Genomic Characterization of Salmonella Isangi: A Global Perspective of a Rare Serovar.

Salmonella Isangi is an infrequent serovar that has recently been reported in several countries due to nosocomial infections. A considerable number of reports indicate Salmonella Isangi multidrug resistance, especially to cephalosporins, which could potentially pose a risk to public health worldwide. Genomic analysis is an excellent tool for monitoring the emergence of microorganisms and related factors. In this context, the aim of this study was to carry out a genomic analysis of Salmonella Isangi isolated from poultry in Brazil, and to compare it with the available genomes from the Pathogen Detection database and Sequence Read Archive. A total of 142 genomes isolated from 11 different countries were investigated. A broad distribution of extended-spectrum beta-lactamase (ESBL) genes was identified in the Salmonella Isangi genomes examined (blaCTX-M-15, blaCTX-M-2, blaDHA-1, blaNDM-1, blaOXA-10, blaOXA-1, blaOXA-48, blaSCO-1, blaSHV-5, blaTEM-131, blaTEM-1B), primarily in South Africa. Resistome analysis revealed predicted resistance to aminoglycoside, sulfonamide, macrolide, tetracycline, trimethoprim, phenicol, chloramphenicol, and quaternary ammonium. Additionally, PMQR (plasmid-mediated quinolone resistance) genes qnr19, qnrB1, and qnrS1 were identified, along with point mutations in the genes gyrAD87N, gyrAS83F, and gyrBS464F, which confer resistance to ciprofloxacin and nalidixic acid. With regard to plasmids, we identified 17 different incompatibility groups, including IncC, Col(pHAD28), IncHI2, IncHI2A, IncM2, ColpVC, Col(Ye4449), Col156, IncR, IncI1(Alpha), IncFIB (pTU3), Col(B5512), IncQ1, IncL, IncN, IncFIB(pHCM2), and IncFIB (pN55391). Phylogenetic analysis revealed five clusters grouped by sequence type and antimicrobial gene distribution. The study highlights the need for monitoring rare serovars that may become emergent due to multidrug resistance.

The antibiotic resistome in Escherichia coli isolated from human, food, and animal sources.

AIMS: The aim of this study was to analyze and compare the prevalence and distribution of resistance genes in Escherichia coli genomes isolated from human clinical samples and animal-based foods worldwide. METHODS AND RESULTS: We download from NCBI Pathogen Detection Database the corresponding metadata of the 7,123 E. coli genome to access the information about the antimicrobial resistance gene content. The geographic location and the source of isolation were also obtained and compiled with the antimicrobial resistance gene for statistical analysis, results and discussion. Our criteria considered four groups for analyzing the antimicrobial resistance gene distribution. The first group of genomes from invasive clinical human (ICH) samples from countries with Human Development Index (HDI) ≥ 0.850; the second group of ICH from countries with an HDI ≤ 0.849; the third group of animal-based foods (ABF) from countries with HDI ≥ 0.850 and the fourth group of ABFs from countries with HDI ≤ 0.849. The most prevalent genes in the first group were blaCTX-M-134 (96.53%) and blaCTX-M-27 (86.35%). In the second group, ere(A) (95.96%), soxS (94.49%), qepA8 (90.81%), blaCTX-M-15 (85.66%), and fosA3 (80.88%). In the third group, the most frequently detected were aadA12 (98.5%), ant(3") (89.92%), and blaCARB-2 (87.2%). In the fourth group, aadA12 and aac(3)-IV were identified in 100% of the analyzed genomes. CONCLUSIONS: It was clear that the use of aminoglycosides in animal production is increasing the selective pressure on micro-organisms in both groups of countries since genes linked to aminoglycoside resistance are related to E. coli from ABF samples. The genomic profile of E. coli from HDI ≥ 0.850 countries indicates a selective pressure aimed at cephalosporins given the high prevalence in both sources.

Food safety concerns on polycyclic aromatic hydrocarbon contamination in fish products from estuarine bays throughout the American continent.

Estuarine environments are highly productive ecosystems exhibiting high fish biodiversity and richness. Estuarine bays yield significant fisheries catches, making them the target of extractive activities by both artisanal and industrial fisheries. These areas, however, are highly vulnerable to chemical contamination, such as polycyclic aromatic hydrocarbons (PAH) associated with oil spills and other anthropogenic activities, which can jeopardize animal health and consumer welfare. In this context, this systematic review aimed to evaluate PAH levels detected in seafood from estuarine bays throughout the entire American continent and assess potential human health risks. The PICO methodology was applied, and 27 experimental papers were evaluated. The findings indicate that naphthalene and pyrene are routinely detected at high concentrations in several species, such as white mullet and catfish, and that biliary metabolites concentrations tend to be higher than tissue levels. Although the effects of PAH on animal health are well defined due to several decades of assessments, food safety evaluations are still not routine, evidencing a significant knowledge gap and the need for legislative measures based on toxicological data.

