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Gut Pathogens Dec 2021Members of the genus Arcobacter are considered as emerging zoonotic food and waterborne pathogens that cause gastroenteritis and bacteremia in humans. However, the...
Prevalence, antimicrobial susceptibility and virulence gene profiles of Arcobacter species isolated from human stool samples, foods of animal origin, ready-to-eat salad mixes and environmental water.
BACKGROUND
Members of the genus Arcobacter are considered as emerging zoonotic food and waterborne pathogens that cause gastroenteritis and bacteremia in humans. However, the potential risk that Arcobacter species pose to public health remains unassessed in various countries, including Baltic states. Therefore, the aim of this study was to determine the prevalence, antimicrobial susceptibility and presence of putative virulence genes of Arcobacter isolates recovered from humans, food products and environmental water in Lithuania.
RESULTS
A total of 1862 samples were collected and examined from 2018 to 2020 in the city of Kaunas. Overall, 11.2% (n = 208) of the samples were positive for the presence of Arcobacter spp. The highest prevalence was detected in chicken meat (36%), followed by environmental water (28.1%), raw cow milk (25%), ready-to-eat salad mixes (7.1%) and human stool (1.7%). A. butzleri was the most frequently isolated species (n = 192; 92.3%), followed by A. cryaerophilus (n = 16; 7.7%). Arcobacter spp. antimicrobial susceptibility testing revealed unimodally distributed aggregated minimal inhibitory concentrations (MICs) for gentamicin, tetracycline, ciprofloxacin, ampicillin and erythromycin. However, a bimodal distribution for azithromycin was found with 96.2% of determined MICs above the epidemiological cut-off value (ECOFF) defined for Campylobacter jejuni (0.25 µg/ml). Majority of the Arcobacter isolates (n = 187; 89.9%) showed high susceptibility to ciprofloxacin with MICs below or equal to the ECOFF value of 0.5 µg/ml. The putative virulence genes cadF (100%), ciaB (100%), cj1349 (99%), tlyA (99%), mviN (97.9%) and pldA (95.8%) were the predominant genes detected among A. butzleri isolates. In contrast, the mviN and ciaB genes were present in all, whereas cj1349 (12.5%), tlyA (25%) and hecA (12.5%) were only detected in few A. cryaerophilus isolates.
CONCLUSIONS
Our results demonstrate that food products and environmental water in Lithuania are frequently contaminated with Arcobacter spp. that carry multiple putative virulence genes. Furthermore, A. butzleri were isolated from 1.7% of inpatients. Fluoroquinolones and aminoglycosides were found to be more effective against Arcobacter in comparison to other antimicrobial agents. However, further studies are needed to determine the pathogenic mechanisms and factors that facilitate the spread of Arcobacter infections.
PubMed: 34930425
DOI: 10.1186/s13099-021-00472-y -
Frontiers in Cellular and Infection... 2023In recent years, has gained clinical significance as an emerging diarrheagenic pathogen associated with poultry and water reservoirs. The full clinical significance of...
In recent years, has gained clinical significance as an emerging diarrheagenic pathogen associated with poultry and water reservoirs. The full clinical significance of remains rather speculative due to variable virulence and antibiotic susceptibility of individual strains. The aims of the present study were (i) to identify antibiotic resistance genes (ARGs) in the genome sequences of two multidrug-resistant isolates, (ii) to use multilocus-sequence typing (MLST) to generate a guiding phylogeny of isolates collected in Kumasi, Ghana, (iii) to examine the distribution of ARGs in the test cohort, and (iv) to assess the strain's virulence and possible antibiotic treatment options for arcobacteriosis based on the genome sequences and the ARG distribution. A total of 48 A isolates obtained from poultry were included in the analysis. These isolates were genotyped by MLST and the antibiotic susceptibilities of isolates to ampicillin, ciprofloxacin, tetracycline, gentamicin, and erythromycin were tested by disk diffusion. Whole genome sequence data of two multidrug-resistant (MDR) isolates were obtained by a combination of single-molecule real-time (SMRT) and Illumina sequencing technology. A total of 14 ARGs were identified in the two generated genome sequences. For all 48 isolates, the frequency of these 14 ARGs was investigated by PCR or amplicon sequencing. With 44 different sequence types found among 48 isolates, strains were phylogenetically heterogeneous. Four of 48 isolates showed an ARG constellation indicating a multidrug-resistant phenotype. The virulence genes in the two genomes showed that the species might be characterized by a somewhat lower virulence as species. The phenotypic susceptibility data combined with the distribution of the particular ARGs especially and the T81I point mutation of the quinolone resistance determining region (QRDR) in a significant percentage of isolates indicated that macrolides and tetracycline can be recommended for calculated antibiotic treatment of arcobacteriosis in Ghana, but not ampicillin and quinolones.
