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Archives of Microbiology Jan 2021Shigella sonnei is the emerging pathogen globally, as it is the second common infectious species of shigellosis (bloody diarrhoea) in low- and middle-income countries... (Review)
Review
Shigella sonnei is the emerging pathogen globally, as it is the second common infectious species of shigellosis (bloody diarrhoea) in low- and middle-income countries (LMICs) and the leading one in developed world. The multifactorial processes and novel mechanisms have been identified in S. sonnei, that are collectively playing apart a substantial role in increasing its prevalence, while replacing the S. flexneri and other Gram-negative gut pathogens niche occupancy. Recently, studies suggest that due to improvement in sanitation S. sonnei has reduced cross-immunization from Plesiomonas shigelliodes (having same O-antigen as S. sonnei) and also found to outcompete the two major species of Enterobacteriaceae family (Shigella flexneri and Escherichia coli), due to encoding of type VI secretion system (T6SS). This review aimed to highlight S. sonnei as an emerging pathogen in the light of recent research with pondering aspects on its epidemiology, transmission, and pathogenic mechanisms. Additionally, this paper aimed to review S. sonnei disease pattern and related complications, symptoms, and laboratory diagnostic techniques. Furthermore, the available treatment reigns and antibiotic-resistance patterns of S. sonnei are also discussed, as the ciprofloxacin and fluoroquinolone-resistant S. sonnei has already intensified the global spread and burden of antimicrobial resistance. In last, prevention and controlling strategies are briefed to limit and tackle S. sonnei and possible future areas are also explored that needed more research to unravel the hidden mysteries surrounding S. sonnei.
Topics: Anti-Bacterial Agents; Ciprofloxacin; Drug Resistance, Bacterial; Dysentery, Bacillary; Escherichia coli; Fluoroquinolones; Humans; Shigella flexneri; Shigella sonnei; Type VI Secretion Systems
PubMed: 32929595
DOI: 10.1007/s00203-020-02034-3 -
TheScientificWorldJournal 2021Fish and fish products are considered a fundamental part of the human diet due to their high nutritional value. Food-borne diseases are considered a major public health... (Review)
Review
Fish and fish products are considered a fundamental part of the human diet due to their high nutritional value. Food-borne diseases are considered a major public health challenge worldwide due to their incidence, associated mortality, and negative economic repercussions. Food safety is the guarantee that foods will not cause harm to the health of those who consume them, and it is a fundamental property of food quality. Food safety can be at risk of being lost at any stage of the food chain if the food is contaminated by pathogenic microorganisms. Many diverse bacteria are present in the environment and as part of the microbiota of food that can be transmitted to humans during the handling and consumption of food. has been mainly associated with outbreaks of gastrointestinal diseases due to the consumption of fish. This bacterium inhabits the environment and aquatic animals and is associated with the microbiota of fish such as tilapia, a fish of importance in fishing, aquaculture, commercialization, and consumption worldwide. The purpose of this document is to provide, through a bibliographic review of databases (Scopus, Web of Science, and Google Scholar, among others), a general informative perspective on food-borne diseases and, in particular, the consumption of fish and tilapia. Diseases derived from contamination by are included, and control and prevention actions and sanitary regulations for fishery products established in several countries around the world are discussed to promote the safety of foods of aquatic origin intended for human consumption and to protect public health.
Topics: Animals; Aquaculture; Bacterial Load; Cryopreservation; Disease Reservoirs; Fish Diseases; Fish Products; Food Contamination; Food Handling; Food Microbiology; Food Preservation; Food Safety; Gastroenteritis; Gram-Negative Bacterial Infections; Humans; Plesiomonas; Prevalence; Quality Control; Seafood; Tilapia; Water Pollution
PubMed: 34594160
DOI: 10.1155/2021/3119958 -
Microbiology Spectrum Oct 2022Maintaining the health of seafarers is a difficult task during long-term voyages. Little is known about the corresponding changes in the gut microbiome-host interaction....
