Salmonella enterica

Disinfectants and one health review: The role of reactive oxygen species in the bactericidal activity of chlorine against Salmonella

Salmonella are among the most common foodborne pathogens in humans, and they are associated with mild to severe diseases commonly referred to as salmonellosis. The genus resides in various animals' intestinal tracts, including humans. It is one of the most diverse genera of bacteria, including over 2500 serovars. Consumption of poultry products contaminated with Salmonella is a significant source of disease transmission in humans. Because of this food safety concern, the poultry industry and governments spend billions of dollars on Salmonella containment methods. However, a completely effective strategy is yet to be established. Chlorine has been commonly used as a disinfectant in the poultry industry. In humans, antibiotic therapy is the primary means for managing Salmonella infection. However, widespread use of both compounds at sub-inhibitory concentrations has allowed resistant strains to emerge and rapidly spread globally. Both antimicrobial compounds involve generating reactive oxygen species (ROS) as a bactericidal mechanism of action. However, ROS generation and its association with bacterial survival and growth inhibition have not been widely explored. Thus, a better understanding of ROS generation during antimicrobial treatments may help devise better Salmonella containment strategies.

Amphiphilic polymer coated carbon nanotubes: A promising platform against Salmonella typhi

Carbon nanotubes (CNTs) are an excellent example of new nanostructures that can penetrate bacterial cell walls. Its remarkable physical features and potent antibacterial activity make it a promising candidate for various applications. However, two significant barriers currently limit the antibacterial potential of CNTs in medical devices: cell toxicity and CNTs aggregation within a polymer matrix. In this study, a simple and cost-effective method was proposed to synthesize multi-walled carbon nanotubes-g-[poly(ethylene glycol)-bpoly(ε-caprolactone)] (PEG-PCL@CNTs) using biocompatible amphiphilic PEG-PCL diblock copolymer via non-covalent functionalization. Furthermore, time-killing kinetic, ROS generation experiments and SEM analysis demonstrated that PEG-PCL@CNTs exhibited antibacterial activities against S. typhi strains through cell membrane disruption with the release of cellular contents and ROS generation. Excellent hemocompatibility with decreased hemolysis ratios was demonstrated by the PEG-PCL@CNTs nanohybrid materials. Thus, PEG-PCL incorporation may successfully lessen both bacterial adhesion and the toxicity of CNT to human cells. These findings suggest a new avenue for rational design of polymer-functionalization of carbon nanomaterials as therapeutic agents for bacterial infections.

Evaluation of the virulence characteristics of ST11 Salmonella enterica from different sources using a 2D cell model

This study aimed to evaluate the virulence characteristics of ST11 Salmonella enterica from various sources and explore its pathogenic mechanisms and the molecular basis of antimicrobial resistance. In total, 20 Salmonella isolates collected between 2017 and 2022 from environmental, animal, clinical, and food sources were analyzed. Comprehensive investigations were conducted using whole-genome sequencing, bioinformatic analysis, broth microdilution methods, a two-dimensional (2D) cell model (Caco-2 cells), and a Galleria mellonella infection model. All tested ST11 strains carried major pathogenicity islands (PAIs) SPI-1salmonella pathogenicity island-1 (SPI-1) to SPI-5, and 90 % of the isolates harbored three or more plasmids, facilitating the horizontal transfer of virulence genes. Expression levels of sopA, ssaV, sipA/sspA, and sipB/sspB virulence genes varied significantly among strains, with sipB/sspB playing a key role in the invasion of ST11 strains. The results of invasion assays using the 2D cell model were consistent with those from the Galleria mellonella infection model, validating the 2D model's effectiveness in evaluating Salmonella's virulence. The findings suggest that Salmonella's virulence is not directly associated with the source of the isolates, and plasmid diversity may impact adaptability and transmission patterns. This study provides new insights into the pathogenic mechanisms of ST11 Salmonella and lays the groundwork for developing a novel 3D cell model to assess bacterial virulence.

Zoonotic infections in semi-domesticated eurasian tundra reindeer (Rangifer tarandus tarandus) in Fennoscandia - a review

Eurasian tundra reindeer (Rangifer tarandus tarandus) make up the basis for reindeer herding in Norway, Sweden and Finland, hosting about 640 000 animals. The animals are mostly free-ranging, with the exception of a few seasonal gatherings. Loss and fragmentation of pastures due to other types of land use, together with climate change and even conservation of predators, are challenging reindeer herding, leading to recent mitigations such as increased feeding. Whereas the average Norwegian consumes about 300 gr/person/year of reindeer meat, Sweden about 100 gr/person/year and Finland about 400 gr/person/year, reindeer meat and products constitutes a much larger part of the diet to members of herding communities. Preparing reindeer meat with no thorough heat treatment (e.g., drying, smoking, curing or raw consumption) can be found in many arctic and sub-arctic people's cultures, and interest for reindeer meat that is not heat-treated has also grown (e.g., carpaccio-style), which can dramatically impact pathogen transmission. There is a wide range of zoonotic parasites, bacteria and viruses that potentially can be transferred from reindeer to human, but it can be concluded that the zoonotic threat from close contact with reindeer or the consumption of reindeer meat and products thereof currently is of restricted magnitude. However, due to the challenges that reindeer populations are facing and the mitigation by increased feeding, the infection biology of zoonotic infections may change and we may face emerging diseases (i.e., pathogens new to the host and region), such as the recently appearing prion disease, Chronic wasting disease (CWD), and re-emerging diseases, such as the alimentary form of necrobacillosis.

Characterization and therapeutic potential of newly isolated bacteriophages targeting the most common Salmonella serovars in Europe

Despite meticulous monitoring of Salmonella spp. throughout the food chain to ensure safer animal food products for consumers, the number of salmonellosis cases in humans continues to rise annually in Europe. Phage therapy emerges as a promising tool for controlling and eradicating Salmonella in primary production. This study aimed to fully characterize new phage therapy candidates isolated from animal sources. To achieve this, a phenotypic and genetic characterization of five phage isolates was conducted. The five phages demonstrated physical stability across a wide range of temperatures and pH levels, effectively lysing 12 different Salmonella serovars, including the most prevalent ones in the European Union in recent years, as well as multidrug-resistant strains isolated from the field. Additionally, four of the phages exhibited depolymerase production in the host range, with genomic analysis confirming that all five possessed sequences encoding for this activity, suggesting their potential as surface-disinfecting agents. Genetic analysis further revealed that the phages belong to distinct genera: Felixounavirus, Cornellvirus, Skatevirus, Agtevirus and Berlinvirus. Notably, none of the phages contained harmful sequences that could compromise their future application, such as virulence factors, antibiotic resistance genes or temperate markers. Overall, these five phages show promise as suitable candidates for phage therapy applications or phage-based Salmonella eradication strategies, where their integration in the existing biocontrol measures may enhance both food safety and public health.

Habitat-Dependent DNA viral communities in atmospheric aerosols: Insights from terrestrial and marine ecosystems in East Asia

The transmission of viruses through aerosols is of growing public health concern, yet research on aerosol-associated viral communities lags behind that of terrestrial and aquatic ecosystems. Here, DNA viral diversity in natural aerosols from both over land and ocean in the East Asia region was examined. The results showed that atmospheric environments harbor a distinct viral community that differs from those present in terrestrial and aquatic ecosystems. A comparison of aerosol samples from different locations revealed that aerosol viruses are strongly influenced by altitude and their sources. Fragments of viruses that can infect pathogenic bacteria, as well as pathogenic viruses (such as herpesviruses, Inoviruses, and Iridovirus) were detected. Anthropogenically-influenced land aerosol samples contained viral communities with greater richness and diversity as well as a higher relative abundance of pathogenic and lytic viruses compared to pristine marine airborne samples. Furthermore, habitat-specific auxiliary metabolic genes (AMGs) were observed, such as the phosphate regulon (phoH), which was more prevalent in ocean aerosol samples and regulates phosphate uptake under low-phosphate conditions, thereby assisting viral hosts in overcoming metabolic challenges in different environmental conditions. This study highlights the ecological distinctness of the airborne viral community and the interconnectedness between those from land, sea, and atmosphere, underscoring the importance of evaluating their potential pathogenicity in future research.

Fangchinoline eliminates intracellular Salmonella by enhancing lysosomal function via the AMPK-mTORC1-TFEB axis

INTRODUCTION

Salmonella, a foodborne zoonotic pathogen, is a significant cause of morbidity and mortality in animals and humans globally. With the prevalence of multidrug-resistant strains, Salmonellosis has become a formidable challenge. Host-directed therapy (HDT) has recently emerged as a promising anti-infective approach for treating intracellular bacterial infections.

OBJECTIVES

Plant-derived natural products, owing to their structural and functional diversity, are increasingly being explored and utilized as encouraging candidates for HDT compounds. This study aims to identify and screen natural compounds with potential as HDT for the treatment of intracellular Salmonella infections.

