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Microbiology Spectrum Aug 2022Aliarcobacter butzleri is an emerging gastrointestinal pathogen found in many countries worldwide. In France, it has become the third most commonly isolated bacterial...
Aliarcobacter butzleri is an emerging gastrointestinal pathogen found in many countries worldwide. In France, it has become the third most commonly isolated bacterial species from the stools of patients with intestinal infections. No interpretative criteria for antimicrobial susceptibility testing have been proposed for A. butzleri, and most strains are categorized using the recommendations of the Clinical and Laboratory Standards Institute or the European Committee on Antimicrobial Susceptibility Testing for Campylobacter or . In the present study, the genomes of 30 resistant A. butzleri isolates were analyzed to propose specific epidemiological cut-off values for ampicillin, ciprofloxacin, erythromycin, and tetracycline. The identification of a β-lactamase and the T85I GyrA mutation associated with ampicillin and ciprofloxacin resistance, respectively, allowed us to adjust the disk diffusion (DD) and MIC cut-off values for these molecules. However, epidemiological cut-off values for erythromycin and tetracycline could not be estimated due to the absence of known resistance mechanisms. The present study paves the way for building a consensus for antimicrobial susceptibility testing for this concerning pathogen. Aliarcobacter butzleri is an emerging and concerning intestinal pathogen. Very few studies have focused on this particular species, and antimicrobial susceptibility testing (AST) is based on methods that have been mostly developed for Campylobacter spp. In fact, no disk diffusion and E-tests adapted cut-offs for A. butzleri are available which leads to misinterpretations. We have shown here that NGS approach to identify genes and mutations in close relation to phenotypic resistance levels is a robust way to solve that issue and precisely differentiate WT and NWT A. butzleri isolates for frequently used antimicrobials. MIC and DD cut-off values have been significantly adjusted and answer the need for a global consensus regarding AST for A. butzleri.
Topics: Ampicillin; Anti-Bacterial Agents; Arcobacter; Ciprofloxacin; Drug Resistance, Bacterial; Erythromycin; Humans; Microbial Sensitivity Tests; Tetracycline
PubMed: 35862990
DOI: 10.1128/spectrum.01003-22 -
Antibiotics (Basel, Switzerland) May 2023Due to the lack of knowledge about in the Chilean poultry industry, the objective of this research was to know the prevalence, resistance, and genotypes of , and in...
Due to the lack of knowledge about in the Chilean poultry industry, the objective of this research was to know the prevalence, resistance, and genotypes of , and in 382 samples of chicken meat purchased in Valdivia, Chile. The samples were analyzed using three isolation protocols. Resistance to four antibiotics was evaluated by phenotypic methods. Genomic analyses were performed on selected resistant strains to detect resistance determinants and their genotypes. A total of 59.2% of the samples were positive. (37.4%) was the most prevalent species, followed by (19.6%), (11.3%), (3.7%) and (1.3%). (14%) was detected by PCR in a subset of samples. was resistant to ciprofloxacin (37.3%) and tetracycline (20%), while and were resistant to ciprofloxacin (55.8% and 2.8%), erythromycin (16.3% and 0.7%) and tetracycline (4.7% and 2.8%), respectively. Molecular determinants were consistent with phenotypic resistance. The genotypes of (CC-21, CC-48, CC-49, CC-257, CC-353, CC-443, CC-446 and CC-658) and (CC-828) coincided with genotypes of Chilean clinical strains. These findings suggest that besides and , chicken meat could play a role in the transmission of other pathogenic and antibiotic-resistant
PubMed: 37237819
DOI: 10.3390/antibiotics12050917 -
MicrobiologyOpen Oct 2019Arcobacter have been frequently detected in and isolated from bivalves, but there is very little information on the genus Arcobacter in the abalone, an important fishery...
Arcobacter have been frequently detected in and isolated from bivalves, but there is very little information on the genus Arcobacter in the abalone, an important fishery resource. This study aimed to investigate the genetic diversity and abundance of bacteria from the genus Arcobacter in the Japanese giant abalone, Haliotis gigantea, using molecular methods such as Arcobacter-specific clone libraries and fluorescence in situ hybridization (FISH). Furthermore, we attempted to isolate the Arcobacter species detected. Twelve genotypes of clones were obtained from Arcobacter-specific clone libraries. These sequences are not classified with any other known Arcobacter species including pathogenic Arcobacter spp., A. butzleri, A. skirrowii, and A. cryaerophilus, commonly isolated or detected from bivalves. From the FISH analysis, we observed that ARC94F-positive cells, presumed to be Arcobacter, accounted for 6.96 ± 0.72% of all EUB338-positive cells. In the culture method, three genotypes of Arcobacter were isolated from abalones. One genotype had a similarity of 99.2%-100.0% to the 16S rRNA gene of Arcobacter marinus, while the others showed only 93.3%-94.3% similarity to other Arcobacter species. These data indicate that abalones carry Arcobacter as a common bacterial genus which includes uncultured species.
Topics: Animals; Arcobacter; Biodiversity; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Gastropoda; Genotype; In Situ Hybridization, Fluorescence; Metagenomics; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 31168933
DOI: 10.1002/mbo3.890 -
Advances in Food and Nutrition Research 2022The concern with food safety in the milk chain begins with the quality of the raw milk. Due to the health hazard that this food can carry when contaminated, the focus of...