Maintaining the health of seafarers is a difficult task during long-term voyages. Little is known about the corresponding changes in the gut microbiome-host interaction. This study recruited 30 seafarers undertaking a 6-month voyage and analyzed their gut microbiota using 16S rRNA gene sequencing. Fecal untargeted metabolomics analysis was performed using liquid chromatography-mass spectrometry. Significant changes in the composition of the gut microbiota and an increased ratio of / at the end (day 180) of the 6-month voyage, relative to the start (day 0), were observed. At the genus level, the abundances of and were significantly increased, while the abundance of was decreased. Predicted microbial functional analysis revealed significant decreases in folate biosynthesis and biotin metabolism. Furthermore, 20 differential metabolites within six differentially enriched human metabolic pathways (including arginine biosynthesis, lysine degradation, phenylalanine metabolism, sphingolipid metabolism, pentose and glucuronate interconversions, and glycine, serine, and threonine metabolism) were identified by comparing the fecal metabolites at day 0 and day 180. Spearman correlation analysis revealed close relationships between the 14 differential microbiota members and the six differential fecal metabolites that might affect specific human metabolic pathways. This study adopted a multi-omics approach and provides potential targets for maintaining the health of seafarers during long-term voyages. These findings are worthy of more in-depth exploration in future studies. Maintaining the health of seafarers undertaking long-term voyages is a difficult task. Apart from the alterations in the gut microbiome and fecal metabolites after a long-term voyage, our study also revealed that 20 differential metabolites within six differentially enriched human metabolic pathways are worthy of attention. Moreover, we found close relationships between the 14 differential microbiota members and the six differential fecal metabolites that might impact specific human metabolic pathways. Accordingly, preventative measures, such as adjusting the gut microbiota by decreasing potential pathobionts or increasing potential probiotics as well as offsetting the decrease in B vitamins and beneficial metabolites (e.g., d-glucuronic acid and citrulline) via dietary adjustment or nutritional supplements, might improve the health of seafarers during long-term sea voyages. These findings provide valuable clues about gut microbiome-host interactions and propose potential targets for maintaining the health of seafarers engaged in long-term sea voyages.
Topics: Humans; Gastrointestinal Microbiome; RNA, Ribosomal, 16S; Vitamin B Complex; Citrulline; Biotin; Lysine; Metabolomics; Feces; Pentoses; Glucuronates; Glycine; Glucuronic Acid; Serine; Phenylalanine; Sphingolipids; Threonine; Arginine; Folic Acid
PubMed: 36197290
DOI: 10.1128/spectrum.01899-22 -
BMC Genomics Mar 2022The ability of animals and their microbiomes to adapt to starvation and then restore homeostasis after refeeding is fundamental to their continued survival and...
BACKGROUND
The ability of animals and their microbiomes to adapt to starvation and then restore homeostasis after refeeding is fundamental to their continued survival and symbiosis. The intestine is the primary site of nutrient absorption and microbiome interaction, however our understanding of intestinal adaptations to starvation and refeeding remains limited. Here we used RNA sequencing and 16S rRNA gene sequencing to uncover changes in the intestinal transcriptome and microbiome of zebrafish subjected to long-term starvation and refeeding compared to continuously fed controls.
RESULTS
Starvation over 21 days led to increased diversity and altered composition in the intestinal microbiome compared to fed controls, including relative increases in Vibrio and reductions in Plesiomonas bacteria. Starvation also led to significant alterations in host gene expression in the intestine, with distinct pathways affected at early and late stages of starvation. This included increases in the expression of ribosome biogenesis genes early in starvation, followed by decreased expression of genes involved in antiviral immunity and lipid transport at later stages. These effects of starvation on the host transcriptome and microbiome were almost completely restored within 3 days after refeeding. Comparison with published datasets identified host genes responsive to starvation as well as high-fat feeding or microbiome colonization, and predicted host transcription factors that may be involved in starvation response.
CONCLUSIONS
Long-term starvation induces progressive changes in microbiome composition and host gene expression in the zebrafish intestine, and these changes are rapidly reversed after refeeding. Our identification of bacterial taxa, host genes and host pathways involved in this response provides a framework for future investigation of the physiological and ecological mechanisms underlying intestinal adaptations to food restriction.
Topics: Animals; Intestines; Microbiota; RNA, Ribosomal, 16S; Transcriptome; Zebrafish
PubMed: 35317738
DOI: 10.1186/s12864-022-08447-2 -
PloS One 2023Diarrheal diseases are a leading cause of mortality and morbidity, disproportionally affecting persons residing in low and middle-income countries. Accessing...