Genomic Analysis of a Community-Acquired Methicillin-Resistant Staphylococcus aureus Sequence Type 1 Associated with Caprine Mastitis.

This study aimed to investigate the genomic and epidemiological features of a methicillin-resistant Staphylococcus aureus sequence type 1 (MRSA ST1) strain associated with caprine subclinical mastitis. An S. aureus strain was isolated from goat's milk with subclinical mastitis in Paraiba, Northeastern Brazil, by means of aseptic procedures and tested for antimicrobial susceptibility using the disk-diffusion method. Whole genome sequencing was performed using the Illumina MiSeq platform. After genome assembly and annotation, in silico analyses, including multilocus sequence typing (MLST), antimicrobial resistance and stress-response genes, virulence factors, and plasmids detection were performed. A comparative SNP-based phylogenetic analysis was performed using publicly available MRSA genomes. The strain showed phenotypic resistance to cefoxitin, penicillin, and tetracycline and was identified as sequence type 1 (ST1) and spa type 128 (t128). It harbored the SCCmec type IVa (2B), as well as the lukF-PV and lukS-PV genes. The strain was phylogenetically related to six community-acquired MRSA isolates (CA-MRSA) strains associated with human clinical disease in North America, Europe, and Australia. This is the first report of a CA-MRSA strain associated with milk in the Americas. The structural and epidemiologic features reported in the MRSA ST1 carrying a mecA-SCCmec type IVa suggest highly complex mechanisms of horizontal gene transfer in MRSA. The SNP-based phylogenetic analysis suggests a zooanthroponotic transmission, i.e., a strain of human origin.

Toxic metal and metalloid contamination in seafood from an eutrophic Brazilian estuary and associated public health risks.

Guanabara Bay (GB) is a highly contaminated estuarine system and an important fishing area in Southeastern Brazil. In this regard, knowledge concerning the association of certain contaminants in seafood to abiotic factors and human health risk assessments is still understudied. Therefore, this study aimed to quantify nine toxic elements in highly consumed crabs, shrimp, and squid, and associate the results with abiotic factors. A human health risk assessment was also performed. Our findings indicate that crabs are the main bioaccumulators. Transparency and depth were noteworthy for all three taxonomic groups. In general, contaminant concentrations were below the limits established by different international agencies, except for As, which was higher than the Brazilian limit (1 mg kg-1). However, the Hazard Index identified risks to consumer health for the ingestion of seafood. This study emphasizes the importance of jointly evaluating different toxic elements, for a more accurate health risk assessment.

Staphylococcus aureus biofilm: the role in disseminating antimicrobial resistance over the meat chain.

Staphylococcus aureus is responsible for severe skin and respiratory infections and food poisoning, resulting in hospitalizations and high morbidity worldwide. Staphylococci have extensive virulence mechanisms and antimicrobial resistance that pose a global challenge to contain the spread of infectious outbreaks. Antimicrobials are used as growth promoters, and for prevention and treatment of infections in animals that provide us with food. The improvement of animal health is undeniable, but the selection of multidrug-resistant strains that can spread resistance genes among microorganisms is undesirable. The administration of sublethal doses of antimicrobials in farm animals causes stress to Staphylococci inducing the formation of a complex extracellular polymeric structure called biofilm. Such a structure may favor the persistence of infection by disseminating antimicrobial-resistant strains that can be consumed in contaminated food of animal origin. In ruminant mastitis and hospitals, the potential of the biofilm structure in the persistence of infections, especially those caused by S. aureus, has already been demonstrated, as well as its role as a source of resistant genes. In the meat production chain, the potential for persistent contamination by biofilm structure is evidently a worrying health risk . This review brings together studies demonstrating that biofilm production facilitates the exchange of mobile genetic elements and random mutations in S. aureus strains within the structure. This contributes to the emergence of more resistant clonal complexes and, with biofilm support, persists in the meat production chain.

Baseline titanium levels of three highly consumed invertebrates from an eutrophic estuary in southeastern Brazil.

