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Microorganisms Jun 2022, the most prevalent species of the genus, has the demonstrated ability to adhere to various surfaces through biofilm production. The biofilm formation capability has...
, the most prevalent species of the genus, has the demonstrated ability to adhere to various surfaces through biofilm production. The biofilm formation capability has been related to the expression of certain genes, which have not been characterized in . In order to increase the knowledge of this foodborne pathogen, the aim of this study was to assess the role of six biofilm-associated genes in campylobacteria (, , , , and ) in the biofilm formation ability of . Knockout mutants were constructed from different foodborne isolates, and static biofilm assays were conducted on polystyrene (PS), reinforced glass and stainless steel. Additionally, motility and Congo red binding assays were performed. In general, mutants in , and showed a decrease in the biofilm production irrespective of the surface; mutants in showed an increase on stainless steel, and mutants in and showed a decrease on reinforced glass but an increase on PS. Our work sheds light on the biofilm-related pathogenesis of , although future studies are necessary to achieve a satisfactory objective.
PubMed: 35888999
DOI: 10.3390/microorganisms10071280 -
The Science of the Total Environment Feb 2023In this study, the DNA metabarcoding technique was used to explore the prokaryote diversity and community structure in wastewater collected in spring and winter...
In this study, the DNA metabarcoding technique was used to explore the prokaryote diversity and community structure in wastewater collected in spring and winter 2020-2021 as well as the efficiency of the treatment in a wastewater treatment plant (WWTP) in Ría de Vigo (NW Spain). The samplings included raw wastewater from the inlet stream (M1), the discharge water after the disinfection treatment (M3) and mussels used as bioindicators of possible contamination of the marine environment. Significant differences were discovered in the microbiome of each type of sample (M1, M3 and mussels), with 92 %, 45 % and 44 % of exclusive OTUs found in mussel, M3 and M1 samples respectively. Seasonal differences were also detected in wastewater samples, with which abiotic parameters (temperature, pH) could be strongly involved. Bacteria present in raw wastewater (M1) were associated with the human gut microbiome, and therefore, potential pathogens that could be circulating in the population in specific periods were detected (e.g., Arcobacter sp. and Clostridium sp.). A considerable decrease in putative pathogenic organisms from the M1 to M3 wastewater fractions and the scarce presence in mussels (<0.5 % total reads) confirmed the effectiveness of pathogen removal in the wastewater treatment plant. Our results showed the potential of the DNA metabarcoding technique for monitoring studies and confirmed its application in wastewater-based epidemiology (WBE) and environmental contamination studies. Although this technique cannot determine if the infective pathogens are present, it can characterize the microbial communities and the putative pathogens that are circulating through the population (microbiome of M1) and also confirm the efficacy of depuration treatment, which can directly affect the aquaculture sector and even human and veterinary health.
Topics: Humans; Animals; Wastewater; Bacteria; Microbiota; Bivalvia; Water Purification; High-Throughput Nucleotide Sequencing
PubMed: 36470389
DOI: 10.1016/j.scitotenv.2022.160531 -
Water Research Oct 2020We describe the technical feasibility of metagenomic water quality analysis using only portable equipment, for example mini-vacuum pumps and filtration units,...
We describe the technical feasibility of metagenomic water quality analysis using only portable equipment, for example mini-vacuum pumps and filtration units, mini-centrifuges, mini-PCR machines and the memory-stick sized MinION of Oxford Nanopore Technologies, for the library preparation and sequencing of 16S rRNA gene amplicons. Using this portable toolbox on site, we successfully characterized the microbiome of water samples collected from Birtley Sewage Treatment Plant, UK, and its environs. We also demonstrated the applicability of the portable metagenomics toolbox in a low-income country by surveying water samples from the Akaki River around Addis Ababa, Ethiopia. The 16S rRNA gene sequencing workflow, including DNA extraction, PCR amplification, sequencing library preparation, and sequencing was accomplished within one working day. The metagenomic data became available within 24-72 h, depending on internet speed. Metagenomic analysis clearly distinguished the microbiome of pristine samples from sewage influenced water samples. Metagenomic analysis identified the potential role of two bacterial genera not conventionally monitored, Arcobacter and Aeromonas, as predominant faecal pollution indicators/waterborne hazards. Subsequent quantitative PCR analysis validated the high Arcobacter butzleri abundances observed in the urban influenced Akaki River water samples by portable next generation sequencing with the MinION device. Overall, our field deployable metagenomics toolbox advances the capability of scientists to comprehensively monitor microbiomes anywhere in the world, including in the water, food and drinks industries, the health services, agriculture and beyond.
Topics: Ethiopia; High-Throughput Nucleotide Sequencing; Metagenome; Metagenomics; RNA, Ribosomal, 16S; Water; Water Quality
PubMed: 32688150
DOI: 10.1016/j.watres.2020.116112 -
Scientific Reports Sep 2020Arcobacter-like species are found associated with many matrices, including shellfish in marine environments. The culture media and conditions play a major role in the...
