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Environmental Pollution (Barking, Essex... Jan 2022Wastewater treatment plant (WWTP) effluents are pointed as hotspots for the introduction of both commensal and pathogenic bacteria as well as their antibiotic resistance... (Review)
Review
Wastewater treatment plant (WWTP) effluents are pointed as hotspots for the introduction of both commensal and pathogenic bacteria as well as their antibiotic resistance genes (ARGs) in receiving water bodies. For the first time, the effect of partially treated submarine effluents was explored at the bottom and surface of the water column to provide a comprehensive overview of the structure of the microbiome and associated AR, and to assess environmental factors leading to their alteration. Seawater samples were collected over a 5-month period from submarine outfalls in central Adriatic Sea, Croatia. 16S rRNA amplicon sequencing was used to establish taxonomic and resistome profiles of the bacterial communities. The community differences observed between the two discharge areas, especially in the abundance of Proteobacteria and Firmicutes, could be due to the origin of wastewaters treated in WWTPs and the limiting environmental conditions such as temperature and nutrients. PICRUSt2 analysis inferred the total content of ARGs in the studied microbiomes and showed the highest abundance of resistance genes encoding multidrug efflux pumps, such as MexAB-OprM, AcrEF-TolC and MdtEF-TolC, followed by the modified peptidoglycan precursors, transporter genes encoding tetracycline, macrolide and phenicol resistance, and the bla operon conferring β-lactam resistance. A number of pathogenic genera introduced by effluents, including Acinetobacter, Arcobacter, Bacteroides, Escherichia-Shigella, Klebsiella, Pseudomonas, and Salmonella, were predicted to account for the majority of efflux pump-driven multidrug resistance, while Acinetobacter, Salmonella, Bacteroides and Pseudomonas were also shown to be the predominant carriers of non-efflux ARGs conferring resistance to most of nine antibiotic classes. Taken together, we evidenced the negative impact of submarine discharges of treated effluents via alteration of physico-chemical characteristics of the water column and enrichment of bacterial community with nonindigenous taxa carrying an arsenal of ARGs, which could contribute to the further propagation of the AR in the natural environment.
Topics: Anti-Bacterial Agents; Croatia; Drug Resistance, Microbial; Genes, Bacterial; Microbiota; RNA, Ribosomal, 16S; Wastewater
PubMed: 34619178
DOI: 10.1016/j.envpol.2021.118282 -
Journal of Environmental Management Jan 2022Woodchip bioreactors are being successfully applied to remove nitrate from commercial land-based recirculating aquaculture system (RAS) effluents. In order to understand...
Woodchip bioreactors are being successfully applied to remove nitrate from commercial land-based recirculating aquaculture system (RAS) effluents. In order to understand and optimize the overall function of these bioreactors, knowledge on the microbial communities, especially on the microbes with potential for production or mitigation of harmful substances (e.g. hydrogen sulfide; HS) is needed. In this study, we quantified and characterized bacterial and fungal communities, including potential HS producers and consumers, using qPCR and high throughput sequencing of 16S rRNA gene. We took water samples from bioreactors and their inlet and outlet, and sampled biofilms growing on woodchips and on the outlet of the three full-scale woodchip bioreactors treating effluents of three individual RAS. We found that bioreactors hosted a high biomass of both bacteria and fungi. Although the composition of microbial communities of the inlet varied between the bioreactors, the conditions in the bioreactors selected for the same core microbial taxa. The HS producing sulfate reducing bacteria (SRB) were mainly found in the nitrate-limited outlets of the bioreactors, the main groups being deltaproteobacterial Desulfobulbus and Desulfovibrio. The abundance of HS consuming sulfate oxidizing bacteria (SOB) was 5-10 times higher than that of SRB, and SOB communities were dominated by Arcobacter and other genera from phylum Epsilonbacteraeota, which are also capable of autotrophic denitrification. Indeed, the relative abundance of potential autotrophic denitrifiers of all denitrifier sequences was even 54% in outlet water samples and 56% in the outlet biofilm samples. Altogether, our results show that the highly abundant bacterial and fungal communities in woodchip bioreactors are shaped through the conditions prevailing within the bioreactor, indicating that the bioreactors with similar design and operational settings should provide similar function even when conditions in the preceding RAS would differ. Furthermore, autotrophic denitrifiers can have a significant role in woodchip biofilters, consuming potentially produced HS and removing nitrate, lengthening the operational age and thus further improving the overall environmental benefit of these bioreactors.
