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Genome Biology and Evolution Feb 2020Arcobacter species are recovered from a wide variety of sources, including animals, food, and both fresh and marine waters. Several Arcobacter species have also been...
Arcobacter species are recovered from a wide variety of sources, including animals, food, and both fresh and marine waters. Several Arcobacter species have also been recovered from human clinical samples and are thus associated tentatively with food- and water-borne human illnesses. Genome sequencing of the poultry isolate Arcobacter cibarius H743 and the Arcobacter acticola, Arcobacter pacificus, and Arcobacter porcinus type strains identified a large number and variety of insertion sequences. This study presents an analysis of these A. acticola, A. cibarius, A. pacificus, and A. porcinus IS elements. The four genomes sequenced here contain 276 complete and degenerate IS elements, representing 13 of the current 29 prokaryotic IS element families. Expansion of the analysis to include 15 other previously sequenced Arcobacter spp. added 73 complete and degenerate IS elements. Several of these IS elements were identified in two or more Arcobacter species, suggesting movement by horizontal gene transfer between the arcobacters. These IS elements are putatively associated with intragenomic deletions and inversions, and tentative movement of antimicrobial resistance genes. The A. cibarius strain H743 megaplasmid contains multiple IS elements common to the chromosome and, unusually, a complete ribosomal RNA locus, indicating that larger scale genomic rearrangements, potentially resulting from IS element-mediated megaplasmid cointegration and resolution may be occurring within A. cibarius and possibly other arcobacters. The presence of such a large and varied suite of mobile elements could have profound effects on Arcobacter biology and evolution.
Topics: Arcobacter; DNA Transposable Elements; Interspersed Repetitive Sequences; Phylogeny; RNA, Ribosomal; Whole Genome Sequencing
PubMed: 32011709
DOI: 10.1093/gbe/evaa014 -
Journal of Food Protection Oct 2017Campylobacter and Arcobacter spp. are common causes of gastroenteritis in humans; these infections are commonly due to undercooked poultry. However, their virulence...
Campylobacter and Arcobacter spp. are common causes of gastroenteritis in humans; these infections are commonly due to undercooked poultry. However, their virulence mechanism is still poorly understood. The aim of this study was to evaluate the presence of genotypic virulence markers in Campylobacter and Arcobacter species using PCR. The prevalence of virulence and cytolethal distending toxin (CDT) genes was estimated in 71 Campylobacteraceae isolates. PCR was used to detect the presence of virulence genes (iam, cadF, virB1, flaA, cdtA, cdtB, and cdtC) using specific primers for a total of 45 Campylobacter isolates, including 37 C. jejuni and 8 C. coli. All the Campylobacter isolates were positive for the cadF gene. The plasmid gene virB11 was not detected in any strain. The invasion associated marker was not detected in C. jejuni. Lower detection rates were observed for flaA, cdtA, cdtB, and cdtC. The presence of nine putative Arcobacter virulence genes (cadF, ciaB, cj1349, mviN, pldA, tlyA, irgA, hecA, and hecB) was checked in a set of 22 Arcobacter butzleri and 4 Arcobacter cryaerophilus isolates. The pldA and mviN genes were predominant (88.64%). Lower detection rates were observed for tlyA (84.76%), ciaB (84.61%), cadF and cj1349 (76.92%), IrgA and hecA (61.53%), and hecB (57.69%). The findings revealed that a majority of the Campylobacteraceae strains have these putative virulence genes that may lead to pathogenic effects in humans.
Topics: Animals; Arcobacter; Campylobacter; Campylobacter jejuni; Humans; Polymerase Chain Reaction; Poultry; Prevalence; Tunisia; Virulence; Virulence Factors
PubMed: 28906158
DOI: 10.4315/0362-028X.JFP-16-509 -
Journal of Applied Microbiology Jan 2010The present study aimed to assess the Arcobacter contamination on bovine carcasses postevisceration and postcooling in two slaughterhouses and in ready-to-eat minced...
AIMS
The present study aimed to assess the Arcobacter contamination on bovine carcasses postevisceration and postcooling in two slaughterhouses and in ready-to-eat minced beef.
