Lies Debruyne

Arcobacter thereius sp. nov., isolated from pigs and ducks.

During a Danish study on the prevalence of campylobacteria in pig abortions and food of animal origin, eight Gram-negative, slightly curved, rod-shaped, non-spore-forming bacteria were clustered by using amplified fragment length polymorphism analysis in a distinct phenon within the genus Arcobacter. In the present study, numerical analysis of whole-cell protein profiles also showed that all isolates clustered in a single group distinct from other recognized Arcobacter species. DNA-DNA hybridization among two representative strains exhibited a mean DNA-DNA relatedness value of 79 %. DNA-DNA hybridization with the type strains of recognized Arcobacter species revealed levels of DNA-DNA relatedness of 41 % or less. The DNA G+C content of the type strain was 28.5 mol%. Pairwise comparison of the 16S rRNA gene sequences with those of the type strains of established species identified Arcobacter cryaerophilus (97.9 %), Arcobacter cibarius (97.5 %) and Arcobacter skirrowii (97.2 %) as the nearest phylogenetic neighbours. The isolates could be distinguished from other Arcobacter species by means of the following biochemical tests: activities of catalase and urease, reduction of nitrate and growth on minimal medium, lack of growth at 37 degrees C under standardized aerobic and microaerobic conditions, in 4 % NaCl and 1 % glycine media. Finally, DNA fingerprints obtained by using enterobacterial repetitive intergenic consenus-PCR showed that the eight isolates represent eight strains of a single novel Arcobacter species, for which the name Arcobacter thereius sp. nov. is proposed. The type strain is LMG 24486(T) (=CCUG 56902(T)).

Novel Campylobacter lari-like bacteria from humans and molluscs: description of Campylobacter peloridis sp. nov., Campylobacter lari subsp. concheus subsp. nov. and Campylobacter lari subsp. lari subsp. nov.

A polyphasic study was undertaken to clarify the taxonomic position of Campylobacter lari-like strains isolated from shellfish and humans. The diversity within the strain collection was initially screened by means of fluorescent amplified fragment length polymorphism analysis and whole-cell protein electrophoresis, revealing the existence of two clusters distinct from C. lari and other Campylobacter species. The divergence of these clusters was confirmed by phenotypic analysis and by 16S rRNA and hsp60 gene sequence analysis. Phylogenetic analysis identified C. lari, Campylobacter jejuni, Campylobacter coli and Campylobacter insulaenigrae as the closest phylogenetic neighbours of both taxa. DNA-DNA hybridizations revealed that one cluster, comprising 10 strains, represented a novel Campylobacter species, for which the name Campylobacter peloridis sp. nov. is proposed, with 2314BVA(T) (=LMG 23910(T) =CCUG 55787(T)) as the type strain. The second cluster, comprising six strains, represents a novel subspecies within the species C. lari, for which the name Campylobacter lari subsp. concheus subsp. nov. is proposed, with 2897R(T) (=LMG 21009(T) =CCUG 55786(T)) as the type strain. The description of C. lari subsp. concheus has the effect of automatically creating the subspecies Campylobacter lari subsp. lari subsp. nov. (type strain LMG 8846(T)=NCTC 11352(T)).

Reclassification of Bacteroides ureolyticus as Campylobacter ureolyticus comb. nov., and emended description of the genus Campylobacter.

The protein profiles, genomic amplified fragment length polymorphism patterns and 16S rRNA and cpn60 gene sequences of a diverse collection of 26 Bacteroides ureolyticus strains, along with published data on their DNA base, respiratory quinone and cellular fatty acid compositions, were used to reassess the taxonomy of this bacterial species. The results demonstrate that this organism is most appropriately allocated in the genus Campylobacter. The presence of much higher amounts of 18 : 1omega7c in its cellular fatty acid profile and its ability to digest gelatin and casein are the characteristics that differentiate it from present species of the genus Campylobacter. Therefore we propose to reclassify this species incertae sedis into the genus Campylobacter as Campylobacter ureolyticus with strain LMG 6451(T) (=CCUG 7319(T) =NCTC 10941(T)) as the type strain.

Quantification of Campylobacter spp. in chicken carcass rinse by real-time PCR

Aims:  In this study, a real‐time quantitative polymerase chain reaction (PCR) method was examined for its ability to quantify Campylobacter spp. in chicken carcass rinses and compared with bacteriological culturing.

Accuracy of the API Campy system, the Vitek 2 Neisseria-Haemophilus card and matrix-assisted laser desorption ionization time-of-flight mass spectrometry for the identification of Campylobacter and related organisms

Biochemical identification of Campylobacter and related organisms is not always specific, and may lead to diagnostic errors. The API Campy, the Vitek 2 system and matrix-assisted desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) are commercially available methods that are routinely used for the identification of these microorganisms. In the present study, we used 224 clinical isolates and ten reference strains previously identified by multiple PCR assays, whole cell protein profiling and either DNA-DNA hybridization or sequencing analysis to compare the reliability of these three methods for the identification of Campylobacter and related pathogens. The API Campy accurately identified 94.4% of Campylobacter jejuni ssp. jejuni and 73.8% of Campylobacter coli, but failed to correctly identify 52.3% of other Epsilobacteria. The Vitek 2 Neisseria-Haemophilus card correctly identified most C. jejuni ssp.jejuni (89.6%) and C. coli (87.7%) strains, which account for the majority of campylobacterioses reported in humans, but it failed in the identification of all of the other species. Despite a good identification rate for both C. jejuni ssp. jejuni and C. coli, both methods showed poor sensitivity in the identification of related organisms, and additional tests were frequently needed. In contrast to API Campy and Vitek, MALDI-TOF MS correctly identified 100% of C. coli and C. jejuni strains tested. With an overall sensitivity of 98.3% and a short response time, this technology appears to be a reliable and promising method for the routine identification of Campylobacter and other Epsilobacteria.

