Arcobacter cloacae sp. nov. and Arcobacter suis sp. nov., two new species isolated from food and sewage

Genus-specific PCR assay for screening Arcobacter spp. in chicken meat

BACKGROUND

The number of emerging pathogenic species described within the genus Arcobacter has increased rapidly during the last few years. In this work a genus-specific polymerase chain reaction (PCR) assay was developed for detection of the species of Arcobacter most commonly associated with foods. The assay uses primers designed to amplify an 85 bp DNA fragment on the 16S rRNA gene and was applied to the detection of Arcobacter spp. in retail chicken meat.

RESULTS

Primer specificity was tested against a panel of Arcobacter spp., related Campylobacter and Helicobacter spp. and other food bacteria. Arcobacter primers consistently and selectively amplified the expected DNA fragment in all tested Arcobacter spp. Bacterial control primers confirmed the presence of amplifiable DNA in the samples. The applicability of the PCR assay to food was validated through screening of fresh retail chicken samples for the presence of Arcobacter spp., with a result of 45% (23 out of 51) positive samples.

CONCLUSION

The genus-specific PCR assay developed has the potential to be used as a quick and sensitive alternative method for the survey of Arcobacter contamination in meats.

A severe case of persistent diarrhoea associated with Arcobacter cryaerophilus but attributed to Campylobacter sp. and a review of the clinical incidence of Arcobacter spp

Although rarely, Arcobacter spp. have been associated with diarrhoea and bacteraemia. We report a persistent case in a healthy 26-year-old Spanish male of bloody diarrhoea, which was attributed to Campylobacter but in fact was caused by Arcobacter cryaerophilus, as determined by sequencing of the rpoB gene. The isolate was re-identified by matrix-assisted laser desorption ionization time of flight (MALDI-TOF) and genotyped for five putative virulence genes and for seven genes included in the Arcobacter multilocus sequence typing database. The low score obtained by MALDI-TOF indicates the need to complement the database with more isolates. Only the ciaB gene, which encodes for an invasin, was detected. Despite the isolate belonging to a new sequence type, three of the alleles (glnA, pgm and tkt) had been found previously in isolates from faeces of patients with diarrhoea. This study, together with the reviewed literature, indicates that Arcobacter can produce bacteraemia and that the isolation from patients with diarrhoea range from 0.11% to 1.25%. This study also demonstrates that Arcobacter species are confused with Campylobacter spp., as previously suggested. This is one of the factors that leads to underestimation of their incidence together with the use of inappropriate detection and identification methods.

Arcobacter anaerophilus sp. nov., isolated from an estuarine sediment and emended description of the genus Arcobacter

Two strains (JC83, JC84T) of obligately anaerobic, H2S-producing bacteria were isolated from estuarine sediment samples collected from Gangasagar, West Bengal, India. Cells were Gram-stain-negative, non-motile rods. Both strains were positive for oxidase, negative for catalase, hydrolysed casein, reduced nitrate and utilized citrate. Both strains grew chemoorganoheterotrophically with optimal pH of 7–8 (range 7–10) and at 30 °C (range 25–37 °C). C16 : 1ω7c, C18 : 1ω7c, C16 : 0 and C12 : 0 were the major fatty acids of both strains with minor amounts of C14 : 0, C12 : 0 3-OH and C18 : 0. Polar lipids of both strains included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, phosphatidylcholine, phosphatidylinositol, an unidentified aminolipid (AL2), an unidentified phospholipid (PL2) and an unidentified lipid (L3). MK-6 was the major respiratory quinone. The DNA G+C content of strains JC83 and JC84T was 25.0 and 24.6 mol%, respectively. The strains showed DNA reassociation >85 % (86.0±0.5 %) (based on DNA–DNA hybridization). Based on 16S rRNA gene sequence analysis, both strains were identified as belonging to the family Campylobacteraceae of the class Epsilonproteobacteria with Arcobacter marinus CL-S1T (95.4 % sequence similarity) as their closest phylogenetic neighbour. On the basis of morphological, physiological and chemotaxonomic characteristics as well as phylogenetic analysis, strains JC83 and JC84T are considered to represent a novel species, for which the name Arcobacter anaerophilus sp. nov. is proposed. The type strain is JC84T ( = KCTC 15071T = MTCC 10956T = DSM 24636T). An emended description of the genus Arcobacter is provided.