METHODS AND RESULTS
Carcasses (n = 247) were sampled at four sites in two slaughterhouses and 100 minced beef samples were collected at retail. Isolation was performed by a quantitative and qualitative Arcobacter selective method, and the isolates were identified by multiplex PCR, after which a part of them were characterized by enterobacterial repetitive intergenic consensus (ERIC)-PCR. Although arcobacters were isolated from 37% of the bovine carcasses postevisceration with the chest and the foreleg as most contaminated sites, cooling the carcasses for at least 24 h reduced the incidence of Arcobacter (7%) on the carcass surface significantly. Arcobacter butzleri was the species most frequently isolated, although co-contamination with multiple species also occurred. At retail, arcobacters were present in 9% of the minced beef samples, with Arcobacter butzleri as the dominant species.
CONCLUSIONS
Forced air cooling of bovine carcasses for at least 24 h decreased the number of positive carcasses, but did not eliminate all arcobacters.
SIGNIFICANCE AND IMPACT OF THE STUDY
This study demonstrates that maintaining good hygiene practices throughout the food supply chain is crucial to ensure safe food products at the consumer level.
Topics: Animals; Arcobacter; Cattle; Food Contamination; Food Handling; Food Microbiology; Meat Products
PubMed: 19614853
DOI: 10.1111/j.1365-2672.2009.04430.x -
FEMS Microbiology Ecology Dec 2022Planktonic particle-associated bacteria comprise particle-attached and motile free-living cells. These groups were obtained by settlement in Imhoff cones. Dilution...
Planktonic particle-associated bacteria comprise particle-attached and motile free-living cells. These groups were obtained by settlement in Imhoff cones. Dilution plating on marine agar 2216 (ZoBell marine agar) and microscopic counts indicated a cultivability of 0.7% (0.4%-1.2%) of bacteria in coastal seawater collected at Helgoland Roads, North Sea. Particle-associated bacteria presented a minority population in seawater, but had a larger cultivability of 25% (0.9%-100%) for populations collected by settlement of particles and 5.7% (0.9%-24%) for populations collected by filtration. Partial 16S rRNA gene sequences indicated that 84% of the cultured taxa were either enriched in particle-associated microbiomes or only found in these microbiomes, including Sulfitobacter and other Rhodobacteraceae, Pseudoalteromonas, Psychromonas, Arcobacter and many Flavobacteriaceae. Illumina-based 16S rRNA V3V4 amplicon sequences of plate communities revealed that nearly all operational taxonomic units had a cultivated and described strain in close phylogenetic proximity. This suggested that decades of strain isolation from seawater on ZoBell marine agar had achieved a very good coverage of cultivable genera abundant in nature. The majority belonged to particle-associated bacteria, complementing observations that abundant free-living seawater bacteria often require cultivation conditions closer to their natural habitat like liquid cultivation in oligotrophic medium.
Topics: Agar; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Sequence Analysis, DNA; Seawater; Flavobacteriaceae; Microbiota
PubMed: 36513318
DOI: 10.1093/femsec/fiac151 -
New Microbes and New Infections Jan 2017is a species associated with human disease. A group of pork strains (represented by strain LMG 24487) clustered separately from the type strain (LMG 24486) in the 16S...
is a species associated with human disease. A group of pork strains (represented by strain LMG 24487) clustered separately from the type strain (LMG 24486) in the 16S rRNA and multilocus phylogenetic trees. DNA-DNA hybridization and average nucleotide identity results between their genomes (93.3 and 51.1%) confirmed '' (LMG 24487) as a new species.
PubMed: 28070334
DOI: 10.1016/j.nmni.2016.11.014 -
Frontiers in Microbiology 2019The Campylobacterota, previously known as Epsilonproteobacteria, are a large group of Gram-negative mainly, spiral-shaped motile bacteria. Some members like the spp.... (Review)
Review
The Campylobacterota, previously known as Epsilonproteobacteria, are a large group of Gram-negative mainly, spiral-shaped motile bacteria. Some members like the spp. are free-living, while others such as spp. can only persist in strict association with a host organism as commensal or as pathogen. Species of this phylum colonize diverse habitats ranging from deep-sea thermal vents to the human stomach wall. Despite their divergent environments, they share common energy conservation mechanisms. The Campylobacterota have a large and remarkable repertoire of electron transport chain enzymes, given their small genomes. Although members of recognized families of transcriptional regulators are found in these genomes, sofar no orthologs known to be important for energy or redox metabolism such as ArcA, FNR or NarP are encoded in the genomes of the Campylobacterota. In this review, we discuss the strategies that members of Campylobacterota utilize to conserve energy and the corresponding regulatory mechanisms that regulate the branched electron transport chains in these bacteria.