Topics: Animals; Poultry; Arcobacter; Multilocus Sequence Typing; Ghana; Gram-Negative Bacterial Infections; Anti-Bacterial Agents; Tetracycline
PubMed: 36761899
DOI: 10.3389/fcimb.2023.1094067 -
Water Research Mar 2021Plastic pollution in aquatic environments, particularly microplastics (<5 mm), is an emerging health threat. The buoyancy, hydrophobic hard surfaces, novel polymer...
Plastic pollution in aquatic environments, particularly microplastics (<5 mm), is an emerging health threat. The buoyancy, hydrophobic hard surfaces, novel polymer carbon sources and long-distance transport make microplastics a unique substrate for biofilms, potentially harbouring pathogens and enabling antimicrobial resistance (AMR) gene exchange. Microplastic concentrations, their polymer types and the associated microbial communities were determined in paired, contemporaneous samples from the Dutch portion of the river Rhine. Microplastics were collected through a cascade of 500/100/10 μm sieves; filtrates and surface water were also analysed. Microplastics were characterized with infrared spectroscopy. Microbial communities and selected virulence and AMR genes were determined with 16S rRNA-sequencing and qPCR. Average microplastic concentration was 213,147 particles/m; polyamide and polyvinylchloride were the most abundant polymers. Microbial composition on 100-500 μm samples differed significantly from surface water and 10-100 μm or smaller samples, with lower microbial diversity compared to surface water. An increasingly 'water-like' microbial community was observed as particles became smaller. Associations amongst specific microbial taxa, polymer types and particle sizes, as well as seasonal and methodological effects, were also observed. Known biofilm-forming and plastic-degrading taxa (e.g. Pseudomonas) and taxa harbouring potential pathogens (Pseudomonas, Acinetobacter, Arcobacter) were enriched in certain sample types, and other risk-conferring signatures like the sul1 and erm(B) AMR genes were almost ubiquitous. Results were generally compatible with the existence of taxon-selecting mechanisms and reduced microbial diversity in the biofilms of plastic substrates, varying over seasons, polymer types and particle sizes. This study provided updated field data and insights on microplastic pollution in a major riverine environment.
Topics: Environmental Monitoring; Microbiota; Microplastics; Netherlands; Plastics; RNA, Ribosomal, 16S; Water Pollutants, Chemical
PubMed: 33517045
DOI: 10.1016/j.watres.2021.116852 -
Journal of Food Protection Apr 2020Cloacal swabs were obtained from live ostriches reared on 30 different farms situated in South Africa (Oudtshoorn) during the period of June 2018 to July 2019 to...
ABSTRACT
Cloacal swabs were obtained from live ostriches reared on 30 different farms situated in South Africa (Oudtshoorn) during the period of June 2018 to July 2019 to determine the prevalence of Campylobacter and Arcobacter species. PCR (n = 168 pooled cloacal swabs), the Cape Town protocol (n = 836 cloacal swabs), International Organization for Standardization ISO 10272-1:2006 (n = 836 cloacal swabs), and a selective Arcobacter spp. method (n = 415 cloacal swabs) were used for detection. PCR determined an average prevalence of 24.63% for species belonging to the Campylobacteraceae family. The ISO 10272-1:2006 method determined a Campylobacter spp. prevalence level of 16.83%, while the Cape Town protocol could not detect Campylobacter spp. For Arcobacter spp., a prevalence of 18.80 and 39.14% was determined with the Cape Town protocol and the selective Arcobacter spp. method, respectively. Results showed that prevalence levels could be influenced by season, the source of water, and the presence of wild water birds. Higher prevalence levels for Campylobacter spp. (23.38%) and Arcobacter spp. (68%) were detected in ostriches sampled during spring and autumn, respectively. Higher prevalence levels for Campylobacter spp. (25.23%) and Arcobacter spp. (44.50%) were detected in ostriches reared on farms that made use of borehole water. Higher prevalence levels for Arcobacter spp. (44.38%) were seen in ostriches reared on farms with wild water birds. This research shows that ostriches from South Africa can be considered as potential carriers of species belonging to the Campylobacteraceae family.
Topics: Animals; Arcobacter; Bird Diseases; Campylobacter; Prevalence; South Africa; Struthioniformes
PubMed: 31855449
DOI: 10.4315/JFP-19-472 -
PloS One 2021Arcobacter butzleri is an emerging zoonotic food-borne and water-borne pathogen that can cause diarrhea in humans. The global prevalence of A. butzleri infection is...
