In vitro virulotyping, antifungal susceptibility testing and DNA fingerprinting of Microsporum canis strains of canine and feline origin

Microsporum canis is considered the common dermatophyte agent associated with ringworm in felines and canines. In the present study, we sampled n = 548 felines and canines for the probable isolation of M. canis. The rate of isolation from the cats and dogs was 70.27 % (52/74) and 1.68 % (8/474), respectively and Persian cats were found to be highly susceptible to M. canis infection. The strains were evaluated for their production of phospholipase, lipase, catalase, and hemolysis and their ability to grow at 35 ℃. All the strains were identified as low producers of catalase and n = 17 strains exhibited high thermotolerance ability. Terbinafine was found to be the most effective antifungal drug and fluconazole was the least effective, in vitro. AFLP analysis revealed three genotypes of M. canis with 15 sub-clusters showing ≥ 90 % similarity and 7 sub-clusters exhibiting 100 % similarity. However, the phenotypic characters cannot be attributed based on the AFLP profiles.

Diagnostic and epidemiological analysis of Trichophyton benhamiae infection on an alpaca (Vicugna pacos) farm in Poland

Alpacas (Vicugna pacos) are growing in popularity and are increasingly being presented for veterinary care. Literature reports indicate that dermatophytosis occurring in alpacas accounted for about 3% of dermatological diagnoses. However, there are no reports regarding species of dermatophytes associated with alpacas and reservoirs of infection. In this study, we investigate the diagnosis and epidemiological origin procedure and the virulence enzymes activities of Trichophyton benhamiae isolates obtained from alpacas from a breeding farm. Identification was carried out traditionally by correlating clinical manifestations with micro- and macroscopic examination, and molecular differentiation methods based on Internal Transcribed Spacer (ITS) sequences. Epidemiological analysis was carried out on the basis of Melting Point PCR (MP -PCR) and Amplified Fragment Lenght Polymorphism (AFLP) genotyping. The production of virulence factors was evaluated phenotypically using specific test media. The results obtained from diagnostic tests indicated that the etiological factor of dermatophytosis is T. benhamiae. The same species was also isolated from cowsheds and insects. The MP-PCR and AFLP analyses indicated high invariability of the genomes of the strains isolated from the animals, cowsheds, and insects. In conclusion, animal husbandry outside the natural ecological niche may increase predisposition to dermatophytosis. The treatment of animals alone is insufficient, one should be aware that only elimination of all fungal sources is a long-term success and the key point of therapy.

Clonal structure in Ichthyobacterium seriolicida, the causative agent of bacterial haemolytic jaundice in yellowtail, Seriola quinqueradiata, inferred from molecular epidemiological analysis

Bacterial haemolytic jaundice caused by Ichthyobacterium seriolicida has been responsible for mortality in farmed yellowtail, Seriola quinqueradiata, in western Japan since the 1980s. In this study, polymorphic analysis of I. seriolicida was performed using three molecular methods: amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). Twenty-eight isolates were analysed using AFLP, while 31 isolates were examined by MLST and MLVA. No polymorphisms were identified by AFLP analysis using EcoRI and MseI, or by MLST of internal fragments of eight housekeeping genes. However, MLVA revealed variation in repeat numbers of three elements, allowing separation of the isolates into 16 sequence types. The unweighted pair group method using arithmetic averages cluster analysis of the MLVA data identified four major clusters, and all isolates belonged to clonal complexes. It is likely that I. seriolicida populations share a common ancestor, which may be a recently introduced strain.

Detection and characterization of amplified fragment length polymorphism markers for clinical mastitis in Canadian Holsteins

Mastitis is the most frequent, complex, and costly disease in dairy cattle. Genetic improvement of milk production traits has accompanied an increased susceptibility to mastitis. To determine genome-wide quantitative trait locus-linked markers for mastitis resistance, a total of 200 cows, comprising 100 top clinical mastitis- (CM) resistant and 100 top CM-susceptible cows, were screened by selective DNA pooling and amplified fragment length polymorphism (AFLP) technique. The AFLP analysis on resistant and susceptible pools using 89 selective primer combinations revealed 27 significant AFLP markers at a false discovery rate (FDR) of < 5%. The most promising AFLP marker was then selected for further characterization. Individual AFLP genotyping of the marker on all selected animals confirmed a significant difference. Sequence analysis detected a single nucleotide polymorphism (A<-->G) responsible for the AFLP polymorphism, which was named CGIL4. The PCR-RFLP analysis indicated that the frequency of allele A was significantly higher in the resistant group. The logistic regression analysis demonstrated that the marker was significantly associated with somatic cell score, CM residual values, and production traits. Radiation hybrid mapping assigned the marker to Bos taurus autosome 22. The present study provides promising markers for marker-assisted selection for CM resistance. Our results also demonstrated the capability of AFLP on selective DNA pools as a method for detection of genome regions containing quantitative trait loci.

