The global burden and epidemiology of invasive non-typhoidal Salmonella infections

First report of third-generation cephalosporin-resistant clinical isolate of Salmonella Bareilly ST203 harbouring plasmid-mediated AmpC β-lactamase CMY6 from India: Genome characteristics and transmissibility

Non-typhoidal Salmonella (NTS) infections are a major public health concern in India because of inadequate knowledge of antimicrobial resistance, limiting therapeutic options. The study aimed to characterize and analyse the genome of a 3rd-generation cephalosporins (3GCs)-resistant clinical isolate of Salmonella Bareilly-harbouring plasmid-mediated AmpC (pAmpC) CMY-6. Identification, antibiotic susceptibility and Whole Genome Sequencing (WGS)-based analysis were performed. Transmissibility, replicon types of blaCMY-6-harbouring plasmid were evaluated. S. Bareilly ST203 (Clonal-Complex 206.2) was isolated from clinical specimen of a paediatric patient and was found to be multidrug-resistant with resistance to 3rd generation cephalosporins, fluoroquinolone and aminoglycosides. WGS revealed pAmpC blaCMY-6 on conjugative IncC plasmid (158,385 kb) which successfully transferred into the transconjugant with other resistance determinants (blaTEM-1A, armA, aac(6')-Ib-cr, sul1), showed higher MICs for 3GCs. Downstream regions of blaCMY-6 include blc (lipocalin), sugE (efflux protein) and truncated ecnR (entericidin R) followed by other resistance genes. Presence of ISEcp1 in the genome facilitated the transfer of blaCMY-6. Several efflux pump genes, two complete CRISPR arrays and intact phage sequences were also detected. Virulence factors associated with Salmonella Pathogenicity Islands SPI-1/SPI-2/SP-3 and their effectors indicated the virulence potential of this strain. To the best of our knowledge, genome of a 3GCs-resistant clinical isolate of S. Bareilly-harbouring pAmpC blaCMY-6 was reported and analysed for the first time in this study. S. Bareilly was found to cause outbreaks in earlier reports but lower resistance was reported in this serovar compared to other NTS. As infections by NTS are concerning, early detection of such strains is of utmost importance.

Immunoinformatic approach for designing a multi-epitope vaccine against non-typhoidal salmonellosis using starvation-stress response proteins from Salmonella Oranienburg

Non-typhoidal Salmonella is responsible for gastrointestinal illnesses worldwide. Therefore, it is important to implement effective therapeutic interventions for preventing these diseases. Vaccines have proven highly efficacious in the treatment and prevention of several illnesses. Nevertheless, there is currently no authorized vaccine available for non-typhoidal salmonellosis. This study aimed to employ in silico techniques to develop a multi-epitope vaccine targeting non-typhoidal salmonellosis. Specifically, we focused on proteins associated with the starvation stress response (SSR) in Salmonella Oranienburg. The presence of these proteins is essential for the survival and disease of the host organism. The vaccine sequence was constructed utilizing B-cell and T-cell epitopes. Linkers, adjuvants and PADRE sequences were used to establish connections between epitopes. The vaccine exhibited no allergenicity, toxigenicity and a significantly high antigenicity score. Docking analysis conducted between the designed vaccine and the TLR-1, TLR-2 and TLR-4 receptors demonstrated favorable interactions and the potential to activate these receptors. In addition, it was found through immunological simulation testing that the vaccine elicits a robust immune response. The use of these proteins in the construction of a multi-epitope vaccine shows potential in terms of both safety and immunogenicity.

Landscape analysis of invasive non-typhoidal salmonella (iNTS) disease and iNTS vaccine use case and demand: Report of a WHO expert consultation

Invasive disease caused by non-typhoidal Salmonella serovars (iNTS) occurs with increased risk in the presence of other comorbidities such as malaria, HIV, malnutrition, anaemia and sickle cell disease. While infection with non-typhoidal (NTS) serovars often results in self-limited enterocolitis in high-income settings, in sub-Saharan Africa (SSA) where these risk-comorbidities are common, an invasive (iNTS) disease phenotype is seen, associated with up to 20 % case-fatality ratio, and antimicrobial resistance is both significant and growing. The need to evaluate the potential public health value of vaccines against iNTS disease is increasingly being recognized, and several candidate vaccines are in early development. A better understanding of the global burden and epidemiology of iNTS disease, as well as the potential public health and socio-economic benefits that iNTS vaccines may offer is fundamental to support and justify the investments in vaccine development. In addition, the pathways for licensure, policy recommendations and eventual vaccine prioritization and use in low- and middle-income countries (LMICs) need to be defined. Here, we report on the proceedings of an expert consultation held on 29 November - 1 December 2021 as part of an overall project to develop a Full Value of Vaccines Assessment (FVVA) for iNTS vaccines and in addition to more recent iNTS vaccine developments. Experts at the consultation reviewed the current evidence on iNTS disease and discussed knowledge gaps to be addressed to accelerate vaccine development, licensure and introduction, as well as LMIC perspectives on potential iNTS vaccine use and demand. The learnings from this consultation are critical inputs to inform remaining work under the iNTS FVVA project.

Prevalence, antimicrobial susceptibility pattern and associated factors of Salmonella and Shigella among under five children with diarrhea attending Bule Hora University Teaching Hospital, Bule Hora, West Guji, Ethiopia

BACKGROUND

Salmonella and Shigella are a critical concern of the developing world and responsible for the high rate of diarrhea-related deaths. The treatment of these infections remains a challenge, due to the global rise in broad-spectrum resistance to many antibiotics. The aim of this study to determine the prevalence, antimicrobial susceptibility patterns, and associated factors of Salmonella and Shigella among under five children with diarrhea attending Bule Hora University Teaching Hospital, Bule Hora, West Guji, Ethiopia.

METHODS

A hospital-based cross-sectional study was conducted from July 01 to October 30, 2023. Three hundred sixty-five under five children with diarrhea were enrolled consecutively using convenient sampling technique. Data about patient socio-demographics, signs, and symptoms was obtained from the parents/guardians of each child using a questionnaire. Stool specimens from diarrheic children were collected and processed for isolation of Salmonella and Shigella using standard bacteriological methods. Antibiotic susceptibility patterns were determined by using the Kirby Bauer disc diffusion method. Data analysis was performed by using SPSS version 25. A p-value < 0.05 at 95% CI was considered statistically significant.

RESULTS

The prevalence of salmonella and Shigella isolates were 6.3% (23/365) and 4.9% (18/365) respectively. The isolates were 95.1% susceptible to ciprofloxacin and 73.2% to ceftriaxone. The isolates were 39.02% multidrug resistance to classes of drug choice for susceptibility tests. Presence of vomiting (AOR = 2.36), contact with diarrhoeal patient (AOR = 3.38), untrimmed fingernail (AOR = 5.20), storing cooked food in open containers (AOR = 6.5), unimproved source of drinking water from well and river (AOR = 3.86 & 3.2) showed statistically significant association with Salmonella and Shigella infections.

CONCLUSION

The prevalence of Salmonella and Shigella isolates were relatively high in the study area. The isolates were found to be sensitive to Ceftriaxone, ciprofloxacin, and cotrimoxazole; and could be possible antimicrobial choices of infection. Contact with diarrhoeal patients, untrimmed fingernails, storing cooked food in open containers and unimproved sources of drinking water were the main sources of infection. Therefore, to alleviate this infection, culture based bacterial species identification and promoting antibiotics sensitivity-based treatment are strongly recommended to avoid empirical treatment in the study area.

Rapid and simple on-site salmonella detection in food via direct sample loading using a lipopolysaccharide-imprinted polymer

Salmonella is a major foodborne pathogen that causes salmonellosis, which is characterized by symptoms such as diarrhea, fever, and abdominal cramps. Existing methods for detecting Salmonella, such as culture plating, ELISA, and PCR, are accurate but time-consuming and unsuitable for on-site applications. In this study, we developed a rapid and sensitive electrochemical sensor using a molecularly imprinted polymer (MIP) to detect Salmonella typhimurium (S. typhimurium) by targeting lipopolysaccharides (LPS). Polydopamine (PDA) was used as the polymer matrix because of its cost-efficiency and functional versatility. The sensor demonstrated high sensitivity and selectivity, with a detection limit of 10 CFU/mL and a linear response over the 10²-10⁸ CFU/mL range. The specificity of the sensor was validated against other gram-positive and gram-negative bacteria and showed no significant cross-reactivity. Furthermore, the sensor performed effectively in real food samples, including tap water, milk, and pork, without complex preprocessing. These results highlight the potential of the LPS-imprinted MIP sensor for practical on-site detection of S. typhimurium, improving food safety monitoring and preventing outbreaks in food-handling environments.

Metal and metal oxide nanoparticle-assisted molecular assays for the detection of Salmonella

This paper provides a comprehensive overview of the diverse applications and innovations of nanoparticles in the detection of Salmonella. It encompasses a comprehensive range of novel methods, including efficient enrichment, nucleic acid extraction, immunoassays, nucleic acid tests, biosensors, and emerging strategies with the potential for future applications. The surface modification of specific antibodies or ligands enables nanoparticles to achieve highly selective capture of Salmonella, while optimizing the nucleic acid extraction process and improving detection efficiency. The employment of nanoparticles in immunological and nucleic acid tests markedly enhances the specificity and sensitivity of the reaction, thereby optimizing the determination of detection results. Moreover, the distinctive physicochemical properties of nanoparticles enhance the sensitivity, selectivity, and stability of biosensors, thereby facilitating the rapid advancement of bio-detection technologies. It is particularly noteworthy that there has been significant advancement in the application and innovative research of nanozymes in molecular assays. This progress has not only resulted in enhanced detection efficiency but has also facilitated innovation and improvement in detection technologies. As nanotechnologies continue to advance, the use of metal and metal oxide nanoparticles in Salmonella detection is likely to become a more promising and reliable strategy for ensuring food safety and public health.