Topics: Aquaculture; Bioreactors; Denitrification; Microbiota; Nitrates; RNA, Ribosomal, 16S
PubMed: 34592671
DOI: 10.1016/j.jenvman.2021.113852 -
Frontiers in Microbiology 2022spp. is a globally emerging zoonotic and foodborne pathogen. However, little is known about its prevalence and antimicrobial resistance in China. To investigate the...
spp. is a globally emerging zoonotic and foodborne pathogen. However, little is known about its prevalence and antimicrobial resistance in China. To investigate the prevalence of spp. isolated from various sources, 396 samples were collected from human feces, chicken cecum, and food specimens including chicken meat, beef, pork, lettuce, and seafood. spp. was isolated by the membrane filtration method. For 92 strains, the agar dilution method and next-generation sequencing were used to investigate their antimicrobial resistance and to obtain whole genome data, respectively. The virulence factor database (VFDB) was queried to identify virulence genes. ResFinder and the Comprehensive Antibiotic Resistance Database (CARD) were used to predict resistance genes. A phylogenetic tree was constructed using the maximum likelihood (ML) method with core single-nucleotide polymorphisms (SNPs). We found that 27.5% of the samples ( = 109) were positive for spp., comprising (53.0%), (39.6%), and (7.4%). Chicken meat had the highest prevalence (81.2%), followed by seafood (51.9%), pork (43.3%), beef (36.7%), lettuce (35.5%), chicken cecum (8%), and human fecal samples (0%, 0/159). Antimicrobial susceptibility tests revealed that 51 and 40 strains were resistant to streptomycin (98.1, 70%), clindamycin (94.1, 90%), tetracycline (64.7, 52.5%), azithromycin (43.1%, 15%), nalidixic acid (33.4, 35%), and ciprofloxacin (31.3, 35%) but were susceptible to erythromycin, gentamicin, chloramphenicol, telithromycin, and clindamycin (≤10%). was sensitive to all experimental antibiotics. The virulence factors A, , and were carried by all spp. strains at 100%, and the following percentages were (95.7%), (23.9%), 2.2%, and (1.1%). Only one strain (F061-2G) carried a macrolide resistance gene (). One and one harbored resistance island gene clusters, which were isolated from pork and chicken. Phylogenetic tree analysis revealed that , and were separated from each other. To our knowledge, this is the first report of the isolation of spp. from vegetables and seafood in China. The resistance island gene cluster found in pork and chicken meat and the presence of virulence factors could be a potential risk to human health.
PubMed: 36532418
DOI: 10.3389/fmicb.2022.1004224 -
Nature Food Aug 2023China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the...
China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.
Topics: Animals; Humans; Anti-Bacterial Agents; Chickens; Drug Resistance, Bacterial; Farms; Metagenomics; Abattoirs; Escherichia coli; Machine Learning
PubMed: 37563495
DOI: 10.1038/s43016-023-00814-w -
Journal of Food Protection Dec 2020Arcobacter is considered an emergent foodborne enteropathogen. Despite the high prevalence of this genus in poultry, the occurrence of Arcobacter spp. contamination in...
ABSTRACT
Arcobacter is considered an emergent foodborne enteropathogen. Despite the high prevalence of this genus in poultry, the occurrence of Arcobacter spp. contamination in Tunisia remains unclear. The objectives of this study were (i) to isolate Arcobacter species (A. butzleri and A. cryaerophilus) by the culture method from different species of raw poultry meat, (ii) to verify the isolates by multiplex PCR (m-PCR) assay and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and (iii) to determine the antibiotic resistance profiles of the isolates. A total of 250 poultry product samples (149 chicken and 101 turkey) were collected from various supermarkets in Sfax. The samples consisted of breasts, wings, legs, and neck skins. The overall isolation frequency of Arcobacter spp. was 10.4%. Arcobacter spp. were found in 13.42% of the chicken samples and in 5.49% of the turkey samples. All the acquired isolates were subject to detailed confirmation with subsequent species classification using m-PCR and MALDI-TOF MS. A. butzleri was found in 22 samples (84.61%) and A. cryaerophilus in 4 samples (15.38%). Thus, m-PCR and MALDI-TOF MS were able to detect A. butzleri significantly better than the conventional method (χ2 = 49.1 and P < 0.001). Arcobacter was isolated from poultry in every season, at contamination levels of 30.76, 23.07, 19.23, and 26.92% in summer, spring, autumn, and winter, respectively. The disk diffusion method was used to determine the susceptibility of Arcobacter isolates to six antimicrobial drugs. All A. butzleri isolates (n = 24) were significantly resistant to erythromycin (P = 0.0015), ampicillin (P = 0.001), and ciprofloxacin (P = 0.05). All tested A. cryaerophilus strains (n = 4) were susceptible to ampicillin, gentamicin, and amoxicillin-clavulanic acid. Multidrug resistance was observed in 83% of the Arcobacter spp. isolates. Our study detected Arcobacter spp. in Tunisian poultry; because of their multidrug resistance, these species may constitute a public health problem.