Molecular typing of Streptococcus agalactiae isolates from fish

The genetic variability among Streptococcus agalactiae isolates recovered from fish was characterized using single-stranded conformation polymorphism (SSCP) analysis of the intergenic spacer region (ISR), and amplified fragment length polymorphism (AFLP) fingerprinting. A total of 46 S. agalactiae cultures isolated from different fish species and geographic origins as well as related reference strains were included in the study. ISR-SSCP divided the S. agalactiae isolates analysed into five distinct genotypes. Genotype 1 grouped all Kuwait isolates while genotype 4 clustered the majority of non-Kuwait isolates (USA, Brazil and Honduras). AFLP analysis offered a higher resolution level by dividing the isolates into 13 different genotypes. Two different AFLP profiles were identified within the Kuwait isolates. When data from both ISR-SSCP and AFLP were combined through a multidimensional analysis (MDS), a good correlation between geographical origin and genotypes was observed. Both AFLP and ISR-SSCP revealed genetic differences between S. agalactiae isolates from fish. While AFLP offered a higher resolution, ISR-SSCP also provided valid information being a simpler and faster method.

Evidence of population genetic effects of long-term exposure to contaminated sediments-a multi-endpoint study with copepods

In the environment, pollution generally acts over long time scales and exerts exposure of multiple toxicants on the organisms living there. Recent findings show that pollution can alter the genetics of populations. However, few of these studies have focused on long-term exposure of mixtures of substances. The relatively short generation time (ca. 4-5 weeks in sediments) of the harpacticoid copepod Attheyella crassa makes it suitable for multigenerational exposure studies. Here, A. crassa copepods were exposed for 60 and 120 days to naturally contaminated sediments (i.e., Svindersviken and Trosa; each in a concentration series including 50% contaminated sediment mixed with 50% control sediment and 100% contaminated sediment), and for 120 days to control sediment spiked with copper. We assayed changes in F(ST) (fixation index), which indicates if there is any population subdivision (i.e., structure) between the samples, expected heterozygosity, percent polymorphic loci, as well as abundance. There was a significant decrease in total abundance after 60 days in both of the 100% naturally contaminated sediments. This abundance bottleneck recovered in the Trosa treatment after 120 days but not in the Svindersviken treatment. After 120 days, there were fewer males in the 100% naturally contaminated sediments compared to the control, possibly caused by smaller size of males resulting in higher surface: body volume ratio in contact with toxic chemicals. In the copper treatment there was a significant decrease in genetic diversity after 120 days, although abundance remained unchanged. Neither of the naturally contaminated sediments (50 and 100%) affected genetic diversity after 120 days but they all had high within treatment F(ST) values, with highest F(ST) in both 100% treatments. This indicates differentiation between the replicates and seems to be a consequence of multi-toxicant exposure, which likely caused selective mortality against highly sensitive genotypes. We further assayed two growth-related measures, i.e., RNA content and cephalothorax length, but none of these endpoints differed between any of the treatments and the control. In conclusion, the results of the present study support the hypothesis that toxicant exposure can reduce genetic diversity and cause population differentiation. Loss of genetic diversity is of great concern since it implies reduced adaptive potential of populations in the face of future environmental change.

Comparison of five allopatric fruit fly parasitoid populations (Psyttalia species) (Hymenoptera: Braconidae) from coffee fields using morphometric and molecular methods

Morphometric studies of five allopatric parasitoid populations (genus Psyttalia Walker) from coffee plantations in Cameroon (Nkolbisson), Ghana (Tafo) and Kenya (Rurima, Ruiru and Shimba Hills) and one non-coffee population (from Muhaka, Kenya) were compared with individuals of Psyttalia concolor (Szépligeti), a species released in several biological control programmes in the Mediterranean Region since the 20th Century. Analyses of wing vein measurements showed the second submarginal cell of the fore wing and its adjoining veins had the heaviest principal component weights and served as the main contributing variables in the diagnostic differentiation of the populations. Two populations (Rurima and Ruiru) were found to be the closest to each other and with the strongest phenetic affinity toward P. concolor (and forming one cluster). Populations from Shimba Hills (of unknown identity), Nkolbisson (P. perproximus (Silvestri)) and Tafo formed a second cluster and were separated from P. concolor. Comparison using amplified fragment length polymorphism (AFLP) also showed the Shimba, Nkolbisson and Tafo populations forming a cluster in a dendrogram generated from their genetic distances, with the Shimba and Tafo populations placed as the most closely related species. Based on consistent morphological similarities, morphometric and ecological data coupled with the genetic evidence from AFLP data, the Shimba population is suggested as belonging to the P. perproximus group and, thus, represents a new occurrence record in Kenya. Our results also support earlier conclusion from cross mating data that populations from Rurima and Ruiru belong to the Psyttalia concolor species-group.