METHODS

A cell-based screening approach was deployed to identify natural compounds capable of mitigating the intracellular replication of S. enterica. Safety and efficacy of the candidate compounds were evaluated using multiple animal models. RNA sequencing, ELISA, and immunoblotting analyses were conducted to elucidate the underlying mechanisms of action.

RESULTS

Our results reveal that fangchinoline (FAN) effectively reduces S. enterica survival both in vitro and in vivo. Meanwhile, FAN also displays anti-infective activity against other intracellular pathogens, including multidrug-resistant isolates. A 14-day safety evaluation in mice showed no significant toxic or adverse effects from FAN administration. RNA sequencing analysis reveals an upregulation of lysosome pathways in S. enterica-infected cells treated with FAN. Mechanistic studies indicate that FAN increases acid lysosomal quantities and fosters autophagic response in Salmonella-infected cells via the AMPK-mTORC1-TFEB axis. In addition, FAN alleviates the inflammatory response in Salmonella-infected cells by inactivating the NF-κB pathway.

CONCLUSION

Our findings suggest that FAN represents a lead HDT compound for tackling recalcitrant infections caused by intracellular bacterial pathogens.

The genetic composition of Anopheles mosquitoes and the diverse population of gut-microbiota within the Anopheles subpictus and Anopheles vagus mosquitoes in Tamil Nadu, India

In recent days, in tropical and subtropical regions, secondary vectors of Anopheles mosquitoes are becoming more important in transmitting diseases to humans as primary vectors. Various molecular techniques have separated closely related Anopheles subpictus and Anopheles vagus mosquitoes based on their diversity with other mosquito species. Despite their widespread distribution, the An. subpictus and An. vagus mosquitoes, which carry Plasmodium in their salivary glands, were not considered primary malaria vectors in India. An. vagus mosquitoes are zoophilic and physically similar to An. subpictus. We intend to identify An. subpictus and An. vagus mosquito's sister species based on their Interspaced Transcribed Region-2 (ITS2). We isolated the midgut gDNA from each mosquito and used ITS2-PCR and Sanger sequencing to characterize the mosquito species. BioEdit software aligned the sequences, and MEGA7 built a phylogenetic tree from them. According to this study, the information gathered from these mosquito samples fits the An. subpictus species A form and the An. vagus Indian form. Furthermore, gut microbiome plays an important role in providing nutrients, immunity, and food processing, whereas mosquitoes' midgut microbiota changes their hosts and spreads illnesses. So, we used the Illumina sequencer to look at the gut microbiome diversity of An. subpictus and An. vagus mosquitoes using 16S rRNA-based metagenomic sequencing. Both mosquito species had an abundant phylum of Pseudomonadota (Proteobacteria), Bacillota, Bacteroidota, and Actinomycetota in their gut microbiomes. Notably, both mosquito species had the genus Serratia in their gut. In the subpictus midgut, the genus of Haematosprillum bacteria was dominant, whereas in the vagus mosquito, the genus of Salmonella was dominant. Notably, current research has observed the Sodalis spp. Bacterial genus for the first time.

Prevalence, antimicrobial resistance, and genomic characterization of Salmonella strains isolated in Hangzhou, China: a two-year study

This study explored the molecular epidemiology and resistance mechanisms of 271 non-duplicate Salmonella enterica (S. enterica) strains, isolated mainly from adults (209/271) in a tertiary hospital in Hangzhou between 2020 and 2021. Through whole-genome sequencing and bioinformatics, the bacterial strains were classified into 46 serotypes and 54 sequence types (ST), with S. Enteritidis, S. 1,4,[5],12:i:-, and S. Typhimurium being the most prevalent serotypes and ST11, ST34, and ST19 the most common STs. The strains isolated from adults were primarily S. Enteritidis (59/209), while from children were mainly S. 1,4,[5],12:i:- (20/62). Worryingly, 12.55% strains were multi-drug resistant (MDR), with resistance rates to cefepime (FEP), ceftazidime (CAZ), ceftriaxone (CRO) and cefotaxime (CTX) of 7.38%, 9.23%, 15.87% and 16.24%, respectively, and resistance rates to levofloxacin (LEV) and ciprofloxacin (CIP) of 8.49% and 19.19%, respectively. It is worth noting that the resistance rates of CRO and CTX in children reached 30.65%. A total of 34 strains carried extended-spectrum β-lactamase (ESBL) genes, dominated by blaCTX-M-65 (13/34) and blaCTX-M-55 (12/34); it is notable that one strain of S. Saintpaul carried both blaCTX-M-27 and blaCTX-M-55. The resistance mechanism to cephalosporins was mainly due to ESBL genes (20/43), and other genes included AmpC and β-lactamase genes. The strains resistant to quinolones mainly carried qnrS1 (27/53), and others included qnrB6, aac(6')-Ib-cr, and mutations in gyrA and parC. One strain did not carry common quinolone resistance genes but had a parC (p.T57S) mutation to cause CIP resistance. This research provides vital insights into the molecular epidemiology and resistance mechanisms of clinical S. enterica, implicating possible infection control strategies.

Assessing antimicrobial resistance profiles of Salmonella enterica in the pork production system

Introduction. Salmonella enterica is a significant enteric pathogen affecting human and livestock health. Pork production is a common source of Salmonella contamination, with emerging multidrug resistance (MDR) posing a global health threat.Gap statement. Salmonella contamination and antimicrobial resistance (AMR) profiles in the pig production chain are underreported.Aim. To investigate the prevalence of S. enterica in the pig production chain and characterise their AMR profiles.Methodology. We collected 485 samples from pig farms, a standard pig abattoir and retail markets in Patthalung and Songkhla provinces in southern Thailand. Antimicrobial susceptibility testing was performed on these samples, and AMR profiles were determined.Results. S. enterica was detected in 68.67% of farm samples, 45.95% of abattoir samples and 50.67% of retail market samples. Analysis of 264 isolates, representing 18 serotypes, identified S. enterica serotype Rissen as the most prevalent. The predominant resistance phenotypes included ampicillin (AMP, 91.29%), tetracycline (TET, 88.26%) and streptomycin (STR, 84.47%). Over 80% of isolates showed resistance to three or more antimicrobial classes, indicating MDR. The AMP-STR-TET resistance pattern was found in nearly 70% of all MDR isolates across the production chain.Conclusions. The high prevalence of MDR is consistent with extensive antimicrobial use in the livestock sector. The presence of extensively resistant S. enterica highlights the urgent need for antimicrobial stewardship. Strengthening preventive strategies and control measures is crucial to mitigate the risk of MDR Salmonella spreading from farm to fork.

Nanozybiotics: Advancing Antimicrobial Strategies Through Biomimetic Mechanisms

Infectious diseases caused by bacterial, viral, and fungal pathogens present significant global health challenges. The rapid emergence of antimicrobial resistance exacerbates this issue, leading to a scenario where effective antibiotics are increasingly scarce. Traditional antibiotic development strategies are proving inadequate against the swift evolution of microbial resistance. Therefore, there is an urgent need to develop novel antimicrobial strategies with mechanisms distinct from those of existing antibiotics. Nanozybiotics, which are nanozyme-based antimicrobials, mimic the catalytic action of lysosomal enzymes in innate immune cells to kill infectious pathogens. This review reinforces the concept of nanozymes and provides a comprehensive summary of recent research advancements on potential antimicrobial candidates. Initially, nanozybiotics are categorized based on their activities, mimicking either oxidoreductase-like or hydrolase-like functions, thereby highlighting their superior mechanisms in combating antimicrobial resistance. The review then discusses the progress of nanozybiotics in treating bacterial, viral, and fungal infections, confirming their potential as novel antimicrobial candidates. The translational potential of nanozybiotic-based products, including hydrogels, nanorobots, sprays, bandages, masks, and protective clothing, is also considered. Finally, the current challenges and future prospects of nanozybiotic-related products are explored, emphasizing the design and antimicrobial capabilities of nanozybiotics for future applications.

Distribution and genetic characterization of fluoroquinolone resistance gene qnr among Salmonella strains from chicken in China

The prevalence and dissemination of the plasmid-mediated fluoroquinolone (FQ) resistance gene qnr in Salmonella are considered serious public health concerns worldwide. So far, no comprehensive large-scale studies have focused on the prevalence and genetic characteristics of the qnr gene in Salmonella isolated from chickens. Herein, this study aimed to investigate the prevalence, antimicrobial resistance (AMR) patterns, and molecular characteristics of chicken-originated qnr-positive Salmonella strains from chicken farms, slaughterhouses, and markets in 12 provinces of China in 2020-2021. The overall prevalence of the qnr gene was 21.13% (56/265), with the highest prevalence in markets (36.11%, 26/72), followed in farms (17.95%, 21/117), and slaughterhouses (10.53%, 9/76). Only the qnrS and qnrB genes were detected, and the prevalence rate of the qnrS gene (19.25%, 51/265) was higher than that of the qnrB gene (1.89%, 5/265). Whole genome sequencing identified 37 distinct AMR genes and 15 plasmid replicons, and the most frequent mutation in quinolone resistance determining regions was parC (T57S; 91.49%, 43/47). Meanwhile, four different qnrS and two qnrB genetic environments were discovered among 47 qnr-positive Salmonella strains. In total, 21.28% (10/47) of the strains were capable of conjugative transfer, and all were qnrS1-positive strains, with the majority of transferable plasmids being IncHI2 types (n = 4). Overall, the prevalence of qnr-positive Salmonella strains from chickens in China and their carriage of multiple resistance and virulence genes and transferable plasmids is a major concern, which calls for continuous surveillance of qnr-positive Salmonella and the development of measures to control its prevalence and transmission.IMPORTANCESalmonella is a common foodborne pathogen responsible for 155,000 deaths annually worldwide. Fluoroquinolones (FQs) are used as first-line drugs for the treatment of Salmonella infections in several countries and regions. However, the emergence and increasing prevalence of the FQ-resistant gene qnr in Salmonella isolated from chickens have been widely reported. Gaining insight into the genetic mechanisms of AMR genes in chicken could lead to the development of preventive measures to control and reduce the risk of drug resistance. In this study, we identified qnr-positive Salmonellae isolated from chickens in different regions of China and their AMR patterns and genome-wide characteristics, providing a theoretical basis for further control of their prevalence and transmission.