Arcobacter butzleri is an emerging zoonotic food-borne and water-borne pathogen that can cause diarrhea in humans. The global prevalence of A. butzleri infection is underestimated, and little is known about their phenotypic and genotypic characterization. The aim of this study was to determine antimicrobial susceptibility (AST) profiles, detect related virulence genes, and classify sequence type (ST) of A. butzleri isolates obtained from human stool and food samples. A total of 84 A. butzleri isolates were obtained from human diarrheal (n = 25), non-diarrheal (n = 24) stool, and food (n = 35) samples in Thailand. They were evaluated for phenotypic identification by conventional microbiological procedures and AST by Kirby-Bauer disc diffusion method as well as virulence genes detection. Representative isolates from each origin were selected based on the presence of virulence genes and AST profiles to analyze genetic diversity by multilocus sequence typing (MLST). All isolates showed resistance to nalidixic acid 40.5% (34/84), ciprofloxacin 11.9% (10/84), azithromycin 8.3% (7/84), and erythromycin 3.6% (3/84). Regarding the ten virulence genes detected, cj1349, mviN and pldA had the highest prevalence 100% (84/84), followed by tlyA 98.8% (83/84), cadF 97.6% (82/84), ciaB 71.4% (60/84), hecA and hecB 22.6% (19/84), iroE 15.5% (13/84) and irgA 10.7% (9/84), respectively. Three virulence genes were present among A. butzleri isolates of human diarrheal stool and food samples, with a significant difference observed among isolates; hecB [36% (9/25) and 8.6% (3/35)], hecA [36% (9/25) and 5.7% (2/35)], and irgA [24% (6/25) and 2.9% (1/35)] (p < 0.05), respectively. The hecA and hecB virulence genes functions are related to the mechanism of hemolysis, while irgA supports a bacterial nutritional requirement. MLST analysis of 26 A. butzleri isolates revealed that 16 novel STs exhibited high genetic diversity. The results of this study is useful for understanding potentially pathogenic and antimicrobial-resistant A. butzleri in Thailand. The pathogenic virulence markers hecB, hecA, and irgA have the potential to be developed for rapid diagnostic detection in human diarrheal stool. No significant relationships among STs and sources of origin were observed. Little is known about A. butzleri, the mechanism of action of these virulence genes, is a topic that needs further investigation.
Topics: Animals; Arcobacter; Diarrhea; Genes, Bacterial; Genotype; Gram-Negative Bacterial Infections; Humans; Multilocus Sequence Typing; Thailand; Virulence Factors
PubMed: 33544770
DOI: 10.1371/journal.pone.0246598 -
Microorganisms Apr 2024In contrast to "frank" pathogens, like , , and , that always have a probability of disease, "opportunistic" pathogens are organisms that cause an infectious disease in a... (Review)
Review
In contrast to "frank" pathogens, like , , and , that always have a probability of disease, "opportunistic" pathogens are organisms that cause an infectious disease in a host with a weakened immune system and rarely in a healthy host. Historically, drinking water treatment has focused on control of frank pathogens, particularly those from human or animal sources (like , , or ), but in recent years outbreaks from drinking water have increasingly been due to opportunistic pathogens. Characteristics of opportunistic pathogens that make them problematic for water treatment include: (1) they are normally present in aquatic environments, (2) they grow in biofilms that protect the bacteria from disinfectants, and (3) under appropriate conditions in drinking water systems (e.g., warm water, stagnation, low disinfectant levels, etc.), these bacteria can amplify to levels that can pose a public health risk. The three most common opportunistic pathogens in drinking water systems are , , and . This report focuses on these organisms to provide information on their public health risk, occurrence in drinking water systems, susceptibility to various disinfectants, and other operational practices (like flushing and cleaning of pipes and storage tanks). In addition, information is provided on a group of nine other opportunistic pathogens that are less commonly found in drinking water systems, including , , , , , , , and several free-living amoebae including and species of The public health risk for these microbes in drinking water is still unclear, but in most cases, efforts to manage , mycobacteria, and risks will also be effective for these other opportunistic pathogens. The approach to managing opportunistic pathogens in drinking water supplies focuses on controlling the growth of these organisms. Many of these microbes are normal inhabitants in biofilms in water, so the attention is less on eliminating these organisms from entering the system and more on managing their occurrence and concentrations in the pipe network. With anticipated warming trends associated with climate change, the factors that drive the growth of opportunistic pathogens in drinking water systems will likely increase. It is important, therefore, to evaluate treatment barriers and management activities for control of opportunistic pathogen risks. Controls for primary treatment, particularly for turbidity management and disinfection, should be reviewed to ensure adequacy for opportunistic pathogen control. However, the major focus for the utility's opportunistic pathogen risk reduction plan is the management of biological activity and biofilms in the distribution system. Factors that influence the growth of microbes (primarily in biofilms) in the distribution system include, temperature, disinfectant type and concentration, nutrient levels (measured as AOC or BDOC), stagnation, flushing of pipes and cleaning of storage tank sediments, and corrosion control. Pressure management and distribution system integrity are also important to the microbial quality of water but are related more to the intrusion of contaminants into the distribution system rather than directly related to microbial growth. Summarizing the identified risk from drinking water, the availability and quality of disinfection data for treatment, and guidelines or standards for control showed that adequate information is best available for management of . For , the risk for this organism has been clearly established from drinking water, cases have increased worldwide, and it is one of the most identified causes of drinking water outbreaks. Water management best practices (e.g., maintenance of a disinfectant residual throughout the distribution system, flushing and cleaning of sediments in pipelines and storage tanks, among others) have been shown to be effective for control of in water supplies. In addition, there are well documented management guidelines available for the control of the organism in drinking water distribution systems. By comparison, management of risks for from water are less clear than for . Treatment of is difficult due to its resistance to disinfection, the tendency to form clumps, and attachment to surfaces in biofilms. Additionally, there are no guidelines for management of in drinking water, and one risk assessment study suggested a low risk of infection. The role of tap water in the transmission of the other opportunistic pathogens is less clear and, in many cases, actions to manage (e.g., maintenance of a disinfectant residual, flushing, cleaning of storage tanks, etc.) will also be beneficial in helping to manage these organisms as well.
PubMed: 38792751
DOI: 10.3390/microorganisms12050916 -
MSystems Aug 2022Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates...
Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes bla, bla, and bla. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.
Topics: Humans; Anti-Bacterial Agents; Bacteria; Microbiota; RNA, Ribosomal, 16S; United States; Wastewater
PubMed: 35762794
DOI: 10.1128/msystems.00118-22 -
Applied and Environmental Microbiology Jan 2022Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that (previously ) often dominate the microbial community and that three genera, , ,...
Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that (previously ) often dominate the microbial community and that three genera, , , and , frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for , , and to quantify their activity using catalyzed-reporter deposition fluorescence hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO in short-term (∼ 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations . Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances. Sulfidic environments worldwide are often dominated by sulfur-oxidizing, carbon-fixing . Environmental factors associated with this group's dominance are now understood, but far less is known about the ecology and physiology of members of subgroups of chemoautotrophic . In this study, we used a novel method to differentiate the genus-specific chemoautotrophic activity of three subtypes of In combination with evidence from microscopic counts, chemical consumption/production during incubations, and DNA-based measurements, our data show that oxygen concentration affects both community composition and chemoautotrophic function . These results help us better understand factors controlling microbial diversity at deep-sea hydrothermal vents, and provide first-order insights into the ecophysiological differences between these distinct microbial taxa.
Topics: Carbon Cycle; Hydrothermal Vents; In Situ Hybridization, Fluorescence; Oxygen; Phylogeny; RNA, Ribosomal, 16S; Seawater
PubMed: 34788061
DOI: 10.1128/AEM.02083-21 -
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 -
Foods (Basel, Switzerland) Dec 2021The bacterial communities and physicochemical characteristics of four types of extremely distinctive traditionally fermented vegetables (pickled pepper (PP), pickled...
The bacterial communities and physicochemical characteristics of four types of extremely distinctive traditionally fermented vegetables (pickled pepper (PP), pickled Brassica napobrassica (PBN), salted flowers of wild chives (SFWC), and pickled cucumber (PC)) were identified and compared from north China. was the main bacterial genus in PP and PBN samples, with only being observed in PBN. The predominant genus in SFWC was , while in PC they were were and . At the species level, , and were abundant in PP and PBN. were enriched in PP, and , and were observed in PBN. and were abundant in SFWC. Moreover, tartaric acid was the most physicochemical factor influencing microbial composition, followed by malic acid, titratable acidity (TA), and lactic acid. Furthermore, functional analysis demonstrated that the most genes of the bacterial profiles correlated with carbohydrate metabolism. However, some foodborne pathogens were existed, such as and . The results of this study provide detailed insight into the relationship between the bacterial communities and physicochemical indices of fermented vegetables, and may improve the quality and safety of traditional Chinese fermented vegetables.
PubMed: 35010147
DOI: 10.3390/foods11010021