The present multicenter study aimed at assessing the performance of air sampling as a novel method for monitoring Campylobacter in biosecure poultry farms. We compared, using a harmonized procedure, the bacteriological isolation protocol (ISO 10272-1:2017) and a real-time PCR method used on air filter samples. Air samples and boot swabs were collected from 62 biosecure flocks from five European countries during the summer of 2019. For air filters, the frequency of PCR-positive findings was significantly higher (n = 36; 58%) than that obtained with the cultivation methods (P < 0.01; standardized residuals). The cultivation protocols (one with Bolton enrichment and one with Preston enrichment) were comparable to each other but returned fewer positive samples (0 to 8%). The association between type of sample and frequency of PCR-positive findings was statistically confirmed (P < 0.01; Fisher´s exact test), although no culture-positive air filters were detected using direct plating. For the boot swabs, the highest number of positive samples were detected after enrichment in Preston broth (n = 23; 37%), followed by direct plating after homogenization in Preston (n = 21; 34%) or Bolton broth (n = 20; 32%). It is noteworthy that the flocks in Norway, a country known to have low Campylobacter prevalence in biosecure chicken flocks, tested negative for Campylobacter by the new sensitive approach. In conclusion, air sampling combined with real-time PCR is proposed as a multipurpose, low-cost, and convenient screening method that can be up to four times faster and four times more sensitive than the current boot-swab testing scheme used for screening biosecure chicken production.IMPORTANCECampylobacter bacteria are the cause of the vast majority of registered cases of foodborne illness in the industrialized world. In fact, the bacteria caused 246,571 registered cases of foodborne illness in 2018, which equates to 70% of all registered cases in Europe that year. An important tool to prevent campylobacters from making people sick is good data on where in the food chain the bacterium is present. The present study reports a new test method that quadruples the likelihood of identifying campylobacter-positive chicken flocks. It is important to identify campylobacter-positive flocks before they arrive at the slaughterhouse, because negative flocks can be slaughtered first in order to avoid cross-contamination along the production line.

• MeSH
• Campylobacter isolation & purification   MeSH
• Campylobacter Infections diagnosis   microbiology   veterinary   MeSH
• Chickens * MeSH
• Poultry Diseases diagnosis   microbiology   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Czech Republic MeSH
• Denmark MeSH
• Italy MeSH
• Norway MeSH
• Poland MeSH

In the Mekong Delta region of Vietnam, small-scale chicken farming is common. However, high levels of disease or mortality in such flocks impair economic development and challenge the livelihoods of many rural households. We investigated 61 diseased small-scale flocks (122 chickens) for evidence of infection with 5 bacteria, 4 viruses, and helminths. Serological profiles (ELISA) were also determined against 6 of these pathogens. The aims of this study were the following: (1) to investigate the prevalence of different pathogens and to compare the probability of detection of bacterial pathogens using PCR and culture; (2) to investigate the relationship between detection of organisms in birds' tissues and the observed morbidity and mortality, as well as their antibody profile; and (3) to characterize risk factors for infection with specific viral or bacterial pathogens. We used PCR to test for viral (viruses causing infectious bronchitis [IB], highly pathogenic avian influenza [HPAI], Newcastle disease, and infectious bursal disease [IBD]) and bacterial pathogens (Mycoplasma gallisepticum, Pasteurella multocida, Avibacterium paragallinarum, and Ornithobacterium rhinotracheale [ORT]). The latter two were also investigated in respiratory tissues by conventional culture. Colisepticemic Escherichia coli was investigated by liver or spleen culture. In 49 of 61 (80.3%) flocks, at least one bacterial or viral pathogen was detected, and in 29 (47.5%) flocks, more than one pathogen was detected. A. paragallinarum was detected in 62.3% flocks, followed by M. gallisepticum (26.2%), viruses causing IBD (24.6%) and IB (21.3%), septicemic E. coli (14.8%), ORT (13.1%), and HPAI viruses (4.9%). Of all flocks, 67.2% flocks were colonized by helminths. Mortality was highest among flocks infected with HPAI (100%, interquartile range [IQR]: 81.6-100%) and lowest with flocks infected with ORT (5.3%, IQR: 1.1-9.0%). The results indicated slight agreement (kappa ≤ 0.167) between detection by PCR and culture for both A. paragallinarum and ORT, as well as between the presence of cestodes and ORT infection (kappa = 0.317). Control of A. paragallinarum, viruses causing HPAI, IBD, and IB, M. gallisepticum, and gastrointestinal helminths should be a priority in small-scale flocks.