Titanium (Ti) is considered a contaminant of emerging interest, as it displays toxic potential and has been increasingly employed in everyday products, pharmaceuticals, and food additives, mainly in nanoparticle form. However, several knowledge gaps are still noted, especially concerning its dynamics in the water. In this context, this study aimed to quantify total Ti concentrations in highly consumed swimming crabs, squid, and shrimp from an important estuary located in southeastern Brazil. Ti concentrations were higher than those reported in most studies carried out worldwide. Animal length and weight, as well as, depth, transparency, dissolved oxygen, and salinity, significantly influence Ti concentrations in the animals. Human health risks were also noted after calculating a simulated exposure to titanium dioxide, especially considering the uncertainties regarding the effects of this element and the absence of regulatory limits.

Multivariate Nature of Fish Freshness Evaluation by Consumers.

The aim of the present study was to evaluate the sensory acceptability limit of refrigerated fish through a multivariate approach, involving classic physicochemical and bacteriological indicators and considering different consumer profiles. The results of the survival analysis demonstrated that, in general, consumers still considered the fish to be suitable for purchase (4.128 days of storage), despite being microbiologically unsuitable for consumption. However, the subsequent division of consumers into clusters indicated that women and individuals with high income and education levels tend to reject fish with few days of storage (3.650 days), mainly due to discoloration, despite still being microbiologically suitable for consumption. Thus, these segments present a safer behavior regarding the purchase of fresh fish. The influence of different frequencies of fish consumption and age of consumers on the assessment of fish freshness was not clarified. The responsibility for ensuring safe and healthy products at the point of sale must lie with the producers and distributors. However, improving consumers' ability to make good choices when buying fresh fish would bring social and economic benefits related to public health and to the seafood industry, because it would enable them to make relevant claims and demand their rights.

Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health.

The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.

Nucleic Acid-Based Nanobiosensor (NAB) Used for Salmonella Detection in Foods: A Systematic Review.

Salmonella bacteria is a foodborne pathogen found mainly in food products causing severe symptoms in the individual, such as diarrhea, fever, and abdominal cramps after consuming the infected food, which can be fatal in some severe cases. Rapid and selective methods to detect Salmonella bacteria can prevent outbreaks when ingesting contaminated food. Nanobiosensors are a highly sensitive, simple, faster, and lower cost method for the rapid detection of Salmonella, an alternative to conventional enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) techniques. This study systematically searched and analyzed literature data related to nucleic acid-based nanobiosensors (NABs) with nanomaterials to detect Salmonella in food, retrieved from three databases, published between 2010 and 2021. We extracted data and critically analyzed the effect of nanomaterial functionalized with aptamer or DNA at the limit of detection (LOD). Among the nanomaterials, gold nanoparticles (AuNPs) were the most used nanomaterial in studies due to their unique optical properties of the metal, followed by magnetic nanoparticles (MNPs) of Fe3O4, copper nanoparticles (CuNPs), and also hybrid nanomaterials multiwalled carbon nanotubes (c-MWCNT/AuNP), QD/UCNP-MB (quantum dotes upconverting nanoparticle of magnetic beads), and cadmium telluride quantum dots (CdTe QDs@MNPs) showed excellent LOD values. The transducers used for detection also varied from electrochemical, fluorescent, surface-enhanced Raman spectroscopy (SERS), RAMAN spectroscopy, and mainly colorimetric due to the possibility of visualizing the detection result with the naked eye. Furthermore, we show the magnetic separation system capable of detecting the target amplification of the genetic material. Finally, we present perspectives, future research, and opportunities to use point-of-care (POC) diagnostic devices as a faster and lower cost approach for detecting Salmonella in food as they prove to be viable for resource-constrained environments such as field-based or economically limited conditions.

Polycyclic aromatic hydrocarbons in aquatic animals: a systematic review on analytical advances and challenges.

Polycyclic aromatic hydrocarbons (PAHs), the main component of petroleum, are a concern due to their environmental persistence, long-range transport, and potential toxic effects on animal, human health, and the environment. PAHs are considered persistent compounds and can be bioaccumulated in sediments and aquatic biota. Determining PAHs in animals and environmental samples consists of three steps: extraction, clean-up or purification, and analytical determination. The matrix complexity and the diversity of environmental contaminants, such as PAHs resulted in the development of numerous analytical techniques and protocols for the extraction of these components and analysis in several samples. This systematic review article seeks to relate the extraction and preparation methods of complex samples from aquatic animals and the two main detection techniques of PAHs. For the elaboration of the research, 67 articles published between 2011 and 2021 were sought, which specifically contemplated the isolation of aquatic extracts and detection and quantification techniques of PAHs.