An electrochemical biosensor based on phage-encoded protein RBP 41 for rapid and sensitive detection of Salmonella

Salmonellosis caused by Salmonella contaminated food poses a serious threat to human health. The rapid and accurate detection of Salmonella is critical for preventing foodborne illness outbreaks. In this study, an electrochemical biosensor was developed using a newly identified biorecognition element, RBP 41, which is capable of specifically recognizing and binding to Salmonella. The biosensor was constructed through a layer-by-layer assembly of graphene oxide (GO), gold nanoparticles (GNPs), and RBP 41 on a glassy carbon electrode (GCE), with the GNPs amplifying the detection signal. The established biosensor was able to detect Salmonella in concentrations ranging from 3 to 106 CFU/mL within approximately 30 min by using differential pulse voltammetry (DPV) signal, and the estimated detection limit was to be 0.2984 Log10 CFU/mL. The biosensor demonstrated excellent specificity and was effective in detecting Salmonella in food matrices, such as skim milk and lettuce. Overall, this study highlights the potential of phage tail receptor binding proteins in biosensing and the proposed biosensor as a promising alternative for rapid and sensitive Salmonella detection in various samples.

Effects of Salmonella Outer Membrane Vesicles on Intestinal Microbiota and Intestinal Barrier Function

Salmonella enterica is one of the most important zoonotic pathogens causing foodborne gastroenteritis worldwide. Outer membrane vesicles (OMVs) are lipid-bilayer vesicles produced by Gram-negative bacteria, which contain biologically active components. We hypothesized that OMVs are an important weapon of S. enterica to initiate enteric diseases pathologies. In this study, the effects of S. enterica OMVs (SeOMVs) on intestinal microbiota and intestinal barrier function were investigated. In vitro fecal culture experiments showed that alpha diversity indexes and microbiota composition were altered by SeOMV supplementation. SeOMV supplementation showed an increase of pH, a decrease of OD630 and total short chain fatty acid (SCFA) concentrations. In vitro IPEC-J2 cells culture experiments showed that SeOMV supplementation did not affect the IPEC-J2 cell viability and the indicated genes expression. In vivo experiments in mice showed that SeOMVs had adverse effects on average daily gain (p < 0.05) and feed:gain ratio (p < 0.05), and had a tendency to decrease the final body weight (p = 0.073) in mice. SeOMV administration decreased serum interleukin-10 level (p < 0.05), decreased the relative abundance of bacteria belonging to the genera BacC-u-018 and Akkermansia (p < 0.05). Furthermore, SeOMV administration damaged the ileum mucosa (p < 0.05). These findings suggest that SeOMVs play an important role in the activation of intestinal inflammatory response induced by S. enterica, and downregulation of SCFA-producing bacteria is a possible mechanism.

Isolation, Identification, Antimicrobial Resistance, Genotyping, and Whole-Genome Sequencing Analysis of Salmonella Enteritidis Isolated from a Food-Poisoning Incident

Salmonella enterica is a common pathogen in humans and animals that causes food poisoning and infection, threatening public health safety. We aimed to investigate the genome structure, drug resistance, virulence characteristics, and genetic relationship of a Salmonella strain isolated from patients with food poisoning. The pathogen strain 21A was collected from the feces of patients with food poisoning, and its minimum inhibitory concentration against commonly used antibiotics was determined using the strip test and Kirby-Bauer disk methods. Subsequently, WGS analysis was used to reveal the genome structural characteristics and the carrying status of resistance genes and virulence genes of strain 21A. In addition, an MLST-based minimum spanning tree and an SNP-based systematic spanning tree were constructed to investigate its genetic evolutionary characteristics. The strain 21A was identified by mass spectrometry as S. enterica, which was found to show resistance to ampicillin, piperacillin, sulbactam, levofloxacin, and ciprofloxacin. The WGS and bioinformatics analyses revealed this strain as Salmonella Enteritidis belonging to ST11, which is common in China, containing various resistance genes and significant virulence characteristics. Strain 21A was closely related to the SJTUF strains, a series strains from animal, food and clinical sources, as well as from Shanghai, China, which were located in the same evolutionary clade. According to the genetic makeup of strain 21A, the change G > A was found to be the most common variation. We have comprehensively analyzed the genomic characteristics, drug resistance phenotype, virulence phenotype, and genetic evolution relationship of S. Enteritidis strain 21A, which will contribute towards an in-depth understanding of the pathogenic mechanism of S. Enteritidis and the effective prevention and control of foodborne diseases.

Microfluidic systems for infectious disease diagnostics

Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.

Protective effects of puerarin on liver tissue in Salmonella-infected chicks: a proteomic analysis

Salmonella enterica is a zoonotic bacterium that not only causes serious economic losses to the livestock and poultry industries but also seriously endangers human health. Long-term indiscriminate use of antibiotics has led to drug resistance in Salmonella, and thus the identification of alternatives to antibiotics is crucial. In this study, the effects of puerarin on the S. enterica-infected chickens were investigated. A total of 360 chicks were randomly assigned as the control group (CON), the S. enterica group (S), and puerarin-treatment group (P). Chicks in the P group were fed the basal diet supplemented with 50 (P50), 100 (P100), 200 (P200), and 400 (P400) mg/kg puerarin, respectively. It was found that puerarin treatment markedly altered the serum activities of aspartate aminotransferase (AST), alanine transaminase (ALT), and superoxide dismutase (SOD), together with the malondialdehyde (MDA) and total antioxidant capacity (T-AOC) contents in the serum. The mRNA expression of IL-6, IL-1β, TNF-α, Bcl-2, and caspase-8 in the livers of S. enterica-infected chicks was increased after infection but significantly reduced after treatment with puerarin. Histologic analysis showed that puerarin effectively mitigated morphological damage in the liver caused by S. enterica. Proteomic analysis revealed that S. enterica infection led to metabolic disorders in the liver, resulting in oxidative stress, increased inflammation, and significantly elevated levels of hepatocellular carcinoma biomarkers. The findings of the filtered sequencing were verified by using quantitative PCR (qPCR). Treatment with 100 mg/mL puerarin thus effectively alleviated disordered liver metabolism, reduced inflammation and oxidative damage and significantly reduced the levels of hepatocellular carcinoma biomarkers in the liver. The results suggest that puerarin has the potential to replace antibiotics to control Salmonella infection in poultry and thus improve food safety.

Salmonella Typhimurium with Eight Tandem Copies of blaNDM-1 on a HI2 Plasmid

Carbapenem-resistant Salmonella has recently aroused increasing attention. In this study, a total of four sequence type 36 Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) isolates were consecutively isolated from an 11-month-old female patient with a gastrointestinal infection, of which one was sensitive to carbapenems and three were resistant to carbapenems. Via antibiotic susceptibility testing, a carbapenemases screening test, plasmid conjugation experiments, Illumina short-reads, and PacBio HiFi sequencing, we found that all four S. Typhimurium isolates contained a blaCTX-M-14-positive IncI1 plasmid. One carbapenem-sensitive S. Typhimurium isolate then obtained an IncHI2 plasmid carrying blaNDM-1 and an IncP plasmid without any resistance genes during the disease progression. The blaNDM-1 gene was located on a new 30 kb multiple drug resistance region, which is flanked by IS26 and TnAs2, respectively. In addition, the ST_F0903R isolate contained eight tandem copies of the ISCR1 unit (ISCR1-dsbD-trpF-ble-blaNDM-1-ISAba125Δ1), but an increase in MICs to carbapenems was not observed. Our work further provided evidence of the rapid spread and amplification of blaNDM-1 through plasmid. Prompting the recognition of carbapenem-resistant Enterobacterales and the initiation of appropriate infection control measures are essential to avoid the spread of these organisms.