The global, regional, and national burden of Invasive Non-typhoidal Salmonella (iNTS): An analysis from the Global Burden of Disease Study 1990-2021

OBJECTIVES

Invasive Non-typhoidal Salmonella (iNTS) can cause serious, life-threatening, and invasive infections, posing great challenges to public health. We aimed to systematically review the burden of iNTS disease based on Global Burden of Diseases (GBD) 2021.

METHODS

We extracted data for the incidence, death, and disability-adjusted life-years (DALYs) associated with iNTS from GBD 2021, providing an overview of its epidemiology while examining trends from 1990 to 2021. Additionally, we decomposed changes of iNTS-related burden, and quantified cross-country inequalities.

RESULTS

GBD 2021 estimated 509976(95%UI,413361 to 606167) incident cases of iNTS worldwide in 2021, with the most cases and highest age-standardized rate (ASR) in Western Sub-Saharan Africa. The low SDI region had the most cases of iNTS in 2021. The incidence and DALYs rates were highest in the Low SDI region. Among all age groups, the incidence, death, and DALYs rate of iNTS were primarily concentrated among the following age groups: <1 year, 1-4 years, 5-9 years, 10-14 years, and 15-19 years. The highest rates were observed in the <1-year group. The results of joinpoint regression analysis revealed that the global burden of iNTS increased overall from 1990 to 2005, followed by notable decrease from 2005 to 2021 at varying rates. Decomposition analysis found that population growth (103.93%) and epidemiological change (48.34%) were responsible for motivating the changes in iNTS global burden. Cross-country inequality analysis revealed that the SDI-related inequalities were moderated from 1990 to 2021.

CONCLUSIONS

The global burden of iNTS is still high, and the distribution patterns vary across different countries and territories. The global burden of iNTS was primarily noteworthy among children and adolescents, with the highest burden among infants. The changes in the iNTS burden were primarily driven by population growth and epidemic transition. Despite varying iNTS burdens across different SDI regions, SDI-related inequalities across countries became moderated gradually over time. This study reported the global disease burden and temporal trends of iNTS disease, and underscores the need for age- and region-specific strategies to mitigate the corresponding global burden.

Epidemiology of Burkholderia pseudomallei, Streptococcus suis, Salmonella spp., Shigella spp. and Vibrio spp. infections in 111 hospitals in Thailand, 2022

The information on notifiable diseases in low- and middle-income countries is often incomplete, limiting our understanding of their epidemiology. Our study addresses this knowledge gap by analyzing microbiology laboratory and hospital admission data from 111 of 127 public referral hospitals in Thailand, excluding Bangkok, from January to December 2022. We evaluated factors associated with the incidence of notifiable bacterial diseases (NBDs) caused by 11 pathogens; including Brucella spp., Burkholderia pseudomallei, Corynebacterium diphtheriae, Neisseria gonorrhoeae, Neisseria meningitidis, non-typhoidal Salmonella spp. (NTS), Salmonella enterica serovar Paratyphi, Salmonella enterica serovar Typhi, Shigella spp., Streptococcus suis, and Vibrio spp.. We used multivariable Poisson random-effects regression models. Additionally, we compared their yearly incidence rates in 2022 with those from 2012-2015 in hospitals where paired data were available. In 2022, the NBD associated with the highest total number of deaths was B. pseudomallei (4,407 patients; 1,219 deaths) infection, followed by NTS (4,501 patients; 461 deaths), S. suis (867 patients, 134 deaths) and Vibrio spp. (809 patients, 122 deaths) infection. The incidence rates of B. pseudomallei, S. suis and Vibrio spp. infections were highest in the northeast, upper central and west, respectively. The incidence rate of NTS infection was generally high across all geographical regions. The yearly incidence rates of B. pseudomallei and S. suis infections in 2022 were higher than those between 2012-2015, while those of fecal-oral transmitted NBDs including NTS infection, typhoid, shigellosis and vibriosis were lower. Overall, B. pseudomallei and S. suis infections are emerging and associated with a very high number of deaths in Thailand. Although the incidence of NTS infection and vibriosis are decreasing, they are still associated with a high number of cases and deaths. Specific public health interventions are warranted.

Non-typhoidal Salmonella in food animals in Paraguay: predominant serovars and resistance phenotypes

Surveillance of antimicrobial resistance (AMR) in Salmonella in livestock (poultry, pig, and cattle) is crucial to maintain food safety. Given the lack of information on the situation in livestock in Paraguay, the aim of this study was to determine the most frequent Salmonella serovars in poultry, pig and cattle sampled in slaughterhouses in the country in 2020-22 along with their AMR phenotypes using data from a national pilot program. Out of 1,161 samples collected from slaughtered animals originating from 189 farms nationwide, Salmonella was isolated from 91/384 (23.7%) samples from poultry, 52/390 (13.3%) from pigs and 6/387 (1.6%) from cattle. Seven serovars were identified in poultry, with Heidelberg being the most frequent (82.4% of 91 isolates), while the most frequent serovars in pigs were Panama (48.1%) and Typhimurium (38.5%), and only two serovars (Cerro and Braenderup) were identified in cattle. The proportion of resistant isolates ranged from extremely high (70-83% for nalidixic acid and tetracycline) and high (25-40% for nitrofurantoin and ampicilin) to low-moderate (8-18% for cefixime, cefotaxime, amoxicillin, and trimethoprim- sulfamethoxazole) and very low-low (<6% for ciprofloxacin and gentamicin) depending on the antimicrobial. Up to 23 different resistance profiles were found, ranging from pansusceptible (18/143 isolates) to resistance to 2-7 antimicrobials (median = 2), with the predominant serovars in poultry and swine typically being resistant to ≥3 antimicrobials. These results should be backed-up with genomic analyses to determine the genetic mechanisms involved in the resistance profiles observed in order to support coordinated actions for AMR surveillance and control in the country.

Bayesian phylogeographic analysis infers cross-border transmission dynamics of drug-resistant Salmonella Enteritidis

Salmonella Enteritidis (S. Enteritidis) stands as a leading cause of human salmonellosis worldwide with a tendency to spread through contaminated foodstuffs and animals. In Hong Kong, a significant proportion of food products are imported, and many cases are often caused by the consumption of contaminated food, hence making the geographical surveillance of drug-resistant S. Enteritidis important for strong public health and food safety measures. We analyzed the whole genomes of 207 S. Enteritidis from Hong Kong, Australia, Canada, mainland China, the United States of America, South Africa, Taiwan, and the United Kingdom to examine associated antimicrobial resistance and the transmission dynamics between continents. Phylogenetic cluster inferences and Bayesian phylogeographical analysis were performed. Overall, sequence type ST11 strains were dominant (92.8%, 192/207). Five phylogenomic clusters A to E were identified, where most isolates from mainland China and Hong Kong were in Cluster E. Among the 22 plasmid types identified, IncX1 was dominant in the Asian isolates. Most of the virulence genes were distributed in Salmonella pathogenicity islands -1 and -2, with two universal virulence operons responsible for the effector delivery system and bacterial cell adhesion. The phylogeographic inference analysis showed a statistically significant link between mainland China and Hong Kong with the highest relative migration rate (relativeGeoRates mean ± standard error = 2.93 ± .07, Bayes Factor [BF] = 1285.5], with some traceable to Canada (0.61 ± 0.03, BF = 6.9) and Australia (1.02 ± 0.04, BF = 4.2). Our analysis suggests hypothetical transmission of S. Enteritidis and its associated antimicrobial resistance across borders.

IMPORTANCE

Antimicrobial resistance and disease severity in nontyphoidal Salmonella have constituted a serious public health challenge worldwide. Drug-resistant Salmonella Enteritidis is a leading pathogen that causes human infections primarily through the consumption of contaminated food products. Previous research focuses on the whole-genome analysis of antimicrobial resistance and virulence factors in S. Enteritidis; however, details on how this bacterium localized, expanded, and diversified from location to location remain unknown. Our study for the first time addresses this gap by investigating the phylogeographic transmission to estimate the frequency and location of cross-border spread. By evidence-based inferred transmission, we aim to uncover novel insights into the dynamic spread of S. Enteritidis, revealing the route of emergence and migration. This research is crucial for enhancing our understanding of the control strategies to safeguard human health.

Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function

BACKGROUND

Promoting resistance to enteric pathogen infection is a core function of the gut microbiota; however, many of the specific host-commensal interactions that mediate this protection remain uncharacterised. To address this knowledge gap, we monocolonised germ-free mice with mouse-derived commensal microbes to screen for microbiota-induced resistance to Salmonella Typhimurium infection.

RESULTS

We identified Enterocloster clostridioformis as a protective species against S. Typhimurium infection. E. clostridioformis selectively upregulates resistin-like molecule β and cell cycle pathway expression at the level of caecal epithelial cells and increases T-regulatory cells in the underlying mucosal immune system, potentially contributing to reduced infection-induced pathology.