Diarrheal diseases are a leading cause of mortality and morbidity, disproportionally affecting persons residing in low and middle-income countries. Accessing high-resolution surveillance data to understand community-level etiology and risk remains challenging, particularly in remote and resource limited populations. A multi-year prospective cohort study was conducted in two rural and two peri-urban villages in Cambodia from 2012 to 2018 to describe the epidemiology and etiology of acute diarrheal diseases within the population. Suspected diarrheal episodes among participants were self-reported or detected via routine weekly household visits. Fresh stool and fecal swabs were tested, and acute-illness and follow-up participant questionnaires collected. Of 5027 enrolled participants, 1450 (28.8%) reported at least one diarrheal incident. A total of 4266 individual diarrhea case events were recorded. Diarrhea incidence rate was calculated to be 281.5 persons per 1000 population per year, with an event rate of 664.3 individual diarrhea events occurring per 1000 population per year. Pathogenic Escherichia coli, Aeromonas spp., and Plesiomonas shigelloides were the most prevalent bacterial infections identified. Hookworm and Strongyloides stercoralis were the predominant helminth species, while Blastocystis hominis and Giardia lamblia were the predominant protozoan species found. Norovirus genotype 2 was the predominant virus identified. Mixed infections of two or more pathogens were detected in 36.2% of positive cases. Risk analyses identified unemployed status increased diarrhea risk by 63% (HR = 1.63 [95% CI 1.46, 1.83]). Individuals without access to protected water sources or sanitation facilities were 59% (HR = 1.59 [95% CI 1.49, 1.69]) and 19% (HR = 1.19 [95% CI 1.12, 1.28]) greater risk of contracting diarrhea, respectively. Patient-level surveillance data captured in this long-term study has generated a unique spatiotemporal profile of diarrheal disease in Cambodia. Understanding etiologies, together with associated epidemiological and community-level risk, provides valuable public health insight to support effective planning and delivery of appropriate local population-targeted interventions.
Topics: Humans; Infant; Urban Population; Cambodia; Prospective Studies; Diarrhea; Risk Factors; Escherichia coli
PubMed: 37000848
DOI: 10.1371/journal.pone.0283871 -
PloS One 2021Acute gastrointestinal infection (AGI) represents a significant public health concern. To control and treat AGI, it is critical to quickly and accurately identify its...
Acute gastrointestinal infection (AGI) represents a significant public health concern. To control and treat AGI, it is critical to quickly and accurately identify its causes. The use of novel multiplex molecular assays for pathogen detection and identification provides a unique opportunity to improve pathogen detection, and better understand risk factors and burden associated with AGI in the community. In this study, de-identified results from BioFire® FilmArray® Gastrointestinal (GI) Panel were obtained from January 01, 2016 to October 31, 2018 through BioFire® Syndromic Trends (Trend), a cloud database. Data was analyzed to describe the occurrence of pathogens causing AGI across United States sites and the relative rankings of pathogens monitored by FoodNet, a CDC surveillance system were compared. During the period of the study, the number of tests performed increased 10-fold and overall, 42.6% were positive for one or more pathogens. Seventy percent of the detections were bacteria, 25% viruses, and 4% parasites. Clostridium difficile, enteropathogenic Escherichia coli (EPEC) and norovirus were the most frequently detected pathogens. Seasonality was observed for several pathogens including astrovirus, rotavirus, and norovirus, EPEC, and Campylobacter. The co-detection rate was 10.2%. Enterotoxigenic E. coli (ETEC), Plesiomonas shigelloides, enteroaggregative E. coli (EAEC), and Entamoeba histolytica were detected with another pathogen over 60% of the time, while less than 30% of C. difficile and Cyclospora cayetanensis were detected with another pathogen. Positive correlations among co-detections were found between Shigella/Enteroinvasive E. coli with E. histolytica, and ETEC with EAEC. Overall, the relative ranking of detections for the eight GI pathogens monitored by FoodNet and BioFire Trend were similar for five of them. AGI data from BioFire Trend is available in near real-time and represents a rich data source for the study of disease burden and GI pathogen circulation in the community, especially for those pathogens not often targeted by surveillance.