Transcriptional Profiling of the Effect of Coleus amboinicus L. Essential Oil against Salmonella Typhimurium Biofilm Formation

Salmonella enterica serovar Typhimurium cause infections primarily through foodborne transmission and remains a significant public health concern. The biofilm formation of this bacteria also contributes to their multidrug-resistant nature. Essential oils from medicinal plants are considered potential alternatives to conventional antibiotics. Therefore, this study assessed the antimicrobial and antibiofilm activities of Coleus amboinicus essential oil (EO-CA) against S. Typhimurium ATCC 14028. Seventeen chemical compounds of EO-CA were identified, and carvacrol (38.26%) was found to be the main constituent. The minimum inhibitory concentration (MIC) of EO-CA for S. Typhimurium planktonic growth was 1024 µg/mL while the minimum bactericidal concentration was 1024 µg/mL. EO-CA at sub-MIC (≥1/16× MIC) exhibited antibiofilm activity against the prebiofilm formation of S. Typhimurium at 24 h. Furthermore, EO-CA (≥1/4× MIC) inhibited postbiofilm formation at 24 and 48 h (p < 0.05). Transcriptional profiling revealed that the EO-CA-treated group at 1/2× MIC had 375 differentially expressed genes (DEGs), 106 of which were upregulated and 269 were downregulated. Five significantly downregulated virulent DEGs responsible for motility (flhD, fljB, and fimD), curli fimbriae (csgD), and invasion (hilA) were screened via quantitative reverse transcription PCR (qRT-PCR). This study suggests the potential of EO-CA as an effective antimicrobial agent for combating planktonic and biofilm formation of Salmonella.

Differences in pathogenic community assembly processes and their interactions with bacterial communities in river and lake ecosystems

Pathogenic bacterial infections caused by water quality degradation are one of the most widespread environmental problems. Clarifying the structure of pathogens and their assembly mechanisms in lake ecosystems is vital to prevent the infestation of waterborne pathogens and maintain human health. However, the composition and assembly mechanisms of pathogenic bacterial communities in river and lake ecosystems are still poorly understood. In this study, we collected 17 water and 17 sediment samples from Lake Chaohu and its 11 inflow rivers. Sequencing of 16S rRNA genes was used to study bacterial pathogen communities. The results of the study showed that there was a significant difference (P < 0.05) in the composition of the pathogen community between riverine and lake habitats. Acinetobacter (36.49%) was the dominant bacterium in the river, whereas Flavobacterium (21.6%) was the most abundant bacterium in the lake. Deterministic processes (i.e., environmental filtering and species interaction) drove the assembly of pathogenic bacterial communities in the lake habitat, while stochastic processes shaped river pathogenic bacterial communities. Spearman correlation analysis showed that the α-diversity of bacterial communities was linearly and negatively linked to the relative abundance of pathogens. Having a higher bacterial community diversity had a suppressive effect on pathogen abundance. In addition, co-occurrence network analysis showed that bacterial communities were tightly linked to pathogenic bacteria. Pseudomonas aeruginosa and Salmonella enterica were identified as keystone species in an inflow water sampling network (W_FR), reducing the complexity of the network. These results provide a reference for assessments of water quality safety and pathogenic bacteria posing risks to human health in large freshwater lakes.

Prevalence of Salmonella species and factors associated with contamination of mechanically recovered poultry meat imported into South Africa, 2016-2017

Background and Aim

Mechanically recovered meat (MRM) products have been linked to outbreaks of human salmonellosis. However, no studies have investigated the prevalence of Salmonella species in MRM products in South Africa despite the products being imported. Therefore, this study aimed to estimate the prevalence and factors associated with Salmonella spp. contamination of mechanically recovered poultry meat (MRPM) imported into South Africa.

Materials and Methods

This study used secondary data of MRPM consignments imported through a port entry into South Africa from May 2016 to December 2017. Crude and factor-specific proportions of Salmonella positive MRPM and their 95% confidence intervals were calculated. A logistic regression model was used to assess the association among country, season, importer, year, and MRPM Salmonella status.

Results

A total of 8127 MRPM consignments were imported. Seventeen percentages (17.18%, 985/5733) of consignments tested positive for Salmonella species and only 364 isolates were serotyped. Salmonella Heidelberg (73.90%, 269/364) was the most common serotype followed by Salmonella Infantis (6.59%, 24/364), Salmonella Salamae (4.67%, 17/364), and Salmonella Schwarzengrund (3.57%, 13/364). The odds of a consignment testing positive for Salmonella spp. was higher among consignments from country-B (Odds Ratio [OR]: 3.958, p < 0.0001) compared to "All others." The odds of testing positive for Salmonella were also higher among consignments imported in autumn (OR: 1.488, p < 0.0001) but lower among those imported in spring (OR: 0.767, p = 0.0004) and summer (OR: 0.843, p < 0.0001) when compared to the winter season. Consignments imported in 2016 compared to 2017 were 1.563 times (p < 0.0001) as likely to test positive for a Salmonella species.

Conclusion

Salmonella species were reported in MRPM consignments in this study with Salmonella Heidelberg being the most common serotype. Furthermore, some Salmonella serotypes reported in this study have been implicated in foodborne disease outbreaks. Country of origin, season, and year of importation were significantly associated with the odds of a consignment testing positive for Salmonella species.

The microbial biodiversity at the archeological site of Tel Megiddo (Israel)

Introduction

The ancient city of Tel Megiddo in the Jezreel Valley (Israel), which lasted from the Neolithic to the Iron Age, has been continuously excavated since 1903 and is now recognized as a World Heritage Site. The site features multiple ruins in various areas, including temples and stables, alongside modern constructions, and public access is allowed in designated areas. The site has been studied extensively since the last century; however, its microbiome has never been studied. We carried out the first survey of the microbiomes in Tel Megiddo. Our objectives were to study (i) the unique microbial community structure of the site, (ii) the variation in the microbial communities across areas, (iii) the similarity of the microbiomes to urban and archeological microbes, (iv) the presence and abundance of potential bio-corroding microbes, and (v) the presence and abundance of potentially pathogenic microbes.

Methods

We collected 40 swab samples from ten major areas and identified microbial taxa using next-generation sequencing of microbial genomes. These genomes were annotated and classified taxonomically and pathogenetically.

Results

We found that eight phyla, six of which exist in all ten areas, dominated the site (>99%). The relative sequence abundance of taxa varied between the ruins and the sampled materials and was assessed using all metagenomic reads mapping to a respective taxon. The site hosted unique taxa characteristic of the built environment and exhibited high similarity to the microbiome of other monuments. We identified acid-producing bacteria that may pose a risk to the site through biocorrosion and staining and thus pose a danger to the site's preservation. Differences in the microbiomes of the publicly accessible or inaccessible areas were insignificant; however, pathogens were more abundant in the former.

Discussion

We found that Tel Megiddo combines microbiomes of arid regions and monuments with human pathogens. The findings shed light on the microbial community structures and have relevance for bio-conservation efforts and visitor health.

Genetic characteristics and integration specificity of Salmonella enterica temperate phages

Introduction

Temperate phages can engage in the horizontal transfer of functional genes to their bacterial hosts. Thus, their genetic material becomes an intimate part of bacterial genomes and plays essential roles in bacterial mutation and evolution. Specifically, temperate phages can naturally transmit genes by integrating their genomes into the bacterial host genomes via integrases. Our previous study showed that Salmonella enterica contains the largest number of temperate phages among all publicly available bacterial species. S. enterica is an important pathogen that can cause serious systemic infections and even fatalities.

Methods

Initially, we extracted all S. enterica temperate phages from the extensively developed temperate phage database established in our previous study. Subsequently, we conducted an in-depth analysis of the genetic characteristics and integration specificity exhibited by these S. enterica temperate phages.

Results

Here we identified 8,777 S. enterica temperate phages, all of which have integrases in their genomes. We found 491 non-redundant S. enterica temperate phage integrases (integrase entries). S. enterica temperate phage integrases were classified into three types: intA, intS, and phiRv2. Correlation analysis showed that the sequence lengths of S. enterica integrase and core regions of attB and attP were strongly correlated. Further phylogenetic analysis and taxonomic classification indicated that both the S. enterica temperate phage genomes and the integrase gene sequences were of high diversities.

Discussion

Our work provides insight into the essential integration specificity and genetic diversity of S. enterica temperate phages. This study paves the way for a better understanding of the interactions between phages and S. enterica. By analyzing a large number of S. enterica temperate phages and their integrases, we provide valuable insights into the genetic diversity and prevalence of these elements. This knowledge has important implications for developing targeted therapeutic interventions, such as phage therapy, to combat S. enterica infections. By harnessing the lytic capabilities of temperate phages, they can be engineered or utilized in phage cocktails to specifically target and eradicate S. enterica strains, offering an alternative or complementary approach to traditional antibiotic treatments. Our study has implications for public health and holds potential significance in combating clinical infections caused by S. enterica.