Campylobacter cuniculorum sp. nov., from rabbits

Eight strains of an unknown thermotolerant Campylobacter species were isolated from the caecal contents of rabbits (Oryctolagus cuniculus). All strains were initially identified as belonging to the genus Campylobacter by means of genus-specific PCR, but none were identified using species-specific PCR for known thermophilic species. Cells were spiral shaped with bipolar unsheathed flagella, with no periplasmic fibres, and appeared coccoid after 10-12 days of incubation. Phylogenetic analyses based on 16S rRNA gene, rpoB and groEL sequences revealed that all strains formed a robust clade that was very distinct from recognized Campylobacter species. 16S rRNA gene sequence pairwise comparisons of strain 150B(T) with the type strains of other Campylobacter species revealed that the nearest phylogenetic neighbour was Campylobacter helveticus NCTC 12470(T), with 96.6 % similarity. The uniqueness of these rabbit isolates was confirmed by whole-cell protein electrophoresis. Taken together, these data indicate that the strains belong to a novel Campylobacter species for which the name Campylobacter cuniculorum sp. nov. is proposed, with 150B(T) (=LMG 24588(T) =CCUG 56289(T)) as the type strain.

Campylobacter volucris sp. nov., isolated from black-headed gulls (Larus ridibundus)

During a study of the prevalence of Campylobacter jejuni in black-headed gulls (Larus ridibundus) in Sweden, three isolates, strains LMG 24379, LMG 24380T and LMG 24381, were initially identified as Campylobacter lari. Further characterization by both AFLP and whole-cell protein SDS-PAGE analyses revealed that they formed a distinct group in the genus Campylobacter. This unique position was confirmed by phenotypic characterization, 16S rRNA and hsp60 gene sequence analysis and DNA-DNA hybridizations. The combined data confirm that these isolates represent a novel species within the genus Campylobacter, for which the name Campylobacter volucris sp. nov. is proposed. The type strain is LMG 24380T (=CCUG 57498T).

Campylobacter avium sp. nov., a hippurate-positive species isolated from poultry.

Three strains of an unusual hippurate-positive Campylobacter species were isolated at 37 degrees C from caecal contents of broiler chickens and a turkey. All strains were initially identified as Campylobacter by means of genus-specific PCR, but none was further identified using specific PCRs for known thermophilic species. Phylogenetic analyses based on 16S rRNA, rpoB and groEL gene sequences revealed that these strains formed a robust clade distinct from other Campylobacter species. Amplified fragment length polymorphism analysis and whole-cell protein electrophoresis were subsequently carried out and confirmed the divergence between the avian strains and other taxa. These data indicate that the unidentified Campylobacter strains belong to a novel taxon which could be distinguished from other campylobacters through its phenotypic and genotypic characteristics. The name Campylobacter avium sp. nov., is proposed for the novel species, with the type strain 86/06T (=LMG 24591T=CCUG 56292T).

Key characteristics for tool choice in indicator-based sustainability assessment at farm level

Although the literature on sustainability assessment tools to support decision making in agriculture is rapidly growing, little attention has been paid to the actual tool choice. We focused on the choice of more complex integrated indicator-based tools at the farm level. The objective was to determine key characteristics as criteria for tool choice. This was done with an in-depth comparison of 2 cases: the Monitoring Tool for Integrated Farm Sustainability and the Public Goods Tool. They differ in characteristics that may influence tool choice: data, time, and budgetary requirements. With an enhanced framework, we derived 11 key characteristics to describe differences between the case tools. Based on the key characteristics, we defined 2 types of indicator-based tools: full sustainability assessment (FSA) and rapid sustainability assessment (RSA). RSA tools are more oriented toward communicating and learning. They are therefore more suitable for use by a larger group of farmers, can help to raise awareness, trigger farmers to become interested in sustainable farming, and highlight areas of good or bad performance. If and when farmers increase their commitment to on-farm sustainability, they can gain additional insight by using an FSA tool. Based on complementary and modular use of the tools, practical recommendations for the different end users, i.e., researchers, farmers, advisers, and so forth, have been suggested.

Campylobacter subantarcticus sp. nov., isolated from birds in the sub-Antarctic region

Six Gram-stain-negative, spiral-shaped, microaerobic isolates were obtained during a sampling from wild birds in the sub-Antarctic region. Based on initial observations, these isolates were classified as Campylobacter lari-like. The isolates were further characterized by whole-cell protein and amplified fragment length polymorphism (AFLP) analysis, which revealed that they were distinct from C. lari and all other known species of the genus Campylobacter. Here, we present comprehensive phylogenetic, genomic and phenotypic evidence that these isolates represent a novel species within the genus Campylobacter, for which the name Campylobacter subantarcticus sp. nov. is proposed. The type strain is R-3023(T) (=LMG 24377(T) =CCUG 38513(T)).