Rapid bacterial genome sequencing: methods and applications in clinical microbiology.

The recent advances in sequencing technologies have given all microbiology laboratories access to whole genome sequencing. Providing that tools for the automated analysis of sequence data and databases for associated meta-data are developed, whole genome sequencing will become a routine tool for large clinical microbiology laboratories. Indeed, the continuing reduction in sequencing costs and the shortening of the 'time to result' makes it an attractive strategy in both research and diagnostics. Here, we review how high-throughput sequencing is revolutionizing clinical microbiology and the promise that it still holds. We discuss major applications, which include: (i) identification of target DNA sequences and antigens to rapidly develop diagnostic tools; (ii) precise strain identification for epidemiological typing and pathogen monitoring during outbreaks; and (iii) investigation of strain properties, such as the presence of antibiotic resistance or virulence factors. In addition, recent developments in comparative metagenomics and single-cell sequencing offer the prospect of a better understanding of complex microbial communities at the global and individual levels, providing a new perspective for understanding host-pathogen interactions. Being a high-resolution tool, high-throughput sequencing will increasingly influence diagnostics, epidemiology, risk management, and patient care.

Monogenean parasitic on marine fishes from Perú and Chile: three new species and two new combinations

Five species of monogeneans collected from marine fishes of the Pacific coast of Chile and Perú were studied. Three of them are new species: Interniloculus chilensis n. sp. (Capsalidae), Neoheterobothrium insalaris n. sp. (Diclidophoridae) and Loxura peruensis n. sp. (Axinidae) parasitic on Sebastes capensis (Scorpaenidae), Paralichthys sp. (Bothiidae) and Belone scapularis (Belonidae), respectively. Two new combinations are proposed, Intracotyle neghmei (Microcotylidae) for Neobivagina neghmei Villalba, 1987 and Hargicotlyle conceptionensis (Diclidophoridae) for Choricotyle conceptionensis Villalba, 1987.

New species of Proteocephalus (Cestoda - Proteocephalidae) parasitic in fishes from the Paraná River, Paraná, Brazil

Two species of the genus Proteocephalus (Cestoda: Proteocephalidae) were collected in fishes from the Paraná River. Proteocephalus vazzolerae n. sp. from Piaractus mesopotamicus and Proteocephalus chubbi, n. sp. from Gymnotus carapo are new species, and are described and illustrated. Proteocephalus vazzolerae n. sp. is characterized mainly by the number of testes and the development of vitellaria. Proteocephalus chubbi n. sp. can be differentiated from its congeners by a combination of characters which include, number of testes, number of proglottids, strobila length, scolex shape and disposition of vitellaria. This is the first record of proteocephalidean in P. mesopotamicus and G. carapo.

Trypanorhynch Cestodes of Commercial Fishes from Northeast Brazilian Coastal Waters

A large scale investigation on trypanorhynch cestode infestation of tropical marine fishes was carried out along the Northeast Brazilian coast in the summer of 1991 and 1993. A total of 798 fish specimens belonging to 57 species and 30 families were examined. Metacestodes of 11 different trypanorhynchs were found: Callitetrarhynchus gracilis, Dasyrhynchus giganteus, Grillotia sp., Nybelinia edwinlintoni, N. indica, N. senegalensis, Nybelinia c.f. lingualis, Otobothrium cysticum, Pseudolacistorhynchus noodti, Pseudotobothrium dipsacum and Pterobothrium kingstoni. Scanning electron microscopy was used to clarify details of the tentacular armature of some species. Rose-thorn shaped hooklets, regularly arranged like microtriches, are described from the bothridial surface of N. edwinlintoni. Of the 57 fish species, 15 harboured trypanorhynch cestodes. Of these the mullid Pseudupeneus maculatus was the most heavily infested fish species, harbouring 5 different trypanorhynch species. P. noodti in P. maculatus had the highest prevalence (87%) and intensity (maximum = 63) of infestation. C. gracilis was the parasite with the lowest host-specificity. It could be isolated from 10 fish species. The cestode fauna of the Northeast Brazilian coast appears to be similar to that of the West African coast. Five of the trypanorhynch cestodes found during this study are common to both localities. The two single cases of intra musculature infestation in Citharichthys spilopterus and Haemulon aurolineatum by trypanorhynch cestodes indicate that marketability of the investigated commercially exploited fish species is inconsequential.