From Eberthella typhi to Salmonella Typhi: The Fascinating Journey of the Virulence and Pathogenicity of Salmonella Typhi

Salmonella Typhi (S. Typhi), the invasive typhoidal serovar of Salmonella enterica that causes typhoid fever in humans, is a severe threat to global health. It is one of the major causes of high morbidity and mortality in developing countries. According to recent WHO estimates, approximately 11-21 million typhoid fever illnesses occur annually worldwide, accounting for 0.12-0.16 million deaths. Salmonella infection can spread to healthy individuals by the consumption of contaminated food and water. Typhoid fever in humans sometimes is accompanied by several other critical extraintestinal complications related to the central nervous system, cardiovascular system, pulmonary system, and hepatobiliary system. Salmonella Pathogenicity Island-1 and Salmonella Pathogenicity Island-2 are the two genomic segments containing genes encoding virulent factors that regulate its invasion and systemic pathogenesis. This Review aims to shed light on a comparative analysis of the virulence and pathogenesis of the typhoidal and nontyphoidal serovars of S. enterica.

Quercitrin Is a Novel Inhibitor of Salmonella enterica Serovar Typhimurium Type III Secretion System

The purpose was to screen type III secretory system (T3SS) inhibitors of Salmonella enterica serovar Typhimurium (S. Typhimurium) from natural compounds. The pharmacological activities and action mechanisms of candidate compounds in vivo and in vitro were systematically studied and analyzed. Using a SipA-β-lactamase fusion reporting system, we found that quercitrin significantly blocked the translocation of SipA into eukaryotic host cells without affecting the growth of bacteria. Adhesion and invasion assay showed that quercitrin inhibited S. Typhimurium invasion into host cells and reduced S. Typhimurium mediated host cell damage. β-galactosidase activity detection and Western blot analysis showed that quercitrin significantly inhibited the expression of SPI-1 genes (hilA and sopA) and effectors (SipA and SipC). The results of animal experiments showed that quercitrin significantly reduced colony colonization and alleviated the cecum pathological injury of the infected mice. Small molecule inhibitor quercitrin directly inhibited the function of T3SS and provided a potential antibiotic alternative against S. Typhimurium infection. Importance: T3SS plays a crucial role in the bacterial invasion and pathogenesis of S. Typhimurium. Compared with conventional antibiotics, small molecules could inhibit the virulence factors represented by S. Typhimurium T3SS. They have less pressure on bacterial vitality and a lower probability of producing drug resistance. Our results provide strong evidence for the development of novel inhibitors against S. Typhimurium infection.

Whole-Genome Subtyping Reveals Population Structure and Host Adaptation of Salmonella Typhimurium from Wild Birds

Within-host evolution of bacterial pathogens can lead to host-associated variants of the same species or serovar. Identification and characterization of closely related variants from diverse host species are crucial to public health and host-pathogen adaptation research. However, the work remained largely underexplored at a strain level until the advent of whole-genome sequencing (WGS). Here, we performed WGS-based subtyping and analyses of Salmonella enterica serovar Typhimurium (n = 787) from different wild birds across 18 countries over a 75-year period. We revealed seven avian host-associated S. Typhimurium variants/lineages. These lineages emerged globally over short timescales and presented genetic features distinct from S. Typhimurium lineages circulating among humans and domestic animals. We further showed that, in terms of virulence, host adaptation of these variants was driven by genome degradation. Our results provide a snapshot of the population structure and genetic diversity of S. Typhimurium within avian hosts. We also demonstrate the value of WGS-based subtyping and analyses in unravelling closely related variants at the strain level.

Using bacterial pan-genome-based feature selection approach to improve the prediction of minimum inhibitory concentration (MIC)

Background: Predicting the resistance profiles of antimicrobial resistance (AMR) pathogens is becoming more and more important in treating infectious diseases. Various attempts have been made to build machine learning models to classify resistant or susceptible pathogens based on either known antimicrobial resistance genes or the entire gene set. However, the phenotypic annotations are translated from minimum inhibitory concentration (MIC), which is the lowest concentration of antibiotic drugs in inhibiting certain pathogenic strains. Since the MIC breakpoints that classify a strain to be resistant or susceptible to specific antibiotic drug may be revised by governing institutes, we refrained from translating these MIC values into the categories "susceptible" or "resistant" but instead attempted to predict the MIC values using machine learning approaches. Results: By applying a machine learning feature selection approach on a Salmonella enterica pan-genome, in which the protein sequences were clustered to identify highly similar gene families, we showed that the selected features (genes) performed better than known AMR genes, and that models built on the selected genes achieved very accurate MIC prediction. Functional analysis revealed that about half of the selected genes were annotated as hypothetical proteins (i.e., with unknown functional roles), and that only a small portion of known AMR genes were among the selected genes, indicating that applying feature selection on the entire gene set has the potential of uncovering novel genes that may be associated with and may contribute to pathogenic antimicrobial resistances. Conclusion: The application of the pan-genome-based machine learning approach was indeed capable of predicting MIC values with very high accuracy. The feature selection process may also identify novel AMR genes for inferring bacterial antimicrobial resistance phenotypes.

The ever-increasing necessity of mass spectrometry in dissecting protein post-translational modifications catalyzed by bacterial effectors

Protein post-translational modifications (PTMs), such as ADP-ribosylation and phosphorylation, regulate multiple fundamental biological processes in cells. During bacterial infection, effector proteins are delivered into host cells through dedicated bacterial secretion systems and can modulate important cellular pathways by covalently modifying their host targets. These strategies enable intruding bacteria to subvert various host processes, thereby promoting their own survival and proliferation. Despite rapid expansion of our understanding of effector-mediated PTMs in host cells, analytical measurements of these molecular events still pose significant challenges in the study of host-pathogen interactions. Nevertheless, with major technical breakthroughs in the last two decades, mass spectrometry (MS) has evolved to be a valuable tool for detecting protein PTMs and mapping modification sites. Additionally, large-scale PTM profiling, facilitated by different enrichment strategies prior to MS analysis, allows high-throughput screening of host enzymatic substrates of bacterial effectors. In this review, we summarize the advances in the studies of two representative PTMs (i.e., ADP-ribosylation and phosphorylation) catalyzed by bacterial effectors during infection. Importantly, we will discuss the ever-increasing role of MS in understanding these molecular events and how the latest MS-based tools can aid in future studies of this booming area of pathogenic bacteria-host interactions.

Pathogen detection in RNA-seq data with Pathonoia

BACKGROUND

Bacterial and viral infections may cause or exacerbate various human diseases and to detect microbes in tissue, one method of choice is RNA sequencing. The detection of specific microbes using RNA sequencing offers good sensitivity and specificity, but untargeted approaches suffer from high false positive rates and a lack of sensitivity for lowly abundant organisms.

RESULTS

We introduce Pathonoia, an algorithm that detects viruses and bacteria in RNA sequencing data with high precision and recall. Pathonoia first applies an established k-mer based method for species identification and then aggregates this evidence over all reads in a sample. In addition, we provide an easy-to-use analysis framework that highlights potential microbe-host interactions by correlating the microbial to the host gene expression. Pathonoia outperforms state-of-the-art methods in microbial detection specificity, both on in silico and real datasets.

CONCLUSION

Two case studies in human liver and brain show how Pathonoia can support novel hypotheses on microbial infection exacerbating disease. The Python package for Pathonoia sample analysis and a guided analysis Jupyter notebook for bulk RNAseq datasets are available on GitHub.

High frequency of non-susceptibility to ciprofloxacin in nontyphoid Salmonella recovered from Brazilian broiler chicken

1. This study evaluated the minimal inhibitory concentration (MIC) of ciprofloxacin and the presence of plasmid-mediated quinolone resistance (PMQR) mechanisms in 97 nontyphoidal Salmonella spp. isolated from broilers and carcases from three different regions in Brazil. The presence of mutations in quinolone resistance determination regions (QRDRS) was investigated in the ciprofloxacin-resistant strain by DNA sequencing.2. Most of the Salmonella spp. (85.6%) had intermediate resistance to ciprofloxacin and only one isolate was resistant. MIC breakpoints ranged from ≤0.03 to 1 µg/ml and 67.0% of the strains had a MIC of 0.25 µg/ml (n=65). Thirteen strains (13.4%) were susceptible to ciprofloxacin with MIC ≤0.06 µg/ml. The qnrB gene was detected in eight isolates with intermediate resistance and in two susceptible strains. The other PMQR genes, qnrA, qnrC, qnrD, qnrS, qnrVC, aac(6')-Ib, qepA, oqxAB and mutations in QRDR were not detected in any strain.3. There was a high frequency of ciprofloxacin intermediate resistant Salmonella from broiler and broiler carcases from Brazil. The presence of these strains in poultry and derived products poses a risk to public health.