The Role of the Ecotoxicology Applied to Seafood as a Tool for Human Health Risk Assessments Concerning Polycyclic Aromatic Hydrocarbons.

BACKGROUND: Polycyclic aromatic hydrocarbons (PAHs) are persistent pollutants routinely detected in aquatic ecosystems. It is, therefore, necessary to assess the link between deleterious marine biota PAH effects, especially in commercialized and consumed animals, environmental health status, and potential human health risks originating from the consumption of contaminated seafood products. Thus, this review seeks to verify the relationships of ecotoxicological studies in determining effect and safety concentrations on animals routinely consumed by humans. METHODS: A total of 52 published studies between 2011 and 2021, indexed in three databases, were selected following the PICO methodology, and information on test animals, evaluated PAH, and endpoints were extracted. RESULTS: Benzo(a)pyrene and phenanthrene were the most investigated PAHs in terms of biomarkers and test organisms, and mussels were the most evaluated bioindicator species, with an emphasis on reproductive responses. Furthermore, despite the apparent correlation between environmental PAH dynamics and effects on aquatic biota and human health, few assessments have been performed in a multidisciplinary manner to evaluate these three variables together. CONCLUSIONS: The links between human and environmental sciences must be strengthened to enable complete and realistic toxicity assessments as despite the application of seafood assessments, especially to mussels, in bioassays, the connection between toxicological animal responses and risks associated with their consumption is still understudied.

Global distribution of plasmid-mediated colistin resistance mcr gene in Salmonella: A systematic review.

This systematic review focuses on obtaining the most relevant information from multiple studies that detected a mobilized colistin resistance mcr gene in Salmonella for a better comprehension of its global distribution. A group of strategic and systematic keywords were combined to retrieve research data on the detection frequency of the mcr gene globally from four database platforms (Google Scholar, Science Direct, PubMed and Scielo). Forty-eight studies attended all the eligibility criteria and were selected. China was the country with the highest frequency of Salmonella strains with the mcr gene, and Europe exhibited a wide diversity of countries with positive mcr strains. In addition, animals and humans carried the highest frequency of positive strains for the mcr gene. Salmonella Typhimurium was the most frequent serovar carrying the mcr gene. Apparently, colistin overuse in animal husbandry has increased the selective pressure of antimicrobial resistance, resulting in the emergence of a plasmid-mediated colistin resistance mcr gene in China. The mcr-positive Salmonella strains are recently predominant worldwide, which is probably due to the capacity of this gene to be swiftly horizontally transmissible. The transmission ability of mcr-positive Salmonella strains to humans through the consumption of contaminated animal-based food is a public health concern.

A Systematic Review on Metal Dynamics and Marine Toxicity Risk Assessment Using Crustaceans as Bioindicators.

Metals, many of which are potentially toxic, are present in the aquatic environment originated from both natural and anthropogenic sources. In these ecosystems, these elements are mostly deposited in the sediment, followed by water dissolution, potentially contaminating resident biota. Among several aquatic animals, crustaceans are considered excellent bioindicators, as they live in close contact with contaminated sediment. The accumulation of metal, whether they are classified as essential, when in excessive quantities or nonessential, not only cause damage to the health of these animals, but also to the man who consumes seafood. Among the main toxic elements to animal and human health are aluminum, arsenic, cadmium, chromium, copper, lead, mercury, nickel and silver. In this context, this systematic review aimed to investigate the dynamics of these metals in water, the main bioaccumulative tissues in crustaceans, the effects of these contaminants on animal and human health, and the regulatory limits for these metals worldwide. A total of 91 articles were selected for this review, and an additional 68 articles not found in the three assessed databases were considered essential and included, totaling 159 articles published between 2010 and 2020. Our results indicate that both chemical speciation and abiotic factors such as pH, oxygen and salinity in aquatic environments affect element bioavailability, dynamics, and toxicity. Among crustaceans, crabs are considered the main bioindicator biological system, with the hepatopancreas appearing as the main bioaccumulator organ. Studies indicate that exposure to these elements may result in nervous, respiratory, and reproductive system effects in both animals and humans. Finally, many studies indicate that the concentrations of these elements in crustaceans intended for human consumption exceed limits established by international organizations, both with regard to seafood metal contents and well as daily, weekly, or monthly intake limits set for humans, indicating consumer health risks.