Topics: Animals; Arcobacter; Drug Resistance, Microbial; Food Microbiology; Poultry; Tunisia
PubMed: 32634222
DOI: 10.4315/JFP-20-056 -
Travel Medicine and Infectious Disease 2022Travellers' diarrhoea (TD) is the most frequent illness experienced by international travellers to lower-income countries with bacterial agents considered to account for... (Review)
Review
Travellers' diarrhoea (TD) is the most frequent illness experienced by international travellers to lower-income countries with bacterial agents considered to account for 80-90% of cases. In this review, we summarise evidence published on bacterial TD over the past 10 years, focusing on the epidemiology and aetiology of TD. Diarrhoeagenic Escherichia coli (DEC) continue to be the most commonly implicated bacteria in TD, although Enteropathogenic E. coli (EPEC) and Enteroaggregative E. coli (EAEC) now appear to be predominant where Enterotoxigenic E. coli (ETEC) was previously considered most prevalent globally. Where fluroquinolone resistance had primarily been documented for Campylobacter in Southeast Asia, widespread resistance has been observed in most regions of the world for multiple enteropathogens, including Shigella, Salmonella, ETEC and EAEC. Implementation of novel molecular methods for pathogen detection has led to identification of bacterial pathogens, including Clostridium difficile (with and without the use of prior antibiotics), Arcobacter species and Bacteroides fragilis, as aetiological agents in TD. The widespread resistance to first-line antibiotics in multiple bacterial enteropathogens warrants continued surveillance and re-evaluation of current treatment practices. Further investigations are required to determine the prevalence and geographical distribution of bacterial enteropathogens that have been more recently implicated in TD.
Topics: Anti-Bacterial Agents; Bacteria; Bacterial Infections; Diarrhea; Enterotoxigenic Escherichia coli; Feces; Humans; Travel
PubMed: 35247581
DOI: 10.1016/j.tmaid.2022.102293 -
Food Microbiology Aug 2020Arcobacter butzleri is a zoonotic foodborne pathogen able to cause enteric and extraintestinal diseases. Its occurrence in foodstuff is well recognized worldwide but...
Arcobacter butzleri is a zoonotic foodborne pathogen able to cause enteric and extraintestinal diseases. Its occurrence in foodstuff is well recognized worldwide but data on its presence in foods from Southern Italy are scarce. In this study the results on the occurrence and genotyping of Arcobacter spp. in bulk milk samples collected in Southern Italy are reported. Out of 484 samples, 64 (13.2%) resulted positive for the presence of Arcobacter spp. Using Real Time PCR but as few as 31.2% of these samples turned out as positive by using the cultural method, showing an overall prevalence of 4.1%. All isolates were identified as A. cryaerophilus using the biochemical identification whilst the sequencing of the atpA gene revealed that all the isolates were A. butzleri. Among the confirmed isolates, 16 different Sequence Types (ST) were identified using the Multi Locus Sequence Typing (MLST), 14 (87.5%) of which were previously unreported. Our survey reveals the presence of A. butzleri in bulk tank milk from Southern Italy and highlights the discrepancy between the two approaches used both for the detection (i.e., real time PCR vs cultural method) and the identification (i.e., biochemical test vs aptA sequencing) of Arcobacter spp In addition, a large genetic diversity among the isolates was detected and this makes the identification of source of the infections very challenging in outbreaks investigation.
Topics: Animals; Arcobacter; Food Microbiology; Food Safety; Genetic Variation; Italy; Milk; Multilocus Sequence Typing
PubMed: 32139002
DOI: 10.1016/j.fm.2019.103403 -
Microbial Ecology Aug 2023Intestinal microbes are essential participants in host vital activities. The composition of the microbiota is closely related to the environmental factors. Predator...