CONCLUSIONS

We highlight novel mechanisms of host-microbe interactions that can mediate microbiota-induced resistance to acute salmonellosis. In the backdrop of increasing antibiotic resistance, this study identifies novel potential avenues for further research into protective host responses against enteric infections and could lead to new therapeutic approaches. Video Abstract.

Worldwide Population Dynamics of Salmonella Saintpaul: Outbreaks, Epidemiology, and Genome Structure

BACKGROUND/OBJECTIVES

Salmonella Saintpaul (SSa) is increasingly linked to foodborne outbreaks in Brazil and globally. Despite its rising public health significance, its epidemiology, genomic diversity, and pathogenic potential remain underexplored. This study addresses these gaps through a comprehensive global analysis of SSa population dynamics, outbreak patterns, and genetic structures, along with an in-depth phenotypic and genomic characterization of strain PP_BR059, isolated from a hospitalized patient in Ceará, Brazil.

METHODS

We analyzed 1,953 publicly available SSa genomes using core-genome multi-locus sequence typing (cgMLST), antimicrobial resistance (AMR) profiling, pan-genome analysis, and phylogenetic inference. A genome-wide association study (GWAS) identified genetic determinants of virulence and AMR. The invasiveness and intracellular survival of PP_BR059 were assessed using in vitro macrophage infection assays, while whole-genome sequencing (WGS) provided genetic insights.

RESULTS

Phylogenetic analysis identified 49 sequence types (STs), with ST-50 (787 genomes) and ST-27 (634 genomes) being most prevalent. ST-50 included all clinical strains from South America, including PP_BR059. AMR analysis showed 60% of SSa genomes were pan-susceptible, while ST-27 had the highest proportion of AMR strains. GWAS revealed distinct evolutionary lineages within ST-50 and ST-27. PP_BR059 exhibited lower macrophage invasion (3.82%) but significantly higher intracellular survival at 2 h (68.72%) and 20 h (25.68%) post-infection. WGS confirmed a pan-susceptible AMR profile and plasmid absence.

CONCLUSIONS

This study highlights SSa's global dissemination, evolutionary trends, and pathogenic variability, emphasizing the need for molecular surveillance to inform public health interventions.

Genomic survey of multidrug resistant Salmonella enterica serovar Minnesota clones in chicken products

Salmonella enterica serovar Minnesota (S. Minnesota) is an emerging serovar that persists within poultry supply chains, potentially causing outbreaks in humans. Understanding its population genomics is crucial for designing preventive measures. We performed a genomic surveillance study of S. Minnesota by analyzing 259 isolates from poultry in Saudi Arabia. Whole-genome sequencing data for these isolates were analyzed to characterize emerging clones and the genetic factors underlying antimicrobial resistance and virulence. We compared the isolates to all available global genomes of S. Minnesota. Our results revealed the emergence of four clones, three of which were mixed with global strains. These clones exhibited higher levels of antimicrobial resistance and virulence due to the acquisition of multiple plasmids, particularly IncC plasmids, carrying resistance and virulence genes. IncC plasmids underwent genomic rearrangements, presenting diverse configurations of resistance genes. Our findings demonstrate the emergence and persistence of pathogenic and multidrug-resistant S. Minnesota clones.

SHASI-ML: a machine learning-based approach for immunogenicity prediction in Salmonella vaccine development

Introduction

Accurate prediction of immunogenic proteins is crucial for vaccine development and understanding host-pathogen interactions in bacterial diseases, particularly for Salmonella infections which remain a significant global health challenge.

Methods

We developed SHASI-ML, a machine learning-based framework for predicting immunogenic proteins in Salmonella species. The model was trained and validated using a curated dataset of experimentally verified immunogenic and non-immunogenic proteins. Three distinct feature groups were extracted from protein sequences: global properties, sequence-derived features, and structural information. The Extreme Gradient Boosting (XGBoost) algorithm was employed for model development and optimization.

Results

SHASI-ML demonstrated robust performance in identifying bacterial immunogens, achieving 89.3% precision and 91.2% specificity. When applied to the Salmonella enterica serovar Typhimurium proteome, the model identified 292 novel immunogenic protein candidates. Global properties emerged as the most influential feature group in prediction accuracy, followed by structural and sequence information. The model showed superior recall and F1-scores compared to existing computational approaches.

Discussion

These findings establish SHASI-ML as an efficient computational tool for prioritizing immunogenic candidates in Salmonella vaccine development. By streamlining the identification of vaccine candidates early in the development process, this approach significantly reduces experimental burden and associated costs. The methodology can be applied to guide and optimize both research and industrial-scale production of Salmonella vaccines, potentially accelerating the development of more effective immunization strategies.

Unraveling the treasure trove of phytochemicals in mitigating the Salmonella enterica infection

Foodborne diseases triggered by various infectious micro-organisms are contributing significantly to the global disease burden as well as to increasing mortality rates. Salmonella enterica belongs to the most prevalent form of bacteria accountable for significant burden of foodborne illness across the globe. The conventional therapeutic approach to cater to Salmonella enterica-based infections relies on antibiotic therapy, but the rapid emergence of the antibiotic resistance strains of Salmonella sp. necessitates the development of alternative treatment and prevention strategies. In light of this growing concern, the scientific community is rigorously exploring novel phytochemicals harnessed from medicinally important plants as a promising approach to curb Salmonella enterica infections. A variety of phytochemicals belonging to alkaloids, phenols, flavonoid, and terpene classes are reported to exhibit their inhibitory activity against bacterial cell communication, membrane proteins, efflux pumps, and biofilm formation among drug resistant Salmonella strains. The present review article delves to discuss the emergence of antibiotic resistance among Salmonella enterica strains, various plant sources, identification of phytochemicals, and the current state of research on the use of phytochemicals as antimicrobial agents against Salmonella enterica, shedding light on the promising potential of phytochemicals in the fight against this pathogen.

Effectiveness of iNTS vaccination in sub-Saharan Africa

Invasive non-Typhoidal Salmonella (iNTS) is one of the leading causes of blood stream infections in Sub-Saharan Africa, especially among children. iNTS can be difficult to diagnose, particularly in areas where malaria is endemic, and difficult to treat, partly because of the emergence of antibiotic resistance. We developed a mathematical model to evaluate the impact of a vaccine for iNTS in 49 countries of sub-Saharan Africa. Without vaccination we estimate 9.2 million new iNTS cases among children below 5 years old in these 49 countries from 2022 to 2038, 6.2 million of which between 2028 and 2038. The introduction of a [Formula: see text] ([Formula: see text]) efficacy vaccine in 2028 would prevent 2.6 (2.9) million of these new infections. We provide the country-specific impact of a iNTS vaccine considering the different age structures and vaccine coverage levels.

Combatting Salmonella: a focus on antimicrobial resistance and the need for effective vaccination

BACKGROUND

Salmonella infections represent a major global public health concern due to their widespread zoonotic transmission, antimicrobial resistance, and associated morbidity and mortality. This review aimed to summarize the zoonotic nature of Salmonella, the challenges posed by antimicrobial resistance, the global burden of infections, and the need for effective vaccination strategies to mitigate the rising threat of Salmonella.

METHODS

A systematic review of literature was conducted using databases such as PubMed, Scopus, Web of Science, and Google Scholar. Relevant studies published in English were identified using keywords including Salmonella, vaccination, antimicrobial resistance, and public health. Articles focusing on epidemiology, vaccine development, and strategies to control Salmonella infections were included, while conference abstracts and non-peer-reviewed studies were excluded.

RESULTS

Salmonella infections result in approximately 95 million global cases annually, with an estimated 150,000 deaths. Regional variations were evident, with higher infection rates in low- and middle-income countries due to poor sanitation and food safety standards. Salmonella Enteritidis and S. Typhimurium were the most prevalent serovars associated with human infections. The review highlighted an alarming rise in multidrug-resistant (MDR) Salmonella strains, particularly due to the overuse of antibiotics in humans and livestock. Despite progress in vaccine development, challenges remain in achieving a universal vaccine that targets diverse Salmonella serovars. Live-attenuated, killed, recombinant, subunit, and conjugate vaccines are currently under development, but limitations such as efficacy, cost, and accessibility persist.

CONCLUSIONS

Salmonella infections continue to impose a significant burden on global health, exacerbated by rising antimicrobial resistance. There is an urgent need for a multifaceted approach, including improved sanitation, prudent antibiotic use, and the development of affordable, broad-spectrum vaccines. Strengthening surveillance systems and promoting collaborative global efforts are essential to effectively control and reduce the burden of Salmonella.

Genomic characterization of antimicrobial-resistance and virulence factors in Salmonella isolates obtained from pig farms in Antioquia, Colombia

BACKGROUND

Occurrence of antimicrobial-resistant Salmonella strains has been reported worldwide, because of inappropriate use of antimicrobial products in either humans or animals. The presence of multidrug resistant Salmonella in pig production systems had been reported in Antioquia, Colombia.

AIM

To identify antimicrobial resistance genes (ARG) in different Salmonella spp. strains isolated from pig productions in Antioquia, Colombia. Methods: Samples were received at the Diagnostic Unit of the Faculty of Agrarian Sciences at the University of Antioquia, from January 1, 2019, to January 2021. A total of 28 isolates of Salmonella spp. were included, which presented phenotypic resistance to more than one antibiotic used in pig farms. Whole genome sequencing (WGS) was performed in the Unit of Genomic of Agrosavia using an automated pipeline from the GHRU- Sanger Institute, employing the Illumina MiSeq platform.