Tracking soil resistance and virulence genes in rice-crayfish co-culture systems across China

Rice-crayfish co-culture (RC) has been widely and rapidly promoted as a sustainable agricultural system in many countries. The accumulation of crayfish residues could enhance soil organic matters; however, impacts of this integrated farming model on the dissemination and pathogenicity of resistance and virulence genes remain poorly understood. Here, we characterized antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence factor genes (VFGs) using metagenomic methods in paired RC and rice monoculture (RM) systems across China. The RC model did not increase the abundance of soil ARGs, BRGs, MRGs, or VFGs in comparison to the RM model, but selectively enriched 35 subtypes of these potential resistance and virulence genes. Network analysis revealed that resistance and virulence genes had a higher number of connections with mobile genetic elements (MGEs) in the RC system than that in the RM system, suggesting a higher horizontal transfer potential of these genes. Moreover, the RC model had a higher abundance of human opportunistic pathogens such as Salmonella enterica, Vibrio cholerae, and Shigella dysenteriae which were potential hosts of VFGs such as phoP, fleS, and gspE, suggesting a potential threat to human health. We further unraveled that stochastic process was the main driver of the assembly of resistance and virulence genes in the RC system. The abundance of ARGs and VFGs were primarily associated with microbial community compositions, while the abundance of BRGs and MRGs were mainly associated with that of MGEs. Taken together, our results suggest that the RC model has potential to cause the dissemination and pathogenicity of resistance and virulence genes, which has important implications for the control of soil-borne biological risks and the strategic management of sustainable agriculture.

Poria cocos Polysaccharide Ameliorated Antibiotic-Associated Diarrhea in Mice via Regulating the Homeostasis of the Gut Microbiota and Intestinal Mucosal Barrier

Poria cocos polysaccharides (PCP) have been validated for several biological activities, including antitumor, anti-inflammatory, antioxidant, immunomodulatory, hepatoprotective and modulation on gut microbiota. In this research, we aim to demonstrate the potential prebiotic effects and the therapeutic efficacies of PCP in the treatment of antibiotic-associated diarrhea (AAD), and confirm the beneficial effects of PCP on gut dysbiosis. Antibiotic-associated diarrhea mice models were established by treating them with broad-spectrum antibiotics in drinking water for seven days. Mice in two groups treated with probiotics and polysaccharide were given Bifico capsules (4.2 g/kg/d) and PCP (250 mg/kg/d) for seven days using intragastric gavage, respectively. To observe the regulatory effects of PCP on gut microbiota and intestinal mucosal barrier, we conducted the following experiments: intestinal flora analysis (16S rDNA sequencing), histology (H&E staining) and tight junction proteins (immunofluorescence staining). The levels of mRNA expression of receptors associated with inflammation and gut metabolism were assessed by real-time reverse transcription-polymerase chain reaction (RT-PCR). The study revealed that PCP can comprehensively improve the clinical symptoms of AAD mice, including fecal traits, mental state, hair quality, etc., similar to the effect of probiotics. Based on histology observation, PCP significantly improved the substantial structure of the intestine of AAD mice by increasing the expression levels of colonic tight junction protein zonula-occludens 1 (ZO-1) and its mRNA. Moreover, PCP not only increased the abundance of gut microbiota, but also increased the diversity of gut microbiota in AAD mice, including alpha diversity and beta diversity. Further analysis found that PCP can modulate seven characteristic species of intestinal flora in AAD mice, including Parabacteroides_distasonis, Akkermansia_muciniphila, Clostridium_saccharolyticum, Ruminoc-occus_gnavus, Lactobacillus_salivarius, Salmonella_enterica and Mucispirillum_schaedleri. Finally, enrichment analysis predicted that PCP may affect intestinal mucosal barrier function, host immune response and metabolic function by regulating the microbiota. RT-PCR experiments showed that PCP can participate in immunomodulatory and modulation on metabolic by regulating the mRNA expression of forkhead-box protein 3 (FOXP3) and G protein-coupled receptor 41 (GPR41). These results indicated that Poria cocos polysaccharide may ameliorate antibiotic-associated diarrhea in mice by regulating the homeostasis of the gut microbiota and intestinal mucosal barrier. In addition, polysaccharide-derived changes in intestinal microbiota were involved in the immunomodulatory activities and modulation of the metabolism.

Pal Affects the Proliferation in Macrophages and Virulence of Brucella, and as Mucosal Adjuvants, Provides an Effective Protection to Mice Against Salmonella Enteritidis

The purpose of this study was to elucidate the roles of peptidoglycan-associated lipoprotein (Pal protein) in the proliferation of Brucella in macrophage and bacterial virulence, and to evaluate the immune effect of Pal protein to Salmonella enteritidis. Murine macrophage-like cell line Raw264.7 was stimulated by recombinant Pal protein, and the expression of TNF-α and IFN-γ were up-regulated, but not it of IL-1β and IL-6. The macrophages infection and in vitro simulated stress assays showed that deletion of pal gene reduced the proliferation of Brucella in macrophages, the survival in acidic, oxidative and polymyxin B-contained environment. The mice infection assay showed that mice challenged with the pal mutant strain were found to have more severe splenomegaly, but less bacterial load. After oral immunization of mice, Pal protein induced a higher titer of mucosal and humoral antibody (IgA and IgG) against heat-killed Salmonella enteritidis, and a stronger Th1 cellular immune response. The challengte experiments showed Pal protein elevated the survival rate and reduced the bacterial load of spleens in immunized mice. In conclusion, our results revealed the important roles of pal gene in Brucella virulence, and Pal protein was a potentially valuable adjuvant against mucosal pathogens, such as Salmonella enteritidis.

A Review of Preclinical Tools to Validate Anti-Diarrheal Agents

BACKGROUND

Since their inception, preclinical experimental models have played an important role in investigating and characterizing disease pathogenesis. These in vivo, ex vivo, and in vitro preclinical tests also aid in identifying targets, evaluating potential therapeutic drugs, and validating treatment protocols.

INTRODUCTION

Diarrhea is a leading cause of mortality and morbidity, particularly among children in developing countries, and it represents a huge health-care challenge on a global scale. Due to its chronic manifestations, alternative anti-diarrheal medications must be tested and developed because of the undesirable side effects of currently existing anti-diarrheal drugs.

METHODS

Several online databases, including Science Direct, PubMed, Web of Science, Google Scholar and Scopus, were used in the literature search. The datasets were searched for entries of studies up to May, 2022.

RESULTS

The exhaustive literature study provides a large number of in vivo, in vitro and ex vivo models, which have been used for evaluating the mechanism of the anti-diarrheal effect of drugs in chemically-, pathogen-, disease-induced animal models of diarrhea. The advances and challenges of each model were also addressed in this review.

CONCLUSION

This review encompasses diverse strategies for screening drugs with anti-diarrheal effects and covers a wide range of pathophysiological and molecular mechanisms linked to diarrhea, with a particular emphasis on the challenges of evaluating and predictively validating these experimental models in preclinical studies. This could also help researchers find a new medicine to treat diabetes more effectively and with fewer adverse effects.

Surface-enhanced Raman spectroscopy for characterization of filtrate portions of blood serum samples of typhoid patients

BACKGROUND

Surface-enhanced Raman spectroscopy (SERS) is explored to design a rapid screening method for the characterization and diagnosis of typhoid fever by employing filtrate fractions of blood serum samples obtained by centrifugal filtration with 50 KDa filters.

OBJECTIVES

The purpose of this study, to separate the filtrate portions of blood serum samples in this way contain proteins smaller than 50 kDa and removal of bigger size protein which allows to acquire the SERS spectral features of smaller proteins more effectively which are probably associated with typhoid disease. Disease caused by Salmonella typhi diagnose more effectively by using surface-enhanced Raman spectroscopy (SERS) and multivariate data analysis tools.

METHODS

SERS was used as a diagnostic tool for typhoid fever by comparison between healthy and diseased samples. For this purpose, all the samples were analyzed by comparing their SERS spectral features. Over the spectral range of 400-1800cm^-1, multivariate data analysis techniques such as Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) are applied to diagnose and differentiate different filtrate fractions of blood serum samples of patients of typhoid fever and healthy ones.

RESULTS

By comparing SERS spectra of healthy filtrate with that of filtrate of typhoid sample, the SERS spectral features associated with disease development are identified including PCA is found to be efficient for the qualitative differentiation of all of the samples analyzed. Moreover, PLS-DA successfully identified and classified healthy and typhoid positive blood serum samples with 97 % accuracy, 99 % specificity, 91 % sensitivity and 0.78 area under the receiver operating characteristic (AUROC) curve.

CONCLUSIONS

Surface enhanced Raman spectroscopy using silver nanoparticles SERS substrate, is found to be useful technique for the quick identification and evaluation of filtrate fractions of the blood serum samples of healthy and typhoid samples for disease diagnosis.

Symbiotic bacteria stabilize the intestinal environment by producing phenylpropanoids

Salmonella enterica serovar Enteritidis (S. Enteritidis) can colonize in the intestinal tract of chickens and transmit to humans. In order to decrypt the mechanism of avian resistance to S. Enteritidis, we utilized two China local chicken breeds to generate the reciprocal crosses (the Cross and the Reverse-cross). The two lines of hybrids were orally inoculated with S. Enteritidis at 2-day old and sampled at 3 days post-inoculation. Along the analysis direction of multi-omics, differential metabolites, functional pathways and correlated microbes, we found that 12 species of microbes thrived upon S. Enteritidis challenge and probably contributed to the intestinal stability in the Cross by enhancing the production of phenylpropanoids. Our findings can help to understand the symbiotic and resistant mechanisms derived from the intestinal microbiota.