Intestinal microbes are essential participants in host vital activities. The composition of the microbiota is closely related to the environmental factors. Predator presence may impact on intestinal microbiota of prey. In the present study, stone crab Charybdis japonica was used as potential predator, an external stress on mussel Mytilus coruscus, to investigate the intestinal microbiota alteration in M. coruscus. We set up two forms of predator presence including free crab and trapped crab, with a blank treatment without crab. The composition of intestinal microbiota in mussels among different treatments showed significant differences by 16S rRNA techniques. The biodiversity increased with trapped crab presence, but decreased with free crab presence. Neisseria, the most abundant genus, fell with the presence of crabs. Besides, the Arcobacter, a kind of pathogenic bacteria, increased with free crab presence. Regarding PICRUTs analysis, Environmental Information Processing, Genetic Information Processing and Metabolism showed differences in crab presence treatments compared with the blank, with a bit higher in the presence of free crab than trapped crab. In conclusion, trapped crab effects activated the metabolism and immunity of the intestinal flora, but free crabs made mussels more susceptible to disease and mortality, corresponding to the decreased biodiversity and the increased Arcobacter in their intestine.
Topics: Animals; Humans; Gastrointestinal Microbiome; RNA, Ribosomal, 16S; Mytilus; Brachyura; Biodiversity
PubMed: 36068360
DOI: 10.1007/s00248-022-02106-5 -
Microorganisms Jul 2021The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding... (Review)
Review
The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude mineralized geothermal springs (temperature range 25.8-70 °C and pH range 6.0-7.5) in Armenia and Nagorno-Karabakh. All these geothermal springs are at altitudes ranging from 960-2090 m above sea level and are located on the Alpide (Alpine-Himalayan) orogenic belt, a seismically active region. A mixed-cation mixed-anion composition, with total mineralization of 0.5 mg/L, has been identified for these thermal springs. The taxonomic diversity of hot spring microbiomes has been examined using culture-independent approaches, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene library construction, 454 pyrosequencing, and Illumina HiSeq. The bacterial phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes are the predominant life forms in the studied springs. Archaea mainly include the phyla Euryarchaeota, Crenarchaeota, and Thaumarchaeota, and comprise less than 1% of the prokaryotic community. Comparison of microbial diversity in springs from Karvachar with that described for other terrestrial hot springs revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Deinococcus-Thermus are the common bacterial groups in terrestrial hot springs. Contemporaneously, specific bacterial and archaeal taxa were observed in different springs. Evaluation of the carbon, sulfur, and nitrogen metabolism in these hot spring communities has revealed diversity in terms of metabolic activity. Temperature seems to be an important factor in shaping the microbial communities of these springs. Overall, the diversity and richness of the microbiota are negatively affected by increasing temperature. Other abiotic factors, including pH, mineralization, and geological history, also impact the structure and function of the microbial community. More than 130 bacterial and archaeal strains (, , and ) have been reported, some of which may be representative of novel species (sharing 91-97% sequence identity with their closest matches in GenBank) and producers of thermozymes and biomolecules with potential biotechnological applications. Whole-genome shotgun sequencing of K1, as well as of the potentially new sp. J25 and sp. K1, were performed. Most of the phyla identified by 16S rRNA were also identified using metagenomic approaches. Detailed characterization of thermophilic isolates indicate the potential of the studied springs as a source of biotechnologically valuable microbes and biomolecules.
PubMed: 34361908
DOI: 10.3390/microorganisms9071473 -
Archives of Microbiology Dec 2019Acanthamoeba castellanii is a free-living amoeba found mainly in humid environments and Arcobacter butzleri is an emerging zoonotic pathogen, both can establish in vitro...
Acanthamoeba castellanii is a free-living amoeba found mainly in humid environments and Arcobacter butzleri is an emerging zoonotic pathogen, both can establish in vitro endosymbiotic relationships in the absence of bacterial replication. We analyzed the localization of A. butzleri within A. castellanii establishing their association with endoplasmic reticulum vesicles and mitochondria. Through confocal microscopy, we observed that during the early stages of endosymbiosis, there is not colocalization between amoebic vacuoles containing A. butzleri and mitochondria or ER vesicles of A. castellanii. Considering that energy production of this bacterium occurs via metabolism of amino acids or the tricarboxylic acid cycle, these results contribute to explain the absence of bacterial replication, since A. butzleri would not have access to the nutrients found in endoplasmic reticulum vesicles and mitochondria. In addition, we observe that A. butzleri induces significantly the actin polymerization of A. castellanii during the early stages of endosymbiosis.
Topics: Acanthamoeba castellanii; Arcobacter; Symbiosis; Vacuoles
PubMed: 31302710
DOI: 10.1007/s00203-019-01699-9