The concern with food safety in the milk chain begins with the quality of the raw milk. Due to the health hazard that this food can carry when contaminated, the focus of studies has turned to microbiological and chemical contaminants that may be present in raw milk. There is an essential concern about conventional pathogens (Shiga toxin-producing Escherichia coli, Salmonella spp., Listeria monocytogenes, Campylobacter spp., Salmonella spp., and coagulase-positive Staphylococcus spp.) and emerging pathogens (Arcobacter butzleri, Yersinia enterocolitica, Mycobacterium avium ssp. paratuberculosis, Helicobacter pylori, and Cronobacter sakazakii) found in raw milk and dairy products. In addition, a growing public health issue has been raised regarding antimicrobial-resistant pathogens and commensal strains found in milk and dairy products. The antibiotic residues in milk can also damage health, such as allergies, and cause technological problems in dairy products processing. This health issue extends to other chemical contaminants such as heavy metals, pesticides, polycyclic aromatic hydrocarbons, melamine, dioxins, polychlorinated biphenyls, plasticizers, and additives in milk and dairy products. Other chemical substances formed by microorganisms are also of high importance, such as biogenic amines and mycotoxins. Therefore, this chapter aimed to revise and discuss relevant biological and chemical risks to ensure the safety and quality of raw milk and dairy products.
Topics: Animals; Food Microbiology; Listeria monocytogenes; Milk; Salmonella
PubMed: 35659353
DOI: 10.1016/bs.afnr.2022.01.001 -
Frontiers in Microbiology 2022species are ubiquitous emerging pathogens with an impact that has been underestimated due to limitations in isolation and detection methods. Our group recently...
species are ubiquitous emerging pathogens with an impact that has been underestimated due to limitations in isolation and detection methods. Our group recently developed the novel NRJ -detection system, with major improvements in specificity and selectivity compared to other culture-based methods. In this work, the NRJ detection system was evaluated using retail whole broiler chicken carcass. Nanopore 16S rRNA gene amplicon sequencing demonstrated that species are found in very low abundance in retail chicken and that indigenous microbiota could be a major factor interfering with detection. Comparison of the microbiome obtained from modified Houf broth (HB) method, as the standard detection system, and the novel NRJ method, showed abundances of <15% and >97%, respectively. The NRJ system significantly inhibits the growth of non-target microbiota, and specifically allows the multiplication of species. In this report, we describe the gold-standard of -specific culture-based method to test food matrices, which can be used for other applications, such as clinical and environmental sampling.
PubMed: 35801110
DOI: 10.3389/fmicb.2022.903079 -
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 -
International Journal of Systematic and... May 2023A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2, was isolated from a seawater sample collected from Roscoff, France....
A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2, was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2 was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2 was closely related to LFT 1.7 and RW17-10(95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2 was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA-DNA hybridization, indicated that strain ARW1-2F2 represents a new species. The predominant fatty acids were C ω7/C ω6 and C ω7/C ω6. The results of a polyphasic analysis supported the description of strain ARW1-2F2 as representing a novel species of the genus , for which the name sp. nov. is proposed with the type strain ARW1-2F2 (DSM 29169=KCTC 52423).
Topics: Fatty Acids; Phospholipids; Arcobacter; RNA, Ribosomal, 16S; Base Composition; Phylogeny; DNA, Bacterial; Sequence Analysis, DNA; Bacterial Typing Techniques; Seawater
PubMed: 37200211
DOI: 10.1099/ijsem.0.005895 -
Journal of Hazardous Materials Jun 2023Antibiotics are increasingly used and released into the marine environment due to the rapid development of mariculture, resulting in spread of antibiotic resistance. The...
Antibiotics are increasingly used and released into the marine environment due to the rapid development of mariculture, resulting in spread of antibiotic resistance. The pollution, distribution, and characteristics of antibiotics, antibiotic resistance genes (ARGs) and microbiomes have been investigated in this study. Results showed that 20 antibiotics were detected in Chinese coastal environment, with predominance of erythromycin-HO, enrofloxacin and oxytetracycline. In coastal mariculture sites, antibiotic concentrations were significantly higher than in control sites, and more types of antibiotics were detected in the South than in the North of China. Residues of enrofloxacin, ciprofloxacin and sulfadiazine posed high resistance selection risks. β-Lactam, multi-drug and tetracycline resistance genes were frequently detected with significantly higher abundance in the mariculture sites. Of the 262 detected ARGs, 10, 26, and 19 were ranked as high-risk, current-risk, future-risk, respectively. The main bacterial phyla were Proteobacteria and Bacteroidetes, of which 25 genera were zoonotic pathogens, with Arcobacter and Vibrio in particular ranking in the top10. Opportunistic pathogens were more widely distributed in the northern mariculture sites. Phyla of Proteobacteria and Bacteroidetes were the potential hosts of high-risk ARGs, while the conditional pathogens were associated with future-risk ARGs, indicating a potential threat to human health.
Topics: Humans; Anti-Bacterial Agents; Genes, Bacterial; Enrofloxacin; Bacteria; Bacteroidetes; Proteobacteria; Microbiota
PubMed: 36966625
DOI: 10.1016/j.jhazmat.2023.131208 -
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 -
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