Antimicrobial Resistance of Salmonella Strains Isolated from Human, Wild Boar, and Environmental Samples in 2018-2020 in the Northwest of Italy

Antimicrobial resistance is one of the most challenging public health problems worldwide, and integrated surveillance is a key aspect in a One Health control strategy. Additionally, Salmonella is the second most common zoonosis in Europe. We aimed to investigate the circulation of Salmonella strains and their related antimicrobial resistance in human, environmental, and wild boar samples from the northwest of Italy, from 2018 to 2020, to obtain a more comprehensive epidemiological picture. Salmonella Typhimurium 1,4,[5],12:i:-, S. Veneziana and S. Newport were the most common serotypes occurring in humans, the environment, and wild boar, respectively. Antimicrobial resistance was rather common in Salmonella isolates, with those from human displaying the highest degree of resistance against sulfadiazine−sulfamerazine−sulfamethazine (>90% of resistance). Moreover, resistance against azithromycin were exclusively observed in environmental samples, while only 7.7% (95% CI = 1.6−20.8) of wild boar isolates experienced resistance against trimethoprim−sulfamethoxazole. Multidrug resistance concurrently involved up to seven antimicrobial classes in human isolates, including third-generation cephalosporins and fluoroquinolones. Salmonella Typhimurium in humans and serotypes Goldcoast and Rissen from environmental sources showed the highest levels of resistance. This study shows diverse antimicrobial resistance patterns in Salmonella strains isolated from different sources and gives a broad picture of antimicrobial resistance spread in wild animals, humans, and the environment.

Metagenomic analysis of diarrheal stools in Kolkata, India, indicates the possibility of subclinical infection of Vibrio cholerae O1

We examined the stools of 23 patients in Kolkata, who were diagnosed as cholera patients because Vibrio cholerae O1 was detected from their stools by culturing methods, and further explored by metagenomic sequencing analysis. Subsequently, the presence of the gene encoding A subunit of cholera toxin (ctxA) and the cholera toxin (CT) level in these stool samples were examined. ctxA was examined by both metagenomic sequencing analysis and polymerase chain reaction. In these examinations, two samples did not show positive in any of these tests. The metagenomic analysis showed that the genes for Streptococcus pneumoniae and Salmonella enterica were present in the stools of these two patients, respectively. Therefore, these two patients were not considered to have diarrhea due to V. cholerae infection. From these results, we predicted that some Kolkata residents harbor a small number of V. cholerae in their intestines as a form of subclinical infection with V. cholerae. Next, we analyzed the stool samples of 22 diarrhea patients from which V. cholerae was not isolated. The results showed that 3 of the patients seemed to have subclinical infection of V. cholerae based on the amount of the genes. These results indicated that subclinical infections with V. cholerae O1 occur in Kolkata.

Endophytic Fungi Associated with Aquilaria sinensis (Agarwood) from China Show Antagonism against Bacterial and Fungal Pathogens

Agarwood is the most expensive non-construction wood product in the world. As a therapeutic agent, agarwood can cure some diseases, but few studies have been carried out on the antagonistic abilities of endophytic fungi associated with agarwood. Agarwood is mainly found in the genus Aquiaria. The objectives of this study are to understand the antimicrobial activities and their potential as biocontrol agents of the endophytic fungi of Aquilaria sinensis. First, fresh samples of A. sinensis were collected from Yunnan and Guangdong Provinces in 2020-2021, and the endophytic fungi were isolated and identified to genus level based on the phylogenetic analyses of the Internal Transcribed Spacer (ITS) region. In this bioassay, 47 endophytic strains were selected to check their bioactivities against three bacterial pathogens viz. Erwinia amylovora, Pseudomonas syringae, and Salmonella enterica; and three fungal pathogens viz. Alternaria alternata, Botrytis cinerea, and Penicillium digitatum. The antibiosis test was carried out by the dual culture assay (10 days), and among the 47 strains selected, 40 strains belong to 18 genera viz. Alternaria, Annulohypoxylon, Aspergillus, Botryosphaeria, Colletotrichum, Corynespora, Curvularia, Daldinia, Diaporthe, Fusarium, Lasiodiplodia, Neofusicoccum, Neopestalotiopsis, Nigrospora, Paracamarosporium, Pseudopithomyces, Trichoderma, Trichosporon and one strain belongs to Xylariaceae had antimicrobial activities. In particular, Lasiodiplodia sp. (YNA-D3) showed the inhibition of all the bacterial and fungal pathogens with a significant inhibition rate. In addition, the strains viz; Curvularia sp. (GDA-3A9), Diaporthe sp. (GDA-2A1), Lasiodiplodia sp. (YNA-D3), Neofusicoccum sp. (YNA-1C3), Nigrospora sp. (GDA-4C1), and Trichoderma sp. (YNA-1C1) showed significant antimicrobial activities and are considered worthy of further studies to identify individual fungal species and their bioactive compounds. This study enriches the diversity of endophytic fungi associated with agarwood, and their potential antagonistic effects against bacterial and fungal pathogens.

Screening and evaluation of lactic acid bacteria with probiotic potential from local Holstein raw milk

There are massive bacteria in the raw milk, especially the lactic acid bacteria (LABs), which have been considered probiotics in humans and animals for a long time. Novel probiotics are still urgently needed because of the rapid development of the probiotic industry. To obtain new LABs with high probiotic potential, we obtained 26 LAB isolates, named L1 ~ L26, from local Holstein raw milk collected from a farm whose milk had never been used for LAB isolation. We identified them at the species level by biochemical and 16S rDNA sequencing methods. Their antagonistic activities against four target pathogens (Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 25923, Pseudomonas aeruginosa PAO1, and Salmonella enterica H9812), co-aggregative ability with these target pathogens, survivability in the simulated gastrointestinal tract conditions and phenol, auto-aggregation and hydrophobicity, hemolytic activity, and antibiotic susceptibility, were evaluated in vitro. Five Lactiplantibacillus plantarum isolates (L5, L14, L17, L19, and L20) showed more promising probiotic potential than others. Specifically, these five isolates conglutinated with and inhibited all the target pathogens, and survived in the simulated gastric juice (92.55 ~ 99.69%), intestinal juice (76.18 ~ 83.39%), and 0.4% phenol (76.95 ~ 88.91%); possessed considerable auto-aggregation (83.91 ~ 90.33% at 24 h) and hydrophobicity (79.32 ~ 92.70%); and were non-hemolytic, sensitive to kinds of common antimicrobials. Our findings demonstrated that these five isolates could be preliminarily determined as probiotic candidates because they have better probiotic potential than those previously reported. Again, this study highlighted the potential of raw milk for probiotic isolating and screening and provided the probiotic industry with five new LAB candidates.

Dysregulation of intestinal flora: excess prepackaged soluble fibers damage the mucus layer and induce intestinal inflammation

Soluble fiber is commonly used as a dietary supplement to improve intestinal flora, and many prepackaged products are sold in the market. However, whether these prepared soluble fibers are harmless for intestinal flora has not been systematically evaluated. Here, we assessed the dose-effect of fructooligosaccharides (FOSs) on obesity and intestinal flora using a mouse model. Gavage of low- and medium-dose FOS improved the microbiota in high-fat diet fed mice, but high-dose FOS leads to intestinal flatulence, diarrhea and flora disorders, including an increase in Akkermansia muciniphila and Clostridium difficile, which disrupt the mucus barrier and cause intestinal inflammation. Besides, a high dose of xylooligosaccharide by gavage induces symptoms similar to those of FOS in mice. These adverse effects can be alleviated by regulating intestinal flora. In addition, we experimentally proved that supplementary probiotics protect against the negative effects of FOS in obese mice. Therefore, prepackaged soluble fiber supplements need to be taken with caution, and excessive consumption of soluble fibers results in intestinal dysfunction and even induces intestinal inflammation. Combining probiotics and soluble fiber can be considered if necessary.

Enterobacterial LPS-inducible LINC00152 is regulated by histone lactylation and promotes cancer cells invasion and migration

Gut microbes participate in pathogenesis by interacting with the host genome through epigenetic mechanisms, such as long non-coding RNAs. However, the mechanisms by which the microbiota induce expression alteration of long non-coding RNAs remains unclear. Here, we quantified the transcriptome alteration of human colon cell lines after being infected by a common enteric pathogen Salmonella typhimurium SL1344. We observed a widespread lncRNAs expression alteration. Among them, the elevated expression of LINC00152 was verified and proved to be induced by enteric bacteria-derived lipopolysaccharide (LPS). The inducible LINC00152 were found to inhibit Salmonella invasion and inflammation response. LINC00152 was overexpressed in tumors of the clinical CRC samples compared with adjacent normal tissues. Accordingly, we also demonstrated that overexpression of LINC00152 promoted the migration and invasion of colorectal cancer cells. Consistently, we observed an increased abundance of gram-negative bacteria and LPS in tumors tissue. Taken together, the above data implicated that enriched gram-negative bacteria in tumor tissue might promote tumor growth through modulating the expression of LINC00152. Furthermore, we demonstrated that LPS upregulated the expression of LINC00152 by introducing histone lactylation on its promoter and decreasing the binding efficiency of the repressor, YY1, to it. Our results provide new insights into how enterobacteria affect host epigenetics in human disease.