Multiplex polymerase chain reaction using ethidium monoazide and propidium monoazide for distinguishing viable and dead cells of arcobacters in biofilm

This paper concerns the formation of biofilm in bacteria of the genus Arcobacter. A multiplex polymerase chain reaction (PCR) method was introduced and optimized for detecting biofilm while using the intercalating dyes ethidium monoazide (EMA) and propidium monoazide (PMA), first for analysis of strains of the genus Arcobacter from a collection, and then applied to samples of prepared biofilms. The results of the study indicate considerable variability among species of bacteria within the genus Arcobacter. The EMA–PMA PCR method can distinguish viable cells from dead cells and is therefore suitable for determining the viability of cells.

Molecular diagnosis of Arcobacter and Campylobacter in diarrhoeal samples among Portuguese patients

The present study was conducted to investigate the prevalence and diversity of Arcobacter and Campylobacter spp. in 298 stool samples of patients with diarrhoea, collected from 22 Portuguese hospitals, between September and November 2012. Detection of Arcobacter and Campylobacter spp. was performed using molecular-based detection techniques, such as real-time fluorescence resonance energy transfer PCR, species-specific PCR, and sequencing of amplified PCR products. Overall, 1.3% of the samples were positive for Arcobacter butzleri and 0.3% for Arcobacter cryaerophilus. Campylobacter spp. were found in 31.9% of diarrhoeic faeces. Campylobacter jejuni and Campylobacter concisus were the most prevalent species (13.7% and 8.0%, respectively). The prevalence of Arcobacter and Campylobacter spp. was significantly different between children and adults (39.7% versus 22.8%, P = 0.003). We underline the high prevalence of these pathogens in diarrhoeal samples among Portuguese patients, with particular relevance in the paediatric age group.

Occurrence of six virulence-associated genes in Arcobacter species isolated from various sources in Shiraz, Southern Iran

In humans, arcobacters are associated with watery diarrhea and septicemia. Although, recently, more cases of diarrhea have been caused by Arcobacter species, very little is known about its pathogenesis. Therefore, the aim of this study was to evaluate the presence of six putative Arcobacter virulence genes (cadF, ciaB, cj1349, mviN, pldA, and tlyA), in a set of 113 Arcobacter butzleri, 40 Arcobacter cryaerophilus, and 15 Arcobacter skirrowii isolates that were recovered from various origins. The isolates were confirmed on the basis of polymerase chain reaction (PCR) amplification of genus and species specific PCR for determining three species. For confirmed isolates, PCR was carried out for the presence of virulence genes using specific primers. All A. butzleri isolates carried all six genes. For A. cryaerophilus and A. skirrowii, the cadF gene was detected just in 55 and 53.3%, ciaB in 97.5 and 86.6%, cj1349 in 45 and 60%, mviN in 90 and 80%, pldA in 32.5 and 13.3%, and tlyA in 37.5 and 40%, respectively. For A. cryaerophilus and A. skirrowii, the genes ciaB and mviN were significantly more prevalent than other virulence markers (P ≤ 0.05). The findings revealed that many of the important Arcobacter strains (86%) have these putative virulence genes which can be potential pathogenic properties for humans.

Performance of five molecular methods for monitoring Arcobacter spp

Background

Bacteria belonging to the Arcobacter genus are emerging enteropathogens and potential zoonotic agents. Their taxonomy has evolved very rapidly, and there are presently 18 recorded species. The prevalence of species belonging to Arcobacter is underestimated because of the limitations of currently available methods for species identification.

The aim of this study was to compare the performance of five PCR based methods that target regions of 16S rRNA, 23S rRNA or gyrA genes to identify Arcobacter species, and to review previous results reported in the literature using these methods.

Results

The five tested methods were found not to be reliable. They misidentified between 16.8% and 67.4% of the studied strains; this was dependent upon the target regions of the tested genes. The worst results obtained were for the identification of Arcobacter cryaerophilus and Arcobacter butzleri when the 23S rRNA gene was used as the target. These species were confused with many non-targeted species.

Conclusion

Our results suggest that the known diversity of Arcobacter spp. in different environments could be expanded if reliable identification methods are applied in future studies.