RESULTS

WGS revealed 34 ARGs among these isolates. In 25 isolates (89%) more than two ARGs were found. Genes encoding resistance were found for 10 different groups of antibiotics (beta-lactam, aminoglycosides, chloramphenicol, rifampicins, lincosamides, fluoroquinolones, tetracyclines, sulfonamides and trimethoprim). The most frequently observed MDR profile in Typhimurium isolates was AMP-CEX-CEP-CEF-EFT-CEQ-FLU-ENR-TE-FFC-SXT.

CONCLUSION

The presence of multi-drug resistant Salmonella strains in pigs destined for human consumption in Antioquia, Colombia was determined. This research emphasizes the utmost importance of epidemiological tools to understand the presence and spreading of antimicrobial resistance genes in pig farms. Additionally, it highlights the critical need for developing educational programs and public policies to help reduce the spread of antimicrobial resistance in production systems.

Foodborne Infections and Salmonella: Current Primary Prevention Tools and Future Perspectives

Salmonella is considered the major zoonotic and foodborne pathogen responsible for human infections. It includes the serovars causing typhoid fever (S. typhi and S. paratyphi) and the non-typhoidal salmonella (NTS) serovars (S. enteritidis and S. typhimurium), causing enteric infections known as "Salmonellosis". NTS represents a major public health burden worldwide. The consumption of S. enteritidis-contaminated animal foods is the main source of this disease in humans, and eradicating bacteria from animals remains a challenge. NTS causes various clinical manifestations, depending on the quantity of bacteria present in the food and the immune status of the infected individual, ranging from localized, self-limiting gastroenteritis to more serious systemic infections. Salmonellosis prevention is based on hygienic and behavioral rules related to food handling that aim to reduce the risk of infection. However, no vaccine against NTS is available for human use. This aspect, in addition to the increase in multidrug-resistant strains and the high morbidity, mortality, and socioeconomic costs of NTS-related diseases, makes the development of new prevention and control strategies urgently needed. The success of the vaccines used to protect against S. typhi encouraged the development of NTS vaccine candidates, including live attenuated, subunit-based, and recombinant-protein-based vaccines. In this review, we discuss the epidemiological burden of Salmonellosis and its primary prevention, focusing on the current status and future perspectives of the vaccines against NTS.

Integron-Mediated Antimicrobial Resistance and Virulence Factors in Salmonella Typhimurium Isolated from Poultry

This study investigates antimicrobial-resistant (AMR) Salmonella Typhimurium in poultry, focusing on how class I integrons contribute to AMR and virulence. Using whole genome sequencing, researchers analyzed 26 S. Typhimurium isolates from U.S. poultry, finding that three isolates contained integrons (1000 base pairs each). These integron-positive isolates exhibited significantly higher resistance to beta-lactams, phenicols, and tetracyclines compared to integron-free isolates (p = 0.004, 0.009, and 0.02, respectively) and harbored genes like ges, imp, and oxa, which are linked to extended-spectrum beta-lactamase resistance. Most AMR gene classes (64%) were chromosome-based, with integron-positive isolates showing a broader array of resistance genes, including catB and tetA. Integron-bearing isolates had higher occurrences of bacteriocin genes and specific AMR genes like aminoglycoside and beta-lactam resistance genes, while integron-free isolates had more fimbrial and pilus genes. The presence of integrons may trend with increased AMR genes and virulence factors, highlighting the role of integron screening in enhancing AMR surveillance and reducing the need for high-priority antimicrobial treatments in poultry. These findings could support better AMR stewardship practices in poultry production, potentially lowering infection risks in humans and livestock.

One Health approach probes zoonotic non-typhoidal Salmonella infections in China: A systematic review and meta-analysis

Background

Zoonotic infections, particularly those caused by non-typhoidal Salmonella (NTS), pose a significant disease burden. However, there is a notable lack of comprehensive and integrated studies employing the One Health approach to address Salmonella prevalence. In this study, we aimed to analyse NTS spatiotemporal prevalence, serovar distribution, and antimicrobial resistance (AMR) across China.

Methods

We conducted a systematic review and meta-analysis to understand the dynamics of NTS in a One Health context in China. We searched the CNKI, Wanfang, and PubMed databases for Chinese and English peer-reviewed articles published before 1 January 2022 dealing with Salmonella in the context of China. We examined the dynamic prevalence along the food chain, the risk of dominant serovars and the carriers' regional contribution by principal component analysis, and the AMR burden before and after the ban on using antimicrobials as feed additives across five decades. We used the inverse variance index as an indicator of the inconsistency across studies, and we adopted the restricted maximum likelihood model due to high heterogeneity for analysis with a 95% confidence level for the pooled prevalence estimate.

Results

Based on 562 retrieved high-quality studies during 1967-2021, representing 5 052 496 samples overall and 80 536 positive samples for NTS isolates, the overall average prevalence was 7.35% (95% confidence interval (CI) = 0.069-0.087), which was regionally relatively higher in northern China (8.19%; 95% CI = 0.078-0.117) than in southern China (6.94%; 95% CI = 0.067-0.088). Poultry was the primary vehicle for serovars Enteritidis and Indiana (especially in the north), while swine and ruminants for Typhimurium and Derby were the first to highlight the regional livestock contribution to serovar prevalence. The overall AMR rate was 73.63% (95% CI = 0.68-0.99), decreasing after the ban on excessive use of feed-based antibiotics in livestock since 2020, with a relatively low resistance towards front-line and last-resort drugs.

Conclusions

Our study emphasises the importance of adopting a One Health framework to better understand the zoonotic nature of human NTS and highlights the dominant serovars on food contamination and human infection. The similarity in AMR patterns between poultry and human isolates further emphasises the integrated approach for evaluating disease burden and implementing targeted interventions.

Biofilm Production and Antibiogram Profiles in Escherichia coli and Salmonella

Salmonella and Escherichia coli are important enteric pathogens associated with a variety of infections. Biofilm formation and antimicrobial resistance are important characteristics making these pathogens a concern in terms of strong attachment to substrates, expression of virulence markers and difficult removal. The present study investigates the biofilm-forming ability and antibiogram patterns among E. coli and Salmonella spp. A total of 200 E. coli and 100 Salmonella isolates received at National Salmonella and Escherichia Centre were identified by biochemical testing, followed by serotyping. Biofilm production was detected by Tissue Culture Plate method. The isolates were further subjected to Antibiotic Susceptibility Testing by the Kirby-Bauer disk diffusion method. 113 (56.5%) E. coli isolates and 79 (79%) Salmonella isolates were detected as biofilm producers. A total of 114(57%)E. coli isolates and 31(31%) Salmonella isolates were found to be resistant to multiple drugs when Antibiotic Susceptibility Testing was carried out. Antibiotic resistance was found to be significantly higher in biofilm producing salmonella (p = 0.001) whereas in the case of E. coli the difference remained non-significant (p = 0.4454). The capability to produce biofilm along with acquiring high level of antimicrobial resistance in salmonella and E. coli provide enhanced survival potential in adverse environments. Therefore, it becomes a serious cause of concern for public health authorities considering the virulence of these bacteria and their association with different disease conditions and requires urgent intervention with regards to control and prevention strategies.

Nationwide trends and features of human salmonellosis outbreaks in China

Salmonellosis is one of the most common causes of diarrhea, affecting 1/10 of the global population. Salmonellosis outbreaks (SO) pose a severe threat to the healthcare systems of developing regions. To elucidate the patterns of SO in China, we conducted a systematic review and meta-analysis encompassing 1,134 reports across 74 years, involving 89,050 patients and 270 deaths. A rising trend of SO reports has been observed since the 1970s, with most outbreaks occurring east of the Hu line, especially in coastal and populated regions. It is estimated to have an overall attack rate of 36.66% (95% CI, 33.88-39.45%), and antimicrobial resistance towards quinolone (49.51%) and beta-lactam (73.76%) remains high. Furthermore, we developed an online website, the Chinese Salmonellosis Outbreak Database (CSOD), for visual presentation and data-sharing purposes. This study indicated that healthcare-associated SO required further attention, and our study served as a foundational step in pursuing outbreak intervention and prediction.

A c-di-GMP binding effector STM0435 modulates flagellar motility and pathogenicity in Salmonella

Flagella play a crucial role in the invasion process of Salmonella and function as a significant antigen that triggers host pyroptosis. Regulation of flagellar biogenesis is essential for both pathogenicity and immune escape of Salmonella. We identified the conserved and unknown function protein STM0435 as a new flagellar regulator. The ∆stm0435 strain exhibited higher pathogenicity in both cellular and animal infection experiments than the wild-type Salmonella. Proteomic and transcriptomic analyses demonstrated dramatic increases in almost all flagellar genes in the ∆stm0435 strain compared to wild-type Salmonella. In a surface plasmon resonance assay, purified STM0435 protein-bound c-di-GMP had an affinity of ~8.383 µM. The crystal structures of apo-STM0435 and STM0435&c-di-GMP complex were determined. Structural analysis revealed that R33, R137, and D138 of STM0435 were essential for c-di-GMP binding. A Salmonella with STM1987 (GGDEF protein) or STM4264 (EAL protein) overexpression exhibits completely different motility behaviours, indicating that the binding of c-di-GMP to STM0435 promotes its inhibitory effect on Salmonella flagellar biogenesis.