PubMed: 31417516
DOI: 10.3389/fmicb.2019.01719 -
BMC Microbiology Jan 2019Arcobacter faecis and A. lanthieri are two newly classified species of genus Arcobacter. The prevalence and distribution of virulence, antibiotic resistance and toxin...
BACKGROUND
Arcobacter faecis and A. lanthieri are two newly classified species of genus Arcobacter. The prevalence and distribution of virulence, antibiotic resistance and toxin (VAT) genes in these species are required to assess their potential pathogenic health impacts to humans and animals. This study (i) developed species- and gene-specific primer pairs for the detection of six virulence, two antibiotic resistance, and three toxin genes in two target species; (ii) optimized eight single-tube multiplex and three monoplex PCR protocols using the newly developed species- and gene-specific primers; and (iii) conducted specificity and sensitivity evaluations as well as validation of eleven mono- and multiplex PCR assays by testing A. faecis (n= 29) and A. lanthieri (n= 10) strains isolated from various fecal and agricultural water sources to determine the prevalence and distribution of VAT genes and assess the degree of pathogenicity within the two species.
RESULTS
Detection of all ten and eleven target VAT genes, and expression of cytolethal distending toxin (cdtA, cdtB and cdtC) genes in A. faecis and A. lanthieri reference strains with high frequency in field isolates suggest that they are potentially pathogenic strains. These findings indicate that these two species can pose a health risk to humans and animals.
CONCLUSIONS
The study results show that the developed mono- and multiplex PCR (mPCR) assays are simple, rapid, reliable and sensitive for the simultaneous assessment of the potential pathogenicity and antibiotic resistance profiling of tet(O) and tet(W) genes in these two newly discovered species. Also, these assays can be useful in diagnostic and analytical laboratories to determine the pathotypes and assessment of the virulence and toxin factors associated to human and animal infections.
Topics: Animals; Arcobacter; Bacterial Toxins; Bacterial Typing Techniques; Drug Resistance, Microbial; Genes, Bacterial; Gram-Negative Bacterial Infections; Humans; Multiplex Polymerase Chain Reaction; Polymerase Chain Reaction; Sensitivity and Specificity; Virulence
PubMed: 30634926
DOI: 10.1186/s12866-018-1357-7 -
IScience Mar 2021Mangrove-dominated estuaries host a diverse microbial assemblage that facilitates nutrient and carbon conversions and could play a vital role in maintaining ecosystem...
Mangrove-dominated estuaries host a diverse microbial assemblage that facilitates nutrient and carbon conversions and could play a vital role in maintaining ecosystem health. In this study, we used 16S rRNA gene analysis, metabolic inference, nutrient concentrations, and δC and δN isotopes to evaluate the impact of land use change on near-shore biogeochemical cycles and microbial community structures within mangrove-dominated estuaries. Samples in close proximity to active shrimp aquaculture were high in NH , NO NO , and PO ; lower in microbial community and metabolic diversity; and dominated by putative nitrifiers, denitrifies, and sulfur-oxidizing bacteria. Near intact mangrove forests we observed the presence of potential nitrogen fixers of the genus and order Rhizobiales. We identified possible indicators of aquaculture effluents such as family Chromatiaceae and genus These results highlight the sensitivity of the estuarine-mangrove microbial community, and their ecosystem functions, to land use changes.
PubMed: 33786421
DOI: 10.1016/j.isci.2021.102204 -
Applied and Environmental Microbiology Apr 2020Pathogenic bacteria in wastewater are generally considered to be efficiently removed in biological wastewater treatment plants. This understanding is almost solely based...