• MeSH
• Bacterial Infections epidemiology   microbiology   veterinary   MeSH
• Chickens * MeSH
• Morbidity MeSH
• Mortality MeSH
• Poultry Diseases epidemiology   microbiology   parasitology   virology   MeSH
• Parasitic Diseases, Animal epidemiology   parasitology   MeSH
• Polymerase Chain Reaction veterinary   MeSH
• Prevalence MeSH
• Risk Factors MeSH
• Antibody Formation MeSH
• Virus Diseases epidemiology   veterinary   virology   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Vietnam MeSH

Commercial small-scale chicken farms managed as all-in-all-out but operating with low standards of hygiene/biosecurity are increasingly common in Vietnam. These conditions facilitate the transmission of gastrointestinal helminths. However, there are no published data on helminths in these systems. We aimed (1) to determine the prevalence/burden of gastrointestinal helminths in small-scale commercial flocks in the Mekong Delta region and (2) to investigate the association between worm burdens and birds' weight and disease status. Randomly selected chickens (n = 120) from 'normal' flocks were investigated at the end of their production cycle (~ 18 weeks), as well as 90 chickens from 'diseased' flocks with signs of respiratory and/or severe disease. The gastrointestinal tract of chickens was dissected and all visible helminths were identified and counted. A total of 54.2% and 54.4% normal and diseased chickens contained helminths. Among colonised birds, the diseased ones harboured a higher mass of helminth worms than normal (healthy) birds (3.8 ± SD 8.6 g vs. 1.9 ± SD 6.3 g, respectively). Eight species were identified, including nematodes (Ascaridia galli, Cheilospirura hamulosa and Heterakis gallinarum), cestodes (Hymenolepis, Raillietina cesticillus, Raillietina echinobothrida, Raillietina tetragona,) and one trematode (Echinostomatidae). Heterakis gallinarum was the most prevalent helminth (43.3% and 42.2% in normal and sick chickens, respectively), followed by A. galli (26.7% and 41.1%). Colonised chickens weighed 101.5 g less than non-colonised birds. Colonisation was higher during the rainy months (May-November) for both H. gallinarum and A. galli. Anthelminthic usage was not associated with reduced helminth burdens. We recommend upgrading cleaning and disinfection and limiting access to ranging areas to control helminths in small-scale chicken flocks.

• MeSH
• Anthelmintics therapeutic use   MeSH
• Cestoda classification   isolation & purification   MeSH
• Helminths classification   isolation & purification   MeSH
• Farms MeSH
• Gastrointestinal Tract parasitology   MeSH
• Helminthiasis, Animal drug therapy   parasitology   MeSH
• Nematoda classification   isolation & purification   MeSH
• Chickens MeSH
• Poultry Diseases parasitology   MeSH
• Prevalence MeSH
• Body Weight drug effects   MeSH
• Trematoda classification   isolation & purification   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Vietnam MeSH

Mycobacterium avium paratuberculosis (Map) is a pathogen which causes a chronic progressive granulomatous enteritis known as paratuberculosis or Johne's disease and it primarily affects wild and domestic ruminants. The aim of this research was to examine a flock which consisted of 294 goats and was located in Garfagnana district (Tuscany, Italy) performing ELISA tests, culture and IS900 PCR assay; direct diagnostic methods were carried out not only on bulk tank milk and cheese samples but also on individual milk and tissue specimens collected from nine subjects positive to ELISA tests. Out of 294 animals, 20 goats (6.8%) were positive to ELISA surveys. Bulk tank milk samples were negative to culture and to PCR assay carried out on the DNA extracted directly from them, while, with respect to cheese, Map was detected by culture in 2/12 (16.66%) cheeses ripened for 3-7 days, and by PCR in 2/12 (16.66%) cheeses ripened for 3-7 days and in 3/12 (25%) cheeses ripened for 45 days. Regarding individual milk samples, Map was detected by culture in 2/9 (22.22%) specimens and by PCR in 5/9 (55.55%) samples. Furthermore, Map was isolated from the intestine in 9/9 (100%) animals, from the mesenteric lymph nodes in 8/9 (88.88%) subjects, from the liver in 4/9 (44.44%) goats, from the spleen in 5/9 (55.55%) animals, while Map DNA was found in all the tissue samples analyzed.The results demonstrated the presence of paratuberculosis in a goat flock located in Garfagnana district (Tuscany, Italy).