Deletion of both anaerobic regulator genes fnr and narL compromises the colonization of Salmonella Typhimurium in mice model

Salmonella Typhimurium (STM), a zoonotic pathogen, can adjust its metabolic pathway according to the variations in the partial pressure of atmospheric oxygen and nitrate via fumarate nitrate reductase regulator (Fnr) and NarL, the response regulator for nitrate reductase. Both Fnr and NarL have been individually reported to be the contributors of virulent phenotypes of STM. Hypoxia along with nitrate-rich environment are prevalent in macrophages and the Salmonella-induced inflammatory lumen of the host's large intestine activates both fnr and narL genes. In this study, the double (fnr and narL) knockout STM showed a synergistic reduction in the swimming (62%), swarming (84%) and biofilm density (86%) phenotypes anaerobically in association with its significant aerobic attenuation. The intracellular replication of the double mutant was reduced by 2.3 logs in chicken monocyte-derived macrophages. Furthermore, the competitive index of the double mutant in liver and spleen was found to be 0.3 and 0.44 respectively at 120 h post-infection (PI) in mice. Surprisingly, no double mutant could be recovered from the infected mouse liver 3 days PI. Histopathological findings showed moderate infiltration of mononuclear cells in the large intestine of mice infected with double mutant, but severe infiltration was seen with the wild-type strain.

Characterization of Virulence Genotypes, Antimicrobial Resistance Patterns, and Biofilm Synthesis in Salmonella spp Isolated from Foodborne Outbreaks

Salmonella is the main bacterial pathogen that causes foodborne disease, particularly in developing countries. Nontyphoidal Salmonella (NTS) include Enteritidis and Typhimurium as the most prevalent strains which are one of the significant causes of acute gastroenteritis in children. Therefore, identifying the most predominant serovars, types of common contaminated food, and paying attention to their antibiotic resistance are the main factors in the prevention and control strategy of salmonellosis. This study was undertaken to evaluate the prevalence rate of serovars, the biofilm formation, antimicrobial resistance (AMR) status, and phenotypic virulence factors of Salmonella strains isolated from diarrhea samples in some cities of Iran. A total of 40 (10.41%) Salmonella isolates were recovered from 384 diarrhea samples processed and the most common serovar was Salmonella serovar Typhimurium (82.5). Also, all isolates belonging to serovar Typhimurium showed more virulence factors compared to other serovars. The isolates showed a high resistance rate to ampicillin (95%) and nalidixic acid (87.5%), while a low resistance rate was found for chloramphenicol (2.5%). Moreover, significant variances in the capacity of biofilm formation were found between different Salmonella serotypes. The resistance of NTS to extant choice drugs is a potential public health problem. Constant monitoring of AMR pattern and virulence profile of NTS serovars is suggested for the prevention of salmonellosis in humans.

Genomic analysis of antibiotic resistance genes and mobile genetic elements in eight strains of nontyphoid Salmonella

Nontyphoidal Salmonella (NTS) is the main etiological agent of human nontyphoidal salmonellosis. The aim of this study was to analyze the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance (AMR) genes from eight strains of NTS detected in Zhenjiang City, Jiangsu Province, China. Fecal samples from outpatients with food-borne diarrhea were collected in 2022. The NTS isolates were identified, and their susceptibility was tested with the Vitek 2 Compact system. The genomes of the NTS isolates were sequenced with the Illumina NovaSeq platform and Oxford Nanopore Technologies platform. The AMR genes and mobile genetic elements (MGEs) were predicted with the relevant open access resources. Eight strains of NTS were isolated from 153 specimens, and Salmonella Typhimurium ST19 was the most prevalent serotype. The AMR gene with the highest detection rate was AAC(6')-Iaa (10.5%) followed by TEM-1 (7.9%), sul2 (6.6%), and tet(A) (5.3%). Eleven MGEs carrying 34 AMR genes were identified on the chromosomes of 3 of the 8 NTS, including 3 resistance islands, 6 composite transposons (Tns), and 2 integrons. Eighteen plasmids carrying 40 AMR genes were detected in the 8 NTS strains, including 6 mobilizable plasmids, 3 conjugative plasmids, and 9 nontransferable plasmids, 7 of which carried 10 composite Tns and 3 integrons. This study provided a theoretical basis, from a genetic perspective, for the prevention and control of NTS resistance in Zhenjiang City.

IMPORTANCE

Human nontyphoidal salmonellosis is one of the common causes of bacterial food-borne illnesses, with significant social and economic impacts, especially those caused by invasive multidrug-resistant nontyphoidal Salmonella, which entails high morbidity and mortality. Antimicrobial resistance is mainly mediated by drug resistance genes, and mobile genetic elements play key roles in the capture, accumulation, and dissemination of antimicrobial resistance genes. Therefore, it is necessary to study the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance genes of nontyphoidal Salmonella to prevent the spread of multidrug-resistant nontyphoidal Salmonella.

Clinical Characteristics, Serotypes and Antimicrobial Resistance of Invasive Salmonella Infections in HIV-Infected Patients in Hangzhou, China, 2012-2023

Purpose

Developing countries, invasive Salmonella infections can cause considerable morbidity and mortality. There is a relative lack of data on coinfection with Salmonella in HIV-infected patients in Hangzhou, China.

Patients and Methods

In this study, we manually collected case data of patients aged >18 years with HIV combined with invasive Salmonella infections admitted to Xixi Hospital in Hangzhou from January 2012 to August 2023 by logging into the Hospital Information System, and identified 26 strains of invasive Salmonella using a fully automated microbiological identification system and mass spectrometer. Serotypes were determined using Salmonella diagnostic sera based on the White-Kauffmann-Le Minor scheme. Drug sensitivity tests were performed using the automated instrumental method of the MIC method.

Results

A total of 26 HIV-infected patients with invasive Salmonella coinfections were identified over 11 years; Twenty-five of the 26 patients (96.2%) were males, with a mean age of 33.5 years (26.75, 46.75). The most common type of infection was bloodstream infection (92.3%). One patient also had concomitant meningitis and osteoarthritis, followed by pneumonia (7.7%). The presence of multiple bacterial infections or even multiple opportunistic pathogens was clearly established in 7 (26.9%) patients. Three (11.6%) patients were automatically discharged from the hospital with deterioration of their condition, and one (3.8%) patient died. Salmonella enteritidis was the most common serotype in 6 patients (23.2%), and Salmonella Dublin was the most common serotype in 6 patients (23.2%). Drug sensitivity results revealed multidrug resistance in a total of 8 (30.8%) patients.

Conclusion

The clinical presentation of invasive Salmonella infection in HIV patients is nonspecific and easily masked by other mixed infections. A CD4+ count <100 cells/µL and comorbid intestinal lesions may be important susceptibility factors. Salmonella has a high rate of resistance to common antibiotics, and the risk of multidrug resistance should not be ignored.

Colorimetry/fluorescence dual-mode detection of Salmonella typhimurium based on a "three-in-one" nanohybrid with high oxidase-like activity for AIEgen

A colorimetry/fluorescence dual-mode assay based on the aptamer-functionalized magnetic covalent organic framework-supported CuO and Au NPs (MCOF-CuO/Au@apt) was developed for Salmonella typhimurium (S. typhimurium) biosensing. The nanohybrid combined three functions in one: good magnetic separation characteristic, excellent oxidase-mimic activity for tetrap-aminophenylethylene (TPE-4A), and target recognition capability. The attachment of MCOF-CuO/Au@apt onto the surface of S. typhimurium resulted in a significant reduction in the oxidase-mimicking activity of the nanohybrid, which could generate dual-signal of colorimetry and fluorescence through the catalytic oxidation of TPE-4A. Based on this, S. typhimurium could be specifically detected in the linear ranges of 102- 106 CFU·mL-1 and 101- 106 CFU·mL-1, with LODs of 7.6 and 2.1 CFU·mL-1, respectively in colorimetry/fluorescence modes. Moreover, the smartphone and linear discrimination analysis-based system could be used for on-site and portable testing. In addition, this platform showed applicability in detecting S. typhimurium in milk, egg liquid and chicken samples.

Frequency, serotyping, antibiogram, and seasonality of Salmonella isolated from red meat markets

Bacterial pathogenic strains are as adaptable as Salmonella strains and cause diverse intestinal and extraintestinal diseases in humans and other mammals worldwide. Red meat and its products are important hosts for many zoonotic diseases. This work was designed to investigate the frequency, serotypes, and antimicrobial resistance profile of isolated Salmonella spp. in red meat (cattle, sheep, and goats) sold in Dhamar Governorate, Yemen. A total of 250 red meat samples were collected from the retail seller market between July and December 2022. All samples were transported immediately to the laboratory, subcultured on selective enrichment agar, and identified by serotyping and antimicrobial susceptibility tests via disk diffusion methods. The results indicated 26 positive samples of Salmonella out of the 250 samples (10.4%). Notably, isolates belong to ten various serotypes: S. Typhimurium 19.2%, S. Anatum 15.4%, S. Newport 11.5%, S. Enteritidis 11.5%, S. Muenchen 11.5%, S. Infantis 7.7%, S. Montevideo 7.7%, S. Dublin 7.7%, S. Senftenberg 3.9%, and S. Arizona 3.9%. The antibiotic resistance profile revealed that 57.5%, 53.9%, and 53.9% of isolates are resistant to erythromycin, tetracycline, and norfloxacin, respectively. This resistance among Salmonella spp. suggests a significant threat to health, which will in turn require an active safety measure and response. On the other hand, the seasonal variations "August and July" were found to be associated with an increased frequency of Salmonella isolation.