On dome-shaped norms of reaction for size-to-age at maturity in fishes

The optimal size-to-age at maturity depends on growth and mortality rates, which vary with environment. Therefore, organisms in spatially or temporaly changing environments should develop adaptative phenotypic plasticity for this trait. Experimental work by Alm (1959) on several fish species shows a dome-shape norm of reaction for size-to-age at maturity: size at maturity is smaller in both fast-growing and slow-growing fishes, than it is in fish with a medium growth rate. Using computer simulations, we show that such a dome-shaped norm of reaction is optimal when assuming a finite life span and a negative relationship between production and survival rates. This latter assumption is supported by empirical data, as well as by physiological and emographic arguments.

Some Aspects of the Development of Lobatostoma jungwirthi Kritscher, 1974 (Aspidogastrea) in Snails and Cichlid Fishes from Buenos Aires, Argentina

The molluscs Heleobia castellanosae and Ampullaria canaliculata and cichlid fishes were collected from an artificial pond at Tres de Febrero Park (Buenos Aires city), between June 1994 and May 1995. One hundred and eighty of 2,467 H. castellanosae examined were infected with pre-adults of Lobatostoma jungwirthi, 112 of them in concurrent infections with digeneans. L. jungwirthi was significantly more prevalent in larger snails, especially those infected with larval digeneans, but the prevalence of infection did not fluctuate significantly throughout the year. A. canaliculata and cichlids smaller than 10 cm were not infected, but larger Cichlasoma facetum harboured adults of L. jungwirthi in their intestines. Experimental infections of C. facetum and Gymnogeophagus meridionalis with pre-adult aspidogastreans obtained from H. castellanosae were successful. The development of L. jungwirthi in the snail host involves five arbitrary growth phases. Its life-cycle is heteroxenous, similar to that described for L. manteri, with H. castellanosae as the intermediate host and cichlid fishes as the definitive host in this pond.

Scolex Morphology of Proteocephalid Cestodes Parasites of Neotropical Freshwater Fishes

The morphology of the scolices and metascolices of 29 proteocephalid species, parasites of freshwater fishes from Brazil was compared by using scanning electron microscope, light and laser microscopy. The following species were evaluated: Proteocephalus vazzolerae, P. piramutab, Robertiella paranaensis, Travassiella avitellina, Monticellia loyolai, M. spinulifera, M. belavistensis, Houssayela sudobim, Zygobothrium megacephalum, Gibsoniela mandube, Cangatiella arandasi, Nomimoscolex sudobim, N. lopesi, N. admonticellia, N. piraeeba, N. pirarara, Harriscolex kaparari, Crepidobothrium eirasi, Spatulifer rugosa, Megathylacus brooksi, Choanoscolex abscisus, Amphoteromorphus peniculus, A. piraeeba, Paramonticellia itaipuensis, Peltidocotyle rugosa, Othinoscolex lenha, Rudolphiella rugata, R. piranabu, Jauella glandicephalus. Some features as overall shape of scolex, suckers, apical sucker, frontal glands and several kinds of metascolex were analyzed. The taxonomic importance of scolex and metascolex is discussed.

Nematodes of elasmobranch fishes from the southern coast of Brazil

New records for nematode species recovered from elasmobranch fishes in Brazil are established and new systematical arrangements proposed. Parascarophis sphyrnae Campana-Rouget, 1955 from the spiral valve of Sphyrna zygaena is referred for the first time in South America as a new host record. Procamallanus (S.) pereirai Annereaux, 1946, from the spiral valve of Raja castelnaui is reported parasitizing an elasmobranch host. Nematode larvae of the genera Anisakis, Contracaecum, Pseudoterranova and Raphidascaris are listed from the stomach and spiral valves of several hosts. Anisakidae larvae previously referred in Brazil in the genus Phocanema should be reallocated in Pseudoterranova. Nematodes of the genera Anisakis, Contracaecum, Pseudoterranova and Raphidascaris are reported for the first time parasitizing elasmobranchs in Brazil.