• MeSH
• Enzyme-Linked Immunosorbent Assay MeSH
• Goats MeSH
• Milk microbiology   MeSH
• Mycobacterium avium subsp. paratuberculosis genetics   immunology   isolation & purification   MeSH
• Goat Diseases diagnosis   epidemiology   microbiology   MeSH
• Paratuberculosis diagnosis   epidemiology   microbiology   MeSH
• Polymerase Chain Reaction MeSH
• Cheese microbiology   MeSH
• Animals MeSH
• Check Tag
• Male MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Italy epidemiology   MeSH

IS901 RFLP analysis of 36 Mycobacterium avium subsp. avium (MAA) isolates from 15 pheasants (Phasianus colchicus) and two goshawks (Accipiter gentilis) from four pheasant farms was performed. Using this method, six different IS901 RFLP types (E, F, G, M, Q, and V) were identified. The distribution of IS901 RFLP profiles was tightly linked to individual flocks. Matching IS901 RFLP profiles observed in the present study indicate MAA transmission between pheasants and goshawks in the same locality. In two flocks, different pheasants within a flock as well as in various organs of five individual pheasants were found to have two distinct IS901 RFLP profiles.

• MeSH
• Galliformes * MeSH
• Liver microbiology   MeSH
• Bone Marrow microbiology   MeSH
• Mycobacterium avium genetics   MeSH
• Poultry Diseases microbiology   MeSH
• Polymorphism, Restriction Fragment Length * MeSH
• Polymorphism, Genetic * MeSH
• Tuberculosis, Avian microbiology   MeSH
• Spleen microbiology   MeSH
• Intestines microbiology   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH

First multilocus analysis of the largest Neotropical cichlid genus Crenicichla combining mitochondrial (cytb, ND2, 16S) and nuclear (S7 intron 1) genes and comprising 602 sequences of 169 specimens yields a robust phylogenetic hypothesis. The best marker in the combined analysis is the ND2 gene which contributes throughout the whole range of hierarchical levels in the tree and shows weak effects of saturation at the 3rd codon position. The 16S locus exerts almost no influence on the inferred phylogeny. The nuclear S7 intron 1 resolves mainly deeper nodes. Crenicichla is split into two main clades: (1) Teleocichla, the Crenicichla wallacii group, and the Crenicichla lugubris-Crenicichla saxatilis groups ("the TWLuS clade"); (2) the Crenicichla reticulata group and the Crenicichla lacustris group-Crenicichla macrophthalma ("the RMLa clade"). Our study confirms the monophyly of the C. lacustris species group with very high support. The biogeographic reconstruction of the C. lacustris group using dispersal-vicariance analysis underlines the importance of ancient barriers between the middle and upper Paraná River (the Guaíra Falls) and between the middle and upper Uruguay River (the Moconá Falls). Our phylogeny recovers two endemic species flocks within the C. lacustris group, the Crenicichla missioneira species flock and the herein discovered Crenicichla mandelburgeri species flock from the Uruguay and Paraná/Iguazú Rivers, respectively. We discuss putative sympatric diversification of trophic traits (morphology of jaws and lips, dentition) and propose these species flocks as models for studying sympatric speciation in complex riverine systems. The possible role of hybridization as a mechanism of speciation is mentioned with a recorded example (Crenicichla scottii).

• MeSH
• Bayes Theorem MeSH
• Cichlids anatomy & histology   classification   genetics   MeSH
• Phylogeny MeSH
• Phylogeography MeSH
• Genetic Variation MeSH
• Multilocus Sequence Typing MeSH
• Likelihood Functions MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Fish Proteins genetics   MeSH
• Sequence Alignment MeSH
• Sympatry MeSH
• Genetic Speciation MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Paraguay MeSH
• Uruguay MeSH

