcus iniae, Streptococcus agalactiae, Carnobacterium maltaromaticum) using serum against V. salmoninarum CECT 5810. Electrophoretic analysis of cell surface proteins and immunoblot supported the antigenic homogeneity within V. salmoninarum strains. Moreover, limited diversity was detected using genomic (RAPD, ERIC-PCR and REP-PCR) and MALDI-TOF-MS analyses. The phenotypic, genomic and proteomic methods tested allowed the rapid differentiation of V. salmoninarum from the other species causing streptococcosis. However, MALDI-TOF-MS is the most promising method for typing and characterization of V. salmoninarum.

Large-scale genomic analyses reveal the population structure and evolutionary trends of Streptococcus agalactiae strains in Brazilian fish farms

Streptococcus agalactiae is a major pathogen and a hindrance on tilapia farming worldwide. The aims of this work were to analyze the genomic evolution of Brazilian strains of S. agalactiae and to establish spatial and temporal relations between strains isolated from different outbreaks of streptococcosis. A total of 39 strains were obtained from outbreaks and their whole genomes were sequenced and annotated for comparative analysis of multilocus sequence typing, genomic similarity and whole genome multilocus sequence typing (wgMLST). The Brazilian strains presented two sequence types, including a newly described ST, and a non-typeable lineage. The use of wgMLST could differentiate each strain in a single clone and was used to establish temporal and geographical correlations among strains. Bayesian phylogenomic analysis suggests that the studied Brazilian population was co-introduced in the country with their host, approximately 60 years ago. Brazilian strains of S. agalactiae were shown to be heterogeneous in their genome sequences and were distributed in different regions of the country according to their genotype, which allowed the use of wgMLST analysis to track each outbreak event individually.