Limosilactobacillus reuteri SLZX19-12 Protects the Colon from Infection by Enhancing Stability of the Gut Microbiota and Barrier Integrity and Reducing Inflammation

Limosilactobacillus reuteri plays an important role in regulating intestinal functions and maintaining barrier integrity in animals. In this study, Limosilactobacillus reuteri strain SLZX19-12 was isolated from the fecal microbiota of Tibetan pigs, and it was found that this strain is sensitive to common antibiotics and has strong resistance to stress. Upon being administered by gavage at different doses, including low, medium, and high doses, for 14 days, Limosilactobacillus reuteri SLZX19-12 may enhance the intestinal barrier. After administration of a high dose of SLZX19-12, mice were challenged with Salmonella enterica serovar Typhimurium SL1344. Infection with Salmonella Typhimurium SL1344 led to disordered colonic microbiotas, colonic inflammation through the S100A8/S100A9-NF-κB pathway and potential apoptosis, and translocation of pathogens to parenteral visceral organs in mice. However, the mice pretreated with Limosilactobacillus reuteri SLZX19-12 showed lower loads of Salmonella in visceral organs, less colonic inflammation, and higher barrier integrity. More importantly, the administration of strain SLZX19-12 resulted in a more stable microbiota structure of the colon, in which the abundance of Alloprevotella was greatly enhanced. Therefore, this study suggests that Limosilactobacillus reuteri SLZX19-12 can protect the colon from infection by enhancing the stability of gut microbiota and barrier integrity and reducing inflammation. IMPORTANCE The use of antibiotics to treat bacterial infections leads to a series of side effects. As an alternative method, the biocontrol strategy, which uses probiotics to suppress pathogens, is considered a potential way to deal with bacterial infections in gut. However, there are few probiotics that are currently safe and can protect against infection. In this study, Limosilactobacillus reuteri strain SLZX19-12 was obtained from Tibetan pigs, which have higher resistance to infection. This strain is sensitive to conventional antibiotics, secretes a wide spectrum of enzymes, and also promotes the intestinal barrier function in mice. In addition, Limosilactobacillus reuteri SLZX19-12 can promote the stability of the gut microbiota to avoid or alleviate the occurrence or development of foodborne infections.

Prevalence and whole-genome sequencing analysis of Salmonella reveal its spread along the duck production chain

Salmonella is the most important foodborne pathogen in poultry production systems and can infect humans via consumption of contaminated food. Ducks, an important waterfowl widely raised in China, are also a vehicle that transmits Salmonella through the food supply chain. In this study, 701 samples were collected from each production stage of the duck production chain. Salmonella was isolated and identified, and the isolates were tested for drug sensitivity and molecular typing based on whole genome sequencing (WGS) to explore the prevalence of Salmonella in the duck production chain. Altogether, a total of 180 Salmonella isolates (25.7%) were obtained from the duck production chain, 82 (35.7%) isolates were from hatchery samples, followed by 64 (29.2%) from market samples, 17 (23.6%) from farm samples, and 17 (9.4%) from slaughterhouse samples. All isolates were divided into 9 serotypes, among which S. Typhimurium, S. Anatum, and S. Enteritidis were the dominant serotypes. The S. Typhimurium was distributed in various production stages in the duck production chain. Among the 16 antibiotics, selected 60 isolates were only resistant to NAL, indicating that resistance of Salmonella in the duck production chain was low. WGS phylogenetic relationship results based on core-genome SNPs showed that S. Typhimurium can spread across geographic regions and along between different stages of the duck production chain, eventually reaching the market where it is a potential threat to consumer health. This study explored the prevalence of Salmonella in the duck production chain which will provide data support for proposing some interventions to control Salmonella.

Behavior and Immune Response of Conventional and Slow-Growing Broilers to Salmonella Typhimurium

Fast growth rate in broiler chickens comes with welfare concerns and the contribution of growth rate to pathogen resistance and sickness behavior is relatively unknown. The objective of this study was to evaluate physiological and behavioral responses of conventional (CONV) and slow-growing (SG) male broilers challenged with Salmonella Typhimurium. CONV (n = 156) and SG (n = 156) chicks were raised in a pen with wood litter shavings until day 7 of age, when birds were transferred to 24 isolators (n = 11 chicks/isolator). On day 14 of age, half of the birds (n = 12 isolators) were challenged with S. Typhimurium (ST) and the other half (n = 12 isolators) received a control (C). On days 7, 13, 17, 21, and 24, body weight was recorded, and blood, jejunum and ileum sections were collected from 2 birds/isolator (n = 48 birds/sampling) to measure plasma IgA and IgG and intestinal histomorphology, respectively. On days 12, 16, 21, and 23, video was recorded to evaluate bird postures (sitting, standing, or locomoting) and behaviors (eating, drinking, preening, stretching, sham foraging, allopreening, and aggression). CONV birds were 70 g heavier (p = 0.03) on day 21 and 140 g heavier (p = 0.007) on day 24 than SG. On day 7, CONV jejunum villus height and crypt depth were 22 and 7 μm greater (p ≤ 0.001), respectively, than SG. On day 24, ST ileum villus height was 95 μm shorter (p = 0.009) than C. IgA increased after day 17 for all birds and at day 21, CONV IgA was greater (p = 0.01) than SG. Although SG IgG was 344 μg/ml greater (p = 0.05) than CONV on day 7, CONV IgG increased with age (p < 0.0001) to greater (p ≤ 0.03) concentrations than SG on day 21 and day 24 by 689 μg/ml and 1,474 μg/ml, respectively, while SG IgG remained at similar concentrations after day 13. Generally, a greater proportion of birds sham foraged as they aged (p < 0.0001). A greater proportion of CONV tended to sit (p = 0.09) and fewer locomoted (p < 0.0001) than SG as they aged. The results illustrate conventional and slow-growing broilers differ in their behavior, immunity, and response to Salmonella.

Catalytic antimicrobial therapy using nanozymes

Nanozymes are nanomaterials with enzyme-like characteristics, which catalyze the conversion of enzyme substrates and follow enzymatic kinetics under physiological conditions. As a new generation of artificial enzymes, nanozymes provide alternative approaches for those upon enzymatic catalysis. Compared with natural enzymes, nanozymes have the advantages of simple preparation, good stability and low cost, which makes nanozymes promising for application in many fields, such as antimicrobial infection treatment. Many studies have reported that nanozymes are capable of killing a number of pathogenic bacteria with resistance, fungi as well as viruses, and have shown great curative effects for diseases caused by these pathogens. Herein, we summarize the application of nanozymes for antibacterial, antiviral, and antifungal therapies and outline the issues needing resolution in the future. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease.

The Leaf Microbiome of Tobacco Plants across Eight Chinese Provinces

Leaf microorganism communities play significant roles in the process of plant growth, but the microbiome profiling of crop leaves is still a relatively new research area. Here, we used 16S rDNA sequencing to profile the microbiomes of 78 primary dried tobacco leaf samples from 26 locations in eight Chinese provinces. Our analyses revealed that the national leaf microbial communities contain 4473 operational taxonomic units (OTU) representing 1234 species, but there is a small, national core microbiome with only 14 OTU representing nine species. The function of this core microbiome is related to processes including nitrogen fixation, detoxification of diverse pollutants, and heavy-metal reduction. The leaf microorganism communities are obviously affected by local environments but did not exhibit obvious relationships to single ecological factors (e.g., temperature, precipitation). Our findings enhance the understanding of microbial diversity of tobacco leaves, which could be utilized for a variety of bioprocess, agricultural, and environmental detoxification applications.

Isolation and Sequencing of the First Case of Symptomatic MDR Salmonella enterica Subsp. Enterica ST40 in Human in Italy, July 2020

Strains of drug-resistant nontyphoidal Salmonella spp. are emerging in livestock worldwide. We describe the first case of symptomatic multidrug-resistant (MDR) Salmonella enterica subsp. enterica in human and the genetic mechanisms at the basis of its antibiotic resistance. To control outbreaks, rapid identification and sequencing are necessary. Proactive research and notification are needed to evaluate the routes of transmission from livestock to humans and risk-management strategies of MDR Salmonella strains.

PRODORIC: state-of-the-art database of prokaryotic gene regulation

PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the PRODORIC website. Missing input and output options from the original Virtual Footprint were added again for position weight matrix pattern-based searches. The whole PRODORIC dataset was reannotated. Every transcription factor binding site was re-evaluated to increase the overall database quality. During this process, additional parameters, like bound effectors, regulation type and different types of experimental evidence have been added for every transcription factor. Additionally, 109 new transcription factors and 6 new organisms have been added. PRODORIC is publicly available at https://www.prodoric.de.