Digenea and acanthocephala of elasmobranch fishes from the southern coast of Brazil

New records for helminth species recovered from elasmobranch fishes in Brazil are established. Digenean and acanthocephalan parasites of elasmobranch fishes are reported from the southern coast of Brazil: Otodistomum veliporum (Creplin, 1837) Stafford, 1904 (Digenea: Azygiidae) in the stomach and spiral valve of Dipturus trachydermus and in the spiral valve of Squatina sp. Cystacanths and juveniles of the acanthocephalans Corynosoma australe Johnston, 1937 and Corynosoma sp., in the spiral valve of Squatina sp., Galeorhinus galeus and Hexanchus griseus and in the stomach of Squalus megalops; a juvenile of Gorgorhynchus sp., in the spiral valve of Sphyrna zygaena. Dipturus trachydermus and Squatina sp. are new host records for O. veliporum. Digeneans and acanthocephalans are reported for the first time parasitizing elasmobranch fishes in Brazil.

Taxonomic reports of Otobothrioidea (Eucestoda, Trypanorhyncha) from elasmobranch fishes of the southern coast off Brazil

Specimens of elasmobranch fishes, captured in the states of Paraná and Santa Catarina, of the southern coast off Brazil, represented by three families, four genera, and four species, were parasitized with otobothrioid trypanorhynch cestodes: Heptranchias perlo (Bonnaterre, 1788), Squalus sp. and Carcharhinus signatus (Poey, 1868) were parasitized with Progrillotia dollfusi Carvajal & Rego,1987; Prionace glauca (Linnaeus, 1758) with Molicola horridus (Goodsir, 1841) Dollfus, 1942. Details of internal morphology and/or scolex and/or proglottids surface ultrastructure, that expanded the description of M. horridus, through observations with lightfield, and/or scanning eletronic microscopy, are provided. The known geographical distribution for the species M. horridus is enlarged. P. dollfusi is reported for the first time in elasmobranchs.

Consumer Food Safety Knowledge, Microbiology & Refrigeration Temperatures in Domestic Kitchens

This study examined consumer food safety knowledge on the island of Ireland. Domestic refrigerators were tested for the presence of a range of pathogenic bacteria.

A Study of Food Safety Knowledge, Microbiology and Refrigeration Temperatures in Restaurant Kitchens on the Island of Ireland

A population-based telephone survey conducted in 2002 estimated that there were 3.2 million episodes of acute gastroenteritis on the island of Ireland each year (Scallon et al., 2004). It is often very dif ficult to definitively identify the source of illness. However, of the respondents in that study suspecting food as the reason for their illness, 74% blamed food consumed from commercial premises such as restaurants, cafés, takeaways, canteens and pubs. Within the food services industry, statistics show a significant level of prosecutions, prohibition and closure orders of restaurants for food hygiene offences. The Food Safety Authority of Ireland has identified the main contributory factors to foodborne infections to be: cross-contamination, inadequate cooking, inadequate storage, inadequate reheating, delayed serving and infected food handlers (FSAI, 2000). Development of appropriate training and education campaigns to target problem areas requires initial understanding of the current level of food safety knowledge and practices in the food services industry.

An Assessment of the Microbiology of Hand Contact Surfaces in the Retail Environment

This study aimed to assess the microbiology of food and hand contact surfaces in the retail environment and the potential for these surfaces to act as vehicles for the spread of foodborne pathogens. During the survey, 10 stores in the Republic of Ireland (ROI) were visited by student Environmental Health Officers (EHOs) who took swab samples from four surfaces: conveyor belts, long-life shopping bags, shopping trolley handles and keypads on card payment units. The swab samples were examined for the presence of the pathogens Salmonella, Campylobacter and Listeria. The Aerobic Colony Counts, as well as the levels of E. coli and Enterobacteriaceae, were also determined. In addition, structured questionnaires were used with retailers to establish the stores’ regimes for the cleaning of conveyor belts. Similarly, shoppers donating their long-life shopping bags for sampling were questioned about how they normally use these bags, and the results were compared with those from the microbiological survey. The results indicated that the hygiene of the surfaces sampled was good, with Salmonella, Campylobacter and Listeria not detected in any of the samples, and levels of both Enterobacteriaceae and E. coli were below the limits of detection in all but one sample. Aerobic Colony Counts varied but none of the results obtained would be deemed ‘unacceptable’ or ‘unsatisfactory’ under guidelines for ready-to-eat foods