Interactions between mercury and environmental factors: A chemometric assessment in seafood from an eutrophic estuary in southeastern Brazil.

Guanabara Bay (GB) is an estuary in Brazil, constantly the target of pollutants, such as mercury (Hg). Thus, our study aimed to evaluate (i) total mercury (THg) content in shrimp and squid species from GB; (ii) associate THg content to contamination in swimming crabs; (iii) explore potential differences between species, and size; (iv) correlate abiotic water data to the determined THg contents; (v) verify if Hg concentrations are below acceptable limits. Swimming crabs showed greater Hg contamination compared to other species. For shrimp only biometric variables are related to Hg, while for squid, only abiotic. Only squids did not show a correlation between Hg and animal size. Finally, the detected Hg values are below the tolerable limits established by legislations. Our results indicate that the dynamics of Hg contamination differs between groups and that further studies are needed to elucidate the mechanisms that affect bioaccumulation in different species.

Antimicrobial Resistance Gene Detection Methods for Bacteria in Animal-Based Foods: A Brief Review of Highlights and Advantages.

Antimicrobial resistance is a major public health problem and is mainly due to the indiscriminate use of antimicrobials in human and veterinary medicine. The consumption of animal-based foods can contribute to the transfer of these genes between animal and human bacteria. Resistant and multi-resistant bacteria such as Salmonella spp. and Campylobacter spp. have been detected both in animal-based foods and in production environments such as farms, industries and slaughterhouses. This review aims to compile the techniques for detecting antimicrobial resistance using traditional and molecular methods, highlighting their advantages and disadvantages as well as the effectiveness and confidence of their results.

Virulence genes identification and characterization revealed the presence of the Yersinia High Pathogenicity Island (HPI) in Salmonella from Brazil.

Salmonella spp. is one of the major agents of foodborne disease worldwide, and its virulence genes are responsible for the main pathogenic mechanisms of this micro-organism. The whole-genome sequencing (WGS) of pathogens has become a lower-cost and more accessible genotyping tool providing many gene analysis possibilities. This study provided an in silico investigation of 129 virulence genes, including plasmidial and bacteriophage genes from Brazilian strains' public Salmonella genomes. The frequency analysis of the four most sequenced serovars and a temporal analysis over the past four decades was also performed. The NCBI sequence reads archive (SRA) database comprised 1077 Salmonella public whole-genome sequences of strains isolated in Brazil between 1968 and 2018. Among the 1077 genomes, 775 passed in Salmonella in silico Typing (SISTR) quality control, which also identified 41 different serovars in which the four most prevalent were S. Enteritidis, S. Typhimurium, S. Dublin, and S. Heidelberg. Among these, S. Heidelberg presented the most distinct virulence profile, besides presenting Yersinia High Pathogenicity Island (HPI), rare and first reported in Salmonella from Brazil. The genes mgtC, csgC, ssaI and ssaS were the most prevalent within the 775 genomes with more than 99% prevalence. On the other hand, the less frequent genes were astA, iucBCD, tptC and shdA, with less than 1% frequency. All of the plasmids and bacteriophages virulence genes presented a decreasing trend between the 2000 s and 2010 s decades, except for the phage gene grvA, which increased in this period. This study provides insights into Salmonella virulence genes distribution in Brazil using freely available bioinformatics tools. This approach could guide in vivo and in vitro studies besides being an interesting method for the investigation and surveillance of Salmonella virulence. Moreover, here we propose the genes mgtC, csgC, ssaI and ssaS as additional targets for PCR identification of Salmonella in Brazil due to their very high frequency in the studied genomes.

Arsenic in shellfish: A systematic review of its dynamics and potential health risks.

Arsenic is the most toxic element for humans. Presenting naturally in aquatic ecosystems and due to anthropogenic action, this semi-metal transfers to shellfish through the food chain. This systematic review aims to explain the dynamic of arsenic in the marine aquatic system, investigating factors that affect its bioaccumulation. A total of 64 articles were considered from three databases. The key abiotic factor influencing the presence of arsenic in shellfish is anthropogenic contamination, followed by geographic location. The crucial biotic factor is the genetics of each species of shellfish, including their diet habits, habitat close to the sediment, metabolic abilities, physiological activities of organisms, and metal levels in their habitats and food. Finally, arsenic presents an affinity for specific tissues in shellfish. Despite containing mostly less toxic organic arsenic, shellfish are a relevant source of arsenic in the human diet.