Topics: Bacteria; Clinical Laboratory Techniques; Cloud Computing; Epidemiological Monitoring; Feces; Gastrointestinal Diseases; Humans; United States; Viruses
PubMed: 33930062
DOI: 10.1371/journal.pone.0250767 -
BMC Veterinary Research Dec 2022Bacterial pathogens are a great threat to fish production. Gram-negative bacteria are among the major bacterial fish pathogens and are zoonotic with the potential to...
Isolation and identification of major bacteria from three Ethiopian rift valley lakes live and processed fish, and water samples: implications in sanitary system of fish products.
Bacterial pathogens are a great threat to fish production. Gram-negative bacteria are among the major bacterial fish pathogens and are zoonotic with the potential to infect humans. This cross-sectional study was conducted to isolate and identify major gram-negative bacteria from live and processed fish, and water samples from Lakes Hawassa, Langanoo and Ziway. A total of 674 different types of samples: 630 tissue samples (210 samples for each intestine, Kkidney and liver collected from 210 live fish (Oreochromis niloticus, Cyprinus carpio and Clarias gariepinus), 20 processed fish samples from lake Ziway fish processing center and 24 lake water samples were included in the study from each lake. The mean values of pH, temperature, dissolved oxygen and nitrate in all water samples were within the normal range at which most freshwater fish species become non-stressed. Of a total of 674 samples included in the study, bacteria were isolated from 154(22.8%) samples with significant difference (P < 0.05) observed in some isolates with respect to sample origin. Of these 154 isolates, 103(66.8%) isolates were gram-negative bacteria consisting of 15 species based on morphology and a range of biochemical tests. From live fish samples, Escherichia coli was the dominant species with 15 isolates followed by Edwardsiella tarda (12), Salmonella Paratyphi (10), Salmonella Typhi (9), Shigella dysenteriae (7), Shigella flexneri (7), Klebsiella pneumonia (7), Enterobacter aerogenes (6), Enterobacter cloacae (5), Pseudomonas aeruginosa (5), Vibrio parahemolyticus (5), Aeromonas sobria (4), Citrobacter freundii (4), Citrobacter koseri (4) and Plesiomonas shigelloides (3). The detection of the common fecal coliforms (E. coli, K. pneumoniae and E. aerogenes) and Salmonella spp. in processed fish indicates the potential danger of passage of pathogenic bacteria and/or their poisons to humans via infected and/or contaminated fish products. Human infection by pathogenic fish bacteria and food poisoning is possible through contamination of fish product in fish production chain due to inadequate handling, poor hygiene and contact with contaminated water. Therefore, producers, consumers and all other stakeholders need to be cautious during handling, processing and consumption of fish harvested from the study lakes.
Topics: Animals; Bacteria; Carps; Cross-Sectional Studies; Escherichia coli; Fish Products; Gram-Negative Bacteria; Lakes; Water; Ethiopia
PubMed: 36517783
DOI: 10.1186/s12917-022-03508-w -
International Journal of Environmental... Nov 2019Drinking water outbreaks occur worldwide and may be caused by several factors, including raw water contamination, treatment deficiencies, and distribution network...
Drinking water outbreaks occur worldwide and may be caused by several factors, including raw water contamination, treatment deficiencies, and distribution network failure. This study describes two drinking water outbreaks in Finland in 2016 (outbreak I) and 2018 (outbreak II). Both outbreaks caused approximately 450 illness cases and were due to drinking water pipe breakage and subsequent wastewater intrusion into the distribution system. In both outbreaks, the sapovirus was found in patient samples as the main causative agent. In addition, adenoviruses and (outbreak I), and noroviruses, astroviruses, enterotoxigenic and enterohemorragic (ETEC and EHEC, respectively) and (outbreak II) were detected in patient samples. Water samples were analyzed for the selected pathogens largely based on the results of patient samples. In addition, traditional fecal indicator bacteria and host-specific microbial source tracking (MST) markers (GenBac3 and HF183) were analyzed from water. In drinking water, sapovirus and enteropathogenic (EPEC) were found in outbreak II. The MST markers proved useful in the detection of contamination and to ensure the success of contaminant removal from the water distribution system. As mitigation actions, boil water advisory, alternative drinking water sources and chlorination were organized to restrict the outbreaks and to clean the contaminated distribution network. This study highlights the emerging role of sapoviruses as a waterborne pathogen and warrants the need for testing of multiple viruses during outbreak investigation.