Infectious Disease Prophylaxis During and After Immunosuppressive Therapy

Immune-mediated renal diseases are a diverse group of disorders caused by antibody, complement, or cell-mediated autosensitization. Although these diseases predispose to infection on their own, a growing array of traditional and newer, more targeted immunosuppressant medications are used to treat these diseases. By understanding their mechanisms of action and the infections associated with suppression of each arm of the immune system, nephrologists can better anticipate these risks and effectively prevent and recognize opportunistic infections. Focusing specifically on nonkidney transplant recipients, this review discusses the infections that can be associated with each of the commonly used immunosuppressants by nephrologists and suggest interventions to prevent infectious complications in patients with immune-mediated renal disease.

The Economic Burden of Non-Typhoidal Salmonella and Invasive Non-Typhoidal Salmonella Infection: A Systematic Literature Review

Non-typhoidal Salmonella (NTS) infection and invasive non-typhoidal Salmonella (iNTS) infection cause a significant global health and economic burden. This systematic review aims to investigate the reported economic burden of NTS and iNTS infection, identify research gaps, and suggest future research directions. Data from PubMed and Embase databases up to April 2022 were reviewed, and articles were screened based on predefined criteria. Cost data were extracted, categorized into direct medical costs (DMCs), direct non-medical costs (DNMCs), and indirect costs (ICs), and converted into US dollars (year 2022). Data primarily originated from high-income countries (37 out of 38), with limited representation from Africa and resource-limited settings. For inpatients, DMCs were the primary cost driver for both NTS and iNTS illnesses, with estimates ranging from USD 545.9 (Taiwan, a region of China) to USD 21,179.8 (Türkiye) for NTS and from USD 1973.1 (Taiwan, a region of China) to USD 32,507.5 (United States of America) for iNTS per case. DNMCs and ICs varied widely across studies. Although study quality improved over time, methodological differences persisted. This review underscores the lack of economic data on NTS and iNTS in resource-limited settings. It also highlights the need for economic burden data in resource-limited settings and a standardized approach to generate global datasets, which is critical for informing policy decisions, especially regarding future vaccines.

Serovar and sequence type distribution and phenotypic and genotypic antimicrobial resistance of Salmonella originating from pet animals in Chongqing, China

A total of 334 Salmonella isolates were recovered from 6,223 pet rectal samples collected at 50 pet clinics, 42 pet shops, 7 residential areas, and 4 plazas. Forty serovars were identified that included all strains except for one isolate that did not cluster via self-agglutination, with Salmonella Typhimurium monophasic variant, Salmonella Kentucky, Salmonella Enteritidis, Salmonella Pomona, and Salmonella Give being the predominant serovars. Fifty-one sequence types were identified among the isolates, and ST198, ST11, ST19, ST451, ST34, and ST155 were the most common. The top four dominant antimicrobials to which isolates were resistant were sulfisoxazole, ampicillin, doxycycline, and tetracycline, and 217 isolates exhibited multidrug resistance. The prevalence of β-lactamase genes in Salmonella isolates was 59.6%, and among these isolates, 185 harbored blaTEM, followed by blaCTX-M (66) and blaOXA (10). Moreover, six PMQR genes, namely, including qnrA (4.8%), qnrB (4.2%), qnrD (0.9%), qnrS (18.9%), aac(6')-Ib-cr (16.5%), and oqxB (1.5%), were detected. QRDR mutations (76.6%) were very common in Salmonella isolates, with the most frequent mutation in parC (T57S) (47.3%). Furthermore, we detected six tetracycline resistance genes in 176 isolates, namely, tet(A) (39.5%), tet(B) (8.1%), tet(M) (7.7%), tet(D) (5.4%), tet(J) (3.3%), and tet(C) (1.8%), and three sulfonamide resistance genes in 303 isolates, namely, sul1 (84.4%), sul2 (31.1%), and sul3 (4.2%). Finally, we found 86 isolates simultaneously harboring four types of resistance genes that cotransferred 2-7 resistance genes to recipient bacteria. The frequent occurrence of antimicrobial resistance, particularly in dogs and cats, suggests that antibiotic misuse may be driving multidrug-resistant Salmonella among pets.IMPORTANCEPet-associated human salmonellosis has been reported for many years, and antimicrobial resistance in pet-associated Salmonella has become a serious public health problem and has attracted increasing attention. There are no reports of Salmonella from pets and their antimicrobial resistance in Chongqing, China. In this study, we investigated the prevalence, serovar diversity, sequence types, and antimicrobial resistance of Salmonella strains isolated from pet fecal samples in Chongqing. In addition, β-lactamase, QRDR, PMQR, tetracycline and sulfonamide resistance genes, and mutations in QRDRs in Salmonella isolates were examined. Our findings demonstrated the diversity of serovars and sequence types of Salmonella isolates. The isolates were widely resistant to antimicrobials, notably with a high proportion of multidrug-resistant strains, which highlights the potential direct or indirect transmission of multidrug-resistant Salmonella from pets to humans. Furthermore, resistance genes were widely prevalent in the isolates, and most of the resistance genes were spread horizontally between strains.

Prevalence and Antimicrobial Resistance Diversity of Salmonella Isolates in Jiaxing City, China

Nontyphoidal Salmonella (NTS) is a cause of foodborne diarrheal diseases worldwide. Important emerging NTS serotypes that have spread as multidrug-resistant high-risk clones include S. Typhimurium monophasic variant and S. Kentucky. In this study, we isolated Salmonella in 5019 stool samples collected from patients with clinical diarrhea and 484 food samples. Antibiotic susceptibility testing and whole-genome sequencing were performed on positive strains. The detection rates of Salmonella among patients with diarrhea and food samples were 4.0% (200/5019) and 3.1% (15/484), respectively. These 215 Salmonella isolates comprised five main serotypes, namely S. Typhimurium monophasic variant, S. Typhimurium, S. London, S. Enteritidis, and S. Rissen, and were mainly resistant to ampicillin, tetracycline, chloramphenicol, and trimethoprim/sulfamethoxazole. The MDR rates of five major serotypes were 77.4%, 56.0%, 66.7%, 53.3%, and 80.0%, respectively. The most commonly acquired extended-spectrum β-lactamase-encoding genes were blaTEM-1B, blaOXA-10, and blaCTX-M-65. The S. Typhimurium monophasic variant strains from Jiaxing City belonged to a unique clone with broad antibiotic resistance. S. Kentucky isolates showed the highest drug resistance, and all were MDR strains. The discovery of high antibiotic resistance rates in this common foodborne pathogen is a growing concern; therefore, ongoing surveillance is crucial to effectively monitor this pathogen.

Loss of function of metabolic traits in typhoidal Salmonella without apparent genome degradation

Salmonella enterica serovar Typhi and Paratyphi A are the cause of typhoid and paratyphoid fever in humans, which are systemic life-threatening illnesses. Both serovars are exclusively adapted to the human host, where they can cause life-long persistent infection. A distinct feature of these serovars is the presence of a relatively high number of degraded coding sequences coding for metabolic pathways, most likely a consequence of their adaptation to a single host. As a result of convergent evolution, these serovars shared many of the degraded coding sequences although often affecting different genes in the same metabolic pathway. However, there are several coding sequences that appear intact in one serovar while clearly degraded in the other, suggesting differences in their metabolic capabilities. Here, we examined the functionality of metabolic pathways that appear intact in S. Typhi but that show clear signs of degradation in S. Paratyphi A. We found that, in all cases, the existence of single amino acid substitutions in S. Typhi metabolic enzymes, transporters, or transcription regulators resulted in the inactivation of these metabolic pathways. Thus, the inability of S. Typhi to metabolize Glucose-6-Phosphate or 3-phosphoglyceric acid is due to the silencing of the expression of the genes encoding the transporters for these compounds due to point mutations in the transcriptional regulatory proteins. In contrast, its inability to utilize glucarate or galactarate is due to the presence of point mutations in the transporter and enzymes necessary for the metabolism of these sugars. These studies provide additional support for the concept of adaptive convergent evolution of these two human-adapted S. enterica serovars and highlight a limitation of bioinformatic approaches to predict metabolic capabilities.

IMPORTANCE

Salmonella enterica serovar Typhi and Paratyphi A are the cause of typhoid and paratyphoid fever in humans, which are systemic life-threatening illnesses. Both serovars can only infect the human host, where they can cause life-long persistent infection. Because of their adaptation to the human host, these bacterial pathogens have changed their metabolism, leading to the loss of their ability to utilize certain nutrients. In this study we examined the functionality of metabolic pathways that appear intact in S. Typhi but that show clear signs of degradation in S. Paratyphi A. We found that, in all cases, the existence of single amino acid substitutions in S. Typhi metabolic enzymes, transporters, or transcription regulators resulted in the inactivation of these metabolic pathways. These studies provide additional support for the concept of adaptive convergent evolution of these two human-adapted S. enterica serovars.