Adaptive radiation occurs when species diversify rapidly to occupy an array of ecological niches. As opportunities for parasite infection and transmission may greatly vary among these niches, adaptive radiation is expected to be associated with a turnover of the parasite community. As major agents of natural and sexual selection, parasites may play a central role in host diversification. The study of parasite turnover may thus be of general relevance and could significantly improve our understanding of adaptive radiation. In this study, we examined the parasite faunas of eleven species belonging to the tribe Tropheini, one of several adaptive radiations of cichlid fishes in Lake Tanganyika. The most parsimonious ancestral foraging strategy among the Tropheini is relatively unselective substrate browsing of aufwuchs. Several lineages evolved more specialized foraging strategies, such as selective combing of microscopic diatoms or picking of macro-invertebrates. We found that representatives of these specialized lineages bear reduced infection with food-web-transmitted acanthocephalan helminths, but not with parasites with a direct life cycle. Possibly, the evolution of selective foraging strategies entailed reduced ingestion of intermediate invertebrate hosts of acanthocephalans. We conclude that some species belonging to the Tropheini virtually escape acanthocephalan infection as a by-product of trophic specialization.

• MeSH
• Biological Evolution * MeSH
• Cichlids parasitology   MeSH
• Helminths pathogenicity   MeSH
• Phylogeny * MeSH
• Parasites MeSH
• Food Chain MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Tanzania MeSH

• Publication type
• Abstracts MeSH

An outbreak of Mycobacterium avium subsp. avium infection was diagnosed in one breed of domestic pigeons (Columba livia f. domestica) in the Czech Republic. Nodular granulomatous lesions were found in 42 (9.7%) pigeons of the 435 examined; histopathologic examination of livers with gross lesions of mycobacteriosis from 15 randomly selected pigeons revealed granulomatous inflammation typical for avian mycobacteriosis in all samples. Direct Ziehl-Neelsen (ZN) microscopy and conventional culture were performed for a total of 117 liver samples (42 pigeons with nodular lesions, 55 randomly selected pigeons without nodular lesions, and 20 randomly selected squabs). Acid-fast bacilli were observed in 19 (16.2%), and conventional culture yielded growth of M. a. avium in 40 (34.2%) liver samples. A triplex quantitative real-time PCR assay based on the IS901 detection system was performed successfully in 115 liver samples and revealed M. a. avium in 63 (54.8%) of them. Mycobacterium a. avium was also detected in two squabs. Eight domestic rabbits (Oryctolagus cuniculus f. domestica) living in the breeding facility were also examined. Pyogranulomatous lesions were only found in one adult male rabbit. At necropsy, both direct ZN microscopy and culture gave negative results for mycobacteria in all examined rabbit tissues. Mycobacterium a. avium was diagnosed in a liver sample of one juvenile rabbit using triplex qPCR, suggesting that M. a. avium infection can occur as early as juvenile animals.

• MeSH
• Columbidae MeSH
• Liver pathology   virology   MeSH
• Rabbits MeSH
• Mycobacterium avium isolation & purification   MeSH
• Liver Diseases veterinary   MeSH
• Bird Diseases epidemiology   pathology   MeSH
• Polymerase Chain Reaction MeSH
• Tuberculosis, Avian epidemiology   virology   MeSH
• Tuberculosis epidemiology   veterinary   MeSH
• Animals MeSH
• Check Tag
• Rabbits MeSH
• Male MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Case Reports MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Czech Republic MeSH

Clades that have undergone episodes of rapid cladogenesis are challenging from a phylogenetic point of view. They are generally characterised by short or missing internal branches in phylogenetic trees and by conflicting topologies among individual gene trees. This may be the case of the subfamily Trematominae, a group of marine teleosts of coastal Antarctic waters, which is considered to have passed through a period of rapid diversification. Despite much phylogenetic attention, the relationships among Trematominae species remain unclear. In contrast to previous studies that were mostly based on concatenated datasets of mitochondrial and/or single nuclear loci, we applied various single-locus and multilocus phylogenetic approaches to sequences from 11 loci (eight nuclear) and we also used several methods to assess the hypothesis of a radiation event in Trematominae evolution. Diversification rate analyses support the hypothesis of a period of rapid diversification during Trematominae history and only a few nodes in the hypothetical species tree were consistently resolved with various phylogenetic methods. We detected significant discrepancies among trees from individual genes of these species, most probably resulting from incomplete lineage sorting, suggesting that concatenation of loci is not the most appropriate way to investigate Trematominae species interrelationships. These data also provide information about the possible effects of historic climate changes on the diversification rate of this group of fish.

• MeSH
• Bayes Theorem MeSH
• Phylogeny MeSH
• Fishes classification   genetics   MeSH
• Sequence Analysis, DNA MeSH
• Genetic Speciation MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Antarctic Regions MeSH