Genetic impact of the Prestige oil spill in wild populations of a poor dispersal marine snail from intertidal rocky shores

In November 2002, the sinking of the Prestige cargo ship produced an oil spill of 60,000 tons that affected many areas along the Galician coast (in the northwest of Spain). In a number of rocky shore sites, most organisms (particularly marine mollusks) were nearly extinct at a local scale. We tested whether the local bottleneck/extinction that occurred in affected localities caused any detectable reduction of the genetic diversity in the marine snail Littorina saxatilis, an ovoviviparous rocky shore model species characterized by a low dispersal ability, high population density, and wide distribution range. We compared the level of genetic variation and population differentiation between affected (polluted) and control sites located in seven geographical areas (three sites per area, one impacted and two controls, and two replicates per site) one and a half years after the spill. The analysis included molecular marker variation (microsatellite and AFLP loci) and quantitative trait genetic variation for shell variables in embryos extracted from pregnant females. Our results indicate that the affected populations did not show a significant overall reduction in genetic diversity when compared to the controls, suggesting that the species is highly resistant to losing genetic variability as a consequence of a local short-term pollution process in spite of its low dispersal ability and direct development. However, some genetic effects were detected in the polluted populations, particularly for quantitative shell traits and AFLPs, consistent with local adaptations resulting from the fuel contamination.

Characterization of AFLP markers associated with growth in the Kuruma prawn, Marsupenaeus japonicus, and identification of a candidate gene

Growth rate of the Kuruma prawn, Marsupenaeus japonicus is an important economic trait, with larger animals commanding higher market prices. To identify gene markers associated with growth, a genetic map of a full-sib F(2) intercross family of M. japonicus has previously been generated and quantitative trait loci (QTL) influencing weight, total length, and carapace length were identified. In this study, amplified fragment length polymorphism (AFLP) markers associated with the major QTL region, contributing 16% to phenotypic variation, were characterized. Flanking sequence has been obtained and allelic variants responsible for segregation patterns of these markers have been identified. The genomic sequence surrounding the AFLP band 7.21a, residing under the QTL peak, contains a gene sequence homologous to the elongation of very long chain fatty acids-like (ELOVL) protein family. A full-length mRNA (ELOVL-MJ) encoding this protein was isolated from M. japonicus, representing both the first ELOVL gene in crustacea and the first candidate gene identified via QTL studies in crustacea.

Bovine Intramammary Infections Caused by Coagulase-Negative Staphylococci May Persist Throughout Lactation According to Amplified Fragment Length Polymorphism-Based Analysis

Persistence of coagulase-negative staphylococci (CNS) in intramammary infections during lactation was studied in a research dairy herd of University of Helsinki. Milk samples from 328 udder quarters of 82 dairy cows (30 primiparous, 52 multiparous) were collected 2 wk before calving, at calving, and every 4 wk thereafter until the end of lactation or until the cow left the herd. The CNS isolated from the milk samples were analyzed with the API Staph ID 32 (bioMérieux, Marcy l'Etoile, France) test (API) and genotyped using amplified fragment length polymorphism (AFLP) analysis. The AFLP patterns were used for similarity analysis between CNS isolates and for species identification. For the latter, AFLP patterns of CNS isolates and staphylococcal type strains were used as operational taxonomic units in numerical analysis. In addition, the somatic cell count (SCC) of the milk samples was measured during lactation. A CNS infection was considered persistent when isolates originating from the same quarter had identical AFLP patterns on at least 3 consecutive samplings. In total, 63 CNS infections were detected during lactation in 30 and 33 quarters in the first and later lactations, respectively. Twenty-nine of these infections persisted and 34 were transient. Most of the persistent infections lasted until the end of lactation. In 57 quarters, CNS infection was detected before calving, at calving, or both, but only half of these quarters were infected by CNS during subsequent lactation. The geometric mean of SCC in quarters during persistent CNS infection was 657,600 cells/mL, and the mean of SCC in quarters with transient CNS infection was 619,100 cells/mL. The median of SCC in quarters during persistent CNS infection was 355,400 cells/mL, and the median of SCC in quarters with transient CNS infection was 133,500 cells/mL. According to both the API test and AFLP results, Staphylococcus chromogenes and Staphylococcus simulans were the CNS species isolated most often. Identification results for API and AFLP corresponded in 71.9% of the isolates.