Adherence to and invasion of human intestinal cells by Arcobacter species and their virulence genotypes

The genus Arcobacter is composed of 17 species which have been isolated from various sources. Of particular interest are A. butzleri, A. cryaerophilus, and A. skirrowii, as these have been associated with human cases of diarrhea, the probable transmission routes being through the ingestion of contaminated drinking water and food. To date, only limited studies of virulence traits in this genus have been undertaken. The present study used 60 Arcobacter strains isolated from different sources, representing 16 of the 17 species of the genus, to investigate their ability to adhere to and invade the human intestinal cell line Caco-2. In addition, the presence of five putative virulence genes (ciaB, cadF, cj1349, hecA, and irgA) was screened for in these strains by PCR. All Arcobacter species except A. bivalviorum and Arcobacter sp. strain W63 adhered to Caco-2 cells, and most species (10/16) were invasive. The most invasive species were A. skirrowii, A. cryaerophilus, A. butzleri, and A. defluvii. All invasive strains were positive for ciaB (encoding a putative invasion protein). Other putative virulence genes were present in other species, i.e., A. butzleri (cadF, cj1349, irgA, and hecA), A. trophiarum (cj1349), A. ellisii (cj1349), and A. defluvii (irgA). No virulence genes were detected in strains which showed little or no invasion of Caco-2 cells. These results indicate that many Arcobacter species are potential pathogens of humans and animals.

Occurrence and genetic diversity of Arcobacter spp. in a spinach-processing plant and evaluation of two Arcobacter-specific quantitative PCR assays

Some species of the genus Arcobacter are considered to be emerging food pathogens. With respect to recent vegetable-borne outbreaks, the aim of this work was to investigate the occurrence and diversity of Arcobacter within the production chain of a spinach-processing plant by a combination of cultivation and molecular methods. Samples including spinach, water, and surface biofilm were taken over a period of three years from the entire processing line. Ten 16S rRNA (rrs) gene clone libraries were constructed and analysed using amplified rRNA gene restriction analysis (ARDRA). Approximately 1200 clones were studied that resulted in 44 operational taxonomic units (OTUs). Sequences with high similarities to Arcobacter cryaerophilus (13% of clones, 3 OTUs), A. ellisii (4%, 6 OTUs), A. suis (15%, 3 OTUs), and the type strain of A. nitrofigilis (1%, 7 OTUs) were identified. This represents the first report of the detection of the recently described species A. ellisii, A. suis and, in addition, A. venerupis from alternative habitats. A total of 67% of the clones (22 OTUs) could not be assigned to a genus, which indicated the presence of uncharacterised Arcobacter species. For the cultivation-independent detection of Arcobacter, two genus-specific quantitative PCR (qPCR) assays were developed and tested on 15 Arcobacter species. When these assays were applied to samples from the spinach-processing plant, they showed positive results for up to 35% of the samples and supported the conclusion that there is a considerable risk for the transfer of pathogenic Arcobacter species on vegetables, which was also verified by a cultivation approach.

Updated 16S rRNA-RFLP method for the identification of all currently characterised Arcobacter spp

BACKGROUND

Arcobacter spp. (family Campylobacteraceae) are ubiquitous zoonotic bacteria that are being increasingly recognised as a threat to human health. A previously published 16S rRNA-RFLP Arcobacter spp. identification method produced specific RFLP patterns for the six species described at that time, using a single endonuclease (MseI). The number of characterised Arcobacter species has since risen to 17. The aim of the present study was to update the 16S rRNA-RFLP identification method to include all currently characterised species of Arcobacter.

RESULTS

Digestion of the 16S rRNA gene with the endonuclease MseI produced clear, distinctive patterns for 10 of the 17 species, while the remaining species shared a common or very similar RFLP pattern. Subsequent digestion of the 16S rRNA gene from these species with the endonucleases MnlI and/or BfaI generated species-specific RFLP patterns.

CONCLUSIONS

16S rRNA-RFLP analysis identified 17 Arcobacter spp. using either polyacrylamide or agarose gel electrophoresis. Microheterogeneities within the 16S rRNA gene, which interfered with the RFLP identification, were also documented for the first time in this genus, particularly in strains of Arcobacter cryaerophilus isolated from animal faeces and aborted foetuses.

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.