Characterization of MLST-99 Salmonella Typhimurium and the monophasic variant I:4,[5],12:i:- isolated from Canadian Atlantic coast shellfish

Salmonella enterica subsp. enterica Typhimurium and its monophasic variant I 1;4,[5],12:i:- (MVST) are responsible for thousands of reported cases of salmonellosis each year in Canada, and countries worldwide. We investigated S. Typhimurium and MVST isolates recovered from raw shellfish harvested in Atlantic Canada by the Canadian Food Inspection Agency (CFIA) over the past decade, to assess the potential impact of these isolates on human illness and to explore possible routes of shellfish contamination. Whole-genome sequence analysis was performed on 210 isolates of S. Typhimurium and MVST recovered from various food sources, including shellfish. The objective was to identify genetic markers linked to ST-99, a sequence type specifically associated with shellfish, which could explain their high prevalence in shellfish. We also investigated the genetic similarity amongst CFIA ST-99 isolates recovered in different years and geographical locations. Finally, the study aimed to enhance the molecular serotyping of ST-99 isolates, as they are serologically classified as MVST but are frequently misidentified as S. Typhimurium through sequence analysis. To ensure recovery of ST-99 from shellfish was not due to favourable growth kinetics, we measured the growth rates of these isolates relative to other Salmonella and determined that ST-99 did not have a faster growth rate and/or shorter lag phase than other Salmonella evaluated. The CFIA ST-99 isolates from shellfish were highly clonal, with up to 81 high-quality single nucleotide variants amongst isolates. ST-99 isolates both within the CFIA collection and those isolated globally carried numerous unique deletions, insertions and mutations in genes, including some considered important for virulence, such as gene deletions in the type VI secretion system. Interestingly, several of these genetic characteristics appear to be unique to North America. Most notably was a large genomic region showing a high prevalence in genomes from Canadian isolates compared to those from the USA. Although the functions of the majority of the proteins encoded within this region remain unknown, the genes umuC and umuD, known to be protective against UV light damage, were present. While this study did not specifically examine the effects of mutations and insertions, results indicate that these isolates may be adapted to survive in specific environments, such as ocean water, where wild birds and/or animals serve as the natural hosts. Our hypothesis is reinforced by a global phylogenetic analysis, which indicates that isolates obtained from North American shellfish and wild birds are infrequently connected to isolates from human sources. These findings suggest a distinct ecological niche for ST-99, potentially indicating their specialization and adaptation to non-human hosts and environments, such as oceanic habitats.

Point-of-Care Diagnostic System for Viable Salmonella Species via Improved Propidium Monoazide and Recombinase Polymerase Amplification Based Nucleic Acid Lateral Flow

Salmonella species are prominent foodborne microbial pathogens transmitted through contaminated food or water and pose a significant threat to human health. Accurate and rapid point-of-care (POC) diagnosis is gaining attention in effectively preventing outbreaks of foodborne disease. However, the presence of dead bacteria can interfere with an accurate diagnosis, necessitating the development of methods for the rapid, simple, and efficient detection of viable bacteria only. Herein, we used an improved propidium monoazide (PMAxx) to develop a nucleic acid lateral flow (NALF) assay based on recombinase polymerase amplification (RPA) to differentiate viable Salmonella Typhimurium. We selected an RPA primer set targeting the invA gene and designed a probe for NALF. RPA-based NALF was optimized for temperature (30-43 °C), time (1-25 min), and endonuclease IV concentration (0.025-0.15 unit/µL). PMAxx successfully eliminated false-positive results from dead S. Typhimurium, enabling the accurate detection of viable S. Typhimurium with a detection limit of 1.11 × 102 CFU/mL in pure culture. The developed method was evaluated with spiked raw chicken breast and milk with analysis completed within 25 min at 39 °C. This study has potential as a tool for the POC diagnostics of viable foodborne pathogens with high specificity, sensitivity, rapidity, and cost-effectiveness.

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.

Loss of function of metabolic traits in typhoidal Salmonella without apparent genome degradation

Salmonella enterica serovar Typhi and Paratyphi A are the cause of typhoid and paratyphoid fever in humans, which are systemic life-threatening illnesses. Both serovars are exclusively adapted to the human host, where they can cause life-long persistent infection. A distinct feature of these serovars is the presence of a relatively high number of degraded coding sequences coding for metabolic pathways, most likely a consequence of their adaptation to a single host. As a result of convergent evolution, these serovars shared many of the degraded coding sequences although often affecting different genes in the same metabolic pathway. However, there are several coding sequences that appear intact in one serovar while clearly degraded in the other, suggesting differences in their metabolic capabilities. Here, we examined the functionality of metabolic pathways that appear intact in S . Typhi but that show clear signs of degradation in S . Paratyphi A. We found that, in all cases, the existence of single amino acid substitutions in S. Typhi metabolic enzymes, transporters, or transcription regulators resulted in the inactivation of these metabolic pathways. Thus, the inability of S . Typhi to metabolize Glucose-6-Phosphate or 3-phosphoglyceric acid is due to the silencing of the expression of the genes encoding the transporters for these compounds due to point mutations in the transcriptional regulatory proteins. In contrast, its inability to utilize glucarate or galactarate is due to the presence of point mutations in the transporter and enzymes necessary for the metabolism of these sugars. These studies provide additional support for the concept of adaptive convergent evolution of these two human-adapted Salmonella enterica serovars and highlight a limitation of bioinformatic approaches to predict metabolic capabilities.

Diverse bacteria elicit distinct neutrophil responses in a physiologically relevant model of infection

An efficient neutrophil response is critical for fighting bacterial infections, which remain a significant global health concern; therefore, modulating neutrophil function could be an effective therapeutic approach. While we have a general understanding of how neutrophils respond to bacteria, how neutrophil function differs in response to diverse bacterial infections remains unclear. Here, we use a microfluidic infection-on-a-chip device to investigate the neutrophil response to four bacterial species: Pseudomonas aeruginosa, Salmonella enterica, Listeria monocytogenes, and Staphylococcus aureus. We find enhanced neutrophil extravasation to L. monocytogenes, a limited overall response to S. aureus, and identify IL-6 as universally important for neutrophil extravasation. Furthermore, we demonstrate a higher percentage of neutrophils generate reactive oxygen species (ROS) when combating gram-negative bacteria versus gram-positive bacteria. For all bacterial species, we found the percentage of neutrophils producing ROS increased following extravasation through an endothelium, underscoring the importance of studying neutrophil function in physiologically relevant models.

Salmonellosis: An Overview of Epidemiology, Pathogenesis, and Innovative Approaches to Mitigate the Antimicrobial Resistant Infections

Salmonella is a major foodborne pathogen and a leading cause of gastroenteritis in humans and animals. Salmonella is highly pathogenic and encompasses more than 2600 characterized serovars. The transmission of Salmonella to humans occurs through the farm-to-fork continuum and is commonly linked to the consumption of animal-derived food products. Among these sources, poultry and poultry products are primary contributors, followed by beef, pork, fish, and non-animal-derived food such as fruits and vegetables. While antibiotics constitute the primary treatment for salmonellosis, the emergence of antibiotic resistance and the rise of multidrug-resistant (MDR) Salmonella strains have highlighted the urgency of developing antibiotic alternatives. Effective infection management necessitates a comprehensive understanding of the pathogen's epidemiology and transmission dynamics. Therefore, this comprehensive review focuses on the epidemiology, sources of infection, risk factors, transmission dynamics, and the host range of Salmonella serotypes. This review also investigates the disease characteristics observed in both humans and animals, antibiotic resistance, pathogenesis, and potential strategies for treatment and control of salmonellosis, emphasizing the most recent antibiotic-alternative approaches for infection control.

Characterization of Antibiotic Treatment among Children Aged 0-59 Months Hospitalized for Acute Bacterial Gastroenteritis in Israel

BACKGROUND

We examined the extent and correlates of appropriate antibiotic use among children hospitalized with bacterial acute gastroenteritis (AGE) in Israel, a high-income country setting.

METHODS

Data were collected from children aged 0-59 months who participated in active hospital-based surveillance of AGE undertaken during 2007-2015. Bacterial AGE was defined as having a positive stool culture for Salmonella, Shigella, Campylobacter, or dysentery. Appropriate antibiotic use was defined as the administration of ciprofloxacin, azithromycin, or third-generation cephalosporins during hospitalization or at discharge.

RESULTS

Overall, 550 children had bacterial AGE; of those, 369 (67.1% [95% CI 63.1-70.9]) received antibiotics, mostly azithromycin (61.8%) and third-generation cephalosporins (37.9%). Appropriate antibiotic treatment was given to 318/550 (57.8% [95% CI 53.7-61.9]). Children aged 0-11 months vs. 24-49 months were more likely to receive appropriate antibiotic treatment (OR = 1.90 [95% CI 1.09-3.33]). Having dysentery (OR = 5.30 [95% CI 3.35-8.39]), performing blood culture (OR = 1.59 [95% CI 1.02-2.48]), and C-reactive protein (CRP) levels (OR = 1.01 [95% CI 1.01-1.02]) were positively associated with receiving appropriate antibiotic treatment.

CONCLUSIONS

Most children with bacterial AGE received appropriate antibiotic treatment, which correlated with young age, dysentery, CRP level, and performing blood culture, suggesting more severe illness, thus supporting the clinical decisions of physicians.