Pathogenic bacteria in wastewater are generally considered to be efficiently removed in biological wastewater treatment plants. This understanding is almost solely based on culture-based control measures, and here we show, by applying culture-independent methods, that the removal of species in the genus was less effective than for many other abundant genera in the influent wastewater. was one of the most abundant genera in influent wastewater at 14 municipal wastewater treatment plants and was also abundant in the "clean" effluent from all the plants, reaching up to 30% of all bacteria as analyzed by 16S rRNA gene amplicon sequencing. Metagenomic analyses, culturing, genome sequencing of isolates, and visualization by fluorescent hybridization (FISH) confirmed the presence of the human-pathogenic and in both influent and effluent. The main reason for the high relative abundance in the effluent was probably that cells, compared to those of other abundant genera in the influent, did not flocculate and attach well to the activated sludge flocs, leaving a relatively large fraction dispersed in the water phase. The study shows there is an urgent need for new standardized culture-independent measurements of pathogens in effluent wastewaters, e.g., amplicon sequencing, and an investigation of the problem on a global scale to quantify the risk for humans and livestock. The genus was unexpectedly abundant in the effluent from 14 Danish wastewater treatment plants treating municipal wastewater, and the species included the human-pathogenic and Recent studies have shown that is common in wastewater worldwide, so the study indicates that discharge of members of the genus may be a global problem, and further studies are needed to quantify the risk and potentially minimize the discharge. The study also shows that culture-based analyses are insufficient for proper effluent quality control, and new standardized culture-independent measurements of effluent quality encompassing most pathogens should be considered.
Topics: Arcobacter; Denmark; RNA, Bacterial; RNA, Ribosomal, 16S; Waste Disposal, Fluid; Wastewater
PubMed: 32111585
DOI: 10.1128/AEM.03044-19 -
Applied and Environmental Microbiology Dec 2019Members of the epsilonproteobacterial genus have been identified to be potentially important sulfide oxidizers in marine coastal, seep, and stratified basin...
Members of the epsilonproteobacterial genus have been identified to be potentially important sulfide oxidizers in marine coastal, seep, and stratified basin environments. In the highly productive upwelling waters off the coast of Peru, cells comprised 3 to 25% of the total microbial community at a near-shore station where sulfide concentrations exceeded 20 μM in bottom waters. From the chemocline where the population exceeded 10 cells ml and where high rates of denitrification (up to 6.5 ± 0.4 μM N day) and dark carbon fixation (2.8 ± 0.2 μM C day) were measured, we isolated a previously uncultivated species, sp. nov. (BCCM LMG-31510). Genomic analysis showed that possesses genes encoding sulfide oxidation and denitrification pathways but lacks the ability to fix CO via autotrophic carbon fixation pathways. Genes encoding transporters for organic carbon compounds, however, were present in the genome. Physiological experiments demonstrated that grew best on a mix of sulfide, nitrate, and acetate. Isotope labeling experiments further verified that completely reduced nitrate to N and assimilated acetate but did not fix CO, thus coupling heterotrophic growth to sulfide oxidation and denitrification. Single-cell nanoscale secondary ion mass spectrometry analysis of samples taken from shipboard isotope labeling experiments also confirmed that the population did not substantially fix CO The efficient growth yield associated with the chemolithoheterotrophic metabolism of may allow this species to rapidly bloom in eutrophic and sulfide-rich waters off the coast of Peru. Our multidisciplinary approach provides new insights into the ecophysiology of a newly isolated environmental species, as well as the physiological flexibility within the genus and sulfide-oxidizing, denitrifying microbial communities within oceanic oxygen minimum zones (OMZs). The chemolithoheterotrophic species may play a substantial role in the diverse consortium of bacteria that is capable of coupling denitrification and fixed nitrogen loss to sulfide oxidation in eutrophic, sulfidic coastal waters. With increasing anthropogenic pressures on coastal regions, e.g., eutrophication and deoxygenation (D. Breitburg, L. A. Levin, A. Oschlies, M. Grégoire, et al., Science 359:eaam7240, 2018, https://doi.org/10.1126/science.aam7240), niches where sulfide-oxidizing, denitrifying heterotrophs such as thrive are likely to expand.
Topics: Arcobacter; Biomass; Carbon; Carbon Cycle; Denitrification; Geologic Sediments; Heterotrophic Processes; Isotope Labeling; Nitrates; Nitrogen Fixation; Oxidation-Reduction; Oxygen; Peru; RNA, Ribosomal, 16S; Seawater; Sulfides; Water; Water Microbiology; Whole Genome Sequencing
PubMed: 31585991
DOI: 10.1128/AEM.01344-19