Arcobacter-like species are found associated with many matrices, including shellfish in marine environments. The culture media and conditions play a major role in the recovery of new Arcobacter-like species. This study was aimed to develop a culture media for isolation and enhanced growth of Arcobacter-like spp. from marine and shellfish matrices. For this purpose, 14 different Arcobacter-like spp. mostly isolated from shellfish, were grown in 24 different formulations of enrichment broths. The enrichment broths consisted of five main groups based on the organic contents (fresh oyster homogenate, lyophilized oyster either alone or in combination with other standard media), combined with artificial seawater (ASW) or 2.5% NaCl. Optical density (OD) measurements after every 24 h were compared with the growth in control media (Arcobacter broth) in parallel. The mean and standard deviation were calculated for each species in each broth and statistical differences (p < 0.05) among broths were calculated by ANOVA. The results indicated that shellfish-associated Arcobacter-like species growth was significantly higher in Arcobacter broth + 50% ASW and the same media supplemented with lyophilized oysters. This is the first study to have used fresh or lyophilized oyster flesh in the enrichment broth for isolation of shellfish-associated Arcobacter-like spp.
Topics: Analysis of Variance; Animals; Arcobacter; Food Microbiology; Marine Biology; Seawater; Shellfish
PubMed: 32884057
DOI: 10.1038/s41598-020-71442-8 -
Frontiers in Microbiology 2019A wide range of species have been described from shellfish in various countries but their presence has not been investigated in Australasia, in which shellfish are a...
A wide range of species have been described from shellfish in various countries but their presence has not been investigated in Australasia, in which shellfish are a popular delicacy. Since several arcobacters are considered to be emerging pathogens, we undertook a small study to evaluate their presence in several different shellfish, including greenshell mussels, oysters, and abalone (paua) in New Zealand. , a species associated with human gastroenteritis, was the only species isolated, from greenshell mussels. Whole-genome sequencing revealed a range of genomic traits in these strains that were known or associated virulence factors. Furthermore, we describe the first putative virulence plasmid in , containing lytic, immunoavoidance, adhesion, antibiotic resistance, and gene transfer traits, among others. Complete genome sequence determination using a combination of long- and short-read genome sequencing strategies, was needed to identify the plasmid, clearly identifying its benefits. The potential for plasmids to disseminate virulence traits among and other species warrants further consideration by researchers interested in the risks to public health from these organisms.
PubMed: 31428079
DOI: 10.3389/fmicb.2019.01802 -
Biomedical and Environmental Sciences :... Dec 2021is an emerging foodborne pathogen worldwide. In this study, the prevalence, antimicrobial susceptibility and genetic characteristics of from different sources were...
is an emerging foodborne pathogen worldwide. In this study, the prevalence, antimicrobial susceptibility and genetic characteristics of from different sources were investigated. Eighteen isolates were obtained from 60 raw chicken meat samples (16/60, 27%) and 150 patients with diarrhea (2/150, 1.3%). The resistance ratios to nalidixic acid, ciprofloxacin, clindamycin, chloramphenicol, and florfenicol were 83.33% (15/18), 38.89% (7/18), 38.89% (7/18), 33.33% (6/18) and 33.33% (6/18), respectively. We performed whole genome sequencing of the 18 isolates, and we predicted antibiotic resistance genes and virulence factors by using assembled genomes through blastx analysis. Two resistance genes, and (H), and the C254T mutation in , were identified in the genomes of some resistant isolates. Furthermore, virulence genes, such as , , , , , , , , , , and , were found in all strains, whereas , and were found in only some strains. Phylogenetic tree analysis of isolates on the basis of the core-genome single nucleotide polymorphisms showed that two isolates from patients with diarrhea clustered together, separately from the isolates from raw chicken and the chicken strains. This study is the first comprehensive analysis of isolated in Beijing.
Topics: Aged; Animals; Arcobacter; Chickens; Diarrhea; Drug Resistance, Bacterial; Genes, Bacterial; Gram-Negative Bacterial Infections; Humans; Male; Meat; Microbial Sensitivity Tests; Phylogeny; Poultry Diseases; Virulence; Virulence Factors
PubMed: 34981728
DOI: 10.3967/bes2021.139 -
Microorganisms Aug 2022Biofilm contamination in food production threatens food quality and safety, and causes bacterial infections. Study of food biofilms (BF) is of great importance. The...
Biofilm contamination in food production threatens food quality and safety, and causes bacterial infections. Study of food biofilms (BF) is of great importance. The taxonomic composition and structural organization of five foods BF taken in different workshops of a meat-processing plant (Moscow, RF) were studied. Samples were taken from the surface of technological equipment and premises. Metagenomic analysis showed both similarities in the presented microorganisms dominating in different samples, and unique families prevailing on certain objects were noted. The bacteria found belonged to 11 phyla (no archaea). The dominant ones were , , , and . The greatest diversity was in BFs taken from the cutting table of raw material. Biofilms' bacteria may be the cause of meat, fish and dairy products spoilage possible representatives include , , , , , , etc.). Opportunistic human and animal pathogens (possible representatives include , , , etc.) were also found. Electron-microscopic studies of BF thin sections revealed the following: (1) the diversity of cell morphotypes specific to multispecies BFs; (2) morphological similarity of cells in BFs from different samples, micro-colonial growth; (3) age heterogeneity of cells within the same microcolony (vegetative and autolyzed cells, resting forms); (4) heterogeneity of the polymer matrix chemical nature according to ruthenium red staining.