Identification and bioinformatic analysis of invA gene of Salmonella in free range chicken

Abstract Salmonella is a serious cause of the health issues in human and animal worldwide. Salmonella has been isolated from different biological samples and it considers as the key role in induction of inflammation of gastrointestinal tract which in turn cause diarrhoea in different species. To further understand the involvement of Salmonella in contaminating and infecting fresh eggs and meat of free-range chicken. This study aimed to establish the microbiological and molecular detections of Salmonella in the cloaca of the free-range chicken and to identify predicted biological functions using Kyoto Encyclopedia of Gene and Genomic (KEGG) pathways and protein-protein interaction. Cloacal swabs were collected from free range chicken raised in the local farm in Duhok city. The isolates were cultured and biochemical test performed using XLD and TSI, respectively. Molecular detection and functional annotation of invA gene was carried out using Conventional PCR and bioinformatics approaches. The present study found that Salmonella was detected in 36 out of 86 samples using microbiological methods. To confirm these findings, invA gene was utilised and 9 out of 36 Salmonella isolates have shown a positive signal of invA by agarose gel. In addition, bioinformatic analysis revealed that invA gene was mainly associated with bacterial secretion processes as well as their KEGG terms and Protein-Protein Interaction were involved in bacterial invasion and secretion pathways. These findings suggested that invA gene plays important role in regulating colonization and invasion processes of Salmonella within the gut host in the free range chicken.

Emergence and genomic characteristics of multi-drug-resistant Salmonella in pet turtles and children with diarrhoea

Pet turtles are a well-recognized source of human salmonellosis, posing a threat to human health, particularly children who commonly keep pet turtles. To date, the genomic characteristics of Salmonella among pet turtles and children has not been well described. We investigated the prevalence, antimicrobial resistance (AMR) and genomic characteristics of Salmonella from pet turtles in Beijing, China. In total, 9.6 % (46/480) of pet turtles were positive for Salmonella with S. Thompson being the dominant serovar (19/46) in 2019. Moreover, 80.4 % of Salmonella were multi-drug resistant (MDR) and 60.7 % were resistant to ampicillin, streptomycin, sulfonamides and tetracycline (ASSuT). We further compared the genomes of S. Thompson isolates from pet turtles (n=19) with those from children with diarrhoea (n=28) in the same region and year, most of which were sequence type (ST)26, with one novel ST7937 identified from a child-associated isolate. S. Thompson isolates from children with diarrhoea exhibited less resistance than isolates from pet turtles. Most MDR isolates possessed multiple AMR genes, including the AmpC β-lactamase-encoding genes bla DHA-15 and bla DHA-1 which co-occurred with the IncA/C and IncHI plasmid replicon types. To the best of our knowledge, this is the first time that the bla DHA-15 gene has been detected from Salmonella. Several pet turtle-associated S. Thompson isolates comprised phylogenetically close clusters with those from children with diarrhoea (<20 SNP differences). Bayesian analysis demonstrated that the Chinese ST26 S. Thompson strains had a recent evolutionary history and evolved into two major clades, with one clade acquiring various resistant plasmids. Our findings revealed the emergence of MDR Salmonella among pet turtles in China and provided evidence for the interspecies transmission of S. Thompson.

Sophy β-Glucan from the Black Yeast Aureobasidium pullulans Attenuates Salmonella-Induced Intestinal Epithelial Barrier Injury in Caco-2 Cell Monolayers via Exerting Anti-Oxidant and Anti-Inflammatory Properties

The zoonotic pathogens Salmonella spp. infection disrupted intestinal epithelial barrier function and induced local gastroenteritis and systemic inflammation in humans and animals. Sophy β-glucan, a water-soluble β-1,3/1,6-glucan synthesized from the black yeast Aureobasidium pullulans, was reported with immune-regulatory, anti-inflammatory, and anti-infective properties. Here, we investigated the protective role of sophy β-glucan on Salmonella enterica serotype Enteritidis (SE)-challenged Caco-2 cells monolayer and explored underlying action mechanisms. The results showed that pretreatment with sophy β-glucan blocked the adhesion and invasion of SE onto Caco-2 cells along with alleviating SE-induced epithelial barrier injury, as evidenced by increased trans-epithelial electrical resistance, decreased fluorescently-labeled dextran 4 flux permeability, and an enhanced Claudin-4 protein level in the SE-stimulated Caco-2 cell monolayer. Moreover, treatment with β-glucan down-regulated pro-inflammatory factors (IL-1β, IL-8, and TNF-α) while up-regulating anti-inflammatory factors IL-10 at mRNA and protein levels in SE-infected Caco-2 cells. Furthermore, sophy β-glucan strengthened the anti-oxidative capacity of Caco-2 monolayers cells by elevating T-AOC and SOD activity and inhibiting MDA production defending SE. Together, our data showed that sophy β-glucan could prevent intestinal epithelial injury induced by SE, possibly by exerting anti-oxidant and anti-inflammatory properties, and it might be helpful for controlling SE infection.

Genomic characterization of Salmonella isolated from retail chicken and humans with diarrhea in Qingdao, China

Salmonella, especially antimicrobial resistant strains, remains one of the leading causes of foodborne bacterial disease. Retail chicken is a major source of human salmonellosis. Here, we investigated the prevalence, antimicrobial resistance (AMR), and genomic characteristics of Salmonella in 88 out of 360 (24.4%) chilled chicken carcasses, together with 86 Salmonella from humans with diarrhea in Qingdao, China in 2020. The most common serotypes were Enteritidis and Typhimurium (including the serotype I 4,[5],12:i:-) among Salmonella from both chicken and humans. The sequence types were consistent with serotypes, with ST11, ST34 and ST19 the most dominantly identified. Resistance to nalidixic acid, ampicillin, tetracycline and chloramphenicol were the top four detected in Salmonella from both chicken and human sources. High multi-drug resistance (MDR) and resistance to third-generation cephalosporins resistance were found in Salmonella from chicken (53.4%) and humans (75.6%). In total, 149 of 174 (85.6%) Salmonella isolates could be categorized into 60 known SNP clusters, with 8 SNP clusters detected in both sources. Furthermore, high prevalence of plasmid replicons and prophages were observed among the studied isolates. A total of 79 antimicrobial resistant genes (ARGs) were found, with aac(6')-Iaa, blaTEM-1B, tet(A), aph(6)-Id, aph(3″)-Ib, sul2, floR and qnrS1 being the dominant ARGs. Moreover, nine CTX-M-type ESBL genes and the genes blaNMD-1, mcr-1.1, and mcr-9.1 were detected. The high incidence of MDR Salmonella, especially possessing lots of mobile genetic elements (MGEs) in this study posed a severe risk to food safety and public health, highlighting the importance of improving food hygiene measures to reduce the contamination and transmission of this bacterium. Overall, it is essential to continue monitoring the Salmonella serotypes, implement the necessary prevention and strategic control plans, and conduct an epidemiological surveillance system based on whole-genome sequencing.

Typhoid and Non-Typhoid Salmonellosis Related Mortality in Iran, National Data from the Ministry of Health

Background

Despite the declining trend, salmonellosis is still an important preventable cause of death in Iran and the world, especially in certain age and occupational subgroups, and the need for preventive measures, especially raising awareness of at-risk groups, is necessary.

Methods

Data were obtained from the Ministry of Health covering the years 2013 to 2019. The data were then stratified by year, season, month, and province of death as well as sex, age group, belonging to rural vs. urban communities and cause of death and were then analyzed using SPSS to report differences in age, sex, seasonal patterns, and spatial distribution.

Results

Non-typhoid salmonellosis (NTS) and typhoid were recorded as the cause of 800 and 32 deaths, respectively, with the highest number in 2015 and 2013. Septicemia was the cause of 87.3% of deaths due to NTS, whereas typhoid was the cause of 62.5% of its respective cases. The highest percentage of death related to both occurred in spring (P<0.001). NTS mortality rates were higher in the 70-80 and 80-90 age groups, while typhoid mortality was greatest in the under 10 yr age group. NTS mortality was higher in urban while typhoid mortality was higher in rural areas (P<0.001). Most deaths occurred in Ardabil, Sistan and Baluchistan and Khorasan Razavi provinces and Sistan and Baluchistan, West Azerbaijan and Khorasan Razavi related to NTS and typhoid, respectively.

Conclusion

Salmonella remains a preventable cause of death, especially among the elderly and children, the data gathered in this study provides important information for priority setting in specific subpopulations and food safety policy.

Genomic Diversity, Antimicrobial Resistance, Plasmidome, and Virulence Profiles of Salmonella Isolated from Small Specialty Crop Farms Revealed by Whole-Genome Sequencing

Salmonella is the leading cause of death associated with foodborne illnesses in the USA. Difficulty in treating human salmonellosis is attributed to the development of antimicrobial resistance and the pathogenicity of Salmonella strains. Therefore, it is important to study the genetic landscape of Salmonella, such as the diversity, plasmids, and presence antimicrobial resistance genes (AMRs) and virulence genes. To this end, we isolated Salmonella from environmental samples from small specialty crop farms (SSCFs) in Northeast Ohio from 2016 to 2021; 80 Salmonella isolates from 29 Salmonella-positive samples were subjected to whole-genome sequencing (WGS). In silico serotyping revealed the presence of 15 serotypes. AMR genes were detected in 15% of the samples, with 75% exhibiting phenotypic and genotypic multidrug resistance (MDR). Plasmid analysis demonstrated the presence of nine different types of plasmids, and 75% of AMR genes were located on plasmids. Interestingly, five Salmonella Newport isolates and one Salmonella Dublin isolate carried the ACSSuT gene cassette on a plasmid, which confers resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline. Overall, our results show that SSCFs are a potential reservoir of Salmonella with MDR genes. Thus, regular monitoring is needed to prevent the transmission of MDR Salmonella from SSCFs to humans.

Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping

The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.