Topics: Bacterial Infections; Disease Outbreaks; Drinking Water; Feces; Finland; Humans; Virus Diseases; Wastewater; Water Microbiology; Water Purification
PubMed: 31717479
DOI: 10.3390/ijerph16224376 -
BMC Microbiology Dec 2022RpoN, also known as σ, first reported in Escherichia coli, is a subunit of RNA polymerase that strictly controls the expression of different genes by identifying...
BACKGROUND
RpoN, also known as σ, first reported in Escherichia coli, is a subunit of RNA polymerase that strictly controls the expression of different genes by identifying specific promoter elements. RpoN has an important regulatory function in carbon and nitrogen metabolism and participates in the regulation of flagellar synthesis, bacterial motility and virulence. However, little is known about the effect of RpoN in Plesiomonas shigelloides.
RESULTS
To identify pathways controlled by RpoN, RNA sequencing (RNA-Seq) of the WT and the rpoN deletion strain was carried out for comparison. The RNA-seq results showed that RpoN regulates ~ 13.2% of the P. shigelloides transcriptome, involves amino acid transport and metabolism, glycerophospholipid metabolism, pantothenate and CoA biosynthesis, ribosome biosynthesis, flagellar assembly and bacterial secretion system. Furthermore, we verified the results of RNA-seq using quantitative real-time reverse transcription PCR, which indicated that the absence of rpoN caused downregulation of more than half of the polar and lateral flagella genes in P. shigelloides, and the ΔrpoN mutant was also non-motile and lacked flagella. In the present study, the ability of the ΔrpoN mutant to kill E. coli MG1655 was reduced by 54.6% compared with that of the WT, which was consistent with results in RNA-seq, which showed that the type II secretion system (T2SS-2) genes and the type VI secretion system (T6SS) genes were repressed. By contrast, the expression of type III secretion system genes was largely unchanged in the ΔrpoN mutant transcriptome and the ability of the ΔrpoN mutant to infect Caco-2 cells was also not significantly different compared with the WT.
CONCLUSIONS
We showed that RpoN is required for the motility and contributes to the killing ability of P. shigelloides and positively regulates the T6SS and T2SS-2 genes.
Topics: Humans; RNA Polymerase Sigma 54; Gene Expression Regulation, Bacterial; Plesiomonas; Bacterial Proteins; Escherichia coli; Caco-2 Cells
PubMed: 36510135
DOI: 10.1186/s12866-022-02722-8 -
Virulence Dec 2023spp. are the causative agent of shigellosis (or bacillary dysentery), a diarrhoeal disease characterized for the bacterial invasion of gut epithelial cells. Among the 4... (Review)
Review
spp. are the causative agent of shigellosis (or bacillary dysentery), a diarrhoeal disease characterized for the bacterial invasion of gut epithelial cells. Among the 4 species included in the genus, is principally responsible for the disease in the developing world while is the main causative agent in high-income countries. Remarkably, as more countries improve their socioeconomic conditions, we observe an increase in the relative prevalence of . To date, the reasons behind this change in aetiology depending on economic growth are not understood. has been widely used as a model to study the pathogenesis of the genus, but as more research data are collected, important discrepancies with have come to light. In comparison to can be differentiated in numerous aspects; it presents a characteristic O-antigen identical to that of one serogroup of the environmental bacterium , a group 4 capsule, antibacterial mechanisms to outcompete and displace gut commensal bacteria, and a poorer adaptation to an intracellular lifestyle. In addition, the World Health Organization (WHO) have recognized the significant threat posed by antibiotic-resistant strains of , demanding new approaches. This review gathers knowledge on what is known about within the context of other spp. and aims to open the door for future research on understanding the increasing spread of this pathogen.
Topics: Humans; Shigella sonnei; Virulence; Prevalence; Anti-Bacterial Agents; Cell Differentiation; Dysentery, Bacillary
PubMed: 37994877
DOI: 10.1080/21505594.2023.2280838