PubMed: 36014001
DOI: 10.3390/microorganisms10081583 -
Microorganisms May 2023, the most widespread species within the genus , is considered as an emerging pathogen causing gastroenteritis in humans. Here, we performed a comparative genome-wide...
, the most widespread species within the genus , is considered as an emerging pathogen causing gastroenteritis in humans. Here, we performed a comparative genome-wide analysis of 40 strains from Lithuania to determine the genetic relationship, pangenome structure, putative virulence, and potential antimicrobial- and heavy-metal-resistance genes. Core genome single nucleotide polymorphism (cgSNP) analysis revealed low within-group variability (≤4 SNPs) between three milk strains (RCM42, RCM65, RCM80) and one human strain (H19). Regardless of the type of input (i.e., cgSNPs, accessory genome, virulome, resistome), these strains showed a recurrent phylogenetic and hierarchical grouping pattern. demonstrated a relatively large and highly variable accessory genome (comprising of 6284 genes with around 50% of them identified as singletons) that only partially correlated to the isolation source. Downstream analysis of the genomes resulted in the detection of 115 putative antimicrobial- and heavy-metal-resistance genes and 136 potential virulence factors that are associated with the induction of infection in host (e.g., , , ), survival and environmental adaptation (e.g., flagellar genes, CheA-CheY chemotaxis system, urease cluster). This study provides additional knowledge for a better -related risk assessment and highlights the need for further genomic epidemiology studies in Lithuania and other countries.
PubMed: 37374927
DOI: 10.3390/microorganisms11061425 -
Current Research in Microbial Sciences Dec 2021An increasing number of species (including several regarded as emerging human foodborne pathogens) have been isolated from shellfish, an important food commodity. A...
An increasing number of species (including several regarded as emerging human foodborne pathogens) have been isolated from shellfish, an important food commodity. A method to distinguish these species and render viable isolates for further analysis would benefit epidemiological and ecological studies. We describe a method based on Elastic Light Scatter analysis (ELSA) for the detection and discrimination of eleven shellfish-associated species. Although substantive differences in the growth rates of some taxa were seen, ELSA was able to differentiate all the species studied, apart from some strains of and , which were nonetheless distinguished from all other species examined. ELSA appears to be a promising new approach for the detection and identification of species in shellfish and may also be applicable for studies in other foods and matrices.
PubMed: 34841324
DOI: 10.1016/j.crmicr.2021.100033 -
Veterinary World Jul 2022Since the past decade, metagenomics has been used to evaluate sequenced deoxyribonucleic acid of all microorganisms in several types of research. Nitrite contamination...
BACKGROUND AND AIM
Since the past decade, metagenomics has been used to evaluate sequenced deoxyribonucleic acid of all microorganisms in several types of research. Nitrite contamination originates from the natural environment in Swiftlet farmhouses (SFHs) and can influence nitrite levels in edible bird's nest (EBN). It is strongly speculated that the conversion process into nitrite is influenced by the bacteria present in SFHs. Nitrite can cause adverse effects on human health. The previous research has focused on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. This study aimed to a metagenomics analysis of bacteria present in the dirt of SFHs and evaluated nitrite levels in EBN on Sumatera Island.
MATERIALS AND METHODS
In total, 18 SFHs on Sumatera Island were selected, and EBN and dirt samples were collected from each SFH, resulting in 18 EBN and 18 dirt SFH samples. Raw uncleaned white EBN and dirt from three areas of SFH were collected. The samples were analyzed for nitrite levels using a spectrophotometer, and the metagenomics sequencing of SFH dirt samples was performed using the MinIon nanopore method. The sequenced data were analyzed using the EPI2ME software.
RESULTS
Of the 18 raw uncleaned white EBN samples, 9 (50%) had <30 ppm nitrite levels. The top five bacterial genera in SFH dirt samples in Group A (nitrite levels >30 ppm) were , , , , and . Those in Group B (nitrite levels <30 ppm) were , , , , and . There were 12 genera of nitrifying bacteria in Group A and 8 in Group B. The total cumulative read of nitrifying bacteria in Groups A and B were 87 and 38 reads, respectively.
CONCLUSION
This is the first study to show that characteristic bacteria present in the dirt of SFHs might significantly influence the conversion from nitrogen to nitrite. Approximately 50% of raw uncleaned EBN samples had <30 ppm nitrite levels. was the most dominant bacterial genus found in Groups A and B. The variations in genus and cumulative reads nitrifying bacteria in group A were greater than those in Group B. This study provides information on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. Metagenomics data were obtained from the reading using the software EPI2ME. Further research is needed on the bacterial target species that can convert nitrite in SFHs.
PubMed: 36185528
DOI: 10.14202/vetworld.2022.1798-1803